Ac8b03157 Si 001

Supporting Information
Computing the 3D Radial Distribution Function

from Particle Positions: An Advanced Analytic Approach
Bernd A. F. Kopera and Markus Retsch
Physikalische Chemie I
Universität Bayreuth
Universitätsstraße 30
95440 Bayreuth
Germany
Corresponding author: markus.retsch@uni-bayreuth.de

Contents
1 Theory S-2
1.1 How to Compute g(r) from Particle Coordinates . . . . . . . . . . . . . . . S-2
1.2 The Effects of Artificial Periodic Boundaries . . . . . . . . . . . . . . . . . S-4
1.3 The Effects of Averaging Over a Small Subvolume . . . . . . . . . . . . . . S-6
1.4 The Intersection Volume Between a Shell and a Box . . . . . . . . . . . . . S-7
1.5 The Volume of a Spherical Cut . . . . . . . . . . . . . . . . . . . . . . . . S-12
2 Mathematical Appendix S-14

2.1 The Volume of a Spherical Segment . . . . . . . . . . . . . . . . . . . . . . S-14
2.2 The Volume of a Spherical Cap . . . . . . . . . . . . . . . . . . . . . . . . S-15
2.3 The Internal Volume Vint . . . . . . . . . . . . . . . . . . . . . . . . . . . . S-16
2.4 Proof for the Integral I1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . S-21
3 Pseudo code S-28
4 Source code S-32

4.1 FCC Coordinate Generation . . . . . . . . . . . . . . . . . . . . . . . . . . S-32
4.2 Simple g(r) Implementation in Python 3 . . . . . . . . . . . . . . . . . . . S-34
4.3 Analytic g(r) Implementation in Python 3 . . . . . . . . . . . . . . . . . . S-35
4.4 Analytic - Internal Volume . . . . . . . . . . . . . . . . . . . . . . . . . . . S-38
4.5 Monte Carlo - Internal Volume . . . . . . . . . . . . . . . . . . . . . . . . S-38
4.6 Numeric Integration - Internal Volume . . . . . . . . . . . . . . . . . . . . S-39
4.7 Analytic - Spherical Cut Volume . . . . . . . . . . . . . . . . . . . . . . . . S-39
4.8 The Octant Sum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . S-39
4.9 The Octant Volume . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . S-39
4.10 Monte Carlo - Spherical Cut Volume . . . . . . . . . . . . . . . . . . . . . S-41
4.11 Monte Carlo - Sphere Volume . . . . . . . . . . . . . . . . . . . . . . . . . S-41
4.12 Simple g(r) in C++ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . S-41
4.13 Analytic g(r) in C++ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . S-46
1 Theory
1.1 How to Compute g(r) from Particle Coordinates
This section describes how the radial distribution function, g(r), is computed from particle
coordinates. First, we look at the relation between g(r) and the local particle density
1
fl(r) = flavg · g(r) … g(r) = · fl(r). (1.1)
flavg
The average density, flavg , is given by the number of all particles, N , divided by the known
sample volume, VSample , like
N
flavg = . (1.2)
VSample
The actual local particle density, flreal (r), at one specific radius, r, is hard to obtain.
Technically, flreal (r), is defined by
r
#P(r ≠ , r + 2r )
flreal (r) = lim 2
. (1.3)
ræ0 VShell (r ≠ r
, r + 2r )
2
Here, #P denotes the number of particles in a spherical shell with the given inner and
outer radii. This definition has some issues when it comes to actually computing fl(r)
and g(r). Both the volume of a spherical shell and the number of particles in the shell
approach zero when r approaches zero. In practice, this issue is solved by using a finite
r. The equation for the estimated local particle density is therefore
r
#P(r ≠ , r + 2r )
flcalc (r, r) = 2
. (1.4)
VShell (r ≠ 2
r
, r + 2
r
)
Before we analyze the implications of using a finite, r, we take a look at the shell volume.
The volume of a spherical shell is given by the difference of the inner and outer bounding
sphere. Therefore, we have
SA B3 A B3 T
r r 4 r r
VShell (r, r) = Vsphere (r + )≠Vsphere (r ≠ ) = fiU r+ ≠ r≠ V (1.5)
2 2 3 2 2
We simplify this equation by expanding the cube roots into

C C DD
4 3 2 r r2 r3 3 2 r r2 r3
fi r + 3r · + 3r · + ≠ r ≠ 3r · + 3r · ≠ . (1.6)
3 2 4 8 2 4 8
Next, we add all terms with equal power, which leaves us with
C D
4 r3 r3
VShell (r, r) = · fi · 3 · r2 · r+ = 4fi · r2 · r+fi· . (1.7)
3 4 3
This equation gives us a simple way to calculate the volume of a spherical shell. Equa-
tion (1.4) becomes
#P(r ≠ 2r , r + 2r )
flcalc (r, r) = 3 . (1.8)
4fir2 r + fi 3r
S-2
(a) (b)
Figure S1: (a) Slightly distorted cubic grid of particles. The red circles create spherical
shells around the central green particle. Each shell has a certain number of blue particles
in it. (b) Histogram showing the particle density, fl(r), as a function of radial distance.
Figure S1 illustrates the procedure defined in equation (1.4). We move the center of
our radial coordinate system onto a single particle. The red shells have a thickness of
r. The average density in each shell is the number of particles divided by the shell
volume (see equation (1.2)). The radial distribution function around a single particle, i,
is therefore given by
1 #P(r ≠ 2r , r + 2r )
gi (r, r) = · 3 . (1.9)
flavg 4fir2 r + fi 3r
We now average over all possible particles
1 ÿ N
gcalc (r, r) = · gi (r, r), (1.10)
N i=1
to get better statistics. Note, that we assumed a homogeneous particle distribution.
S-3
1.2 The Effects of Artificial Periodic Boundaries
In this section, we look at the effecs of applying artificial periodic boundaries to our
sample. Figure S2 shows a small sample volume with periodic boundaries. The spherical
shells for the g(r) computation are now always inside the sample volume.
Figure S2: Small sample volume extended to infinity by periodic boundary conditions.
Note the creation of artificial periodicities.
(a) (b)
Figure S3: (a) Colloidal assemble measured with confocal scanning microscopy and an-
alyzed with TrackPy. (b) Radial distributiong function for the particle assembly in a.
Periodic boundaries distort the peak shape and position.
The effects of periodic boundaries are most pronounced for small samples. Larger finite
sample volumes are less affected by periodic boundaries. The main effects are:
• Stitching errors from unknown sample boundary positions
• Artificial periodicities, especially in small samples
• Rough boundaries from missing particles distort g(r)
S-4
Figure S4: a) Simple cubic lattice with periodic boundaries a half next neighbor distance
away from the outer most particles. No stitching errors (artificial periodicities) are created.
b) Same lattice as in a) but with a tighter boundary. The red distance is artificial. c) g(r)
of a simple cubic lattice with 2197 particles arranged in a cubic sample volume. The unit
cell has size 1 and the particle positions are distorted with a 3D Gaussian blur (‡ = 0.07).
The graph labeled true boundary corresponds to a) and the tight boundary to b). Our
analytic solution uses a tight boundary but reproduces the true boundary case well. Note
the large peak at r < 1 created by the stitching error when a tight periodic boundary is
used. The size of this peak strongly depends on the particle number in the sample and
the sample shape. The position of the peak is at r > 1 when the boundary is more then
a half next neighbor distance away from the outer most particle.
Figure S5: g(r) of a simple cubic lattice arranged in a cubic sample volume similar to
Figure S4 c). We increase the number of particles in the sample volume from 729 to 9261.
The unit cell is 1. The artificial peak at r < 1 is reduced when the particle number is
increased. We attribute this decrease to the decreasing surface to volume ratio.
S-5
1.3 The Effects of Averaging Over a Small Subvolume
In this section we look at a way of avoiding the normalization problem. We avoid it by
confining the averaging over the local g(r) to a small sub-volume. At the same time,
we limit the radial distance as shown in Figure S6. The spherical bins now never reach
beyond the finite sample volume.
Figure S6: Finite sample volume with a smaller subvolume (dashed lines). The radial dis-
tance is limited to Rmax . Averaging is only perfomed over the particles in the subvolume.
The spherical bins (yellow) never reach beyond the sample boundaries.
Figure S7: Radial distribution function for our FCC test data set. The confined average
algorithm produces the same g(r) as the analytic algorithm. However, radial distances
beyond Rmax are not accessible and information is lost.
The main effect of this method is a limited radial distance. There is also a trade-off
between radial distance and noise reduction. Less particles are available for averaging,
increasing the noise.
S-6
1.4 The Intersection Volume Between a Shell and a Box
In this section, we derive the intersection volume between a spherical shell and a rectan-
gular box. During the calculation of g(r), the volume of a spherical shell, occupied by
particles, is needed. In practice, the box where we have information about the particle
positions is finite. Therefore, we need the intersection volume between the spherical shell
and the box to properly normalize g(r). We assume that the center of the spherical shell
is always inside the box. This assumption is valid since the center of our shell is a known
particle. Furthermore, we assume that the walls of the box are perpendicular to each
other.
Figure S8: Intersection volume (red) between a spherical shell and a rectangular box
(blue). The green particle is at the center of the spherical shell. The red volume is needed
to normalize g(r).
An example rendering of a spherical shell, protruding outside of a box, is shown in

Figure S8. The red volume is the intersection volume between the spherical shell and the
blue box.
Figure S9: Definition of the box boundaries. Without loss of generality, we assume that
the center of this coordinate system is at the center of the current particle. We can always
shift the center of the COSY because the coordinates of the central particle are known.
S-7
The boundaries of the box are defined in Figure S9. The center of our Cartesian
coordinate system is at the center of the special shell. To calculate the red intersection
volume we proceed as follows. First, we dived the problem into smaller subproblems that
are easier to solve. We then solve the subproblems and reassemble their solutions into the
final solution.
We note that the volume of a spherical shell is given by the volume of the inner sphere
minus the outer sphere like
Vshell = Vouter sphere ≠ Vinner sphere . (1.11)
Figure S10: The volume of a spherical shell is given by the difference of the inner and
outer sphere. This is true as long as the inner sphere is fully inside the outer sphere.
A graphical proof of equation (1.11) is given in Figure S10. The intersection volume
between the smaller sphere and the box is always completely inside the intersection volume
of the larger sphere and the box. Therefore, equation (1.11) also holds when both spheres
are intersected by a box. We reduced our original problem to the problem of finding the
intersection volume of a sphere and a box.
(a) (b)
Figure S11: Separation of s sphere (a) into eight octants (b) along the planes of the
Cartesian coordinate system. The octants are moved away from the center for clarity.
Next, we use the intrinsic symmetries present in a sphere and a box. To do so, we
split the sphere into eight octants as shown in Figure S11. Note, that the walls of our
rectangular box are perpendicular to the axes of the Cartesian coordinate system. Three
walls of our box cut into each octant at most, since the center of the sphere is always inside
S-8
the box. Therefore, we reduced the original problem to finding the remaining volume of
an octant intersected by three perpendicular boundaries. Overall, the sphere volume is
then given by the sum of the remaining octant - box intersection volumes like
8
ÿ
Vsphere = VOctant (i). (1.12)
i=1
For simplicity, we mirror all octants into the first octant bounded by three positive axes.
This mirroring reduces the number of different cases significantly. Mirroring preserves the
volume. The labels for the new boundaries are shown in Figure S12.
Figure S12: The three boundaries: xb , yb , and zb , defining the dimensions of the corner.
Note that we can always mirror a corner into the all positive octant of the COSY. This
does not affect the intersection volume between the corner and the sphere octant.
We are looking for a simple algorithm to calculate the intersection volume between
a sphere and a box. Using the above definitions and simplifications we arrive at the
following function:
1 d e f SphereVolume ( Rs , Xmin , Xmax, Ymin , Ymax, Zmin , Zmax ) :
2
3 VSphere = 0
4
5 # abs ( ) m i r r o r s t h e b o u n d a r i e s i n t o t h e f i r s t o c t a n t
6 f o r xb i n [ abs ( Xmin ) , abs (Xmax ) ] :
7 f o r yb i n [ abs ( Ymin ) , abs (Ymax ) ] :
8 f o r zb i n [ abs ( Zmin ) , abs (Zmax ) ] :
9
10 VSphere += OctVolume ( Rs , xb , yb , zb )
11
12 r e t u r n VSphere
This leaves us with the challenge of finding a simple solution for the intersection volume of
a box corner with a sphere octant (OctVolume(Rs , xb , yb , zb )). Again we look for patterns
that might simplify this task. First we look at the case that the intersection volume is
only bounded by the box and not by the sphere. This is the case when
x2b + yb2 + zb2 Æ Rs2 . (1.13)
S-9
Figure S13: Intersection volume (red) between a box corner and an octant. The box
corner is fully inside the octant.
Figure S13 shows the case of a box corner inside the octant. In this case, the orange
box corner in Figure S12 is inside or on the sphere. Therefore, the intersection volume is
given by:
OctVolume(Rs , xb , yb , zb ) = xb · yb · zb . (1.14)
This is a special case and we have to treat it as such. Next, we look at a single plane
intersecting the octant. This situation is shown in Figure S14.
Figure S14: Single boundary intersecting the sphere octant. A quarter of a spherical cap
(red) is removed from the octant by the plane (blue).
A single plane removes a quarter of a spherical cap (red) from the octant. For now, we
assume that the three planes do not intersect themselves. A boundary plane, B, intersects
the octant only when it is closer to the origin than the sphere radius:
B < Rs . (1.15)
In this case, we subtract a quarter of a spherical cap, derived in appendix 2.2,
5 6
1 fi 2 1
· Vcap (Rs , B) = · · Rs3 ≠ Rs2 · B + · B 3 (1.16)
4 4 3 3
S-10
from the octant. The last thing left to consider is the overlap between two spherical caps.
Two boundary planes, a, and b, intersect each other inside the octant, when
a2 + b2 < Rs2 . (1.17)
This case is shown in Figure S15.
Figure S15: Two boundaries intersecting the octant. The boundaries also intersect them-
selves inside the octant. During the first step, we subtracted the red volume twice from
the octant. Therefore, we have to add the intersection volume between the two spherical
caps (red).
For simplicity, we name the intersection volume of two spherical caps a spherical cut.
The volume of a spherical cut is derived in section 1.5. For every pair of boundaries, we
have to check if they intersect. If they do, we need to add the spherical cut volume, since
we removed it twice when we removed the spherical caps. Overall, we obtain the following
algorithm for the volume of a sphere octant intersected by up to three planes:
1 d e f OctVolume ( Rs , xb , yb , zb ) :
2
3 # i f a l l boundaries i n t e r s e c t i n s i d e the octant
4 i f xb 2 + yb 2 + zb 2 < Rs 2 :
5
6 r e t u r n xb yb zb
7
8 # i f t h e y dont i n t e r s e c t we s t a r t with a f u l l o c t a n t
9 VOctant = 1/8 4/3 pi Rs 3
10
11 # then , we remove t h e s p h e r i c a l c a p s
12 f o r B i n [ xb , yb , zb ] :
13
14 i f B < Rs :
15 VOctant ≠= p i / 4 ( 2 / 3 Rs 3≠B Rs 2+1/3 B 3)
16
17 # f i n a l l y , we add t h e i n t e r s e c t i o n s o f t h e c a p s
18 f o r ( a , b ) i n [ ( xb , yb ) , ( xb , zb ) , ( yb , zb ) ] :
19
20 if a 2 + b 2 < Rs 2:
21
22 VOctant += VSphereCut ( Rs , a , b )
23
24 r e t u r n VOctant
With these two algorithms and equation (1.11) we are able to efficiently calculate the
intersection volume between a spherical shell and a rectangular box.
S-11
1.5 The Volume of a Spherical Cut
In this section, we derive the volume of a spherical cut. Without loss of generality,
we limit ourselves to the X- and Z-boundary planes. Figure S16 shows a 3D rendering
of the spherical cut in red. The red volume is created by slicing a sphere twice, once
perpendicular to the X-, and once perpendicular to the Z-axis.
Figure S16: Spherical cut (red) created by slicing a sphere with two planes perpendicular
to the X and Z axis. The parts created by the cuts are exploded for better visualization.
Note that we defined the cut volume to be half of the red volume.
The integral to obtain the red volume directly is hard to solve. Therefore, we look for a
decomposition into easier integrals. We choose the decomposition shown in Figure S17.
Figure S17: Decomposition used to calculate the volume of a spherical cut (red) by
adding and subtracting different volumes from the spherical part. Note that the volumes
are rendered from two octants for easier understanding. Only the internal volume (green)
is hard to obtain.
Using this decomposition, the volume of a spherical cut is given by

1 1 1
Vcut (Rs , xb , zb ) = · Vsphere (Rs ) ≠ · Vseg (Rs , xb ) ≠ · Vseg (Rs , zb ) + Vint (Rs , xb , zb ). (1.18)
8 4 4
All volumes, except for the green, internal volume, Vint are known. We insert the volume
of the spherical segment derived in section 2.1 and get
C D C D
1 4 fi x3 fi z3
Vcut (Rs , xb , zb ) = · fiRs3 ≠ · Rs2 · xb ≠ b ≠ · Rs2 · zb ≠ b +Vint (Rs , xb , zb ). (1.19)
8 3 4 3 4 3
S-12
The analytic solution for the internal volume, Vint , is given in appendix 2.3. We insert
the solution for Vint into equation (1.19) and obtain
C D C D
1 4 fi x3 fi z3
Vcut (Rs , xb , zb ) = · fiRs3 ≠ · Rs2 · xb ≠ b ≠ · Rs2 · zb ≠ b + (1.20)
8 3 4 3 4 3
Ò Q R C D
zb · xb · Rs2 ≠ x2b ≠ zb2 1 xb z3
+ · arctan a Ò b · R2 · zb ≠ b +
3 2 R 2 ≠ x2 ≠ z 2
s
3
s b b
Q R C D Q R
1 zb b · R 2 · xb ≠
x3b Rs3 zb · xb
· arctan a Ò ≠ · arctan a Ò b.
2 2 2
R ≠x ≠z 2
s
3 3 Rs · Rs2 ≠ x2b ≠ zb2
s b b
Next, we factor out the Rs3/6 terms in the square brackets to simplify the equation into
S Q RT
R3 zb · xb
Vcut (Rs , xb , zb ) = s · Ufi ≠ 2 · arctan a Ò bV (1.21)
6 Rs · R 2 ≠ x2 ≠ z 2 s b b
S Q R T C D
1 U zb fi x3
b ≠ V · R 2 · xb ≠ b
+ · arctan a Ò
2 R 2 ≠ x2 ≠ z 2 2 s
3
s b b
S Q R T C D
1 xb fi z3
b ≠ V · R2 · zb ≠ b
+ · Uarctan a Ò
2 R 2 ≠ x2 ≠ z 2 2 s
3
s b b
Ò
zb · xb · Rs2 ≠ x2b ≠ zb2
+ .
3
This is the final analytic solution for the volume of the spherical cut, Vcut . In general, a
boundary pair, (a, b), for which
a2 + b2 < Rs2 (1.22)
holds, creates the following spherical cut volume:
S Q RT
R3 a·b
Vcut (Rs , a, b) = s · Ufi ≠ 2 · arctan a Ò bV (1.23)
6 2 2
Rs · Rs ≠ a ≠ b 2
S Q R T C D
1 a fi
b ≠ V · R2 · b ≠
b3
+ · Uarctan a Ò
2 Rs2 ≠ a2 ≠ b2 2 s
3
S Q R T C D
1 U b fiV 2 a3
+ · arctan a Ò b ≠ · Rs · a ≠
2 Rs2 ≠ a2 ≠ b2 2 3
Ò
a·b· Rs2 ≠ a2 ≠ b2
+ .
3
S-13
2 Mathematical Appendix
2.1 The Volume of a Spherical Segment
In this section, we derive the volume of a spherical segment. A spherical segment of
height, B, is shown in Figure S18.
Figure S18: Spherical segment (green) of height, B, inside a sphere of radius, Rs .
A spherical segment can be viewed as a rotation body. The rotation axis is vertical (z)
and the radius, R, depends on the height. Using Pythagoreans theorem, we see that
R2 + z 2 = Rs2 … R2 = Rs2 ≠ z 2 . (2.1)
To get the volume of the spherical segment, Vseg , we integrate over tiny discs along the
z-axis like
⁄B ⁄B Ë È
2
Vseg (Rs , B) = fi · R dz = fi · Rs2 ≠ z 2 dz. (2.2)
0 0
Then, we split the integral at the minus sign and factor out the sphere radius, Rs , to get
SB T S T
⁄ ⁄B ⁄B ⁄B
fi · U R2 s dz ≠ z 2 dz V = fi · URs2 · 1 dz ≠ z 2 dz V . (2.3)
0 0 0 0
Finally, we solve the integrals by

C 5 6B D 5 5 66
1 3 1 1
fi· Rs2 · [z]B
0 ≠ ·z =fi· Rs2 · [B ≠ 0] ≠ · B 3 ≠ · 03 , (2.4)
3 0 3 3
which leaves us with 5 6

1
Vseg (Rs , B) = fi · Rs2 · B ≠ · B3 . (2.5)
3
This is the final equation for the volume of a spherical segment as a function of the
boundary position, B, and the sphere radius, Rs .
S-14
2.2 The Volume of a Spherical Cap
In this section, we derive the volume of a spherical cap. A spherical cap is shown in
Figure S19. This volume is very similar to the volume of a spherical segment.
Figure S19: Spherical cap (green) with radius, Rs , and height, Rs ≠ B.
First, we note that a spherical cap is just a hemi-sphere minus a spherical segment:
1 4 3
Vcap (Rs , B) = · fiR ≠ Vseg (Rs , B) (2.6)
2 3 s
We insert the equation for a spherical segment, derived in appendix 2.1, and simplify the
first term to get 5 6
2 3 2 1 3
Vcap (Rs , B) = fiRs ≠ fi · Rs · B ≠ · B . (2.7)
3 3
Finally, we factor out fi and obtain
5 6
2 1
Vcap (Rs , B) = fi · · Rs3 ≠ Rs2 · B + · B 3 . (2.8)
3 3
This is the final equation for the volume of a spherical cap as a function of the boundary
position, B, from the sphere center.
S-15
2.3 The Internal Volume Vint
In this section, we derive the volume of the internal element, Vint . Figure S20 shows a
rotated drawing of Vint inside a Cartesian coordinate system.
Figure S20: Integration in Cartesian coordinates yields the volume under a 3D surface.
In our case, the 3D surface (green) is part of the surface of a sphere.
To obtain Vint , we integrate a section of the surface of a sphere. The section is bounded
by perpendicular planes through xb and zb . These planes are also orthogonal to their
respective coordinate axis. A sphere, with its center at the origin, is defined by
x2 + y 2 + z 2 = Rs2 . (2.9)
The height, h(x, z) = y, is therefore
Ò
h(x, z) = Rs2 ≠ z 2 ≠ x2 . (2.10)
To obtain the volume under the green surface, we integrate along the x and z coordinate.
The integration boundaries are from 0 to the values xb and zb respectively, like
⁄xb ⁄zb ⁄xb ⁄zb Ò
Vint (Rs , xb , zb ) = h(x, z) dz dx = Rs2 ≠ z 2 ≠ x2 dz dx. (2.11)
0 0 0 0
We solve the two nested integrals one after another. First we integrate over the z-
coordinate. Applying the anti-derivative, given in appendix 2.4, we get
S S Q RTT zb
⁄xb
1 Ò 1 2
U · Uz · R2 ≠ z 2 ≠ x2 + R2 ≠ x2 · arctan a Ò
z
Vint = bVV dx.
2 s s
Rs2 ≠ z 2 ≠ x2
0 0
(2.12)
We insert the upper and lower bound, yielding
S Q RT
⁄xb
1 U Ò 1 2 zb
Vint = · zb · Rs2 ≠ zb2 ≠ x2 + Rs2 ≠ x2 · arctan a Ò bV (2.13)
2 R 2 ≠ z 2 ≠ x2
0 s b
S Q RT
1 Ò 1 2 0
≠ · U0 · Rs2 ≠ 02 ≠ x2 + Rs2 ≠ x2 · arctan a Ò bV dx.
2 Rs ≠ 0 ≠ x
2 2 2
S-16
Since arctan(0) = 0, we are left with
S Q RT
⁄xb
1 U Ò 1 2 zb
Vint = · zb · Rs2 ≠ zb2 ≠ x2 + Rs2 ≠ x2 · arctan a Ò bV dx. (2.14)
2 2 2
R ≠z ≠x 2
0 s b
Next, we split the remaining integral into three parts. We also bring the factor of 2 onto
the side of Vint . This gives us
⁄xb Ò
2 · Vint = zb · Rs2 ≠ zb2 ≠ x2 dx (2.15)
0
Q R
⁄xb
zb
+Rs2 · arctan a Ò b dx
0 Rs2 ≠ zb2 ≠ x2
Q R
⁄xb
zb
≠ x2 · arctan a Ò b dx.
0 Rs2 ≠ zb2 ≠ x2
We now have three individual integrals to solve. We label them according to
2 · Vint = zb · I1 + Rs2 · I2 ≠ I3 . (2.16)
For simplicity, we define the terms

Ò Ò
A = Rs2 ≠ zb2 and S = Rs2 ≠ zb2 ≠ x2b = A ≠ x2b , (2.17)
that are always greater than 0. The anti-derivative of the first integral,
⁄xb Ò ⁄xb Ô
I1 = Rs2 ≠ zb2 ≠ x2 dx = A ≠ x2 dx (2.18)
0 0
is solved in appendix 2.4 and yields

C C A BDDxb
1 Ô x
I1 = · x · A ≠ x2 + A · arctan Ô . (2.19)
2 A ≠ x2 0
Inserting the upper and lower boundaries gives us

S Q RT
1 Ò xb
I1 = · Uxb · A ≠ x2b + A · arctan a Ò bV (2.20)
2 A≠x 2
b
C A BD
1 Ô 0
≠ · 0· A ≠ 02 + A · arctan Ô .
2 A ≠ 02
5 3 46
1 xb
I1 = · xb · S + A · arctan . (2.21)
2 S
The second integral,
Q R A B
⁄xb ⁄xb
zb zb
I2 = arctan a Ò b dx = arctan Ô dx, (2.22)
0 Rs2 ≠ zb2 ≠ x2 0
A ≠ x2
S-17
is solved in appendix 2.5 and yields
S A B
x
I2 = Uzb · arctan Ô (2.23)
A ≠ x2
A B
zb
+x· arctan Ô
A ≠ x2
A B Txb
x · zb
≠Rs · arctan Ô V .
Rs · A ≠ x 2
0

Q R
xb
I2 = zb · arctan a Ò b (2.24)
A≠ x2b
Q R
zb
+xb · arctan a Ò b
A ≠ x2b
Q R
xb · zb
≠Rs · arctan a Ò b
Rs · A≠ x2b
S A B
0
≠Uzb · arctan Ô
A ≠ 02
A B
zb
+0· arctan Ô
A ≠ 02
A BT
0 · zb
≠Rs · arctan Ô V
Rs · A ≠ 02

3 4 3 4 3 4
xb zb xb · zb
I2 = zb · arctan + xb · arctan ≠ Rs · arctan . (2.25)
S S Rs · S
The third integral,

Q R A B
⁄xb ⁄xb
2 zb 2 zb
I3 = x · arctan a Ò b dx = x · arctan Ô dx, (2.26)
0 Rs2 ≠ zb2 ≠ x2 0
A ≠ x2
is solved in the appendix 2.6, like

S A B
z Ô z 1 2 x
U ≠ b · x · A ≠ x2 ≠ b · z 2 ≠ 3 · R2 · arctan Ô (2.27)
6 6 b s
A ≠ x2
A B A B Txb
x3 zb R3 zb · x
+ · arctan Ô ≠ s · arctan Ô V .
3 A ≠ x2 3 Rs · A ≠ x 2
0
S-18
Q R
zb Ò zb 1 2 xb
≠ · xb · A ≠ x2b ≠ · zb2 ≠ 3 · Rs2 · arctan a Ò b (2.28)
6 6 A ≠ x2 b
Q R Q R
x3 zb R3 zb · xb
+ b · arctan a Ò b ≠ s · arctan a Ò b
3 A≠x 2 3 Rs · A ≠ x 2
b b
S A B
zb Ô zb 1 2 0
≠U ≠ ·0· A≠ 02 ≠ · zb2 ≠ 3 · Rs2 · arctan Ô
6 6 A ≠ 02
A B A BT
03 zb R3 zb · 0
+ · arctan Ô ≠ s · arctan Ô V.
3 A ≠ 02 3 Rs · A ≠ 02

3 4 3 4 3 4
≠xb zb S zb 1 2 2 xb x3 zb R3 zb xb
I3 = ≠ zb ≠ 3Rs2 arctan + b arctan ≠ s arctan .
6 6 S 3 S 3 Rs S
(2.29)
Now, we combine the solutions for the three integrals and get:
5 5 3 466
1 1 2 xb
2 · Vint = zb · · xb · S + Rs2 ≠ zb2 · arctan (2.30)
5
2 3 4 3 4
S 3 46
xb zb zb · xb
+ Rs2 · zb · arctan + xb · arctan ≠ Rs · arctan
S S Rs · S
C 3 4 3 4 3 4D
3
≠xb · zb · S zb 1
2 2
2 xb xb zb Rs3 zb · xb
≠ ≠ · zb ≠ 3Rs · arctan + · arctan ≠ · arctan .
6 6 S 3 S 3 Rs · S
Next, we expand all products to remove the brackets

3 4
zb · xb · S zb · (Rs2 ≠ zb2 ) xb
2 · Vint = + · arctan (2.31)
2 3 4 2 3 4
S 3 4
2 x 2 z 3 zb · xb
+ Rs · zb · arctan + Rs · xb · arctan ≠ Rs · arctan
b b
S S Rs · S
1 2 3 4 3 3 4
xb · zb · S zb xb x zb
+ + · zb2 ≠ 3Rs2 · arctan ≠ b · arctan
6 6 S 3 S
3 3 4
R zb · xb
+ s · arctan .
3 Rs · S
We then factor out the arcus tangens functions
zb · xb · S xb · zb · S
2 · Vint = + (2.32)
2 C 6 D
3 4
xb zb · (Rs ≠ zb2 )
2
z 1 2
+ arctan + Rs2 · zb + · zb2 ≠ 3Rs2
b
·
S 2 6
3 4 C 3
D 3 4 C 3 D
zb 2 xb zb · xb Rs 3
+ arctan · Rs · x b ≠ + arctan · ≠ Rs .
S 3 Rs · S 3
S-19
Next, we take a closer look at the term in the square brackets containing zb and see that
zb · (Rs2 ≠ zb2 ) zb 1 2
+ Rs2 · zb + · zb2 ≠ 3Rs2 = (2.33)
2 6
2 3
zb · Rs zb z 3 zb · Rs2
≠ + Rs2 · zb + b ≠ =
2 2 6 2
z3
Rs2 · zb ≠ b
3
Using equation (2.33), we simplify the terms into
3 4 C D
2 · zb · xb · S xb z3
2 · Vint = + arctan · Rs2 · zb ≠ b (2.34)
3 S 3
3 4 C D 3 4 5 6
zb 2 x3b zb · xb 3 2
+ arctan · Rs · x b ≠ + arctan · Rs · ≠ .
S 3 Rs · S 3
Finally, we bring the factor of 2 on the other side

3 4 C D
zb · xb · S 1 xb z3
Vint = + · arctan · Rs2 · zb ≠ b (2.35)
3 2 S 3
3 4 C D 3 4
1 zb 2 x3b Rs3 zb · xb
+ · arctan · Rs · x b ≠ ≠ · arctan ,
2 S 3 3 Rs · S
Ò
and substitute S = Rs2 ≠ x2b ≠ zb2 back into the equation
Ò Q R C D
zb · xb · Rs2 ≠ x2b ≠ zb2 1 xb 2 zb3
Vint = + · arctan a Ò b · Rs · zb ≠ (2.36)
3 2 R 2 ≠ x2 ≠ z 2 3
s b b
Q R C D Q R
1 zb x3 R3
b · R2 · xb ≠ b ≠ s · arctan a
zb · xb
+ · arctan a Ò Ò b.
2 2 2
R ≠x ≠z 2
s
3 3 2
Rs · R ≠ x ≠ z2 2
s b b s b b
This is the final equation for the internal volume, Vint , as a function of the octant radius,
Rs , and the boundary positions, xb and zb .
S-20
2.4 Proof for the Integral I1
In this section, we proof that the integral
⁄ Ô
I1 = A ≠ x2 dx, (A ≠ x2 ) > 0 (2.37)
is solved by C A BD
1 Ô x
· x · A ≠ x2 + A · arctan Ô + C. (2.38)
2 A ≠ x2
To do so, we take the derivative of equation (2.38) with respect to x. Note that
d 1
arctan (x) = . (2.39)
dx 1 + x2
The derivative is then given by
C A BD
d 1 Ô x
· x · A ≠ x2 + A · arctan Ô +C = (2.40)
dx 2 A ≠ x2
S Ô 1
T
1 U Ô 1 1 A ≠ x2 ≠ x · 2ÔA≠x 2 · (≠2x)
· 1 · A ≠ x2 + x · Ô · (≠2x) + A · · V.
2 2 A ≠ x2 x2
1 + A≠x 2 A ≠ x 2
We combine all fractions to get

C C DD
1 Ô x2 A Ô x2
· A ≠ x2 ≠ Ô + · A ≠ x 2+ Ô . (2.41)
2 A ≠ x2 A ≠ x2 + x2 A ≠ x2
Finally, we simplify the fractions and see that

C D
1 Ô x2 Ô x2 Ô
· A ≠ x2 ≠ Ô + A ≠ x 2+ Ô = A ≠ x2 , (2.42)
2 A ≠ x2 A ≠ x2
which is the integrand we were looking for. Therefore, the integral, I1 , is solved by the
anti-derivative given in equation (2.38).
S-21
In this section, we prove that the integral
⁄ A B
zb
I2 = arctan Ô dx, (A ≠ x2 ) > 0 (2.43)
A ≠ x2
is solved by the following anti-derivative
A B A B A B
x z x · zb
zb · arctan Ô + x · arctan Ô b ≠ R s · arctan Ô + C. (2.44)
A ≠ x2 A ≠ x2 Rs · A ≠ x 2
To prove that, we calculate the derivative with respect to x like
A B
d x
zb · arctan Ô (2.45)
dx A ≠ x2
A B
d zb
+ x· arctan Ô
dx A ≠ x2
A B
d x · zb
≠ Rs · arctan Ô +C
dx Rs · A ≠ x 2
We calculate the three derivatives individually. The first derivative is given by
A B Ô 1
d x 1 1 · A ≠ x2 ≠ x · 2·ÔA≠x 2 · (≠2x)
zb · arctan Ô = z · 2 · (2.46)
1 + A≠x A ≠ x2
b
dx A ≠ x2 x
2
we simplify the fractions and get

C D
zb Ô
2+ Ô
x2
· A ≠ x . (2.47)
A ≠ x2 + x2 A ≠ x2
The x2 cancel each other out, leaving us with
C D
zb Ô x2
· A ≠ x2 + Ô . (2.48)
A A ≠ x2
Next, we create equal denominators in the square brackets
C D
zb A ≠ x2 x2
· Ô + Ô , (2.49)
A A ≠ x2 A ≠ x2
which leaves us with
A B
d x zb
zb · arctan Ô =Ô . (2.50)
dx A ≠ x2 A ≠ x2
The second derivative is

A B
d zb
x· arctan Ô = (2.51)
dx A ≠ x2
A B Ô 1
zb 1 A ≠ x2 · 0 ≠ zb · 2ÔA≠x 2 · (≠2x)
1 · arctan Ô +x · 2 · 2
.
A ≠ x2 1 + A≠x
z b
2
A≠x
S-22
We combine the main fractions and get
A B
zb x zb · x
arctan Ô + ·Ô . (2.52)
A ≠ x2 A ≠ x + zb
2 2
A ≠ x2
Using our definition A = Rs2 ≠ zb2 we have

A B A B
d zb zb zb · x2
x · arctan Ô = arctan Ô + Ô . (2.53)
dx A ≠ x2 A ≠ x2 (Rs2 ≠ x2 ) · A ≠ x2
The third derivative is given by

A B
d zb · x
Rs · arctan Ô = (2.54)
dx Rs · A ≠ x 2
Ô
1 Rs · A ≠ x2 · zb ≠ zb · x · Rs · Ô1 · (≠2x)
2 A≠x2
Rs · · .
zb2 ·x2
1 + R2 ·(A≠x 2)
Rs2 · (A ≠ x2 )
s
We combine the main fraction while factoring out zb · Rs from the numerator, to get
C D
Rs2 · zb Ô
2+ Ô
x2
· A ≠ x (2.55)
Rs2 · (A ≠ x2 ) + zb2 · x2 A ≠ x2
Next, we create identical denominators in the square brackets
C D
Rs2 · zb A ≠ x2 x2
· Ô + Ô , (2.56)
Rs2 · (A ≠ x2 ) + zb2 · x2 A ≠ x2 A ≠ x2
Rs2 · zb A
·Ô , (2.57)
Rs · (A ≠ x ) + zb · x
2 2 2 2
A ≠ x2
Before we proceed, we take a closer look at the largest denominator and see that
1 2
Rs2 · A ≠ x2 + zb2 · x2 = (2.58)
Rs2 · A ≠ Rs2 · x2 + zb2 · x2 =
1 2
Rs2 · A + x2 · zb2 ≠ Rs2 .
Since
A = Rs2 ≠ zb2 … ≠A = (zb2 ≠ Rs2 ), (2.59)
we have 1 2
Rs2 · A ≠ A · x2 = A · Rs2 ≠ x2 . (2.60)
Using this identity in equation (2.57), we get
Rs2 · zb A
·Ô , (2.61)
A · (Rs ≠ x )
2 2
A ≠ x2
A B
d zb · x Rs2 · zb
Rs · arctan Ô = Ô . (2.62)
dx Rs · A ≠ x 2 (Rs2 ≠ x2 ) · A ≠ x2
S-23
Finally, we combine all the separate derivatives like
A B
z zb zb · x2 Rs2 · zb
Ô b + arctan Ô + Ô ≠ Ô . (2.63)
A≠x 2 A ≠ x2 (Rs2 ≠ x2 ) · A ≠ x2 (Rs2 ≠ x2 ) · A ≠ x2
We expand the first fraction to create equal denominators like
A B
(Rs2 ≠ x2 ) · zb z zb · x2 Rs2 · zb
Ô + arctan Ô b + Ô ≠ Ô .
(Rs2 ≠ x2 ) · A ≠ x2 A ≠ x2 (Rs2 ≠ x2 ) · A ≠ x2 (Rs2 ≠ x2 ) · A ≠ x2
(2.64)
Then, we add all fractions
A B
zb · (Rs2 ≠ x2 ) + zb · x2 ≠ Rs2 · zb zb
Ô + arctan Ô , (2.65)
(Rs ≠ x ) · A ≠ x
2 2 2 A ≠ x2
and expand the round brackets into
A B
zb · Rs2 ≠ zb · x2 + zb · x2 ≠ Rs2 · zb z
Ô + arctan Ô b . (2.66)
(Rs2 ≠ x2 ) · A ≠ x2 A ≠ x2
We see, that all terms in the numerator cancel each other out, leaving us with
A B
zb
arctan Ô , (2.67)
A ≠ x2
which is the integrand we were looking for. Therefore, the integral, I2 , is solved by the
anti-derivative given in equation (2.44).

In this section, we proof that the integral
⁄ A B
2 zb
I3 = x · arctan Ô dx, (A ≠ x2 ) > 0 (2.68)
A ≠ x2
is solved by
A B
zb Ô zb 1 2 x
≠ · x · A ≠ x2 ≠ · zb2 ≠ 3 · Rs2 · arctan Ô (2.69)
6 6 A ≠ x2
A B A B
3 3
x zb Rs zb · x
+ · arctan Ô ≠ · arctan Ô + C.
3 A ≠ x2 3 Rs · A ≠ x 2
To do so, we take the derivative of this solution with respect to x like
zb d Ô
· x· A ≠ x2
≠ (2.70)
6 dx A B
zb 1 2 2
2 d x
≠ · zb ≠ 3 · Rs · arctan Ô
6 dx A ≠ x2
A B
d x3 zb
+ · arctan Ô
dx 3 A ≠ x2
A B
Rs3 d zb · x
≠ · arctan Ô .
3 dx Rs · A ≠ x 2
S-24
We calculate the derivatives separately. The first derivative is given by
C D
zb d Ô zb Ô 1
≠ · x · A ≠ x2 = ≠ · 1 · A ≠ x2 + x · Ô · (≠2x) . (2.71)
6 dx 6 2 A ≠ x2
We simplify the terms in the square brackets and get
C D
zb x2 Ô
· Ô ≠ A ≠ x2 . (2.72)
6 A≠x 2
Then, we expand the second term in the square bracket

C D
zb x2 A ≠ x2
· Ô ≠ Ô , (2.73)
6 A ≠ x2 A ≠ x2
and simplify, which leaves us with
zb d Ô zb 2 · x2 ≠ A
≠ · x · A ≠ x2 = · Ô . (2.74)
6 dx 6 A ≠ x2
The second derivative is given by

A B
zb 1 2 d x
≠ · zb2 ≠ 3 · Rs2 · arctan Ô = (2.75)
6 dx A ≠ x2
Ô 1
zb 1 2 2
2 1 1 · A ≠ x2 ≠ x · 2ÔA≠x 2 · (≠2x)
≠ · zb ≠ 3 · Rs · · .
6 1 + A≠x2
x 2
A≠x 2
We multiply the fractions

C D
zb 1 2 1 Ô x2
≠ · zb2 ≠ 3 · Rs2 · A ≠ x 2+ Ô , (2.76)
6 A ≠ x2 + x2 A ≠ x2
and simplify to get
C D
zb · (zb2 ≠ 3 · Rs2 ) Ô x2
≠ · A≠x +
2 Ô . (2.77)
6·A A ≠ x2
Then, we expand the terms in the square brackets
C D
zb · (zb2 ≠ 3 · Rs2 ) A ≠ x2 x2
≠ · Ô + Ô , (2.78)
6·A A ≠ x2 A ≠ x2
A B
zb 1 2 2
2 d x zb · (zb2 ≠ 3 · Rs2 )
≠ · zb ≠ 3 · Rs · arctan Ô = ≠ Ô . (2.79)
6 dx A ≠ x2 6 · A ≠ x2
The third derivative is given by

A B
d x3 zb
· arctan Ô = (2.80)
dx 3 A ≠ x2
A B Ô 1
2 z x 3
1 A ≠ x2 · 0 ≠ zb · 2ÔA≠x 2 · (≠2x)
x · arctan Ô +
b
· · .
A ≠ x2 3 1+ b 2 z 2
A≠x 2
A≠x
S-25
We combine the fractions
A B
2 zb x3 1 x · zb
x · arctan Ô + · ·Ô , (2.81)
A ≠ x2 3 A ≠ x + zb
2 2
A ≠ x2
and simplify the denominator, using A = Rs2 ≠ zb2 , yielding
A B A B
d x3 zb 2 zb x4 · zb
· arctan Ô = x · arctan Ô + Ô .
dx 3 A ≠ x2 A ≠ x2 3 · (Rs2 ≠ x2 ) · A ≠ x2
(2.82)
The last derivative is given by
A B
R3 d zb · x
≠ s· arctan Ô = (2.83)
3 dx Rs · A ≠ x 2
Ô
Rs3 1 Rs · A ≠ x2 · zb ≠ zb · x · Rs · Ô1 · (≠2x)
2 A≠x2
≠ · · .
3 1 + 2 zb2 ·x2 2 Rs2 · (A ≠ x2 )
Rs ·(A≠x )
We combine the fractions, leaving us with

C D
zb · Rs4 1 Ô
2+ Ô
x2
≠ · 2 · A ≠ x . (2.84)
3 Rs · (A ≠ x2 ) + zb2 · x2 A ≠ x2
Before we proceed, we take a closer look at the largest denominator and see that
1 2
Rs2 · A ≠ x2 + zb2 · x2 = (2.85)
Rs2 · A ≠ Rs2 · x2 + zb2 · x2 =
1 2
Rs2 · A + x2 · zb2 ≠ Rs2 .
Since A = Rs2 ≠ zb2 … ≠A = zb2 ≠ Rs2 we get

1 2
Rs2 · A ≠ A · x2 = A · Rs2 ≠ x2 (2.86)
Using this identity, we combine the fractions to get
C D
Rs4 · zb Ô
2+ Ô
x2
≠ · A ≠ x . (2.87)
3 · A · (Rs2 ≠ x2 ) A ≠ x2
Next, we create equal denominator in the square brackets
C D
Rs4 · zb A ≠ x2 x2
≠ · Ô + Ô , (2.88)
3 · A · (Rs2 ≠ x2 ) A ≠ x2 A ≠ x2
A B
R3 d zb · x Rs4 · zb
≠ s· arctan Ô =≠ Ô . (2.89)
3 dx Rs · A ≠ x 2 3 · (Rs2 ≠ x2 ) · A ≠ x2
Finally, we sum up all the individual derivatives and get

A B
zb 2 · x2 ≠ A zb · (zb2 ≠ 3 · Rs2 ) zb
· Ô ≠ Ô + x2 · arctan Ô (2.90)
6 A≠x 2 6· A≠x 2 A ≠ x2
x4 · zb Rs4 · zb
+ Ô ≠ Ô .
3 · (Rs2 ≠ x2 ) · A ≠ x2 3 · (Rs2 ≠ x2 ) · A ≠ x2
S-26
We add the fractions like
A B
2 · x2 · zb ≠ A · zb ≠ zb3 + 3 · Rs2 · zb zb
Ô + x2 · arctan Ô (2.91)
6· A≠x 2 A ≠ x2
zb · (x4 ≠ Rs4 )
+ Ô .
3 · (Rs2 ≠ x2 ) · A ≠ x2
We simplify the second fraction with the third binomic equation:
(a + b) · (a ≠ b) = a2 ≠ b2 . (2.92)
This leaves us with

A B
2 · x2 · zb ≠ A · zb ≠ zb3 + 3 · Rs2 · zb zb · (x2 ≠ Rs2 ) · (x2 + Rs2 )
zb
Ô + x2 · arctan Ô+ Ô
6· A≠x 2 3 · (Rs2 ≠ x2 ) · A ≠ x2
A ≠ x2
(2.93)
We now cancel the Rs ≠ x = ≠(x ≠ Rs ) terms and are left with
2 2 2 2
A B
2 · x2 · zb ≠ A · zb ≠ zb3 + 3 · Rs2 · zb 2 z 2 · zb · (x2 + Rs2 )
Ô + x · arctan Ô b ≠ Ô . (2.94)
6 · A ≠ x2 A ≠ x2 6 · A ≠ x2
Again, we add the fractions with identical denominators. We also use A = Rs2 ≠ zb2 in the
numerator, giving us
A B
2 · x2 · zb ≠ (Rs2 ≠ zb2 ) · zb ≠ zb3 + 3 · Rs2 · zb ≠ 2 · zb · (x2 + Rs2 ) zb
Ô + x2 · arctan Ô
6· A≠x 2 A ≠ x2
(2.95)
We expand the terms in the round brackets
A B
2 · x2 · zb ≠ Rs2 · zb + zb3 ≠ zb3 + 3 · Rs2 · zb ≠ 2 · zb · x2 ≠ 2 · zb · Rs2 zb
Ô +x2 ·arctan Ô .
6· A≠x 2 A ≠ x2
(2.96)
All terms in the numerator cancel each other out, which leaves us with
A B
2 zb
x · arctan Ô . (2.97)
A ≠ x2
Therefore, the integral, I3 , is solved by the anti-derivative given in equation (2.69).
S-27
3 Pseudo code
Algorithm 1 Overlap volume between an octant and a corner

Ensure: R, xb , yb , zb Ø 0 Û Mirror into the all positive octant
1: procedure OctantVolume(R, xb , yb , zb )
2: if x2b + yb2 + zb2 Æ R2 then
3: return xb · yb · zb Û The corner is inside the octant
4: end if
5: VOctant Ω 18 · 43 · fi · R3 Û Start with a complete octant
6: for b œ [xb , yb , zb ] do
7: if b < R then Û Remove the spherical caps
8: VOctant Ω VOctant ≠ 12 · (2 · R ≠ 3 · b · R + b )
fi 3 2 3
9: end if
10: end for
11: for (a, b) œ [(xb , yb ), (xb , zb ), (yb , zb )] do
12: if a2 + b2 < R2 then Û Add the cap intersections
13: VOctant Ω VOctant + SphereCutVol(R, a, b)
14: end if
15: end for
16: return VOctant
17: end procedure
Algorithm 2 Compute the volume of a spherical cut.

Ensure: R, A, B Ø 0, A2 + B 2 < R2
1: procedure Ô SphereCutVol(R, A, B)
2: Root Ω R12 ≠ A2 ≠ B 2 1 22
3
3: Vcut Ω R6 · fi ≠ 2 · arctan R·Root
A·B
1 1 2 2 1 2
B3
4: Vcut Ω Vcut + 12 · arctan A
≠ fi
22
· R2 · B ≠ 3 2
1 1 Root 2 1
A3
5: Vcut Ω Vcut + 12 · arctan Root
B
≠ fi
2
· R2 · A ≠ 3
6: Vcut Ω Vcut + 13 · A · B · Root
7: return Vcut
8: end procedure
Algorithm 3 Compute the shell-box intersection volume.

Ensure: Rmin Ø 0, Rmax > 0, Rmin < Rmax , xmin < xmax , ymin < ymax , zmin < zmax
1: procedure ShellVolume(Rmin , Rmax , xmin , xmax , ymin , ymax , zmin , zmax )
2: InnerShell Ω SphereVolume(Rmin , xmin , xmax , ymin , ymax , zmin , zmax )
3: OuterShell Ω SphereVolume(Rmax , xmin , xmax , ymin , ymax , zmin , zmax )
4: return OuterShell ≠ InnerShell
5: end procedure
S-28
Algorithm 4 Compute the sphere-box intersection volume.
Ensure: R Ø 0, xmin < xmax , ymin < ymax , zmin < zmax
1: procedure SphereVolume(R, Boundaries)
2: VSphere Ω 0 Û Start with an empty volume
3: for xb œ [|xmin |, |xmax |] do
4: for yb œ [|ymin |, |ymax |] do
5: for zb œ [|zmin |, |zmax |] do
6: VSphere Ω VSphere + OctantVolume(R, xb , yb , zb )
7: end for
8: end for
9: end for
10: return VSphere
11: end procedure
Algorithm 5 Compute the shell-sphere intersection volume.

Ensure: Rmin Ø 0, Rmax > 0, Rmin < Rmax
1: procedure ShellSphereVolume(Rmin , Rmax , Rboundary , xc , yc , zc , CentralP )
2: dx Ω xc ≠ CentralP.XP os
3: dy Ω yc ≠ CentralP.Y P os
4: dz Ω zc ≠ Ô
CentralP.ZP os
5: P artD Ω dx2 + dy 2 + dz 2 Û Distance between the sphere and the shell centers
6: InnerSphere Ω SphereSphereVolume(Rmin , Rboundary , P artD)
7: OuterSphere Ω SphereSphereVolume(Rmax , Rboundary , P artD)
8: return OuterSphere ≠ InnerSphere
9: end procedure
Algorithm 6 Compute the sphere-sphere intersection volume.

Ensure: Rsphere Ø 0, Rboundary > 0, Dist > 0
1: procedure SphereSphereVolume(Rsphere , Rboundary , Dist)
2: if P artD > Rsphere + Rboundary then Û Check if the spheres intersect
3: return 0
4: end if
R2 2
≠Rsphere +Dist2
5: A Ω Rboundary ≠ boundary 2·Dist
R2 ≠R2 +P artD2
6: B Ω boundary 2·Dist
sphere
≠ (Dist ≠ Rsphere )
7: InnerCap Ω A · (3 · Rboundary ≠ A)
8: OuterCap Ω B · (3 · Rsphere ≠ B)
9: IntersectV ol Ω fi3 · (OuterCap + InnerCap)
10: return IntersectVol
11: end procedure
S-29
Algorithm 7 Compute g(r) from a particle set bounded by a rectangular box.
Ensure: r > 0, Rectangular box boundary. Û Positive radial bin size
1: procedure RDF(P articles, r)
2: Bounds Ω FindBoundary(P articles) Û Determine the sample boundaries
3: VSample Ω Bounds.Lx · Bounds.Ly · Bounds.Lz
4: RhoM ean Ω P articles.size()
VSample
Û Mean particle density
Ò
5: Rmax Ω 12 · Bounds.L2x + Bounds.L2y + Bounds.L2z Û Maximal radial distance
6: BinN um Ω Â Rmax r
Ê Û Number of radial bins
7: rΩ[] Û Empty list for the radial bins
8: for k = 0, k < BinN um do
9: r.append((k + 0.5) · r) Û List with radial bin centers
10: k Ωk+1
11: end for
12: Gr Ω [0...] Û Empty bins for g(r)
13: N onEmptyShells Ω [0...] Û Keeps track of non empty shells
14: for CentralP œ P articles do Û Use every particle as the center
15: LocalGr Ω [0...] Û Empty bins for the local g(r)
16: for N eighbor œ P articles · N eighbor ”= CentralP do
17: D Ω Distance(N eighbor, CentralP ) Û Inter particle distance
1
18: Idx Ω Â r · DÊ Û Index into LocalGr
19: LocalGr[Idx] Ω LocalGr[Idx] + 1 Û Bin the particle
20: end for
21: Shif tBounds Ω ShiftCenter(Bounds, CentralP ) Û Shift the COSY center
to CentralP
22: for k = 0, k < BinN um do Û Compute the local particle density
23: Vshell Ω ShellVolume(r[k] ≠ 2r , r[k] + 2r , Shif tBounds)
24: if Vshell > 0 then
25: LocalGr[k] Ω LocalGr[k]/Vshell Û Use the shell-box intersection volume
26: N onEmptyShells[k] Ω N onEmptyShells[k] + 1
27: end if Û Empty intersection volumes are not used
28: end for
29: Gr Ω Gr + LocalGr Û Add up all local g(r) bins for averaging
30: end for
32: Gr[k] Ω Gr[k]/N onEmptyShells[k] Û Average over all non emtpy shells
33: end for
34: Gr Ω RhoM Gr
ean
Û Final normalization by the average particle density
35: return r, Gr
36: end procedure
S-30
Algorithm 8 Compute g(r) from a particle set bounded by a sphere.
Ensure: r > 0, Rectangular box boundary. Û Positive radial bin size
1: procedure RDF(P articles, r)
2: xc Ω Mean(P articles.XP os) Û Determine the boundary sphere center
3: yc Ω Mean(P articles.Y P os)
4: zc Ω Mean(P articles.ZP os)
5: Radii Ω Distance(P articles, (xcenter , ycenter , zcenter )) Û Radial particle distances
from the center
6: Rboundary Ω Max(Radii) Û Sphere surrounding all particles
4 3
7: VSample Ω 3 · fi · Rboundary
8: RhoM ean Ω P articles.size()
VSample
Û Mean particle density
Û Number of radial bins
R
9: BinN um Ω Â boundary r
Ê
10: rΩ[] Û Empty list for the radial bins
12: r.append((k + 0.5) · r) Û List with radial bin centers
13: k Ωk+1
14: end for
15: Gr Ω [0...] Û Empty bins for g(r)
16: for CentralP œ P articles do Û Use every particle as the center
17: LocalGr Ω [0...] Û Empty bins for the local g(r)
18: for N eighbor œ P articles · N eighbor ”= CentralP do
19: dx Ω N eighbor.XP os ≠ CentralP.XP os Û Inter particle distance
20: dy Ω N eighbor.Y P os ≠ CentralP.Y P os
21: dz Ω N eighbor.ZP
1
Ô 2 os ≠2 CentralP.ZP os
22: Idx Ω Â r · dx + dy + dz Ê 2 Û Index into LocalGr
23: LocalGr[Idx] Ω LocalGr[Idx] + 1 Û Bin the particle
24: end for
25: for k = 0, k < BinN um do Û Compute the local particle density
26: Vshell Ω ShellSphereVolume(r[k] ≠ 2
r
, r[k] +
2
r
, Rboundary , xc , yc , zc , CentralP )
27: if Vshell > 0 then
28: LocalGr[k] Ω LocalGr[k]/Vshell Û Use the shell-box intersection volume
29: end if
30: end for
31: Gr Ω Gr + LocalGr Û Add up all local g(r) bins for averaging
32: end for
33: Gr
Gr Ω P articles.size() Û Average over all particles
34: Gr
Gr Ω RhoM ean Û Final normalization by the average particle density
35: return r, Gr
36: end procedure
S-31
4 Source code
4.1 FCC Coordinate Generation
1 from numpy i mp ort s q r t
2 from random i mpo rt random
3 from numpy . random i mpo rt normal
4 from m a t p l o t l i b . p y p l o t i mpo rt
5 from m p l _ t o o l k i t s . mplot3d i mp ort Axes3D
6
7 """
8 This program c a l c u l a t e s FCC c o o r d i n a t e s .
9 A 3D Gaussian d i s t u r b a n c e can be added .
10 Random Sph ere P o i n t P i c k i n g Algorithm from :
11 G. M a r s a g l i a , The Annals o f Mathematical S t a t i s t i c s ,
12 1 9 7 2 , Vol . 4 3 , No . 2 , 845 ≠646
13 """
14
15 ### DASHBOARD
16
17 SimuName = " FCC_Blurr_Cube " # Name o f t h e Experiment and t h e F i l e s
18 GitterKonst = sqrt (2) # C e l l c o n s t a n t f o r t h e FCC u n i t c e l l
19 PartDiam = 1 # Diameter o f t h e P a r t i c l e s
20 B l u r r = True # add a 3D g a u s s i a n b l u r r ?
21 sigma = 0 . 0 7 # standard d e v i a t i o n of the b l u r r
22 Lx = 4 # D i s t a n c e i n x≠d i r e c t i o n from ≠Lx t o Lx
23 Ly = 4 # D i s t a n c e i n y≠d i r e c t i o n from ≠Ly t o Ly
24 Lz = 4 # D i s t a n c e i n z≠d i r e c t i o n from ≠Lz t o Lz
25
26 """ """
27
28 d e f calcFCCCoor ( G i t t e r K o n s t , Lx , Ly , Lz ) :
29
30 CoorList = [ ]
31
32 XLim = i n t ( Lx/ G i t t e r K o n s t 5 )
33 YLim = i n t ( Ly/ G i t t e r K o n s t 5 )
34 ZLim = i n t ( Lz/ G i t t e r K o n s t 5 )
35
36 L = G i t t e r K o n s t /2
37
38 A = [0 , L, L]
39 B = [L, 0 , L]
40 C = [L, L, 0]
41
42 f o r h i n r a n g e (≠ZLim 2 , ZLim 2 , 1 ) :
43 f o r k i n r a n g e (≠YLim 2 , YLim 2 , 1 ) :
44 f o r l i n r a n g e (≠XLim 2 , XLim 2 , 1 ) :
45
46 NewX = h A[ 0 ] + k B[ 0 ] + l C[ 0 ]
47 NewY = h A[ 1 ] + k B[ 1 ] + l C[ 1 ]
48 NewZ = h A[ 2 ] + k B[ 2 ] + l C[ 2 ]
49
50 i f abs (NewX) < Lx and \
51 abs (NewY) < Ly and \
52 abs (NewZ) < Lz :
53
54 C o o r L i s t . append ( [ NewX, NewY, NewZ ] )
55
56 return CoorList
57
58 """ """
59
60 d e f g e t R a n d O f f s e t ( sigma ) :
61
62 x1 = 2
63 x2 = 2
64
65 w h i l e x1 2 + x2 2 >= 1 :
66
67 x1 = random () 2 ≠1
68 x2 = random () 2 ≠1
S-32
69
70 R = normal ( 0 , sigma )
71
72 Wurzel = s q r t ( 1 ≠ x1 2 ≠ x2 2)
73 x = 2 x1 Wurzel
74 y = 2 x2 Wurzel
75 z = 1 ≠ 2 ( x1 2 + x2 2 )
76
77 return [ x R, y R, z R]
78
79 """ """
80
81 d e f a d d G a u s s i a n B l u r r ( C o o r L i s t , sigma ) :
82
83 BlurrList = [ ]
84
85 f o r P in CoorList :
86
87 O f f s e t = g e t R a n d O f f s e t ( sigma )
88
89 NewX = P [ 0 ] + O f f s e t [ 0 ]
90 NewY = P [ 1 ] + O f f s e t [ 1 ]
91 NewZ = P [ 2 ] + O f f s e t [ 2 ]
92
93 B l u r r L i s t . append ( [ NewX, NewY, NewZ ] )
94
95 return BlurrList
96
97 """ """
98
99 d e f p l o t C o r r ( C o o r L i s t , SimuName ) :
100
101 X = [0] len ( CoorList )
102 Y = [0] len ( CoorList )
103 Z = [0] len ( CoorList )
104
105 f o r P in range (0 , len ( CoorList ) , 1 ) :
106
107 X[ P ] = C o o r L i s t [ P ] [ 0 ]
108 Y[ P ] = C o o r L i s t [ P ] [ 1 ]
109 Z [P] = CoorList [P ] [ 2 ]
110
111 fig = figure ()
112 ax = f i g . add_subplot ( 1 1 1 , p r o j e c t i o n = " 3d " , a s p e c t = " e q u a l " )
113
114 ax . s c a t t e r (X, Y, Z )
115
116 ax . s e t _ x l a b e l ( "X" )
117 ax . s e t _ y l a b e l ( "Y" )
118 ax . s e t _ z l a b e l ( " Z " )
119
120 s a v e f i g ( SimuName + "_3D . png " , d p i = 6 0 0 )
121 show ( )
122
123 r e t u r n True
124
125 """ """
126
127 d e f saveData ( C o o r L i s t , SimuName ) :
128
129 D a t a F i l e = open ( SimuName + " _rawCoor . t x t " , "w" )
130
131 f o r P a r t i c l e in CoorList :
132
133 D a t a F i l e . w r i t e ( s t r ( P a r t i c l e [ 0 ] ) + " \ t " +\
134 s t r ( P a r t i c l e [ 1 ] ) + " \ t " +\
135 s t r ( P a r t i c l e [ 2 ] ) + " \n " )
136
137 DataFile . c l o s e ()
138
140
141 """ """
S-33
142
143 d e f createAutoCADFile ( C o o r L i s t , PartDiam , SimuName ) :
144
145 CADFile = open ( SimuName + "_CAD. s c r " , "w" )
146
147 f o r P a r t i c l e in CoorList :
148
149 CADFile . w r i t e ( "SPHERE\n " ) # SPHERE command
150 CADFile . w r i t e ( s t r ( round ( P a r t i c l e [ 0 ] , 5 ) ) + " , " ) # X≠P o s i t i o n
151 CADFile . w r i t e ( s t r ( round ( P a r t i c l e [ 1 ] , 5 ) ) + " , " ) # Y≠P o s i t i o n
152 CADFile . w r i t e ( s t r ( round ( P a r t i c l e [ 2 ] , 5 ) ) + " \n " )# Z≠P o s i t i o n
153 CADFile . w r i t e ( s t r ( PartDiam / 2 ) + " \n " ) # Radius
154
155 CADFile . w r i t e ( " \n " ) # Blank l i n e a t t h e end
156 CADFile . c l o s e ( )
157
159
160 """ """
161
162 ###MAIN
163
164 p r i n t ( " C a l c u l a t i n g FCC C o o r d i n a t e s . " )
165 FCC = calcFCCCoor ( G i t t e r K o n s t , Lx , Ly , Lz )
166
167 p r i n t ( " P a r t i c l e Number : " + s t r ( l e n (FCC) ) )
168
169 i f B l u r r == True :
170
171 p r i n t ( " Adding a Gaussian b l u r r with Sigma = " + s t r ( sigma ) )
172 FCC = a d d G a u s s i a n B l u r r (FCC, sigma )
173
174 p r i n t ( " Saveing the Coordinats to a . txt file .")
175 saveData (FCC, SimuName )
176
177 p r i n t ( " C r e a t i n g a AutoCAD f i l e . " )
178 createAutoCADFile (FCC, PartDiam , SimuName )
179
180 p r i n t ( " P l o t t i n g the Coordinates . " )
181 p l o t C o r r (FCC, SimuName )
4.2 Simple g(r) Implementation in Python 3

1 from s c i p y im po rt s p a t i a l
2 from numpy i mp ort s q r t , pi , z e r o s
3
4 """
5 This f u n c t i o n c a l c u l a t e s t h e p a i r c o r r e l a t i o n f u n c t i o n g ( 2 ) ( r )
6 f o r a d e n s e s e t o f p a r t i c l e s i n a r e c t e n g u l a r box . The p a r t i c l e
7 c o o r d i n a t e s are supplied as [ [ x , y , z ] , . . . ] l i s t s .
8 A l l p a r t i c l e s a r e used a s c e n t r a l p a r t i c l e s .
9 The s p h e r i c a l s h e l l might e x t e n d beyond t h e known r e g i o n .
10 A KDTree data s t r u c t u r e i s used f o r e f f i c i e n c y .
11 """
12
13 """ """
14
15 d e f RDF_Simple ( P a r t i c l e s , r , dr ) :
16
17 # p r e a l l o c a t e l i s t f o r Gr
18 Gr = z e r o s ( l e n ( r ) )
19
20 # maximal r a d i a l d i s t a n c e
21 MaxDist = r [ ≠ 1 ] + dr /2
22
23 # s o r t a l l P a r t i c l e s i n a KDTree
24 P a r t i c l e T r e e = s p a t i a l . KDTree ( P a r t i c l e s )
25
26 # u s e e v e r y p a r t i c l e a s t h e c e n t e r once
27 k = 0
28 f o r C ent ralP i n P a r t i c l e s :
S-34
29
30 # t h e s e a r e t h e i n d i c e s f o r t h e p a r t i c l e s a t most MaxDist away :
31 NNIndices = P a r t i c l e T r e e . q u e r y _ b a l l _ p o i n t ( CentralP , \
32 MaxDist , p = 2 , e p s = 0 )
33
34 # l o o k a t e v e r y o t h e r p a r t i c l e a t most MaxDist away :
35 f o r Neighbour i n NNIndices :
36
37 i f Ce ntr alP != P a r t i c l e s [ Neighbour ] :
38
39 # c a l c the d i s t a n c e to the neighbour
40 dx = C ent ral P [ 0 ] ≠ P a r t i c l e s [ Neighbour ] [ 0 ]
41 dy = C ent ral P [ 1 ] ≠ P a r t i c l e s [ Neighbour ] [ 1 ]
42 dz = Ce ntr alP [ 2 ] ≠ P a r t i c l e s [ Neighbour ] [ 2 ]
43
44 d = s q r t ( dx 2 + dy 2 + dz 2)
45
46 # what b i n s i s t h e p a r t i c l e i n ?
47 I d x L i s t = [ k f o r k in range (0 , len ( r ) , 1)\
48 i f abs ( r [ k ] ≠ d ) <= dr ]
49
50 # add one t o e v e r y b i n t h e p a r t i c l e i s in
51 f o r Pos i n I d x L i s t :
52
53 # count t h e p a r t i c l e
54 Gr [ Pos ] += 1
55 k += 1
56 print ( " Finished Particle " + st r (k) + " of " + st r ( len ( P a r t i c l e s ) ) )
57
58 # f i n a l normalization
59 Gr [ 0 ] = 0
60
61 BoxVol = (max( P a r t i c l e s [ 0 ] ) ≠ min ( P a r t i c l e s [ 0 ] ) ) \
62 (max( P a r t i c l e s [ 1 ] ) ≠ min ( P a r t i c l e s [ 1 ] ) ) \
63 (max( P a r t i c l e s [ 2 ] ) ≠ min ( P a r t i c l e s [ 2 ] ) )
64
65 f o r i in range (1 , len ( r ) , 1 ) :
66
67 Gr [ i ] /= l e n ( P a r t i c l e s ) # a v e r a g e o v e r a l l c e n t r a l p a r t i c l e s
68
69 # t h e most i n n e r s h e l l s a r e s p h e r e s !
70 i f r [ i ]≠ dr /2 > 0 :
71
72 # by t h e s h e l l volume
73 Gr [ i ] /= 4/3 p i ( ( r [ i ] + dr / 2 ) 3 ≠ ( r [ i ]≠ dr / 2 ) 3)
74
75 else :
76 Gr [ i ] /= 4/3 pi ( r [ i ] + dr / 2 ) 3 # by t h e s h e l l volume
77
78 Gr [ i ] = BoxVol / l e n ( P a r t i c l e s ) # by t h e number d e n s i t y
79
80 r e t u r n Gr
81
82 """ """
4.3 Analytic g(r) Implementation in Python 3

1 from numpy i mp ort s q r t , pi , z e r o s , ones , a r c t a n
2 from random i mpo rt random , s e e d
3 from time im po rt time
4 s e e d ( time ( ) )
5
6 """
7 This f u n c t i o n c a l c u l a t e s t h e p a i r c o r r e l a t i o n f u n c t i o n g ( 2 ) ( r )
8 f o r a d e n s e s e t o f p a r t i c l e s i n a r e c t e n g u l a r box . The p a r t i c l e
9 c o o r d i n a t e s are supplied as [ [ x , y , z ] , . . . ] l i s t s .
10 A l l p a r t i c l e s a r e used a s c e n t r a l p a r t i c l e s .
11 The s p h e r i c a l s h e l l might e x t e n d beyond t h e known r e g i o n .
12 An empty s o u r r o u n d i n g i s assumed .
13 """
14
S-35
15 """ """
16
17 d e f SphereCutVol ( Rs , A, B ) :
18
19 Root = s q r t ( Rs 2≠A 2≠B 2)
20
21 Vcut = 1/6 Rs 3 ( p i ≠ 2 a r c t a n (A B/ ( Rs Root ) ) )
22 Vcut += 1/2 ( a r c t a n (A/ Root ) ≠ p i / 2 ) ( Rs 2 B≠1/3 B 3)
23 Vcut += 1/2 ( a r c t a n (B/ Root ) ≠ p i / 2 ) ( Rs 2 A≠1/3 A 3)
24 Vcut += 1/3 A B Root
25
26 r e t u r n Vcut
27
28 """ """
29
31
32 # i f a l l boundaries are f u l l y in the octant
33 i f xb 2 + yb 2 + zb 2 < Rs 2 :
34
36
37 # i f no boundary i n t e r s e c t s we s t a r t with
38 VOctant = 1/8 4/3 pi Rs 3
39
40 # remove t h e s p h e r i c a l c a p s
41 f o r B i n [ xb , yb , zb ] :
42
43 i f B < Rs :
44
46
47 # add t h e i n t e r s e c t i o n s o f t h e c a p s
49
50 if a 2 + b 2 < Rs 2:
51
52 VOctant += SphereCutVol ( Rs , a , b )
53
55
56 """ """
57
58 d e f SphereVolume ( Rs , BoxBounds ) :
59
60 [ Xmin , Xmax, Ymin , Ymax, Zmin , Zmax ] = BoxBounds
61
62 VSphere = 0
63
65 f o r xb i n [ Xmin , Xmax ] :
66 f o r yb i n [ Ymin , Ymax ] :
67 f o r zb i n [ Zmin , Zmax ] :
68
69 VSphere += OctVolume ( Rs , abs ( xb ) , abs ( yb ) , abs ( zb ) )
70
72
73 """ """
74
75 d e f S h e l lV o l u m e ( Rmin , Rmax , BoxBounds ) :
76
77 # c h e c k f o r n e g a t i v e Rmin v a l u e s
78 Rmin = max ( [ Rmin , 0 ] )
79
80 I n n e r S h e l l = SphereVolume ( Rmin , BoxBounds )
81 O u t e r S h e l l = SphereVolume (Rmax , BoxBounds )
82
83 Volume = O u t e r S h e l l ≠ I n n e r S h e l l
84
85 ## i f Volume <= 0 :
86 ## p r i n t ( " Volume = " + s t r ( Volume ) )
87 ## p r i n t ( " Rmin = " + s t r ( Rmin ) )
S-36
88 ## p r i n t ( " Rmax = " + s t r (Rmax ) )
89 ## p r i n t ( " BoxBounds : " + s t r ( BoxBounds ) )
90
91 r e t u r n Volume
92
93 """ """
94
95 d e f RDF_AnalyticNorm ( P a r t i c l e s , r , dr ) :
96
97 # Gr a v e r a g e d o v e r a l l p a r t i c l e s
98 Global_Gr = z e r o s ( l e n ( r ) )
99
100 # Keep t r a c k o f t h e u s e f u l l s h e l l volumes
101 NonEmptyShells = z e r o s ( l e n ( r ) )
102
103 # maximal r a d i a l d i s t a n c e
104 MaxDist = r [ ≠ 1 ] + dr /2
105
106 # Box boundaries
107 X Li s t = [ Particles [k ] [ 0 ] f o r k in range (0 , len ( P a r t i c l e s ) , 1 ) ]
108 Y Li s t = [ Particles [k ] [ 1 ] f o r k in range (0 , len ( P a r t i c l e s ) , 1 ) ]
109 ZList = [ Particles [k ] [ 2 ] f o r k in range (0 , len ( P a r t i c l e s ) , 1 ) ]
110
111 BoxBounds = [ min ( X Li s t ) , max( X Li s t ) , \
112 min ( Y Li s t ) , max( Y Li s t ) , \
113 min ( Z L i s t ) , max( Z L i s t ) ]
114
115 # box s i z e
116 Lx = BoxBounds [ 1 ] ≠ BoxBounds [ 0 ]
117 Ly = BoxBounds [ 3 ] ≠ BoxBounds [ 2 ]
118 Lz = BoxBounds [ 5 ] ≠ BoxBounds [ 4 ]
119
120 p r i n t ( " Lx = " + s t r ( Lx ) )
121 p r i n t ( " Ly = " + s t r ( Ly ) )
122 p r i n t ( " Lz = " + s t r ( Lz ) )
123
124 MeanDensity = l e n ( P a r t i c l e s ) / ( Lx Ly Lz )
125
126 # u s e e v e r y p a r t i c l e a s t h e c e n t e r once
127 f o r Ce ntr alP i n r a n g e ( 0 , l e n ( P a r t i c l e s ) , 1 ) :
128
129 # l o c a l Gr around t h e c u r r e n t p a r t i c l e
130 Local_Gr = z e r o s ( l e n ( r ) )
131
132 # l o o k a t e v e r y o t h e r p a r t i c l e a t most MaxDist away :
133 f o r Neighbour i n r a n g e ( 0 , l e n ( P a r t i c l e s ) , 1 ) :
134
135 i f Ce ntr alP != Neighbour :
136
137 # c a l c the d i s t a n c e to the neighbour
138 dx = P a r t i c l e s [ C ent ral P ] [ 0 ] ≠ P a r t i c l e s [ Neighbour ] [ 0 ]
139 dy = P a r t i c l e s [ C ent ral P ] [ 1 ] ≠ P a r t i c l e s [ Neighbour ] [ 1 ]
140 dz = P a r t i c l e s [ Ce ntr alP ] [ 2 ] ≠ P a r t i c l e s [ Neighbour ] [ 2 ]
141
142 d = s q r t ( dx 2 + dy 2 + dz 2)
143
144 # what b i n s i s t h e p a r t i c l e i n ?
145 I d x L i s t = [ k f o r k i n r a n g e ( 0 , l e n ( r ) , 1 ) i f abs ( r [ k ] ≠ d ) <= dr / 2 ]
146
147 # add one t o e v e r y b i n t h e p a r t i c l e i s in
148 f o r Pos i n I d x L i s t :
149
150 # count t h e p a r t i c l e
151 Local_Gr [ Pos ] += 1
152
153 # s h i f t t h e c e n t e r o f box c o s y
154 LocalBox = [ BoxBounds [ 0 ] ≠ P a r t i c l e s [ Ce ntralP ] [ 0 ] , \
155 BoxBounds [ 1 ] ≠ P a r t i c l e s [ Ce ntralP ] [ 0 ] , \
159 BoxBounds [ 5 ] ≠ P a r t i c l e s [ Ce ntralP ] [ 2 ] ]
160
S-37
161 # n o r m a l i z e with t h e s h e l l volume
162 f o r RIdx i n r a n g e ( 0 , l e n ( r ) , 1 ) :
163
164 SVolume = S h e l l V o l u m e ( r [ RIdx]≠ dr / 2 , r [ RIdx]+ dr / 2 , LocalBox )
165
166 i f SVolume > 0 . 0 :
167
168 Local_Gr [ RIdx ] /= SVolume
169 NonEmptyShells [ RIdx ] += 1
170
171 # n o r m a l i z e by t h e mean p a r t i c l e d e n s i t y
172 Local_Gr = Local_Gr / MeanDensity
173
174 # save in the g l o b a l gr f o r the average over p a r t i c l e s
175 Global_Gr = Global_Gr + Local_Gr
176
177 p r i n t ( " F i n i s h e d P a r t i c l e " + s t r ( Cen tra lP ) + " o f " + s t r ( l e n ( P a r t i c l e s ) ) )
178
179 # f i n a l n o r m a l i z a t i o n c o n s i d e r i n g t h e non empty s h e l l volumes
180
181 f o r k i n r a n g e ( 0 , l e n ( Global_Gr ) , 1 ) :
182
183 i f NonEmptyShells [ k ] != 0 :
184
185 Global_Gr [ k ] /= NonEmptyShells [ k ]
186
187 else :
188 p r i n t ( " All S h e l l s at R = " + s t r ( r [ k ] ) + " a r e Empty ! " )
189
190 r e t u r n Global_Gr
191
192 """ """
4.4 Analytic - Internal Volume

1 d e f VInt_Analytic ( Rs , xb , zb ) :
2
3 S = s q r t ( Rs 2≠xb 2≠zb 2)
4
5 Vint = 1/3 ( xb zb S)
6 Vint += 1/2 a r c t a n ( xb/S ) ( Rs 2 zb ≠(1/3) zb 3)
7 Vint += 1/2 a r c t a n ( zb /S ) ( Rs 2 xb ≠(1/3) xb 3)
8 Vint ≠= 1/3 Rs 3 a r c t a n ( xb zb / ( Rs S))
9
10 r e t u r n Vint
4.5 Monte Carlo - Internal Volume

1 d e f VInt_MC( Rs , xb , zb , NPoints ) :
2
3 InsidePoints = 0
4
5 f o r k i n r a n g e ( 0 , NPoints , 1 ) :
6
7 # random p o i n t i n t h e f i r s t ( Rs , Rs , Rs ) o c t a n t
8 XRand = random ( ) Rs
9 YRand = random ( ) Rs
10 ZRand = random ( ) Rs
11
12 i f XRand 2 + YRand 2 + ZRand 2 < Rs 2 and \
13 XRand < xb and ZRand < zb :
14
15 I n s i d e P o i n t s += 1
16
17 r e t u r n I n s i d e P o i n t s / NPoints Rs 3
S-38
4.6 Numeric Integration - Internal Volume
1 from numpy i mp ort s q r t , pi , a r c t a n , l i n s p a c e , a r r a y
2 from s c i p y . i n t e g r a t e i mpo rt quad
3
4 d e f VInt_Num( Rs , xb , zb ) :
5
6 d e f h e i g h t ( x , z , Rs ) :
7
8 r e t u r n s q r t ( Rs 2 ≠ x 2 ≠ z 2)
9
10 d e f VInt ( zb , Rs ) :
11
12 r e t u r n quad ( h e i g h t , 0 , xb , a r g s = ( zb , Rs ) ) [ 0 ]
13
14 Volume = quad ( VInt , 0 , zb , a r g s = ( Rs ) ) [ 0 ]
15
16 r e t u r n Volume
4.7 Analytic - Spherical Cut Volume

1 d e f SphereCutVol ( Rs , A, B ) :
2
3 Root = s q r t ( Rs 2≠A 2≠B 2)
4
5 Vcut = 1/6 Rs 3 ( p i ≠ 2 a r c t a n (A B/ ( Rs Root ) ) )
6 Vcut += 1/2 ( a r c t a n (A/ Root ) ≠ p i / 2 ) ( Rs 2 B≠1/3 B 3)
7 Vcut += 1/2 ( a r c t a n (B/ Root ) ≠ p i / 2 ) ( Rs 2 A≠1/3 A 3)
8 Vcut += 1/3 A B Root
9
10 r e t u r n Vcut
4.8 The Octant Sum

1 d e f SphereVolume ( Rs , Xmin , Xmax, Ymin , Ymax, Zmin , Zmax ) :
2
3 VSphere = 0
4
6 f o r xb i n [ abs ( Xmin ) , abs (Xmax ) ] :
7 f o r yb i n [ abs ( Ymin ) , abs (Ymax ) ] :
8 f o r zb i n [ abs ( Zmin ) , abs (Zmax ) ] :
9
10 VSphere += OctVolume ( Rs , xb , yb , zb )
11
4.9 The Octant Volume

2
3 # i f a l l boundaries i n t e r s e c t i n s i d e the octant
4 i f xb 2 + yb 2 + zb 2 < Rs 2 :
5
7
8 # i f t h e y dont i n t e r s e c t we s t a r t with a f u l l o c t a n t
9 VOctant = 1/8 4/3 pi Rs 3
10
11 # then , we remove t h e s p h e r i c a l c a p s
12 f o r B i n [ xb , yb , zb ] :
13
14 i f B < Rs :
16
S-39
17 # f i n a l l y , we add t h e i n t e r s e c t i o n s o f t h e c a p s
19
20 if a 2 + b 2 < Rs 2:
21
22 VOctant += VSphereCut ( Rs , a , b )
23
S-40
4.10 Monte Carlo - Spherical Cut Volume
1 d e f SphereCutVol_MC ( Rs , A, B, NPoints ) :
2
3 InsidePoints = 0
4
6
7 # random p o i n t i n t h e f i r s t ( Rs , Rs , Rs ) o c t a n t
8 XRand = random ( ) Rs
9 YRand = random ( ) Rs
10 ZRand = random ( ) Rs
11
12 i f XRand 2 + YRand 2 + ZRand 2 < Rs 2 and \
13 XRand > A and YRand > B :
14
15 I n s i d e P o i n t s += 1
16
17 r e t u r n I n s i d e P o i n t s / NPoints Rs 3
4.11 Monte Carlo - Sphere Volume

1 d e f SphereVolume_MC ( Rs , Xmin , Xmax, Ymin , Ymax, Zmin , Zmax , NPoints ) :
2
3 InsidePoints = 0
4
6
7 # random p o i n t i n t h e box
8 XRand = random ( ) (Xmax≠Xmin ) + Xmin
9 YRand = random ( ) (Ymax≠Ymin ) + Ymin
10 ZRand = random ( ) (Zmax≠Zmin ) + Zmin
11
12 # i f the point i s i n s i d e the sphere
13 i f XRand 2 + YRand 2 + ZRand 2 < Rs 2:
14
15 I n s i d e P o i n t s += 1
16
17 r e t u r n I n s i d e P o i n t s / NPoints (Xmax≠Xmin ) ( Ymax≠Ymin ) ( Zmax≠Zmin )
4.12 Simple g(r) in C++

1 #i n c l u d e 
2 #i n c l u d e <s s t r e a m >
3 #i n c l u d e <chrono>
4 #i n c l u d e <cmath>
5 #i n c l u d e <c s t d l i b >
6 #i n c l u d e <s t r i n g >
7 #i n c l u d e <f s t r e a m >
8 #i n c l u d e 
9 #i n c l u d e <v e c t o r >
10 #i n c l u d e <s t r ea m b uf >
11
12 long double pi = 3.1415926535897932384626433;
13
14 / /
15 struct Box
16 {
17 long d o u b l e Xmin = 0;
18 long d o u b l e Xmax = 0;
19 long d o u b l e Ymin = 0;
20 long d o u b l e Ymax = 0;
21 long d o u b l e Zmin = 0;
22 long d o u b l e Zmax = 0;
23 long i n t PartNum = 0;
24 };
25
S-41
26 / /
27
28 struct Particle
29 {
30 long d o u b l e XPos = 0 ;
31 long d o u b l e YPos = 0 ;
32 long d o u b l e ZPos = 0 ;
33 };
34
35 / /
36
37 s t d : : v e c t o r <s t d : : s t r i n g > s p l i t ( c o n s t s t d : : s t r i n g& s , c h a r d e l i m i t e r )
38 {
39 s t d : : v e c t o r <s t d : : s t r i n g > t o k e n s ;
40 std : : s t r i n g token ;
41 s t d : : i s t r i n g s t r e a m tokenStream ( s ) ;
42
43 w h i l e ( s t d : : g e t l i n e ( tokenStream , token , d e l i m i t e r ) )
44 {
45 t o k e n s . push_back ( t o k e n ) ;
46 }
47 return tokens ;
48 };
49
50 / /
51
52 i n l i n e s t d : : v e c t o r r e a d P a r t C o o r ( c o n s t s t d : : s t r i n g FileName )
53 {
54 // open t h e raw data f i l e
55 s t d : : i f s t r e a m D a t a F i l e ( FileName + " . t x t " ) ;
56 s t d : : s t r i n g TxtData ;
57
58 // g e t l e n g t h o f f i l e :
59 D a t a F i l e . s e e k g ( 0 , s t d : : i o s : : end ) ; // go t o t h e end o f t h e f i l e
60 TxtData . r e s e r v e ( D a t a F i l e . t e l l g ( ) ) ; // a l l o c a t e enough s p a c e
61 D a t a F i l e . s e e k g ( 0 , s t d : : i o s : : beg ) ; // go t o t h e b e g i n n i n g o f t h e f i l e
62
63 TxtData . a s s i g n ( ( s t d : : i s t r e a m b u f _ i t e r a t o r <char >( D a t a F i l e ) ) ,
64 s t d : : i s t r e a m b u f _ i t e r a t o r <char > ( ) ) ;
65
66 DataFile . c l o s e ( ) ;
67
68 // s p l i t t h e data i n t o l i n e s
69 s t d : : v e c t o r <s t d : : s t r i n g > d a t a l i n e s = s p l i t ( TxtData , ’ \n ’ ) ;
70
71 Particle P; // s i n g l e p a r t i c l e s t r u c t
72 s t d : : v e c t o r P a r t i c l e s ; // l i s t of p a r t i c l e s
73
74 std :: cout << " The f i r s t l i n e s i n t h e raw data f i l e a r e : " << s t d : : e n d l ;
75 std :: cout << d a t a l i n e s . a t ( 0 ) << s t d : : e n d l ;
79
80 s t d : : c o u t << " The RawDataFile has " << d a t a l i n e s . s i z e ( ) << " l i n e s . " << s t d : : e n d l ;
81
82 f o r ( l o n g i n t k = 0 ; k < d a t a l i n e s . s i z e ( ) ; k++)
83 {
84 s t d : : v e c t o r <s t d : : s t r i n g > r e s u l t s ;
85
86 // s p l i t t h e i n d i v i d u a l l i n e s (X, Y, Z )
87 r e s u l t s = s p l i t ( d a t a l i n e s . at ( k ) , ’ \ t ’ ) ;
88
89 // s a v e t h e s i n g l e p a r t i c l e positions
90 P . XPos = s t d : : s t o l d ( r e s u l t s . at ( 0 ) ) ;
91 P . YPos = s t d : : s t o l d ( r e s u l t s . at ( 1 ) ) ;
92 P . ZPos = s t d : : s t o l d ( r e s u l t s . at ( 2 ) ) ;
93
94 P a r t i c l e s . push_back (P ) ;
95 }
96
97 return Particles ;
98 };
S-42
99
100 / /
101
102 i n l i n e Box FindBoxBounds ( c o n s t s t d : : v e c t o r P a r t i c l e s )
103 {
104 // Box b o u n d a r i e s
105 Box BoxBounds ;
106
107 // i n i t i a l i z e t h e b o u n d a r i e s with t h e f i r s t particle
108 BoxBounds . Xmin = P a r t i c l e s . a t ( 0 ) . XPos ;
109 BoxBounds . Xmax = P a r t i c l e s . a t ( 0 ) . XPos ;
110 BoxBounds . Ymin = P a r t i c l e s . a t ( 0 ) . YPos ;
111 BoxBounds . Ymax = P a r t i c l e s . a t ( 0 ) . YPos ;
112 BoxBounds . Zmin = P a r t i c l e s . a t ( 0 ) . ZPos ;
113 BoxBounds . Zmax = P a r t i c l e s . a t ( 0 ) . ZPos ;
114 BoxBounds . PartNum = P a r t i c l e s . s i z e ( ) ;
115
116 // l o o p o v e r a l l o t h e r p a r t i c l e s and f i n d minima and maxima
117 f o r ( l o n g i n t Pos = 1 ; Pos < P a r t i c l e s . s i z e ( ) ; Pos++)
118 {
119 i f ( P a r t i c l e s . a t ( Pos ) . XPos < BoxBounds . Xmin )
120 BoxBounds . Xmin = P a r t i c l e s . a t ( Pos ) . XPos ;
121
122 i f ( P a r t i c l e s . a t ( Pos ) . XPos > BoxBounds . Xmax)
123 BoxBounds . Xmax = P a r t i c l e s . a t ( Pos ) . XPos ;
124
125 i f ( P a r t i c l e s . a t ( Pos ) . YPos < BoxBounds . Ymin )
126 BoxBounds . Ymin = P a r t i c l e s . a t ( Pos ) . YPos ;
127
128 i f ( P a r t i c l e s . a t ( Pos ) . YPos > BoxBounds . Ymax)
129 BoxBounds . Ymax = P a r t i c l e s . a t ( Pos ) . YPos ;
130
131 i f ( P a r t i c l e s . a t ( Pos ) . ZPos < BoxBounds . Zmin )
132 BoxBounds . Zmin = P a r t i c l e s . a t ( Pos ) . ZPos ;
133
134 i f ( P a r t i c l e s . a t ( Pos ) . ZPos > BoxBounds . Zmax)
135 BoxBounds . Zmax = P a r t i c l e s . a t ( Pos ) . ZPos ;
136 };
137
138 / p r i n t the boundaries to the c o n s o l e
139 s t d : : c o u t << " I found t h e Box B o u n d a r i e s : " << s t d : : e n d l ;
140 s t d : : c o u t << " Xmin = " << BoxBounds . Xmin << std : : endl ;
141 s t d : : c o u t << "Xmax = " << BoxBounds . Xmax << std : : endl ;
142 s t d : : c o u t << " Ymin = " << BoxBounds . Ymin << std : : endl ;
143 s t d : : c o u t << "Ymax = " << BoxBounds . Ymax << std : : endl ;
144 s t d : : c o u t << " Zmin = " << BoxBounds . Zmin << std : : endl ;
145 s t d : : c o u t << " Zmax = " << BoxBounds . Zmax << std : : endl ;
146 /
147
148 r e t u r n BoxBounds ;
149 };
150
151 / /
152
153 i n l i n e s t d : : v e c t o r <l o n g double> RDF_AnalyticNorm ( c o n s t s t d : : v e c t o r P a r t i c l e s ,
154 c o n s t s t d : : v e c t o r <l o n g double> r ,
155 c o n s t l o n g d o u b l e dr , c o n s t Box BoxBounds )
156 {
157 // Gr a v e r a g e d o v e r a l l p a r t i c l e s
158 s t d : : v e c t o r <l o n g double> Global_Gr ( r . s i z e ( ) , 0 ) ;
159
160 // maximal r a d i a l d i s t a n c e
161 l o n g d o u b l e MaxDist = r . a t ( r . s i z e () ≠1) + dr / 2 . 0 ;
162
163 // box s i z e
164 l o n g d o u b l e Lx = BoxBounds . Xmax ≠ BoxBounds . Xmin ;
165 l o n g d o u b l e Ly = BoxBounds . Ymax ≠ BoxBounds . Ymin ;
166 l o n g d o u b l e Lz = BoxBounds . Zmax ≠ BoxBounds . Zmin ;
167
168 // Show t h i s t o t h e u s e r
169 s t d : : c o u t << " The Sample Volume has t h e f o l l o w i n g s i z e : " << s t d : : e n d l ;
170 s t d : : c o u t << " Lx = " << Lx << s t d : : e n d l ;
171 s t d : : c o u t << " Ly = " << Ly << s t d : : e n d l ;
S-43
172 s t d : : c o u t << " Lz = " << Lz << s t d : : e n d l ;
173
174 l o n g d o u b l e MeanDensity = P a r t i c l e s . s i z e ( ) / ( Lx Ly Lz ) ;
175
176 // u s e e v e r y p a r t i c l e a s t h e c e n t e r once
177 f o r ( l o n g i n t Ce ntr alP = 0 ; Ce ntr alP Local_Gr ( r . s i z e ( ) , 0 ) ;
181
182 // l o o k a t e v e r y o t h e r p a r t i c l e a t most MaxDist away :
183 f o r ( l o n g i n t Neighbour = 0 ; Neighbour < P a r t i c l e s . s i z e ( ) ; Neighbour++)
184 {
185 i f ( Cen tra lP != Neighbour )
186 {
187 // c a l c t h e d i s t a n c e to the neighbour
188 long double dx = P a r t i c l e s . a t ( Ce ntra lP ) . XPos ≠ P a r t i c l e s . a t ( Neighbour ) . XPos ;
189 long double dy = P a r t i c l e s . a t ( Ce ntra lP ) . YPos ≠ P a r t i c l e s . a t ( Neighbour ) . YPos ;
190 long double dz = P a r t i c l e s . a t ( C ent ral P ) . ZPos ≠ P a r t i c l e s . a t ( Neighbour ) . ZPos ;
191
192 l o n g d o u b l e d = s t d : : s q r t ( dx dx + dy dy + dz dz ) ;
193
194 // what b i n s i s t h e p a r t i c l e i n ?
195 f o r ( l o n g i n t RPos = 0 ; RPos < r . s i z e ( ) ; RPos++)
196 {
197 i f ( s t d : : abs ( r . a t ( RPos ) ≠ d ) <= dr / 2 . 0 )
198 {
199 Local_Gr . a t ( RPos ) += 1 ;
200 }
201 }
202 }
203 }
204
205 // l o c a l box f o r t h e s h e l l box i n t e r s e c t i o n volume
206 Box LocalBox = BoxBounds ;
207
208 // s h i f t t h e c e n t e r o f t h e box cosy
209 LocalBox . Xmin = BoxBounds . Xmin ≠ Particles . a t ( Ce ntralP ) . XPos ;
210 LocalBox . Xmax = BoxBounds . Xmax ≠ Particles . a t ( Ce ntralP ) . XPos ;
211 LocalBox . Ymin = BoxBounds . Ymin ≠ Particles . a t ( Ce ntralP ) . YPos ;
212 LocalBox . Ymax = BoxBounds . Ymax ≠ Particles . a t ( Ce ntralP ) . YPos ;
213 LocalBox . Zmin = BoxBounds . Zmin ≠ Particles . a t ( Ce ntralP ) . ZPos ;
214 LocalBox . Zmax = BoxBounds . Zmax ≠ Particles . a t ( Ce ntralP ) . ZPos ;
215
217 s t d : : c o u t << " The l o c a l Box B o u n d a r i e s a r e : " << s t d : : e n d l ;
218 s t d : : c o u t << " Xmin = " << LocalBox . Xmin << s t d : : e n d l ;
219 s t d : : c o u t << "Xmax = " << LocalBox . Xmax << s t d : : e n d l ;
220 s t d : : c o u t << " Ymin = " << LocalBox . Ymin << s t d : : e n d l ;
221 s t d : : c o u t << "Ymax = " << LocalBox . Ymax << s t d : : e n d l ;
222 s t d : : c o u t << " Zmin = " << LocalBox . Zmin << s t d : : e n d l ;
223 s t d : : c o u t << " Zmax = " << LocalBox . Zmax << s t d : : e n d l ;
224 /
225
226 // n o r m a l i z e with t h e s h e l l volume
227 f o r ( l o n g i n t RIdx = 0 ; RIdx < r . s i z e ( ) ; RIdx++)
228 {
229 // c a l c u l a t e t h e s h e l l box i n t e r s e c t i o n volume
230 l o n g d o u b l e SVolume = 4 . 0 / 3 . 0 pi ( s t d : : pow ( r . a t ( RIdx)+ dr / 2 . 0 , 3 ) ≠ s t d : : pow ( r . a t ( RIdx)≠d
231 Local_Gr . a t ( RIdx ) /= SVolume ;
232
233 // n o r m a l i z e by t h e mean p a r t i c l e d e n s i t y
234 Local_Gr . a t ( RIdx ) /= MeanDensity ;
235
236 // s a v e i n t h e g l o b a l g r f o r t h e a v e r a g e o v e r p a r t i c l e s
237 Global_Gr . a t ( RIdx ) += Local_Gr . a t ( RIdx ) ;
238 }
239
240 i f ( Cen tra lP % 1000 == 0 )
241 s t d : : c o u t << " F i n i s h e d P a r t i c l e " << C ent ral P << " o f " << P a r t i c l e s . s i z e ( ) << s t d : : e n d l ;
242 }
243
244 // f i n a l a v e r a g e o v e r a l l particles
S-44
245 f o r ( l o n g i n t k = 0 ; k < Global_Gr . s i z e ( ) ; k++)
246 {
247 Global_Gr . a t ( k ) /= P a r t i c l e s . s i z e ( ) ;
248 }
249
250 r e t u r n Global_Gr ;
251 };
252
253 / /
254
255 v o i d SaveData ( c o n s t s t d : : s t r i n g SimuName , c o n s t s t d : : s t r i n g FileName , c o n s t s t d : : v e c t o r <l o n g double> Gr
256 c o n s t s t d : : v e c t o r <l o n g double> r , c o n s t l o n g d o u b l e dr , c o n s t l o n g d o u b l e ComputeTime ,
257 Box BoxBounds )
258 {
259 // box s i z e
263
264 l o n g d o u b l e RmaxNatural = s t d : : s q r t ( Lx Lx + Ly Ly + Lz Lz ) / 2 . 0 ;
265
266 std : : ofstream DataFile ;
267 D a t a F i l e . open ( SimuName + " . t x t " , s t d : : i o s : : out ) ;
268 DataFile . p r e c i s i o n ( 2 5 ) ;
269
270 DataFile << " R e s u l t s f o r t h e r a d i a l d i s t r i b u t i o n f u n c t i o n computation . " << s t d : : e n d l ;
271 DataFile << " P a r t i c l e F i l e Name : " << FileName << s t d : : e n d l ;
272 DataFile << " Computation time f o r g ( r ) : " << ComputeTime << " n a n o s e c o n d s . " << s t d : : e n d l ;
273 DataFile << " R a d i a l Bin Width dr : " << dr << s t d : : e n d l ;
274 DataFile << " Number o f r a d i a l Bins : " << r . s i z e ( ) << s t d : : e n d l ;
275 DataFile << " Number o f P a r t i c l e s i n t h e sample : " << BoxBounds . PartNum << s t d : : e n d l ;
276 DataFile << " Average P a r t i c l e Number D e n s i t y : " << BoxBounds . PartNum / ( Lx Ly Lz ) << s t d : : e n d l ;
277 DataFile << " Maximal u s e f u l r a d i a l d i s t a n c e : " << RmaxNatural << s t d : : e n d l ;
278 DataFile << " Box Boundary Xmin : " << BoxBounds . Xmin << s t d : : e n d l ;
279 DataFile << " Box Boundary Xmax : " << BoxBounds . Xmax << s t d : : e n d l ;
280 DataFile << " Box Boundary Ymin : " << BoxBounds . Ymin << s t d : : e n d l ;
281 DataFile << " Box Boundary Ymax : " << BoxBounds . Ymax << s t d : : e n d l ;
282 DataFile << " Box Boundary Zmin : " << BoxBounds . Zmin << s t d : : e n d l ;
283 DataFile << " Box Boundary Zmax : " << BoxBounds . Zmax << s t d : : e n d l ;
284
285 D a t a F i l e << " Box Boundary X≠l e n g t h : " << Lx << s t d : : e n d l ;
286 D a t a F i l e << " Box Boundary Y≠l e n g t h : " << Ly << s t d : : e n d l ;
287 D a t a F i l e << " Box Boundary Z≠l e n g t h : " << Lz << s t d : : e n d l ;
288
289 D a t a F i l e << " Box Volume : " << Lx Ly Lz << s t d : : e n d l ;
290
291 D a t a F i l e << "# r \ t g ( r ) " << s t d : : e n d l ;
292
293 f o r ( l o n g i n t l = 0 ; l < r . s i z e ( ) ; l ++)
294 {
295 D a t a F i l e << r . a t ( l ) << " \ t " ;
296 D a t a F i l e << Gr . a t ( l ) << s t d : : e n d l ;
297 }
298
300 };
301
302 / /
303
304 i n t main ( v o i d )
305 {
306 // Dashboard
307 s t d : : s t r i n g SimuName = " " ; // Name o f t h e s i m u l a t i o n
308 s t d : : s t r i n g FileName = " " ; // Name o f t h e s i m u l a t i o n
309 l o n g i n t Bins = 1 ; // number o f sample c a l c u l a t i o n s
310 l o n g d o u b l e dr = 1 ; // b i n s i z e
311
312 // User I n p u t
313 s t d : : c o u t << " P l e a s e e n t e r t h e f o l l o w i n g i n f o r m a t i o n : " << s t d : : e n d l ;
314 s t d : : c o u t << "Name f o r t h e s i m u l a t i o n : " ;
315 s t d : : c i n >> SimuName ;
316 s t d : : c o u t << " P a r t i c l e F i l e Name : " ;
317 s t d : : c i n >> FileName ;
S-45
318 s t d : : c o u t << " Bin s i z e ( dr ) : " ;
319 s t d : : c i n >> dr ;
320 s t d : : c o u t << " S t a r t i n g g ( r ) computation . " << s t d : : e n d l ;
321
322 // o ut pu t p r e c i s i o n
323 std : : cout . p r e c i s i o n ( 2 0 ) ;
324
325 // r e a d i n t h e raw p a r t i c l e c o o r d i n a t e s
326 s t d : : v e c t o r P a r t i c l e s = r e a d P a r t C o o r ( FileName ) ;
327
328 // benchmark t h e g ( r ) c a l c u l a t i o n
329 auto s t a r t = s t d : : c hro no : : s t e a d y _ c l o c k : : now ( ) ;
330
331 // f i n d t h e Box B o u n d a r i e s
332 Box BoxBounds = FindBoxBounds ( P a r t i c l e s ) ;
333
334 // box size
335 long d o u b l e Lx = BoxBounds . Xmax ≠ BoxBounds . Xmin ;
336 long d o u b l e Ly = BoxBounds . Ymax ≠ BoxBounds . Ymin ;
337 long d o u b l e Lz = BoxBounds . Zmax ≠ BoxBounds . Zmin ;
338
339 // maximal u s e f u l r a d i a l d i s t a n c e
340 l o n g d o u b l e RMAX = s t d : : s q r t ( Lx Lx + Ly Ly + Lz Lz ) / 2 . 0 ;
341
342 // show t h e maximal u s e f u l l r a d i u s t o t h e u s e r
343 s t d : : c o u t << " Maximal u s e f u l l r a d i u s : " << RMAX << s t d : : e n d l ;
344
345 // Number o f Bins
346 Bins = s t a t i c _ c a s t <l o n g i n t >(RMAX / dr ) ;
347
348 // t h e r a d i a l p o s i t i o n and g ( r ) v e c t o r
349 s t d : : v e c t o r <l o n g double> r ( Bins , 0 ) ;
350 s t d : : v e c t o r <l o n g double> Gr ( Bins , 0 ) ;
351
352 // c r e a t e t h e r a d i a l d i s t a n c e v e c t o r
353 f o r ( l o n g i n t k = 0 ; k < Bins ; k++)
354 {
355 r . at ( k ) = k RMAX/ Bins ;
356 }
357
358 // compute t h e r a d i a l d i s t r i b u t i o n f u n c t i o n
359 Gr = RDF_AnalyticNorm ( P a r t i c l e s , r , dr , BoxBounds ) ;
360
361 auto end = s t d : : c hro no : : s t e a d y _ c l o c k : : now ( ) ;
362 auto d i f f = end ≠ s t a r t ;
363 d o u b l e ComputeTime = s t d : : chr ono : : d u r a t i o n <double , s t d : : nano> ( d i f f ) . count ( ) ;
364
365 // i n f o r m a t i o n f o r t h e u s e r
366 s t d : : c o u t << " Time f o r t h e g ( r ) computation : " ;
367 s t d : : c o u t << ComputeTime ;
368 s t d : : c o u t << " n a n o s e c o n d s " << s t d : : e n d l ;
369
370 // s a v e a l l t h e data i n t o a f i l e
371 SaveData ( SimuName , FileName , Gr , r , dr , ComputeTime , BoxBounds ) ;
372
373 s t d : : c o u t << " Program F i n i s h e d ! " << s t d : : e n d l ;
374 };
4.13 Analytic g(r) in C++

1 #i n c l u d e 
2 #i n c l u d e <s s t r e a m >
3 #i n c l u d e <chrono>
4 #i n c l u d e <cmath>
5 #i n c l u d e <c s t d l i b >
6 #i n c l u d e <s t r i n g >
7 #i n c l u d e <f s t r e a m >
8 #i n c l u d e 
9 #i n c l u d e <v e c t o r >
10 #i n c l u d e <s t r ea m b uf >
11
S-46
12 long double pi = 3.1415926535897932384626433;
13
14 / /
15 struct Box
16 {
17 long d o u b l e Xmin = 0;
18 long d o u b l e Xmax = 0;
19 long d o u b l e Ymin = 0;
20 long d o u b l e Ymax = 0;
21 long d o u b l e Zmin = 0;
22 long d o u b l e Zmax = 0;
23 long i n t PartNum = 0;
24 };
25
26 / /
27
28 struct Particle
29 {
30 long d o u b l e XPos = 0 ;
31 long d o u b l e YPos = 0 ;
32 long d o u b l e ZPos = 0 ;
33 };
34
35 / /
36
37 s t d : : v e c t o r <s t d : : s t r i n g > s p l i t ( c o n s t s t d : : s t r i n g& s , c h a r d e l i m i t e r )
38 {
39 s t d : : v e c t o r <s t d : : s t r i n g > t o k e n s ;
40 std : : s t r i n g token ;
41 s t d : : i s t r i n g s t r e a m tokenStream ( s ) ;
42
43 w h i l e ( s t d : : g e t l i n e ( tokenStream , token , d e l i m i t e r ) )
44 {
45 t o k e n s . push_back ( t o k e n ) ;
46 }
47 return tokens ;
48 };
49
50 / /
51
52 i n l i n e s t d : : v e c t o r r e a d P a r t C o o r ( c o n s t s t d : : s t r i n g FileName )
53 {
54 // open t h e raw data f i l e
55 s t d : : i f s t r e a m D a t a F i l e ( FileName + " . t x t " ) ;
56 s t d : : s t r i n g TxtData ;
57
58 // g e t l e n g t h o f f i l e :
59 D a t a F i l e . s e e k g ( 0 , s t d : : i o s : : end ) ; // go t o t h e end o f t h e f i l e
60 TxtData . r e s e r v e ( D a t a F i l e . t e l l g ( ) ) ; // a l l o c a t e enough s p a c e
61 D a t a F i l e . s e e k g ( 0 , s t d : : i o s : : beg ) ; // go t o t h e b e g i n n i n g o f t h e f i l e
62
63 TxtData . a s s i g n ( ( s t d : : i s t r e a m b u f _ i t e r a t o r <char >( D a t a F i l e ) ) ,
64 s t d : : i s t r e a m b u f _ i t e r a t o r <char > ( ) ) ;
65
67
68 // s p l i t t h e data i n t o l i n e s
69 s t d : : v e c t o r <s t d : : s t r i n g > d a t a l i n e s = s p l i t ( TxtData , ’ \n ’ ) ;
70
71 Particle P; // s i n g l e p a r t i c l e s t r u c t
72 s t d : : v e c t o r P a r t i c l e s ; // l i s t of p a r t i c l e s
73
74 std :: cout << " The f i r s t l i n e s i n t h e raw data f i l e a r e : " << s t d : : e n d l ;
79
80 s t d : : c o u t << " The RawDataFile has " << d a t a l i n e s . s i z e ( ) << " l i n e s . " << s t d : : e n d l ;
81
82 f o r ( l o n g i n t k = 0 ; k < d a t a l i n e s . s i z e ( ) ; k++)
83 {
84 s t d : : v e c t o r <s t d : : s t r i n g > r e s u l t s ;
S-47
85
86 // s p l i t t h e i n d i v i d u a l l i n e s (X, Y, Z )
87 r e s u l t s = s p l i t ( d a t a l i n e s . at ( k ) , ’ \ t ’ ) ;
88
89 // s a v e t h e s i n g l e p a r t i c l e positions
90 P . XPos = s t d : : s t o l d ( r e s u l t s . at ( 0 ) ) ;
91 P . YPos = s t d : : s t o l d ( r e s u l t s . at ( 1 ) ) ;
92 P . ZPos = s t d : : s t o l d ( r e s u l t s . at ( 2 ) ) ;
93
94 P a r t i c l e s . push_back (P ) ;
95 }
96
97 return Particles ;
98 };
99
100 / /
101
102 i n l i n e l o n g d o u b l e SphereCutVol ( c o n s t l o n g d o u b l e Rs ,
103 c o n s t l o n g d o u b l e A,
104 c o n s t l o n g d o u b l e B)
105 {
106 l o n g d o u b l e Root = s t d : : s q r t ( Rs Rs≠A A≠B B ) ;
107
108 l o n g d o u b l e Vcut = Rs Rs Rs ( p i ≠ 2 . 0 s t d : : atan (A B/ ( Rs Root ) ) ) / 6 . 0 ;
109 Vcut += ( s t d : : atan (A/ Root ) ≠ p i / 2 . 0 ) ( Rs Rs B≠ 1 . 0 / 3 . 0 B B B) / 2 . 0 ;
110 Vcut += ( s t d : : atan (B/ Root ) ≠ p i / 2 . 0 ) ( Rs Rs A≠ 1 . 0 / 3 . 0 A A A) / 2 . 0 ;
111 Vcut += A B Root / 3 . 0 ;
112
113 /
114 i f ( Vcut <= 0 )
115 {
116 s t d : : c o u t << " Vcut i s l e s s than 0 ! = " << Vcut << s t d : : e n d l ;
117 s t d : : c o u t << " Rs i s = " << Rs << s t d : : e n d l ;
118 s t d : : c o u t << "A = " << A << s t d : : e n d l ;
119 s t d : : c o u t << "B = " << B << s t d : : e n d l ;
120 } /
121
122 r e t u r n Vcut ;
123 };
124
125 / /
126
127 i n l i n e l o n g d o u b l e OctVolume ( c o n s t l o n g d o u b l e Rs ,
128 c o n s t l o n g d o u b l e xb ,
129 c o n s t l o n g d o u b l e yb ,
130 c o n s t l o n g d o u b l e zb )
131 {
132
133 /
134 std :: cout << " Box Corner Bounds : " << s t d : : e n d l ;
135 std :: cout << xb << s t d : : e n d l ;
136 std :: cout << yb << s t d : : e n d l ;
137 std :: cout << zb << s t d : : e n d l ;
138 /
139
140 // i f a l l b o u n d a r i e s a r e f u l l y i n t h e o c t a n t
141 i f ( xb xb + yb yb + zb zb < Rs Rs )
142 {
143 r e t u r n xb yb zb ;
144 }
145
146 // i f no boundary i n t e r s e c t s we s t a r t with a f u l l o c t a n t
147 l o n g d o u b l e VOctant = p i Rs Rs Rs / 6 . 0 ;
148
149 // remove t h e s p h e r i c a l c a p s
150
151 i f ( xb < Rs )
152 {
153 VOctant ≠= p i / 4 . 0 ( 2 . 0 / 3 . 0 Rs Rs Rs≠xb Rs Rs + 1 . 0 / 3 . 0 xb xb xb ) ;
154 }
155
156 i f ( yb < Rs )
157 {
S-48
158 VOctant ≠= p i / 4 . 0 ( 2 . 0 / 3 . 0 Rs Rs Rs≠yb Rs Rs + 1 . 0 / 3 . 0 yb yb yb ) ;
159 }
160
161 i f ( zb < Rs )
162 {
163 VOctant ≠= p i / 4 . 0 ( 2 . 0 / 3 . 0 Rs Rs Rs≠zb Rs Rs + 1 . 0 / 3 . 0 zb zb zb ) ;
164 }
165
166 // add t h e i n t e r s e c t i o n s o f t h e c a p s
167
168 i f ( ( xb xb + yb yb ) < ( Rs Rs ) )
169 {
170 VOctant += SphereCutVol ( Rs , xb , yb ) ;
171 }
172
173 i f ( ( xb xb + zb zb ) < ( Rs Rs ) )
174 {
175 VOctant += SphereCutVol ( Rs , xb , zb ) ;
176 }
177
178 i f ( ( yb yb + zb zb ) < ( Rs Rs ) )
179 {
180 VOctant += SphereCutVol ( Rs , yb , zb ) ;
181 }
182
183 r e t u r n VOctant ;
184 };
185
186 / /
187
188 i n l i n e l o n g d o u b l e SphereVolume ( c o n s t l o n g d o u b l e Rs , c o n s t Box BoxSize )
189 {
190 l o n g d o u b l e VSphere = 0 . 0 ;
191
192 // s t d : : abs ( ) m i r r o r s t h e b o u n d a r i e s i n t o t h e f i r s t o c t a n t
193 VSphere += OctVolume ( Rs , s t d : : abs ( BoxSize . Xmin ) ,
194 s t d : : abs ( BoxSize . Ymin ) , s t d : : abs ( BoxSize . Zmin ) ) ;
196 s t d : : abs ( BoxSize . Ymin ) , s t d : : abs ( BoxSize . Zmax ) ) ;
198 s t d : : abs ( BoxSize . Ymax) , s t d : : abs ( BoxSize . Zmin ) ) ;
200 s t d : : abs ( BoxSize . Ymax) , s t d : : abs ( BoxSize . Zmax ) ) ;
201 VSphere += OctVolume ( Rs , s t d : : abs ( BoxSize . Xmax) ,
202 s t d : : abs ( BoxSize . Ymin ) , s t d : : abs ( BoxSize . Zmin ) ) ;
204 s t d : : abs ( BoxSize . Ymin ) , s t d : : abs ( BoxSize . Zmax ) ) ;
206 s t d : : abs ( BoxSize . Ymax) , s t d : : abs ( BoxSize . Zmin ) ) ;
208 s t d : : abs ( BoxSize . Ymax) , s t d : : abs ( BoxSize . Zmax ) ) ;
209
210 r e t u r n VSphere ;
211 };
212
213 / /
214
215 i n l i n e l o n g d o u b l e S h e l l V ol u m e ( c o n s t l o n g d o u b l e Rmin , c o n s t l o n g d o u b l e Rmax ,
216 c o n s t Box BoxSize )
217 {
218 l o n g d o u b l e I n n e r S p h e r e = SphereVolume ( Rmin , BoxSize ) ;
219 l o n g d o u b l e OuterSphere = SphereVolume (Rmax , BoxSize ) ;
220
221 l o n g d o u b l e S h e l l V o l = OuterSphere ≠ I n n e r S p h e r e ;
222
223 /
224 i f ( S h e l l V o l <= 0 . 0 )
225 {
226 s t d : : c o u t << S h e l l V o l << s t d : : e n d l ;
227 } /
228
229 return ShellVol ;
230 };
S-49
231
232 / /
233
234 i n l i n e Box FindBoxBounds ( c o n s t s t d : : v e c t o r P a r t i c l e s )
235 {
236 // Box b o u n d a r i e s
237 Box BoxBounds ;
238
239 // i n i t i a l i z e t h e b o u n d a r i e s with t h e f i r s t particle
240 BoxBounds . Xmin = P a r t i c l e s . a t ( 0 ) . XPos ;
241 BoxBounds . Xmax = P a r t i c l e s . a t ( 0 ) . XPos ;
242 BoxBounds . Ymin = P a r t i c l e s . a t ( 0 ) . YPos ;
243 BoxBounds . Ymax = P a r t i c l e s . a t ( 0 ) . YPos ;
244 BoxBounds . Zmin = P a r t i c l e s . a t ( 0 ) . ZPos ;
245 BoxBounds . Zmax = P a r t i c l e s . a t ( 0 ) . ZPos ;
246 BoxBounds . PartNum = P a r t i c l e s . s i z e ( ) ;
247
248 // l o o p o v e r a l l o t h e r p a r t i c l e s and f i n d minima and maxima
249 f o r ( l o n g i n t Pos = 1 ; Pos < P a r t i c l e s . s i z e ( ) ; Pos++)
250 {
251 i f ( P a r t i c l e s . a t ( Pos ) . XPos < BoxBounds . Xmin )
252 BoxBounds . Xmin = P a r t i c l e s . a t ( Pos ) . XPos ;
253
254 i f ( P a r t i c l e s . a t ( Pos ) . XPos > BoxBounds . Xmax)
255 BoxBounds . Xmax = P a r t i c l e s . a t ( Pos ) . XPos ;
256
257 i f ( P a r t i c l e s . a t ( Pos ) . YPos < BoxBounds . Ymin )
258 BoxBounds . Ymin = P a r t i c l e s . a t ( Pos ) . YPos ;
259
260 i f ( P a r t i c l e s . a t ( Pos ) . YPos > BoxBounds . Ymax)
261 BoxBounds . Ymax = P a r t i c l e s . a t ( Pos ) . YPos ;
262
263 i f ( P a r t i c l e s . a t ( Pos ) . ZPos < BoxBounds . Zmin )
264 BoxBounds . Zmin = P a r t i c l e s . a t ( Pos ) . ZPos ;
265
266 i f ( P a r t i c l e s . a t ( Pos ) . ZPos > BoxBounds . Zmax)
267 BoxBounds . Zmax = P a r t i c l e s . a t ( Pos ) . ZPos ;
268 };
269
271 s t d : : c o u t << " I found t h e Box B o u n d a r i e s : " << s t d : : e n d l ;
272 s t d : : c o u t << " Xmin = " << BoxBounds . Xmin << std : : endl ;
273 s t d : : c o u t << "Xmax = " << BoxBounds . Xmax << std : : endl ;
274 s t d : : c o u t << " Ymin = " << BoxBounds . Ymin << std : : endl ;
275 s t d : : c o u t << "Ymax = " << BoxBounds . Ymax << std : : endl ;
276 s t d : : c o u t << " Zmin = " << BoxBounds . Zmin << std : : endl ;
277 s t d : : c o u t << " Zmax = " << BoxBounds . Zmax << std : : endl ;
278 /
279
280 r e t u r n BoxBounds ;
281 };
282
283 / /
284
285 i n l i n e s t d : : v e c t o r <l o n g double> RDF_AnalyticNorm ( c o n s t s t d : : v e c t o r P a r t i c l e s ,
286 c o n s t s t d : : v e c t o r <l o n g double> r , c o n s t l o n g d o u b l e dr , c o n s t Box BoxBounds )
287 {
288 // Gr a v e r a g e d o v e r a l l p a r t i c l e s
289 s t d : : v e c t o r <l o n g double> Global_Gr ( r . s i z e ( ) , 0 ) ;
290
291 // Keep t r a c k o f t h e u s e f u l l ( non≠empty ) s h e l l volumes
292 s t d : : v e c t o r <l o n g double> NonEmptyShells ( r . s i z e ( ) , 0 ) ;
293
294 // maximal r a d i a l d i s t a n c e
295 l o n g d o u b l e MaxDist = r . a t ( r . s i z e () ≠1) + dr / 2 . 0 ;
296
297 // box s i z e
301
302 // Show t h i s t o t h e u s e r
303 s t d : : c o u t << " The Sample Volume has t h e f o l l o w i n g s i z e : " << s t d : : e n d l ;
S-50
304 s t d : : c o u t << " Lx = " << Lx << s t d : : e n d l ;
305 s t d : : c o u t << " Ly = " << Ly << s t d : : e n d l ;
306 s t d : : c o u t << " Lz = " << Lz << s t d : : e n d l ;
307
308 l o n g d o u b l e MeanDensity = P a r t i c l e s . s i z e ( ) / ( Lx Ly Lz ) ;
309
310 // u s e e v e r y p a r t i c l e a s t h e c e n t e r once
311 f o r ( l o n g i n t Ce ntr alP = 0 ; Ce ntr alP Local_Gr ( r . s i z e ( ) , 0 ) ;
315
316 // l o o k a t e v e r y o t h e r p a r t i c l e a t most MaxDist away :
317 f o r ( l o n g i n t Neighbour = 0 ; Neighbour < P a r t i c l e s . s i z e ( ) ; Neighbour++)
318 {
319 i f ( Cen tra lP != Neighbour )
320 {
321 // c a l c t h e d i s t a n c e to the neighbour
322 long double dx = P a r t i c l e s . a t ( Ce ntra lP ) . XPos ≠ P a r t i c l e s . a t ( Neighbour ) . XPos ;
323 long double dy = P a r t i c l e s . a t ( Ce ntra lP ) . YPos ≠ P a r t i c l e s . a t ( Neighbour ) . YPos ;
324 long double dz = P a r t i c l e s . a t ( C ent ral P ) . ZPos ≠ P a r t i c l e s . a t ( Neighbour ) . ZPos ;
325
326 l o n g d o u b l e d = s t d : : s q r t ( dx dx + dy dy + dz dz ) ;
327
328 // what b i n s i s t h e p a r t i c l e i n ?
329 f o r ( l o n g i n t RPos = 0 ; RPos < r . s i z e ( ) ; RPos++)
330 {
331 i f ( s t d : : abs ( r . a t ( RPos ) ≠ d ) <= dr / 2 . 0 )
332 {
333 Local_Gr . a t ( RPos ) += 1 ;
334 }
335 }
336 }
337 }
338
339 // l o c a l box f o r t h e s h e l l box i n t e r s e c t i o n volume
340 Box LocalBox = BoxBounds ;
341
342 // s h i f t t h e c e n t e r o f t h e box cosy
343 LocalBox . Xmin = BoxBounds . Xmin ≠ Particles . a t ( Ce ntralP ) . XPos ;
344 LocalBox . Xmax = BoxBounds . Xmax ≠ Particles . a t ( Ce ntralP ) . XPos ;
345 LocalBox . Ymin = BoxBounds . Ymin ≠ Particles . a t ( Ce ntralP ) . YPos ;
346 LocalBox . Ymax = BoxBounds . Ymax ≠ Particles . a t ( Ce ntralP ) . YPos ;
347 LocalBox . Zmin = BoxBounds . Zmin ≠ Particles . a t ( Ce ntralP ) . ZPos ;
348 LocalBox . Zmax = BoxBounds . Zmax ≠ Particles . a t ( Ce ntralP ) . ZPos ;
349
351 s t d : : c o u t << " The l o c a l Box B o u n d a r i e s a r e : " << s t d : : e n d l ;
352 s t d : : c o u t << " Xmin = " << LocalBox . Xmin << s t d : : e n d l ;
353 s t d : : c o u t << "Xmax = " << LocalBox . Xmax << s t d : : e n d l ;
354 s t d : : c o u t << " Ymin = " << LocalBox . Ymin << s t d : : e n d l ;
355 s t d : : c o u t << "Ymax = " << LocalBox . Ymax << s t d : : e n d l ;
356 s t d : : c o u t << " Zmin = " << LocalBox . Zmin << s t d : : e n d l ;
357 s t d : : c o u t << " Zmax = " << LocalBox . Zmax << s t d : : e n d l ;
358 /
359
360 // n o r m a l i z e with t h e s h e l l volume
361 f o r ( l o n g i n t RIdx = 0 ; RIdx < r . s i z e ( ) ; RIdx++)
362 {
363 // c a l c u l a t e t h e s h e l l box i n t e r s e c t i o n volume
364 l o n g d o u b l e SVolume = S he l l V o l u m e ( r . a t ( RIdx)≠dr / 2 . 0 , r . a t ( RIdx)+ dr / 2 . 0 , LocalBox ) ;
365
366 i f ( SVolume > 0 . 0 )
367 {
368 Local_Gr . a t ( RIdx ) /= SVolume ;
369 NonEmptyShells . a t ( RIdx ) += 1 ;
370 }
371
372 // n o r m a l i z e by t h e mean p a r t i c l e d e n s i t y
373 Local_Gr . a t ( RIdx ) /= MeanDensity ;
374
375 // s a v e i n t h e g l o b a l g r f o r t h e a v e r a g e o v e r p a r t i c l e s
376 Global_Gr . a t ( RIdx ) += Local_Gr . a t ( RIdx ) ;
S-51
377 }
378
379 i f ( Cen tra lP % 1000 == 0 )
380 s t d : : c o u t << " F i n i s h e d P a r t i c l e " << C ent ral P << " o f " << P a r t i c l e s . s i z e ( ) << s t d : : e n d l ;
381 }
382
383 // f i n a l n o r m a l i z a t i o n c o n s i d e r i n g t h e non empty s h e l l volumes
384 f o r ( l o n g i n t k = 0 ; k < Global_Gr . s i z e ( ) ; k++)
385 {
386 i f ( NonEmptyShells . a t ( k ) != 0 )
387 {
388 Global_Gr . a t ( k ) /= NonEmptyShells . a t ( k ) ;
389 }
390
391 else
392 {
393 s t d : : c o u t << " A l l S h e l l s a t R = " << r . a t ( k ) << " a r e Empty ! " << s t d : : e n d l ;
394 }
395 }
396
397 r e t u r n Global_Gr ;
398 };
399
400 / /
401
402 v o i d SaveData ( c o n s t s t d : : s t r i n g SimuName , c o n s t s t d : : s t r i n g FileName , c o n s t s t d : : v e c t o r <l o n g double> Gr
403 c o n s t s t d : : v e c t o r <l o n g double> r , c o n s t l o n g d o u b l e dr , c o n s t l o n g d o u b l e ComputeTime ,
404 Box BoxBounds )
405 {
406 // box s i z e
410
411 l o n g d o u b l e RmaxNatural = s t d : : s q r t ( Lx Lx + Ly Ly + Lz Lz ) / 2 . 0 ;
412
413 std : : ofstream DataFile ;
414 D a t a F i l e . open ( SimuName + " . t x t " , s t d : : i o s : : out ) ;
415 DataFile . p r e c i s i o n ( 2 5 ) ;
416
417 DataFile << " R e s u l t s f o r t h e r a d i a l d i s t r i b u t i o n f u n c t i o n computation . " << s t d : : e n d l ;
418 DataFile << " P a r t i c l e F i l e Name : " << FileName << s t d : : e n d l ;
419 DataFile << " Computation time f o r g ( r ) : " << ComputeTime << " n a n o s e c o n d s . " << s t d : : e n d l ;
420 DataFile << " R a d i a l Bin Width dr : " << dr << s t d : : e n d l ;
421 DataFile << " Number o f r a d i a l Bins : " << r . s i z e ( ) << s t d : : e n d l ;
422 DataFile << " Number o f P a r t i c l e s i n t h e sample : " << BoxBounds . PartNum << s t d : : e n d l ;
423 DataFile << " Average P a r t i c l e Number D e n s i t y : " << BoxBounds . PartNum / ( Lx Ly Lz ) << s t d : : e n d l ;
424 DataFile << " Maximal u s e f u l r a d i a l d i s t a n c e : " << RmaxNatural << s t d : : e n d l ;
425 DataFile << " Box Boundary Xmin : " << BoxBounds . Xmin << s t d : : e n d l ;
426 DataFile << " Box Boundary Xmax : " << BoxBounds . Xmax << s t d : : e n d l ;
427 DataFile << " Box Boundary Ymin : " << BoxBounds . Ymin << s t d : : e n d l ;
428 DataFile << " Box Boundary Ymax : " << BoxBounds . Ymax << s t d : : e n d l ;
429 DataFile << " Box Boundary Zmin : " << BoxBounds . Zmin << s t d : : e n d l ;
430 DataFile << " Box Boundary Zmax : " << BoxBounds . Zmax << s t d : : e n d l ;
431
432 D a t a F i l e << " Box Boundary X≠l e n g t h : " << Lx << s t d : : e n d l ;
433 D a t a F i l e << " Box Boundary Y≠l e n g t h : " << Ly << s t d : : e n d l ;
434 D a t a F i l e << " Box Boundary Z≠l e n g t h : " << Lz << s t d : : e n d l ;
435
436 D a t a F i l e << " Box Volume : " << Lx Ly Lz << s t d : : e n d l ;
437
438 D a t a F i l e << "# r \ t g ( r ) " << s t d : : e n d l ;
439
440 f o r ( l o n g i n t l = 0 ; l < r . s i z e ( ) ; l ++)
441 {
442 D a t a F i l e << r . a t ( l ) << " \ t " ;
443 D a t a F i l e << Gr . a t ( l ) << s t d : : e n d l ;
444 }
445
447 };
448
449 / /
S-52
450
451 i n t main ( v o i d )
452 {
453 // Dashboard
454 s t d : : s t r i n g SimuName = " " ; // Name o f t h e s i m u l a t i o n
455 s t d : : s t r i n g FileName = " " ; // Name o f t h e s i m u l a t i o n
456 l o n g i n t Bins = 1 ; // number o f sample c a l c u l a t i o n s
457 l o n g d o u b l e dr = 1 ; // b i n s i z e
458
459 // User I n p u t
460 s t d : : c o u t << " P l e a s e e n t e r t h e f o l l o w i n g i n f o r m a t i o n : " << s t d : : e n d l ;
461 s t d : : c o u t << "Name f o r t h e s i m u l a t i o n : " ;
462 s t d : : c i n >> SimuName ;
463 s t d : : c o u t << " P a r t i c l e F i l e Name : " ;
464 s t d : : c i n >> FileName ;
465 s t d : : c o u t << " Bin s i z e ( dr ) : " ;
466 s t d : : c i n >> dr ;
467 s t d : : c o u t << " S t a r t i n g g ( r ) computation . " << s t d : : e n d l ;
468
469 // o ut pu t p r e c i s i o n
470 std : : cout . p r e c i s i o n ( 2 0 ) ;
471
472 // r e a d i n t h e raw p a r t i c l e c o o r d i n a t e s
473 s t d : : v e c t o r P a r t i c l e s = r e a d P a r t C o o r ( FileName ) ;
474
475 // benchmark t h e g ( r ) c a l c u l a t i o n
476 auto s t a r t = s t d : : c hro no : : s t e a d y _ c l o c k : : now ( ) ;
477
478 // f i n d t h e Box B o u n d a r i e s
479 Box BoxBounds = FindBoxBounds ( P a r t i c l e s ) ;
480
481 // box size
482 long d o u b l e Lx = BoxBounds . Xmax ≠ BoxBounds . Xmin ;
483 long d o u b l e Ly = BoxBounds . Ymax ≠ BoxBounds . Ymin ;
484 long d o u b l e Lz = BoxBounds . Zmax ≠ BoxBounds . Zmin ;
485
486 // maximal u s e f u l r a d i a l d i s t a n c e
487 l o n g d o u b l e RMAX = s t d : : s q r t ( Lx Lx + Ly Ly + Lz Lz ) / 2 . 0 ;
488
489 // show t h e maximal u s e f u l l r a d i u s t o t h e u s e r
490 s t d : : c o u t << " Maximal u s e f u l l r a d i u s : " << RMAX << s t d : : e n d l ;
491
492 // Number o f Bins
493 Bins = s t a t i c _ c a s t <l o n g i n t >(RMAX / dr ) ;
494
495 // t h e r a d i a l p o s i t i o n and g ( r ) v e c t o r
496 s t d : : v e c t o r <l o n g double> r ( Bins , 0 ) ;
497 s t d : : v e c t o r <l o n g double> Gr ( Bins , 0 ) ;
498
499 // c r e a t e t h e r a d i a l d i s t a n c e v e c t o r
500 f o r ( l o n g i n t k = 0 ; k < Bins ; k++)
501 {
502 r . at ( k ) = k RMAX/ Bins ;
503 }
504
505 // compute t h e r a d i a l d i s t r i b u t i o n f u n c t i o n
506 Gr = RDF_AnalyticNorm ( P a r t i c l e s , r , dr , BoxBounds ) ;
507
508 auto end = s t d : : c hro no : : s t e a d y _ c l o c k : : now ( ) ;
509 auto d i f f = end ≠ s t a r t ;
510 d o u b l e ComputeTime = s t d : : chr ono : : d u r a t i o n <double , s t d : : nano> ( d i f f ) . count ( ) ;
511
512 // i n f o r m a t i o n f o r t h e u s e r
513 s t d : : c o u t << " Time f o r t h e g ( r ) computation : " ;
514 s t d : : c o u t << ComputeTime ;
515 s t d : : c o u t << " n a n o s e c o n d s " << s t d : : e n d l ;
516
517 // s a v e a l l t h e data i n t o a f i l e
518 SaveData ( SimuName , FileName , Gr , r , dr , ComputeTime , BoxBounds ) ;
519
520 s t d : : c o u t << " Program F i n i s h e d ! " << s t d : : e n d l ;
521 };
S-53

Ac8b03157 Si 001

Uploaded by

Document Information

Original Title

Copyright

Available Formats

Share this document

Share or Embed Document

Sharing Options

Did you find this document useful?

Is this content inappropriate?

Copyright:

Available Formats

Ac8b03157 Si 001

Uploaded by

Copyright:

Available Formats

Supporting Information

Computing the 3D Radial Distribution Function

Bernd A. F. Kopera and Markus Retsch

Corresponding author: markus.retsch@uni-bayreuth.de

2 Mathematical Appendix S-14

3 Pseudo code S-28

4 Source code S-32

We simplify this equation by expanding the cube roots into

We now average over all possible particles

to get better statistics. Note, that we assumed a homogeneous particle distribution.

• Stitching errors from unknown sample boundary positions

• Artificial periodicities, especially in small samples

• Rough boundaries from missing particles distort g(r)

An example rendering of a spherical shell, protruding outside of a box, is shown in

Vshell = Vouter sphere ≠ Vinner sphere . (1.11)

x2b + yb2 + zb2 Æ Rs2 . (1.13)

a2 + b2 < Rs2 . (1.17)

This case is shown in Figure S15.

Using this decomposition, the volume of a spherical cut is given by

Figure S18: Spherical segment (green) of height, B, inside a sphere of radius, Rs .

R2 + z 2 = Rs2 … R2 = Rs2 ≠ z 2 . (2.1)

Finally, we solve the integrals by

which leaves us with 5 6

Figure S19: Spherical cap (green) with radius, Rs , and height, Rs ≠ B.

We now have three individual integrals to solve. We label them according to

2 · Vint = zb · I1 + Rs2 · I2 ≠ I3 . (2.16)

For simplicity, we define the terms

is solved in appendix 2.4 and yields

Inserting the upper and lower boundaries gives us

Inserting the upper and lower boundaries gives us

Since arctan(0) = 0, we are left with

The third integral,

is solved in the appendix 2.6, like

Since arctan(0) = 0, we are left with

Next, we expand all products to remove the brackets

Finally, we bring the factor of 2 on the other side

We combine all fractions to get

Finally, we simplify the fractions and see that

we simplify the fractions and get

The second derivative is

Using our definition A = Rs2 ≠ zb2 we have

The third derivative is given by

2.6 Proof for the Integral I3

Then, we expand the second term in the square bracket

The second derivative is given by

We multiply the fractions

The third derivative is given by

We combine the fractions, leaving us with

Since A = Rs2 ≠ zb2 … ≠A = zb2 ≠ Rs2 we get

Finally, we sum up all the individual derivatives and get

We simplify the second fraction with the third binomic equation:

This leaves us with

Therefore, the integral, I3 , is solved by the anti-derivative given in equation (2.69).

Algorithm 1 Overlap volume between an octant and a corner

Algorithm 2 Compute the volume of a spherical cut.

Algorithm 3 Compute the shell-box intersection volume.

Algorithm 5 Compute the shell-sphere intersection volume.

Algorithm 6 Compute the sphere-sphere intersection volume.

4.2 Simple g(r) Implementation in Python 3

4.3 Analytic g(r) Implementation in Python 3

4.4 Analytic - Internal Volume

4.5 Monte Carlo - Internal Volume

4.7 Analytic - Spherical Cut Volume