commit 177fcc9099dab15613e5324d8cf5841d36166861
parent ee92bede9dff7368844e371e2ecfb1c27e17f9a6
Author: Vincent Forest <vincent.forest@meso-star.com>
Date: Mon, 18 May 2026 13:54:16 +0200
Translate schiff-geometry man page from man to mdoc macros
During the translation process, the content has been updated,
particularly the overall structure. Grammar is no longer presented as a
single block followed by a section explaining its specific rules.
Grammar rules are now incorporated into the text that explains the
grammar and outlines the file structure. The aim is to make the
documentation easier to read.
Diffstat:
2 files changed, 394 insertions(+), 320 deletions(-)
diff --git a/Makefile b/Makefile
@@ -113,6 +113,7 @@ lint: doc/schiff.1
shellcheck -o all src/test_schiff_cylinder.sh
shellcheck -o all src/test_schiff_sphere.sh
mandoc -Tlint -Wwarning doc/schiff.1
+ mandoc -Tlint -Wwarning doc/schiff-geometry.5
################################################################################
# Test
diff --git a/doc/schiff-geometry.5 b/doc/schiff-geometry.5
@@ -1,260 +1,343 @@
-.\" Copying and distribution of this file, with or without modification,
-.\" are permitted in any medium without royalty provided the copyright
-.\" notice and this notice are preserved. This file is offered as-is,
-.\" without any warranty.
-.TH SCHIFF-GEOMETRY 5
-.SH NAME
-schiff-geometry \- control the shape of soft particles
-.SH DESCRIPTION
-\fBschiff-geometry\fR is a YAML file [1] that controls the geometry
-distribution of soft particles. The
-.BR schiff (1)
-program relies on this description to generate the shape of the sampled soft
+.\" Copyright (C) 2015, 2016, 2026 Centre National de la Recherche Scientifique
+.\" Copyright (C) 2026 Clermont Auvergne INP
+.\" Copyright (C) 2026 Institut Mines Télécom Albi-Carmaux
+.\" Copyright (C) 2017, 2019-2021, 2026 |Méso|Star> (contact@meso-star.com)
+.\" Copyright (C) 2026 Université de Lorraine
+.\" Copyright (C) 2026 Université de Toulouse
+.\"
+.\" This program is free software: you can redistribute it and/or modify
+.\" it under the terms of the GNU General Public License as published by
+.\" the Free Software Foundation, either version 3 of the License, or
+.\" (at your option) any later version.
+.\"
+.\" This program is distributed in the hope that it will be useful,
+.\" but WITHOUT ANY WARRANTY; without even the implied warranty of
+.\" MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+.\" GNU General Public License for more details.
+.\"
+.\" You should have received a copy of the GNU General Public License
+.\" along with this program. If not, see <http://www.gnu.org/licenses/>.
+.Dd May 18, 2026
+.Dt SCHIFF-GEOMETRY 5
+.Os
+.\""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+.Sh NAME
+.Nm schiff-geometry
+.Nd control the shape of soft particles
+.\""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+.Sh DESCRIPTION
+.Nm
+is a plain text file format that controls the geometry distribution of soft
particles.
-.PP
-A geometry is defined by a type and a set of parameters whose value is
-controlled by a distribution. Several geometries with their own probability can
-be declared in the same \fBschiff-geometry\fR file to define a discrete random
-variate of geometries. This allow to finely tune the shapes of the soft
-particles with a collection of geometries, each representing a specific sub-set
-of shapes of the soft particles to handle.
-.SH GRAMMAR
-This section describes the \fBschiff\-geometry\fR grammar based on the YAML
-human readable data format [1]. The YAML format provides several ways to define
-a mapping or a sequence of data. The following grammar always uses the more
-verbose form but any alternative YAML formatting can be used instead. Refer to
-the example section for illustrations of such alternatives.
-.PP
-When the \fBradius_sphere\fR optional parameter is defined, the relative shape
-of the geometry must be fixed, i.e. all other parameters must be constants. In
-this situation, only the volume of the geometry is variable; it is equal to the
-volume of an equivalent sphere whose radius is controlled by the distribution
-of the \fBradius_sphere\fR parameter.
-.PP
-The \fBslices\fR optional attribute controls the discretization of the
-geometries in triangular meshes, i.e. the number of discrete steps around 2PI.
-When not defined it is assumed to be 64. Note that the \fBhelical_pipe\fR
-geometry exposes 2 discretization parameters: \fBslices_circle\fR and
-\fBslices_helicoid\fR. The former controls the discretization of the meridian
-around 2PI while the later defines the total number of discrete steps along the
-helicoid curve. When not defined \fBslices_circle\fR and \fBslices_helicoid\fR
+The
+.Xr schiff 1
+program relies on this description to generate the shape of the sampled
+soft particles.
+.Pp
+A
+.Nm
+may contain one or more geometric shapes to be distributed
+In the latter case, each geometric shape is assigned a probability such
+that the set defines a discrete random variable comprising the geometric
+shapes that make up the mixture.
+This allow to finely tune the shapes of the soft particles with a
+collection of geometries, each representing a specific sub-set of shapes
+of the soft particles to handle:
+.Bl -column (helical-pipe-geometry) (::=) ()
+.It Ao Va schiff-geometry Ac Ta ::= Ta Ao Va geometry Ac |
+.Aq Va geometry-list
+.It \ Ta Ta
+.It Ao Va geometry-list Ac Ta ::= Ta Qo - Qc Ao Va geometry Ac
+.It Ta Ta ...
+.El
+.Pp
+A geometry is defined by its type
+.Pq section Sx GEOMETRIC SHAPES
+and a set of parameters whose value is controlled by a distribution
+.Pq section Sx DISTRIBUTION OF PARAMETERS .
+.Pp
+Note that a
+.Nm
+file is actually a YAML file.
+This format provides several ways to define a mapping or a sequence of
+data.
+In grammar rules, the most detailed form is always used, but it is
+possible to opt for any other, more concise form instead
+.Pq see section Sx EXAMPLES .
+.\""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+.Sh GEOMETRIC SHAPES
+The list of supported geometric shapes are as follows:
+.Bl -column (helical-pipe-geometry) (::=) ()
+.It Ao Va geometry Ac Ta ::= Ta Ao Va cylinder-geometry Ac
+.It Ta \ | Ta Ao Va ellipsoid-geometry Ac
+.It Ta \ | Ta Ao Va helical-pipe-geometrya Ac
+.It Ta \ | Ta Ao Va sphere-geometry Ac
+.It Ta \ | Ta Ao Va supershape-geometry Ac
+.El
+.Pp
+Each of these geometries has an optional parameter
+.Ql radius_sphere
+that defines the radius of a sphere whose volume would correspond to
+that of the geometry.
+If defined, all other parameters of the geometric distribution must be
+constant, in order to fix the shape of the geometry and allow the
+.Ql radius_sphere
+parameter to control only its scaling.
+.Pp
+There are parameters that control the discretisation of geometries.
+Such as the
+.Ql slices
+optional parameter that defines the number of discrete steps around 2PI.
+When not defined it is assumed to be 64.
+Note that the
+.Ql helical_pipe
+geometry exposes 2 discretization parameters:
+.Ql slices_circle
+and
+.Ql slices_helicoid .
+The former controls the discretisation of the meridian around 2PI while
+the later defines the total number of discrete steps along the helicoid
+curve.
+When not defined
+.Ql slices_circle
+and
+.Ql slices_helicoid
are set to 64 and 128, respectively.
-.PP
-All the geometries have the \fBproba\fR optional attribute that defines the
-unnormalized probability to sample the geometry. If it is not defined, it is
-assumed to be equal to 1.
-.PP
-.RS 4
-.nf
-<schiff\-geometry> ::= <geometry> | <geometry\-list>
-
-<geometry\-list> ::= \- <geometry>
- [ \- <geometry> ]
-
-<geometry> ::= <cylinder\-geometry>
- | <ellipsoid\-geometry>
- | <helical\-pipe\-geometry>
- | <sphere\-geometry>
- | <supershape\-geometry>
-
-<cylinder\-geometry> ::= cylinder:
- radius: <distribution>
- height: <distribution>
- [ radius_sphere: <distribution> ]
- [ slices: INTEGER ]
- [ proba: REAL ]
-
-<ellipsoid\-geometry> ::= ellipsoid:
- a: <distribution>
- c: <distribution>
- [ radius_sphere: <distribution> ]
- [ slices: INTEGER ]
- [ proba: REAL ]
-
-<helical\-pipe\-geometry> ::= helical_pipe:
- pitch: <distribution>
- height: <distribution>
- radius_helicoid: <distribution>
- radius_circle: <distribution>
- [ radius_sphere: <distribution> ]
- [ slices_helicoid: INTEGER ]
- [ slices_circle: INTEGER ]
-
-<sphere\-geometry> ::= sphere:
- radius: <distribution>
- [ slices: INTEGER ]
- [ proba: REAL ]
-
-<supershape\-geometry> ::= supershape:
- formula0: <superformula>
- formula1: <superformula>
- [ radius_sphere: <distribution> ]
- [ slices: INTEGER ]
- [ proba: REAL ]
-
-<superformula> ::= A: <distribution>
- B: <Idistribution>
- M: <distribution>
- N0: <distribution>
- N1: <distribution>
- N2: <distribution>
-
-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-
-
-<distribution> ::= <constant>
- | <gaussian>
- | <histogram>
- | <lognormal>
-
-<constant> ::= REAL
-
-<lognormal> ::= lognormal:
- mu: REAL
- sigma: REAL
-
-<gaussian> ::= gaussian:
- mu: REAL
- sigma: REAL
-
-<histogram> ::= histogram:
- lower: REAL
- upper: REAL
- probabilities:
- <probabilities\-list>
-
-<probabilities\-list> ::= \- REAL
- [ \- <probabilities\-list> ]
-.fi
-.SH GEOMETRY TYPES
-.PP
-\fBcylinder\fR
-.PP
-.RS 4
-A cylinder is simply defined by its \fBheight\fR and a its \fBradius\fR.
-.RE
-.PP
-\fBellipsoid\fR
-.PP
-.RS 4
+.Pp
+All geometric shapes have the optional attribute
+.Ql proba ,
+which defines the unnormalised probability of selecting them from the
+set of geometric shapes.
+If it is not defined, it is assumed to be equal to 1.
+.Pp
+The rest of this section describes each of the geometric shapes.
+.\""""""""""""""""""""""""""""""""""
+.Ss Cylinder
+A cylinder is simply defined by its
+.Ql height
+and a its
+.Ql radius .
+.Pp
+Its grammar is as follows:
+.Bl -column (helical-pipe-geometry) (::=) ()
+.It Ao Va cylinder-geometry Ac Ta ::= Ta \& Qq cylinder\&:
+.It Ta Ta \& Qo \& \& radius: Qc Aq Va distribution
+.It Ta Ta \& Qo \& \& height: Qc Aq Va distribution
+.It Ta Ta Op Qo \& \& radius_sphere: Qc Aq Va distribution
+.It Ta Ta Op Qq \& \& slices: Vt integer
+.It Ta Ta Op Qq \& \& proba: Vt real
+.El
+.\""""""""""""""""""""""""""""""""""
+.Ss Ellipsoid
The shape of an ellipsoid geometry is controlled by the length of its
-semi\-principal axises \fBa\fR and \fBc\fR used to evaluate the following
-equation:
-.PP
-.RS 8
-.nf
-(x/\fBa\fR)^2 + (y/\fBa\fR)^2 + (z/\fBc\fR)^2 = 1
-.fi
-.RE
-.RE
-.PP
-\fBhelical_pipe\fR
-.RS 4
-.PP
-Helicoid whose meridian shape is a circle that is orthogonal to the helicoid
-slope. Its \fBpitch\fR defines the width of a complete helicoid turn and its
-\fBheight\fR controls the overall distance between the beginning and the end of
-the helicoid. Finally, the \fBradius_helicoid\fR and the \fBradius_circle\fR
+semi-principal axises
+.Ql a
+and
+.Ql c
+used to evaluate the following equation:
+.Bd -literal -offset Ds
+(x/a)^2 + (y/a)^2 + (z/c)^2 = 1
+.Ed
+.Pp
+Its grammar is as follows:
+.Bl -column (helical-pipe-geometry) (::=) ()
+.It Ao Va ellipsoid-geometry Ac Ta ::= Ta \& Qq ellipsoid\&:
+.It Ta Ta \& Qo \& \& a: Qc Aq Va distribution
+.It Ta Ta \& Qo \& \& c: Qc Aq Va distribution
+.It Ta Ta Op Qo \& \& radius_sphere: Qc Aq Va distribution
+.It Ta Ta Op Qq \& \& slices: Vt integer
+.It Ta Ta Op Qq \& \& proba: Vt real
+.El
+.\""""""""""""""""""""""""""""""""""
+.Ss Helical pipe
+An helical pipe has a circle as a meredian shape that is orthogonal to
+the helicoid slope.
+Its
+.Ql pitch
+defines the width of a complete helicoid turn and its
+.Ql height
+controls the overall distance between the beginning and the end of
+the helicoid.
+Finally, the
+.Ql radius_helicoid
+and the
+.Ql radius_circleR
defines the radius of the helicoid and the radius of its meridian,
-respectively. Let "u" in [0, \fBheight\fR * 2PI / \fBpitch\fR] and "t" in [0,
-2PI], the "X", "Y" and "Z" 3D coordinates of the helicoid points are computed
-from the following equations:
-.PP
-.RS 8
-.nf
+respectively.
+Let
+.Qq u
+in
+.Bq 0,height*2PI/pitch
+and
+.Qq t
+in
+.Bq 0,2PI ,
+the
+.Qq X ,
+.Qq Y
+and
+.Qq Z
+3D coordinates of the helicoid points are computed from the following
+equations:
+.Bd -literal -offset Ds
X(t, u) = x(t)*cos(u) - y(t)*sin(u)
Y(t, u) = x(t)*sin(u) + y(t)*cos(u)
Z(t, u) = z(t) + c*u
-.PP
-x(t) = \fBradius_helicoid\fR + \fBradius_circle\fR*cos(t)
-y(t) = -\fBradius_circle\fR * c / A * sin(t)
-z(t) = \fBradius_circle\fR*\fBradius_helicoid\fR / A * sin(t)
-.PP
-c = \fBpitch\fR / 2PI
-A = sqrt(\fBradius_helicoid\fR^2 + c^2)
-.fi
-.RE
-.RE
-.PP
-\fBsphere\fR
-.RS 4
-.PP
-A sphere is simply defined by its \fBradius\fR.
-.RE
-.PP
-\fBsupershape\fR
-.RS 4
-.PP
-Generalisation of the superellipsoid that is well suited to represent many
-complex shapes found in the nature. It is controlled by 2 superformulas, each
-defining a radius "r" for a given angle "a":
-.PP
-.RS 8
-.nf
-r(a) = ( |cos(\fBM\fR*a/4)/\fBA\fR)|^\fBN1\fR + |sin(\fBM\fR*a/4)/\fBB\fR|^\fBN2\fR )^{-1/\fBN0\fR}
-.fi
-.RE
-.PP
-Assuming a point with the spherical coordinates {theta, phi}, the corresponding
-3D coordinates onto the supershape is obtained by evaluating the following
-relations:
-.RS 8
-.PP
-.nf
+.Ed
+.Pp
+with:
+.Bd -literal -offset Ds
+x(t) = radius_helicoid + radius_circle*cos(t)
+y(t) = -radius_circle * c/A*sin(t)
+z(t) = radius_circle * radius_helicoid/A*sin(t)
+
+c = pitch/2PI
+A = sqrt(Bradius_helicoid^2 + c^2)
+.Ed
+.Pp
+Its grammar is as follows:
+.Bl -column (helical-pipe-geometry) (::=) ()
+.It Ao Va helical-pipe-geometry Ac Ta ::= Ta \& Qq helical_pipe\&:
+.It Ta Ta \& Qo \& \& pitch: Qc Aq Va distribution
+.It Ta Ta \& Qo \& \& height: Qc Aq Va distribution
+.It Ta Ta \& Qo \& \& radius_helicoid: Qc Aq Va distribution
+.It Ta Ta \& Qo \& \& radius_circle: Qc Aq Va distribution
+.It Ta Ta Op Qo \& \& radius_sphere: Qc Aq Va distribution
+.It Ta Ta Op Qq \& \& slices_helicoid: Vt integer
+.It Ta Ta Op Qq \& \& slices_circle: Vt integer
+.El
+.\""""""""""""""""""""""""""""""""""
+.Ss Sphere
+A sphere is simply defined by its
+.Ql radius .
+.Pp
+Its grammar is as follows:
+.Bl -column (helical-pipe-geometry) (::=) ()
+.It Ao Va sphere-geometry Ac Ta ::= Ta \& Qq sphere\&:
+.It Ta Ta \& Qo \& \& radius: Qc Aq Va distribution
+.It Ta Ta Op Qq \& \& slices: Vt integer
+.It Ta Ta Op Qq \& \& proba: Vt real
+.El
+.\""""""""""""""""""""""""""""""""""
+.Ss Supershape
+A supershape is a generalisation of the superellipsoid that is well
+suited to represent many complex shapes found in the nature.
+It is controlled by 2 superformulas, each
+defining a radius
+.Qq r
+for a given angle
+.Qq a :
+.Bd -literal -offset Ds
+r(a) = ( |cos(M*a/4)/A)|^N1 + |sin(M*a/4)/B|^N2 )^{-1/N0}
+.Ed
+.Pp
+Assuming a point with the spherical coordinates
+.Pq theta,phi ,
+the corresponding 3D coordinates onto the supershape is obtained by
+evaluating the following relations:
+.Bd -literal -offset Ds
x = r0(theta)*cos(theta) * r1(phi)*cos(phi)
y = r0(theta)*sin(theta) * r1(phi)*cos(phi)
z = r1(phi)*sin(phi)
-.fi
-.SH PARAMETER DISTRIBUTIONS
-.PP
-\fBconstant\fR
-.RS 4
-.PP
-Fixe the value of the parameter.
-.RE
-.PP
-\fBgaussian\fR
-.RS 4
-.PP
-Use the following probability distribution to define the parameter according to
-the mean value \fBmu\fR and the standard deviation \fBsigma\fR:
-.PP
-.RS 8
-.nf
-P(x) dx = 1 / (\fBsigma\fR*sqrt(2*PI)) * exp(1/2*((x-\fBmu\fR)/\fBsigma\fR)^2) dx
-.fi
-.RE
-.RE
-.PP
-\fBhistogram\fR
-.RS 4
-.PP
-Split the parameter domain [\fBlower\fR, \fBupper\fR] in \fIN\fR intervals of
-length (\fBupper\fR-\fBlower\fR)/\fIN\fR. The list of unnormalized
-probabilities of the interval bounds are listed in the \fBprobabilities\fR
-array and are used to build the cumulative distribution of the parameter. Let a
-random number "r" in [0, 1], the corresponding parameter value is computed by
-retrieving the interval of the parameter from the aforementioned cumulative,
-before linearly interpolating its bounds with respect to "r";
-.RE
-.PP
-\fBlognormal\fR
-.RS 4
-.PP
-Distribute the parameter with respect to a mean value \fBmu\fR and a standard
-deviation \fBsigma\fR as follow:
-.PP
-.RS 8
-.nf
-P(x) dx = 1/(log(\fBsigma\fR)*x*sqrt(2*PI) *
- exp(-(ln(x)-log(\fBmu\fR))^2 / (2*log(\fBsigma\fR)^2)) dx
-.fi
-.SH EXAMPLES
-.PP
+.Ed
+.Pp
+Its grammar is as follows:
+.Bl -column (helical-pipe-geometry) (::=) ()
+.It Ao Va supershape-geometry Ac Ta ::= Ta \& Qq supershape\&:
+.It Ta Ta \& Qo \& \& formula0: Qc Aq Va superformula
+.It Ta Ta \& Qo \& \& formula1: Qc Aq Va superformula
+.It Ta Ta Op Qo \& \& radius_sphere: Qc Aq Va distribution
+.It Ta Ta Op Qq \& \& slices: Vt integer
+.It Ta Ta Op Qq \& \& proba: Vt real
+.It Ao Va superformula Ac Ta ::= Ta \& Qo A: Qc Aq Va distribution
+.It Ta Ta \& Qo B: Qc Aq Va distribution
+.It Ta Ta \& Qo M: Qc Aq Va distribution
+.It Ta Ta \& Qo N0: Qc Aq Va distribution
+.It Ta Ta \& Qo N1: Qc Aq Va distribution
+.It Ta Ta \& Qo N2: Qc Aq Va distribution
+.El
+.\""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+.Sh DISTRIBUTIONS OF PARAMETERS
+Supported distributions are as follows:
+.Bl -column (helical-pipe-geometry) (::=) ()
+.It Ao Va distribution Ac Ta ::= Ta Aq Va constant
+.It Ta \ | Ta Aq Va gaussian
+.It Ta \ | Ta Aq Va histogram
+.It Ta \ | Ta Aq Va lognormal
+.El
+.\""""""""""""""""""""""""""""""""""
+.Ss Constant
+The constant distribution fix the value of the parameter:
+.Bl -column (helical-pipe-geometry) (::=) ()
+.It Ao Va constant Ac Ta ::= Ta Qq Vt real
+.El
+.\""""""""""""""""""""""""""""""""""
+.Ss Gaussian
+The gaussian distribution defines the parameter according to the mean
+value
+.Ql mu
+and the standard deviation
+.Ql sigma :
+.Bl -column (helical-pipe-geometry) (::=) ()
+.It Ao Va gaussian Ac Ta ::= Ta Qq gaussian\&:
+.It Ta Ta Qq \& \& mu: Vt real
+.It Ta Ta Qq \& \& sigma: Vt real
+.El
+.\""""""""""""""""""""""""""""""""""
+.Ss Histogram
+An histogram splits the parameter domain
+.Bq lower,upper
+in
+.Qq N
+intervals of
+length
+.Po upper-lower Pc Ns /N .
+The unnormalized
+probabilities of the interval bounds are listed in the
+.Ql probabilities
+array and are used to build the cumulative distribution of the
+parameter.
+Let a random number
+.Qq r
+in
+.Bq 0,1 ,
+the corresponding parameter value is computed by retrieving the interval
+of the parameter from the aforementioned cumulative, before linearly
+interpolating its bounds with respect to
+.Qq r .
+.Pp
+Its grammar is as follows:
+.Bl -column (helical-pipe-geometry) (::=) ()
+.It Ao Va histogram Ac Ta :: Ta Qq histogram\&:
+.It Ta Ta Qq \& \& lower: Vt real
+.It Ta Ta Qq \& \& upper: Vt real
+.It Ta Ta Qq \& \& probabilities\&:
+.It Ta Ta Qq \& \& \& \& - Vt real
+.It Ta Ta \& \& \& \& \& ...
+.El
+.\""""""""""""""""""""""""""""""""""
+.Ss Lognormal
+The lognormal distribution is controlled by the mean value
+.Ql mu
+and the standard deviation
+.Ql sigma
+as follows:
+.Bd -literal -offset Ds
+P(x) dx = 1/(log(sigma)*x*sqrt(2*PI) *
+ exp(-(ln(x)-log(mu))^2 / (2*log(sigma)^2)) dx
+.Ed
+.Pp
+Its grammar is as follows:
+.Bl -column (helical-pipe-geometry) (::=) ()
+.It Ao Va lognormal Ac Ta ::= Ta Qq lognormal\&:
+.It Ta Ta Qq \& \& mu: Vt real
+.It Ta Ta Qq \& \& sigma: Vt real
+.El
+.\""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+.Sh EXAMPLES
Soft particles are spheres whose radius is distributed according to an
histogram:
-.PP
-.RS 4
-.nf
+.Bd -literal -offset Ds
sphere:
radius:
histogram:
@@ -266,29 +349,25 @@ sphere:
- 0.4
- 1.23
- 3
-.fi
-.RE
-.PP
+.Ed
+.\""""""""""""""""""""""""""""""""""
+.Pp
Soft particles are ellipsoids whose one of its semi-principal axis is
distributed with respect to a lognormal distribution:
-.PP
-.RS 4
-.nf
+.Bd -literal -offset Ds
ellipsoid:
a: 1.0
c:
lognormal:
sigma: 0.2
mu: 1.3
-.fi
-.RE
-.PP
-Soft particles are ellipsoids whose semi\-principal axises are fixed. Its
-volume is equal to the volume of an equivalent sphere whose radius follows an
-histogram distribution:
-.PP
-.RS 4
-.nf
+.Ed
+.\""""""""""""""""""""""""""""""""""
+.Pp
+Soft particles are ellipsoids whose semi-principal axises are fixed.
+Its volume is equal to the volume of an equivalent sphere whose radius
+follows an histogram distribution:
+.Bd -literal -offset Ds
ellipsoid:
a: 1.1
b: 0.3
@@ -297,28 +376,25 @@ ellipsoid:
lower: 1
upper: 2.5
probabilities: [ 0.5, 2, 1 ]
-.fi
-.RE
-.PP
-Soft particles are cylinders. Their radius is constant and their height is
-distributed according to a gaussian distribution. The cylinder geometry is
-discretized in 128 slices along 2PI:
-.PP
-.RS 4
-.nf
+.Ed
+.\""""""""""""""""""""""""""""""""""
+.Pp
+Soft particles are cylinders.
+Their radius is constant and their height is distributed according to a
+gaussian distribution.
+The cylinder geometry is discretized in 128 slices along 2PI:
+.Bd -literal -offset Ds
cylinder:
slices: 128
radius: 1
height: { gaussian: { mu: 1.3, sigma: 0.84 } }
-.fi
-.RE
-.PP
-Soft particles are cylinders whose height and radius are fixed. Their volume
-is equal to the volume of a sphere whose radius is distributed with respect to
-an histogram:
-.PP
-.RS 4
-.nf
+.Ed
+.\""""""""""""""""""""""""""""""""""
+.Pp
+Soft particles are cylinders whose height and radius are fixed.
+Their volume is equal to the volume of a sphere whose radius is
+distributed with respect to an histogram:
+.Bd -literal -offset Ds
cylinder:
height: 1.2
radius: 3.4
@@ -327,16 +403,15 @@ cylinder:
lower: 1.24
upper: 4.56
probabilities: [ 2, 1.2, 3, 0.2 ]
-.fi
-.RE
-.PP
+.Ed
+.\""""""""""""""""""""""""""""""""""
+.Pp
Soft particle are helical pipes whose attributes are controlled by several
-distribution types. Their helicoid curve is split in 256 steps while its
-meridian is discretized in 128 slices:
-.PP
-.RS 4
-.nf
+distribution types.
+Their helicoid curve is split in 256 steps while its meridian is
+discretized in 128 slices:
helical_pipe:
+.Bd -literal -offset Ds
slices_helicoid: 256
slices_circle: 128
height : 4
@@ -347,14 +422,12 @@ helical_pipe:
lower: 1
upper: 1.5
probabilities: [ 1, 1.2, 0.2, 0.5, 1.4 ]
-.fi
-.RE
-.PP
-Soft particles are supershapes whose 2 parameters of each of its superformulas
-are controlled by gaussian distributions:
-.PP
-.RS 4
-.nf
+.Ed
+.\""""""""""""""""""""""""""""""""""
+.Pp
+Soft particles are supershapes whose 2 parameters of each of its
+superformulas are controlled by gaussian distributions:
+.Bd -literal -offset Ds
supershape:
formula0:
A: 1
@@ -370,38 +443,38 @@ supershape:
N0: 1
N1: 1
N2: { gaussian: { mu: 1, sigma: 0.3 } }
-.fi
-.RE
-.PP
-Soft particles are supershapes with the same shape. Their volume is controlled
-by an equivalent sphere whose radius follows a lognormal distribution:
-.PP
-.RS 4
-.nf
+.Ed
+.\""""""""""""""""""""""""""""""""""
+.Pp
+Soft particles are supershapes with the same shape.
+Their volume is controlled by an equivalent sphere whose radius follows
+a lognormal distribution:
+.Bd -literal -offset Ds
supershape:
formula0: { A: 1, B: 1, M: 3, N0: 3, N1: 3, N2: 5 }
formula1: { A: 2, B: 1.1, M: 3, N0: 1, N1: 1, N2: 1 }
radius_sphere : { lognormal: { mu: 2.2, sigma: 1.3 } }
-.fi
-.RE
-.PP
+.Ed
+.\""""""""""""""""""""""""""""""""""
+.Pp
Soft particles are spheres and cylinders with 2 times more spheres than
-cylinders. The cylinder parameters are controlled by lognormal distributions
-and spherical soft particles have a fixed radius:
-.PP
-.RS 4
-.nf
+cylinders.
+The cylinder parameters are controlled by lognormal distributions and
+spherical soft particles have a fixed radius:
+.Bd -literal -offset Ds
- sphere: { radius: 1.12, proba: 2.0, slices: 64 }
-
- cylinder:
- radius: {lognormal: { sigma: 2.3, mu: 0.2 } }
- height: {lognormal: { mu: 1, sigma: 1.5 } }
+ radius: { lognormal: { sigma: 2.3, mu: 0.2 } }
+ height: { lognormal: { mu: 1, sigma: 1.5 } }
slices: 32 # Discretisation in 32 slices
proba: 1
-.fi
-.RE
-.SH NOTES
-.PP
-[1] YAML Ain't Markup Language \- http://yaml.org
-.SH SEE ALSO
-.BR schiff (1)
+.Ed
+.\""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+.Sh SEE ALSO
+.Xr schiff 1
+.Rs
+.%T YAML Ain't Markup Language
+.%A Clark C. Evans et al
+.%D 2009
+.%U https://yaml.org/
+.Re
