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inclusion of reference links in the text

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Evangelos Voyiatzis 2019-10-26 18:09:11 +02:00
parent b7fbb36b81
commit e263890a6b
2 changed files with 18 additions and 9 deletions
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14
doc/src/compute_gyration_shape.txt
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@ -10,7 +10,7 @@ compute gyration/shape command :h3
[Syntax:]
compute ID group-ID gyration compute-ID :pre
compute ID group-ID gyration/shape compute-ID :pre
ID, group-ID are documented in "compute"_compute.html command
gyration/shape = style name of this compute command
@ -24,14 +24,16 @@ compute 1 molecule gyration/shape pe :pre
Define a computation that calculates the eigenvalues of the gyration tensor of a
group of atoms and three shape parameters. The computation includes all effects
due to atoms passing thru periodic boundaries.
due to atoms passing through periodic boundaries.
The three computed shape parameters are the asphericity, b, the acylindricity, c,
and the relative shape anisotropy, k:
:c,image(Eqs/compute_shape_parameters.jpg)
where lx <= ly <= lz are the three eigenvalues of the gyration tensor.
where lx <= ly <= lz are the three eigenvalues of the gyration tensor. A general description
of these parameters is provided in "(Mattice)"_#Mattice while an application to polymer systems
can be found in "(Theodorou)"_#Theodorou.
The asphericity is always non-negative and zero only when the three principal
moments are equal. This zero condition is met when the distribution of particles
is spherically symmetric (hence the name asphericity) but also whenever the particle
@ -81,7 +83,9 @@ package"_Build_package.html doc page for more info.
:line
[(Theodorou)] Theodorou, Suter, Macromolecules, 18, 1206 (1985).
:link(Mattice)
[(Mattice)] Mattice, Suter, Conformational Theory of Large Molecules, Wiley, New York, 1994.
:link(Theodorou)
[(Theodorou)] Theodorou, Suter, Macromolecules, 18, 1206 (1985).

13
doc/src/compute_gyration_shape_chunk.txt
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@ -31,10 +31,11 @@ and the relative shape anisotropy, k:
:c,image(Eqs/compute_shape_parameters.jpg)
where lx <= ly <= lz are the three eigenvalues of the gyration tensor.
The asphericity is always non-negative and zero only when the three principal
moments are equal. This zero condition is met when the distribution of particles
is spherically symmetric (hence the name asphericity) but also whenever the particle
where lx <= ly <= lz are the three eigenvalues of the gyration tensor. A general description
of these parameters is provided in "(Mattice)"_#Mattice while an application to polymer systems
can be found in "(Theodorou)"_#Theodorou. The asphericity is always non-negative and zero
only when the three principal moments are equal. This zero condition is met when the distribution
of particles is spherically symmetric (hence the name asphericity) but also whenever the particle
distribution is symmetric with respect to the three coordinate axes, e.g.,
when the particles are distributed uniformly on a cube, tetrahedron or other Platonic
solid. The acylindricity is always non-negative and zero only when the two principal
@ -84,5 +85,9 @@ package"_Build_package.html doc page for more info.
:line
:link(Mattice)
[(Mattice)] Mattice, Suter, Conformational Theory of Large Molecules, Wiley, New York, 1994.
:link(Theodorou)
[(Theodorou)] Theodorou, Suter, Macromolecules, 18, 1206 (1985).