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make links to papers unique across files

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Axel Kohlmeyer
2018-02-02 10:10:27 +01:00
parent 2ff278defa
commit 85fdf9eaba
2 changed files with 8 additions and 8 deletions
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10
doc/src/fix_ti_spring.txt
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@ -34,7 +34,7 @@ by performing a nonequilibrium thermodynamic integration between the
solid of interest and an Einstein crystal. A detailed explanation of
how to use this command and choose its parameters for optimal
performance and accuracy is given in the paper by
"Freitas"_#Freitas. The paper also presents a short summary of the
"Freitas"_#Freitas1. The paper also presents a short summary of the
theory of nonequilibrium thermodynamic integrations.
The thermodynamic integration procedure is performed by rescaling the
@ -67,13 +67,13 @@ of lambda is kept equal to zero and the fix has no other effect on the
dynamics of the system.
The processes described above is known as nonequilibrium thermodynamic
integration and is has been shown ("Freitas"_#Freitas) to present a
integration and is has been shown ("Freitas"_#Freitas1) to present a
much superior efficiency when compared to standard equilibrium
methods. The reason why the switching it is made in both directions
(potential to Einstein crystal and back) is to eliminate the
dissipated heat due to the nonequilibrium process. Further details
about nonequilibrium thermodynamic integration and its implementation
in LAMMPS is available in "Freitas"_#Freitas.
in LAMMPS is available in "Freitas"_#Freitas1.
The {function} keyword allows the use of two different lambda
paths. Option {1} results in a constant rate of change of lambda with
@ -94,7 +94,7 @@ thermodynamic integration. The use of option {2} is recommended since
it results in better accuracy and less dissipation without any
increase in computational resources cost.
NOTE: As described in "Freitas"_#Freitas, it is important to keep the
NOTE: As described in "Freitas"_#Freitas1, it is important to keep the
center-of-mass fixed during the thermodynamic integration. A nonzero
total velocity will result in divergences during the integration due
to the fact that the atoms are 'attached' to their equilibrium
@ -156,7 +156,7 @@ The keyword default is function = 1.
:line
:link(Freitas)
:link(Freitas1)
[(Freitas)] Freitas, Asta, and de Koning, Computational Materials
Science, 112, 333 (2016).

6
doc/src/pair_ufm.txt
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@ -62,7 +62,7 @@ of a run:
variable prefactor equal ramp(10,100)
fix 1 all adapt 1 pair ufm epsilon * * v_prefactor :pre
NOTE: The thermodynamic integration procedure can be performed with this potential using "fix adapt"_fix_adapt.html. This command will rescale the force on each atom by varying a scale variable, which always starts with value 1.0. The syntax is the same described above, however, changing epsilon to scale. A detailed explanation of how to use this command and perform nonequilibrium thermodynamic integration in LAMMPS is given in the paper by "(Freitas)"_#Freitas.
NOTE: The thermodynamic integration procedure can be performed with this potential using "fix adapt"_fix_adapt.html. This command will rescale the force on each atom by varying a scale variable, which always starts with value 1.0. The syntax is the same described above, however, changing epsilon to scale. A detailed explanation of how to use this command and perform nonequilibrium thermodynamic integration in LAMMPS is given in the paper by "(Freitas)"_#Freitas2.
:line
@ -131,5 +131,5 @@ This pair style can only be used via the {pair} keyword of the
[(Paula Leite2016)] Paula Leite , Freitas, Azevedo, and de Koning, J Chem Phys, 126,
044509 (2016).
:link(Freitas)
[(Freitas)] Freitas, Asta, and de Koning, Computational Materials Science, 112, 333 (2016).
:link(Freitas2)
[(Freitas)] Freitas, Asta, and de Koning, Computational Materials Science, 112, 333 (2016).