diff --git a/doc/src/fix_ti_spring.txt b/doc/src/fix_ti_spring.txt index afb1dcf8fffe855b41ac19f62e6504afd8b13540..191f9e7c6b8d8667b5baef112f20d16fb435a382 100644 --- a/doc/src/fix_ti_spring.txt +++ b/doc/src/fix_ti_spring.txt @@ -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). diff --git a/doc/src/pair_ufm.txt b/doc/src/pair_ufm.txt index 2be35b0d4bb834231cf51efe2a7b6ac58906b64c..88a22864ccaf960472dbe5ea3f985ea2d375ab23 100644 --- a/doc/src/pair_ufm.txt +++ b/doc/src/pair_ufm.txt @@ -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). \ No newline at end of file +:link(Freitas2) +[(Freitas)] Freitas, Asta, and de Koning, Computational Materials Science, 112, 333 (2016).