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final set of bibliography updates

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@ -721,17 +721,14 @@ Bibliography
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The spline-based MEAM+SW format was first devised and used to develop potentials for bcc transition metals by Jeremy Nicklas, Michael Fellinger,
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doc/src/Howto_moltemplate.rst
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@ -367,5 +367,4 @@ And execute the simulation with the following:
.. _OPLSAA96:
**(OPLS-AA)** Jorgensen, Maxwell, Tirado-Rives, J Am Chem Soc,
118(45), 11225-11236 (1996).
**(OPLS-AA)** Jorgensen, Maxwell, Tirado-Rives, J Am Chem Soc, 118(45), 11225-11236 (1996).

3
doc/src/create_atoms.rst
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@ -643,5 +643,4 @@ checked, *maxtry* = 10, and *units* = lattice.
.. _Roberts2019:
**(Roberts)** R. Roberts (2019) "Evenly Distributing Points in a Triangle." Extreme Learning.
`<http://extremelearning.com.au/evenly-distributing-points-in-a-triangle/>`_
**(Roberts)** R. Roberts (2019) "Evenly Distributing Points in a Triangle." Extreme Learning. `<http://extremelearning.com.au/evenly-distributing-points-in-a-triangle/>`_

10
doc/src/fix_dpd_energy.rst
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@ -83,14 +83,8 @@ none
.. _Lisal1:
**(Lisal)** M. Lisal, J.K. Brennan, J. Bonet Avalos, "Dissipative
particle dynamics at isothermal, isobaric, isoenergetic, and
isoenthalpic conditions using Shardlow-like splitting algorithms.",
J. Chem. Phys., 135, 204105 (2011).
**(Lisal)** M. Lisal, J.K. Brennan, J. Bonet Avalos, J. Chem. Phys., 135, 204105 (2011).
.. _Larentzos3:
**(Larentzos)** J.P. Larentzos, J.K. Brennan, J.D. Moore, and
W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative
Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research
Laboratory, Aberdeen Proving Ground, MD (2014).
**(Larentzos)** J.P. Larentzos, J.K. Brennan, J.D. Moore, and W.D. Mattson, ARL-TR-6863, U.S. Army Research Laboratory, Aberdeen Proving Ground, MD (2014).

48
doc/src/fix_shardlow.rst
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@ -29,25 +29,28 @@ Description
Specifies that the Shardlow splitting algorithm (SSA) is to be used to
integrate the DPD equations of motion. The SSA splits the integration
into a stochastic and deterministic integration step. The fix
*shardlow* performs the stochastic integration step and must be used
in conjunction with a deterministic integrator (e.g. :doc:`fix nve <fix_nve>` or :doc:`fix nph <fix_nh>`). The stochastic
integration of the dissipative and random forces is performed prior to
the deterministic integration of the conservative force. Further
details regarding the method are provided in :ref:`(Lisal) <Lisal>` and
*shardlow* performs the stochastic integration step and must be used in
conjunction with a deterministic integrator (e.g. :doc:`fix nve
<fix_nve>` or :doc:`fix nph <fix_nh>`). The stochastic integration of
the dissipative and random forces is performed prior to the
deterministic integration of the conservative force. Further details
regarding the method are provided in :ref:`(Lisal) <Lisal>` and
:ref:`(Larentzos1) <Larentzos1sh>`.
The fix *shardlow* must be used with the :doc:`pair_style dpd/fdt <pair_style>` or :doc:`pair_style dpd/fdt/energy <pair_style>` command to properly initialize the
fluctuation-dissipation theorem parameter(s) sigma (and kappa, if
necessary).
The fix *shardlow* must be used with the :doc:`pair_style dpd/fdt
<pair_style>` or :doc:`pair_style dpd/fdt/energy <pair_style>` command
to properly initialize the fluctuation-dissipation theorem parameter(s)
sigma (and kappa, if necessary).
Note that numerous variants of DPD can be specified by choosing an
appropriate combination of the integrator and :doc:`pair_style dpd/fdt <pair_style>` command. DPD under isothermal conditions can
be specified by using fix *shardlow*, fix *nve* and pair_style
*dpd/fdt*\ . DPD under isoenergetic conditions can be specified by
using fix *shardlow*, fix *nve* and pair_style *dpd/fdt/energy*\ . DPD
under isobaric conditions can be specified by using fix shardlow, fix
*nph* and pair_style *dpd/fdt*\ . DPD under isoenthalpic conditions can
be specified by using fix shardlow, fix *nph* and pair_style
appropriate combination of the integrator and :doc:`pair_style dpd/fdt
<pair_style>` command. DPD under isothermal conditions can be specified
by using fix *shardlow*, fix *nve* and pair_style *dpd/fdt*\ . DPD
under isoenergetic conditions can be specified by using fix *shardlow*,
fix *nve* and pair_style *dpd/fdt/energy*\ . DPD under isobaric
conditions can be specified by using fix shardlow, fix *nph* and
pair_style *dpd/fdt*\ . DPD under isoenthalpic conditions can be
specified by using fix shardlow, fix *nph* and pair_style
*dpd/fdt/energy*\ . Examples of each DPD variant are provided in the
examples/PACKAGES/dpd-react directory.
@ -88,21 +91,12 @@ none
.. _Lisal:
**(Lisal)** M. Lisal, J.K. Brennan, J. Bonet Avalos, "Dissipative
particle dynamics as isothermal, isobaric, isoenergetic, and
isoenthalpic conditions using Shardlow-like splitting algorithms.",
J. Chem. Phys., 135, 204105 (2011).
**(Lisal)** M. Lisal, J.K. Brennan, J. Bonet Avalos, J. Chem. Phys., 135, 204105 (2011).
.. _Larentzos1sh:
**(Larentzos1)** J.P. Larentzos, J.K. Brennan, J.D. Moore, M. Lisal and
W.D. Mattson, "Parallel Implementation of Isothermal and Isoenergetic
Dissipative Particle Dynamics Using Shardlow-Like Splitting
Algorithms", Comput. Phys. Commun., 185, 1987-1998 (2014).
**(Larentzos1)** J.P. Larentzos, J.K. Brennan, J.D. Moore, M. Lisal and W.D. Mattson, Comput. Phys. Commun., 185, 1987-1998 (2014).
.. _Larentzos2sh:
**(Larentzos2)** J.P. Larentzos, J.K. Brennan, J.D. Moore, and
W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative
Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research
Laboratory, Aberdeen Proving Ground, MD (2014).
**(Larentzos2)** J.P. Larentzos, J.K. Brennan, J.D. Moore, and W.D. Mattson, ARL-TR-6863, U.S. Army Research Laboratory, Aberdeen Proving Ground, MD (2014).

5
doc/src/pair_dpd_fdt.rst
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@ -183,7 +183,4 @@ none
.. _Lisal3:
**(Lisal)** M. Lisal, J.K. Brennan, J. Bonet Avalos, "Dissipative
particle dynamics at isothermal, isobaric, isoenergetic, and
isoenthalpic conditions using Shardlow-like splitting algorithms.",
J. Chem. Phys., 135, 204105 (2011).
**(Lisal)** M. Lisal, J.K. Brennan, J. Bonet Avalos, J. Chem. Phys., 135, 204105 (2011).

3
doc/src/pair_kolmogorov_crespi_z.rst
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@ -86,5 +86,4 @@ none
.. _vanWijk:
**(vanWijk)** M. M. van Wijk, A. Schuring, M. I. Katsnelson, and A. Fasolino,
Physical Review Letters, 113, 135504 (2014)
**(vanWijk)** M. M. van Wijk, A. Schuring, M. I. Katsnelson, and A. Fasolino, Physical Review Letters, 113, 135504 (2014)

6
doc/src/pair_spin_dmi.rst
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@ -100,8 +100,6 @@ none
.. _Tranchida5:
**(Rohart)** Rohart and Thiaville,
Physical Review B, 88(18), 184422. (2013).
**(Rohart)** Rohart and Thiaville, Physical Review B, 88(18), 184422. (2013).
**(Tranchida)** Tranchida, Plimpton, Thibaudeau and Thompson,
Journal of Computational Physics, 372, 406-425, (2018).
**(Tranchida)** Tranchida, Plimpton, Thibaudeau and Thompson, Journal of Computational Physics, 372, 406-425, (2018).