bibliography cleanup

doc/src/Bibliography.rst

@@ -1,6 +1,12 @@
 Bibliography
 ************
 
+**(Abascal1)**
+   Abascal, Sanz, Fernandez, Vega, J Chem Phys, 122, 234511 (2005)
+
+**(Abascal2)**
+   Abascal, J Chem Phys, 123, 234505 (2005)
+
 **(Ackland)**
    Ackland, Jones, Phys Rev B, 73, 054104 (2006).
 
@@ -22,21 +28,24 @@ Bibliography
 **(Agnolin and Roux 2007)**
    Agnolin, I. & Roux, J-N. (2007). Internal states of model isotropic granular packings. I. Assembling process, geometry, and contact networks. Phys. Rev. E, 76, 061302.
 
+**(Ahrens-Iwers2022)**
+   Ahrens-Iwers *et al.*, J. Chem. Phys. 157, 084801 (2022).
+
+**(Ahrens-Iwers)**
+   Ahrens-Iwers and Meissner, J. Chem. Phys. 155, 104104 (2021).
+
 **(Aktulga)**
    Aktulga, Fogarty, Pandit, Grama, Parallel Computing, 38, 245-259 (2012).
 
 **(Albe)**
    J.\  Nord, K. Albe, P. Erhart, and K. Nordlund, J. Phys.: Condens. Matter, 15, 5649(2003).
 
-**(Albe)**
+**(Albe1)**
    K.\  Albe, K. Nordlund, J. Nord, and A. Kuronen, Phys. Rev. B, 66, 035205 (2002).
 
 **(Allen)**
    Allen and Germano, Mol Phys 104, 3225-3235 (2006).
 
-**(Allen)**
-   Allen and Tildesley, Computer Simulation of Liquids, Clarendon Press, Oxford, 1987.
-
 **(AllenTildesley)**
    Allen and Tildesley, Computer Simulation of Liquids, Oxford University Press (1987)
 
@@ -49,6 +58,9 @@ Bibliography
 **(Anderson)**
    Anderson, Mukherjee, Critchley, Ziegler, and Lipton "POEMS: Parallelizable Open-source Efficient Multibody Software ", Engineering With Computers (2006).
 
+**(Appshaw)**
+   Appshaw, Seddon, Hanna, Soft. Matter,18, 1747(2022).
+
 **(Avendano)**
    C.\  Avendano, T. Lafitte, A. Galindo, C. S. Adjiman, G. Jackson, E. Muller, J Phys Chem B, 115, 11154 (2011).
 
@@ -58,7 +70,7 @@ Bibliography
 **(Babadi)**
    Babadi, Ejtehadi, Everaers, J Comp Phys, 219, 770-779 (2006).
 
-**(Babadi)**
+**(Babadi2)**
    Babadi and Ejtehadi, EPL, 77 (2007) 23002.
 
 **(Baczewski)**
@@ -73,23 +85,23 @@ Bibliography
 **(Ballenegger)**
    Ballenegger, Arnold, Cerda, J Chem Phys, 131, 094107 (2009).
 
-**(Banna)**
-   Volkov, Banna, Comp. Mater. Sci. 176, 109410 (2020).
-
 **(Barrat)**
    Barrat and Rodney, J. Stat. Phys, 144, 679 (2011).
 
 **(Barrett)**
    Barrett, Tschopp, El Kadiri, Scripta Mat. 66, p.666 (2012).
 
+**(Barros)**
+   Barros, Sinkovits, Luijten, J. Chem. Phys, 140, 064903 (2014)
+
 **(Bartok)**
    Bartok, Payne, Risi, Csanyi, Phys Rev Lett, 104, 136403 (2010).
 
 **(Bartok2010)**
    Bartok, Payne, Risi, Csanyi, Phys Rev Lett, 104, 136403 (2010).
 
-**(Bartok_2010)**
+**(Bartok2013)**
-   AP Bartok, MC Payne, R Kondor, and G Csanyi, Physical Review Letters 104, 136403 (2010).
+   Bartok, Kondor, Csanyi, Phys Rev B, 87, 184115 (2013).
 
 **(Bartok_PhD)**
    A Bartok-Partay, PhD Thesis, University of Cambridge, (2010).
@@ -97,30 +109,36 @@ Bibliography
 **(Baskes)**
    Baskes, Phys Rev B, 46, 2727-2742 (1992).
 
+**(Baskes2)**
+   Baskes, Phys Rev B, 75, 094113 (2007).
+
 **(Beck)**
    Beck, Molecular Physics, 14, 311 (1968).
 
+**(Becton)**
+   Becton, Averett, Wang, Biomech. Model. Mechanobiology, 18, 425-433(2019).
+
+**(Behler and Parrinello 2007)**
+   Behler, J.; Parrinello, M. Phys. Rev. Lett.  2007, 98 (14), 146401.
+
 **(Bennet)**
    Bennet, J Comput Phys, 22, 245 (1976)
 
 **(Berardi)**
    Berardi, Fava, Zannoni, Chem Phys Lett, 297, 8-14 (1998). Berardi, Muccioli, Zannoni, J Chem Phys, 128, 024905 (2008).
 
-**(Berendsen)**
-   Berendsen, Grigera, Straatsma, J Phys Chem, 91, 6269-6271 (1987).
-
 **(Berendsen)**
    Berendsen, Postma, van Gunsteren, DiNola, Haak, J Chem Phys, 81, 3684 (1984).
 
+**(Berendsen2)**
+   Berendsen, Grigera, Straatsma, J Phys Chem, 91, 6269-6271 (1987).
+
 **(Bessarab)**
    Bessarab, Uzdin, Jonsson, Comp Phys Comm, 196, 335-347 (2015).
 
 **(Beutler)**
    Beutler, Mark, van Schaik, Gerber, van Gunsteren, Chem Phys Lett, 222, 529 (1994).
 
-**(Bialke)**
-   J.\  Bialke, T. Speck, and H Loewen, Phys. Rev. Lett. 108, 168301, 2012.
-
 **(Bird)**
    G.\  A. Bird, "Molecular Gas Dynamics and the Direct Simulation of Gas Flows" (1994).
 
@@ -310,6 +328,9 @@ Bibliography
 **(Erdmann)**
    U.\  Erdmann , W. Ebeling, L. Schimansky-Geier, and F. Schweitzer, Eur. Phys. J. B 15, 105-113, 2000.
 
+**(Eshelby)**
+  J.D. Eshelby, Philos. Trans. Royal Soc. London A, Math. Phys. Sci., Vol. 244, No. 877 (1951) pp. 87-112; J. Elasticity, Vol. 5, Nos. 3-4 (1975) pp. 321-335]
+
 **(Espanol and Revenga)**
    Espanol, Revenga, Physical Review E, 67, 026705 (2003).
 

doc/src/Howto_spc.rst

@@ -33,7 +33,7 @@ the partial charge assignments change:
 | O charge = -0.8476
 | H charge = 0.4238
 
-See the :ref:`(Berendsen) <howto-Berendsen>` reference for more details on both
+See the :ref:`(Berendsen2) <howto-Berendsen>` reference for more details on both
 the SPC and SPC/E models.
 
 Below is the code for a LAMMPS input file and a molecule file
@@ -149,4 +149,4 @@ Wikipedia also has a nice article on `water models <https://en.wikipedia.org/wik
 
 .. _howto-Berendsen:
 
-**(Berendsen)** Berendsen, Grigera, Straatsma, J Phys Chem, 91, 6269-6271 (1987).
+**(Berendsen2)** Berendsen, Grigera, Straatsma, J Phys Chem, 91, 6269-6271 (1987).

doc/src/angle_dipole.rst

@@ -49,7 +49,7 @@ angle.
 
 The torque on the dipole can be obtained by differentiating the
 potential using the 'chain rule' as in appendix C.3 of
-:ref:`(Allen) <Allen1>`:
+:ref:`(AllenTildesley) <Allen1>`:
 
 .. math::
 
@@ -129,5 +129,5 @@ lipid membranes, PloS ONE 6(12): e28637, 2011.
 
 .. _Allen1:
 
-**(Allen)** Allen & Tildesley, Computer Simulation of Liquids,
+**(AllenTildesley)** Allen & Tildesley, Computer Simulation of Liquids,
 Clarendon Press, Oxford, 1987.

doc/src/atc_hardy_fields.rst

@@ -34,7 +34,7 @@ Syntax
   - internal_energy : total internal energy (potential + thermal) per unit volume
   - energy : total energy (potential + kinetic) per unit volume
   - number_density : number of atoms per unit volume
-  - eshelby_stress : configurational stress (energy-momentum) tensor defined by [Eshelby]_
+  - eshelby_stress : configurational stress (energy-momentum) tensor defined by :ref:`(Eshelby) <Eshelby1>`
   - vacancy_concentration : volume fraction of vacancy content
   - type_concentration : volume fraction of a specific atom type
 
@@ -83,4 +83,6 @@ By default, no fields are output.
 References
 """"""""""
 
-.. [Eshelby] J.D. Eshelby, Philos. Trans. Royal Soc. London A, Math. Phys. Sci., Vol. 244, No. 877 (1951) pp. 87-112; J. Elasticity, Vol. 5, Nos. 3-4 (1975) pp. 321-335]
+.. _Eshelby1:
+
+**(Eshelby)** J.D. Eshelby, Philos. Trans. Royal Soc. London A, Math. Phys. Sci., Vol. 244, No. 877 (1951) pp. 87-112; J. Elasticity, Vol. 5, Nos. 3-4 (1975) pp. 321-335]

doc/src/atc_hardy_gradients.rst

@@ -32,7 +32,7 @@ Syntax
   - internal_energy : total internal energy (potential + thermal) per unit volume
   - energy : total energy (potential + kinetic) per unit volume
   - number_density : number of atoms per unit volume
-  - eshelby_stress : configurational stress (energy-momentum) tensor defined by [Eshelby]_
+  - eshelby_stress : configurational stress (energy-momentum) tensor defined by :ref:`(Eshelby) <Eshelby3>`
   - vacancy_concentration : volume fraction of vacancy content
   - type_concentration : volume fraction of a specific atom type
 
@@ -72,3 +72,10 @@ Default
 """""""
 
 None.
+
+References
+""""""""""
+
+.. _Eshelby3:
+
+**(Eshelby)** J.D. Eshelby, Philos. Trans. Royal Soc. London A, Math. Phys. Sci., Vol. 244, No. 877 (1951) pp. 87-112; J. Elasticity, Vol. 5, Nos. 3-4 (1975) pp. 321-335]

doc/src/atc_hardy_rates.rst

@@ -32,7 +32,7 @@ Syntax
   - internal_energy : total internal energy (potential + thermal) per unit volume
   - energy : total energy (potential + kinetic) per unit volume
   - number_density : number of atoms per unit volume
-  - eshelby_stress : configurational stress (energy-momentum) tensor defined by [Eshelby]_
+  - eshelby_stress : configurational stress (energy-momentum) tensor defined by :ref:`(Eshelby) <Eshelby2>`
   - vacancy_concentration : volume fraction of vacancy content
   - type_concentration : volume fraction of a specific atom type
 
@@ -72,3 +72,10 @@ Default
 """""""
 
 None.
+
+References
+""""""""""
+
+.. _Eshelby2:
+
+**(Eshelby)** J.D. Eshelby, Philos. Trans. Royal Soc. London A, Math. Phys. Sci., Vol. 244, No. 877 (1951) pp. 87-112; J. Elasticity, Vol. 5, Nos. 3-4 (1975) pp. 321-335]

doc/src/fix_neb_spin.rst

@@ -44,7 +44,7 @@ energy relaxes toward the saddle point (i.e. the point of highest energy
 along the MEP), and a second relaxation is performed.
 
 The nudging forces are calculated as explained in
-:ref:`(BessarabB) <BessarabB>`).
+:ref:`(Bessarab) <BessarabB>`).
 See this reference for more explanation about their expression.
 
 Restart, fix_modify, output, run start/stop, minimize info
@@ -81,5 +81,5 @@ none
 
 .. _BessarabB:
 
-**(BessarabB)** Bessarab, Uzdin, Jonsson, Comp Phys Comm, 196,
+**(Bessarab)** Bessarab, Uzdin, Jonsson, Comp Phys Comm, 196,
 335-347 (2015).

doc/src/fix_wall_ees.rst

@@ -71,7 +71,7 @@ energy of wall-particle interactions E is given by:
    \sigma_{n}^5 \left(r^2-\sigma_{n}^2\right)} \right]\qquad \sigma_n
    < r < r_c
 
-Introduced by Babadi and Ejtehadi in :ref:`(Babadi)
+Introduced by Babadi and Ejtehadi in :ref:`(Babadi2)
 <BabadiEjtehadi>`. Here, *r* is the distance from the particle to the
 wall at position *coord*, and Rc is the *cutoff* distance at which
 the particle and wall no longer interact. Also, :math:`\sigma_n` is
@@ -182,4 +182,4 @@ none
 
 .. _BabadiEjtehadi:
 
-**(Babadi)** Babadi and Ejtehadi, EPL, 77 (2007) 23002.
+**(Babadi2)** Babadi and Ejtehadi, EPL, 77 (2007) 23002.

doc/src/neb_spin.rst

@@ -56,7 +56,7 @@ of the energy barrier associated with a transition state, e.g.
 spins to perform a collective rotation from one energy basin to
 another.
 The implementation in LAMMPS follows the discussion in the
-following paper: :ref:`(BessarabA) <BessarabA>`.
+following paper: :ref:`(Bessarab) <BessarabA>`.
 
 Each replica runs on a partition of one or more processors.  Processor
 partitions are defined at run-time using the :doc:`-partition command-line switch <Run_options>`.  Note that if you have MPI installed, you
@@ -129,7 +129,7 @@ is assigned to be a fraction of the angular distance.
 
    The "angular distance" between the starting and final point is
    evaluated in the geodesic sense, as described in
-   :ref:`(BessarabA) <BessarabA>`.
+   :ref:`(Bessarab) <BessarabA>`.
 
 .. note::
 
@@ -224,7 +224,7 @@ For intermediate replicas, it is the cumulative angular distance
 (normalized by the total cumulative angular distance) between adjacent
 replicas, where "distance" is defined as the length of the 3N-vector of
 the geodesic distances in spin coordinates, with N the number of
-GNEB spins involved (see equation (13) in :ref:`(BessarabA) <BessarabA>`).
+GNEB spins involved (see equation (13) in :ref:`(Bessarab) <BessarabA>`).
 These outputs allow you to monitor NEB's progress in
 finding a good energy barrier.  *N1* and *N2* must both be multiples
 of *Nevery*\ .
@@ -243,7 +243,7 @@ In the second stage of GNEB, the replica with the highest energy is
 selected and the inter-replica forces on it are converted to a force
 that drives its spin coordinates to the top or saddle point of the
 barrier, via the barrier-climbing calculation described in
-:ref:`(BessarabA) <BessarabA>`.  As before, the other replicas rearrange
+:ref:`(Bessarab) <BessarabA>`.  As before, the other replicas rearrange
 themselves along the MEP so as to be roughly equally spaced.
 
 When both stages are complete, if the GNEB calculation was successful,
@@ -321,11 +321,11 @@ maximum torque component of any atom in any replica.  The potential
 gradients are the two-norm of the 3N-length magnetic precession vector
 solely due to the interaction potential i.e. without adding in
 inter-replica forces, and projected along the path tangent (as detailed
-in Appendix D of :ref:`(BessarabA) <BessarabA>`).
+in Appendix D of :ref:`(Bessarab) <BessarabA>`).
 
 The "reaction coordinate" (RD) for each replica is the two-norm of the
 3N-length vector of geodesic distances between its spins and the preceding
-replica's spins (see equation (13) of :ref:`(BessarabA) <BessarabA>`), added to
+replica's spins (see equation (13) of :ref:`(Bessarab) <BessarabA>`), added to
 the RD of the preceding replica. The RD of the first replica RD1 = 0.0;
 the RD of the final replica RDN = RDT, the total reaction coordinate.
 The normalized RDs are divided by RDT, so that they form a monotonically
@@ -340,9 +340,9 @@ screen and master log.lammps file by adding the *verbose* keyword. This
 information include the following.
 The "GradVidottan" are the projections of the potential gradient for
 the replica i on its tangent vector (as detailed in Appendix D of
-:ref:`(BessarabA) <BessarabA>`).
+:ref:`(Bessarab) <BessarabA>`).
 The "DNi" are the non normalized geodesic distances (see equation (13)
-of :ref:`(BessarabA) <BessarabA>`), between a replica i and the next replica
+of :ref:`(Bessarab) <BessarabA>`), between a replica i and the next replica
 i+1. For the last replica, this distance is not defined and a "NAN"
 value is the corresponding output.
 
@@ -372,7 +372,7 @@ parameters.
 A c file script in provided in the tool/spin/interpolate_gneb
 directory, that interpolates the MEP given the information provided
 by the *verbose* output option (as detailed in Appendix D of
-:ref:`(BessarabA) <BessarabA>`).
+:ref:`(Bessarab) <BessarabA>`).
 
 ----------
 
@@ -403,5 +403,5 @@ none
 
 .. _BessarabA:
 
-**(BessarabA)** Bessarab, Uzdin, Jonsson, Comp Phys Comm, 196,
+**(Bessarab)** Bessarab, Uzdin, Jonsson, Comp Phys Comm, 196,
 335-347 (2015).

doc/src/pair_dipole.rst

@@ -124,7 +124,7 @@ and the vector r = Ri - Rj is the separation vector between the two
 particles.  Note that Eqq and Fqq are simply Coulombic energy and
 force, Fij = -Fji as symmetric forces, and Tij != -Tji since the
 torques do not act symmetrically.  These formulas are discussed in
-:ref:`(Allen) <Allen2>` and in :ref:`(Toukmaji) <Toukmaji2>`.
+:ref:`(AllenTildesley) <Allen2>` and in :ref:`(Toukmaji) <Toukmaji2>`.
 
 Also note, that in the code, all of these terms (except Elj) have a
 :math:`C/\epsilon` prefactor, the same as the Coulombic term in the
@@ -140,7 +140,7 @@ moment. In general, a shifted-force potential is a (slightly) modified
 potential containing extra terms that make both the energy and its
 derivative go to zero at the cutoff distance; this removes
 (cutoff-related) problems in energy conservation and any numerical
-instability in the equations of motion :ref:`(Allen)
+instability in the equations of motion :ref:`(AllenTildesley)
 <Allen2>`. Shifted-force interactions for the Lennard-Jones (E_LJ),
 charge-charge (Eqq), charge-dipole (Eqp), dipole-charge (Epq) and
 dipole-dipole (Epp) potentials are computed by these formulas for the
@@ -221,10 +221,10 @@ shifted-force formula for the Lennard-Jones potential is reported in
 :ref:`(Stoddard) <Stoddard>`.  The original (non-shifted) formulas for
 the electrostatic potentials, forces and torques can be found in
 :ref:`(Price) <Price2>`. The shifted-force electrostatic potentials
-have been obtained by applying equation 5.13 of :ref:`(Allen)
+have been obtained by applying equation 5.13 of :ref:`(AllenTildesley)
 <Allen2>`. The formulas for the corresponding forces and torques have
 been obtained by applying the 'chain rule' as in appendix C.3 of
-:ref:`(Allen) <Allen2>`.
+:ref:`(AllenTildesley) <Allen2>`.
 
 If one cutoff is specified in the pair_style command, it is used for
 both the LJ and Coulombic (q,p) terms.  If two cutoffs are specified,
@@ -378,7 +378,7 @@ none
 
 .. _Allen2:
 
-**(Allen)** Allen and Tildesley, Computer Simulation of Liquids,
+**(AllenTildesley)** Allen and Tildesley, Computer Simulation of Liquids,
 Clarendon Press, Oxford, 1987.
 
 .. _Toukmaji2:

doc/src/pair_hdnnp.rst

@@ -210,21 +210,12 @@ The default options are *dir* = "hdnnp/", *showew* = yes, *showewsum* = 0, *maxe
 
 .. _Behler_Parrinello_2007:
 
-**(Behler and Parrinello 2007)** `Behler, J.; Parrinello, M. Generalized
+**(Behler and Parrinello 2007)** Behler, J.; Parrinello, M. Phys. Rev. Lett.  2007, 98 (14), 146401.
-Neural-Network Representation of High-Dimensional Potential-Energy Surfaces.
-Phys. Rev. Lett.  2007, 98 (14), 146401.
-<https://doi.org/10.1103/PhysRevLett.98.146401>`__
 
 .. _Singraber_Behler_Dellago_2019:
 
-**(Singraber, Behler and Dellago 2019)** `Singraber, A.; Behler, J.; Dellago, C.
+**(Singraber, Behler and Dellago 2019)** Singraber, A.; Behler, J.; Dellago, C. J., Chem.  Theory Comput. 2019, 15 (3), 1827-1840
-Library-Based LAMMPS Implementation of High-Dimensional Neural Network
-Potentials. J. Chem.  Theory Comput. 2019, 15 (3), 1827-1840
-<https://doi.org/10.1021/acs.jctc.8b00770>`__
 
 .. _Singraber_et_al_2019:
 
-**(Singraber et al 2019)** `Singraber, A.; Morawietz, T.; Behler, J.; Dellago,
+**(Singraber et al 2019)** Singraber, A.; Morawietz, T.; Behler, J.; Dellago, C., J. Chem. Theory Comput.  2019, 15 (5), 3075-3092.
-C. Parallel Multistream Training of High-Dimensional Neural Network Potentials.
-J. Chem. Theory Comput.  2019, 15 (5), 3075-3092.
-<https://doi.org/10.1021/acs.jctc.8b01092>`__

doc/src/pair_polymorphic.rst

@@ -75,7 +75,7 @@ instance, the potential reduces to a Stillinger-Weber potential
    G_{JIK}\left(\cos\theta\right) & = \left(\cos\theta+\frac{1}{3}\right)^2
 
 The potential reduces to a Tersoff potential (:ref:`Tersoff <Tersoff>`
-or :ref:`Albe <poly-Albe>`) if we set
+or :ref:`Albe1 <poly-Albe>`) if we set
 
 .. math::
 
@@ -351,7 +351,7 @@ Related commands
 
 .. _poly-Albe:
 
-**(Albe)** K. Albe, K. Nordlund, J. Nord, and A. Kuronen, Phys. Rev. B, 66, 035205 (2002).
+**(Albe1)** K. Albe, K. Nordlund, J. Nord, and A. Kuronen, Phys. Rev. B, 66, 035205 (2002).
 
 .. _Wang3:
 

doc/src/pair_quip.rst

@@ -29,7 +29,7 @@ from GitHub:
 `https://github.com/libAtoms/QUIP <https://github.com/libAtoms/QUIP>`_. The
 interface is chiefly intended to be used to run Gaussian Approximation
 Potentials (GAP), which are described in the following publications:
-:ref:`(Bartok et al) <Bartok_2010>` and :ref:`(PhD thesis of Bartok) <Bartok_PhD>`.
+:ref:`(Bartok et al) <Bartok2010>` and :ref:`(PhD thesis of Bartok) <Bartok_PhD>`.
 
 Only a single pair_coeff command is used with the *quip* style that
 specifies a QUIP potential file containing the parameters of the
@@ -103,7 +103,7 @@ Related commands
 
 .. _Bartok_2010:
 
-**(Bartok_2010)** AP Bartok, MC Payne, R Kondor, and G Csanyi, Physical
+**(Bartok2010)** AP Bartok, MC Payne, R Kondor, and G Csanyi, Physical
 Review Letters 104, 136403 (2010).
 
 .. _Bartok_PhD: