diff --git a/doc/src/Bibliography.rst b/doc/src/Bibliography.rst index 9778340c94..6e0c257ba3 100644 --- a/doc/src/Bibliography.rst +++ b/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)** - AP Bartok, MC Payne, R Kondor, and G Csanyi, Physical Review Letters 104, 136403 (2010). +**(Bartok2013)** + 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). diff --git a/doc/src/Howto_spc.rst b/doc/src/Howto_spc.rst index 6dedfe40c4..e4dadb20e7 100644 --- a/doc/src/Howto_spc.rst +++ b/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) ` reference for more details on both +See the :ref:`(Berendsen2) ` 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 `: +:ref:`(AllenTildesley) `: .. 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. diff --git a/doc/src/atc_hardy_fields.rst b/doc/src/atc_hardy_fields.rst index 0159bb55ab..f8ab82eb58 100644 --- a/doc/src/atc_hardy_fields.rst +++ b/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) ` - 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] diff --git a/doc/src/atc_hardy_gradients.rst b/doc/src/atc_hardy_gradients.rst index 52d05eac7c..93770b2249 100644 --- a/doc/src/atc_hardy_gradients.rst +++ b/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) ` - 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] diff --git a/doc/src/atc_hardy_rates.rst b/doc/src/atc_hardy_rates.rst index 0c23e211ba..7ed09eff83 100644 --- a/doc/src/atc_hardy_rates.rst +++ b/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) ` - 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] diff --git a/doc/src/fix_neb_spin.rst b/doc/src/fix_neb_spin.rst index d04ba367c4..8afe18aa0d 100644 --- a/doc/src/fix_neb_spin.rst +++ b/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) `). +:ref:`(Bessarab) `). 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). diff --git a/doc/src/fix_wall_ees.rst b/doc/src/fix_wall_ees.rst index 7bcfc830e2..e154d57dea 100644 --- a/doc/src/fix_wall_ees.rst +++ b/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) `. 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. diff --git a/doc/src/neb_spin.rst b/doc/src/neb_spin.rst index 1d42ff884c..62ca9f32cb 100644 --- a/doc/src/neb_spin.rst +++ b/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) `. +following paper: :ref:`(Bessarab) `. 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 `. 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) `. + :ref:`(Bessarab) `. .. 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) `). +GNEB spins involved (see equation (13) in :ref:`(Bessarab) `). 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) `. As before, the other replicas rearrange +:ref:`(Bessarab) `. 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) `). +in Appendix D of :ref:`(Bessarab) `). 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) `), added to +replica's spins (see equation (13) of :ref:`(Bessarab) `), 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) `). +:ref:`(Bessarab) `). The "DNi" are the non normalized geodesic distances (see equation (13) -of :ref:`(BessarabA) `), between a replica i and the next replica +of :ref:`(Bessarab) `), 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) `). +:ref:`(Bessarab) `). ---------- @@ -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). diff --git a/doc/src/pair_dipole.rst b/doc/src/pair_dipole.rst index bea80bfc45..06c95ba149 100644 --- a/doc/src/pair_dipole.rst +++ b/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) ` and in :ref:`(Toukmaji) `. +:ref:`(AllenTildesley) ` and in :ref:`(Toukmaji) `. 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) `. 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) `. The original (non-shifted) formulas for the electrostatic potentials, forces and torques can be found in :ref:`(Price) `. 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) `. The formulas for the corresponding forces and torques have been obtained by applying the 'chain rule' as in appendix C.3 of -:ref:`(Allen) `. +:ref:`(AllenTildesley) `. 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: diff --git a/doc/src/pair_hdnnp.rst b/doc/src/pair_hdnnp.rst index 1bd3030bf5..f07a0f08a3 100644 --- a/doc/src/pair_hdnnp.rst +++ b/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 -Neural-Network Representation of High-Dimensional Potential-Energy Surfaces. -Phys. Rev. Lett. 2007, 98 (14), 146401. -`__ +**(Behler and Parrinello 2007)** Behler, J.; Parrinello, M. Phys. Rev. Lett. 2007, 98 (14), 146401. .. _Singraber_Behler_Dellago_2019: -**(Singraber, Behler and Dellago 2019)** `Singraber, A.; Behler, J.; Dellago, C. -Library-Based LAMMPS Implementation of High-Dimensional Neural Network -Potentials. J. Chem. Theory Comput. 2019, 15 (3), 1827-1840 -`__ +**(Singraber, Behler and Dellago 2019)** Singraber, A.; Behler, J.; Dellago, C. J., Chem. Theory Comput. 2019, 15 (3), 1827-1840 .. _Singraber_et_al_2019: -**(Singraber et al 2019)** `Singraber, A.; Morawietz, T.; Behler, J.; Dellago, -C. Parallel Multistream Training of High-Dimensional Neural Network Potentials. -J. Chem. Theory Comput. 2019, 15 (5), 3075-3092. -`__ +**(Singraber et al 2019)** Singraber, A.; Morawietz, T.; Behler, J.; Dellago, C., J. Chem. Theory Comput. 2019, 15 (5), 3075-3092. diff --git a/doc/src/pair_polymorphic.rst b/doc/src/pair_polymorphic.rst index 8968c9d7d2..2c9f118a86 100644 --- a/doc/src/pair_polymorphic.rst +++ b/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 ` -or :ref:`Albe `) if we set +or :ref:`Albe1 `) 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: diff --git a/doc/src/pair_quip.rst b/doc/src/pair_quip.rst index 1cb6cf6f08..d40d4c3179 100644 --- a/doc/src/pair_quip.rst +++ b/doc/src/pair_quip.rst @@ -29,7 +29,7 @@ from GitHub: `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) ` and :ref:`(PhD thesis of Bartok) `. +:ref:`(Bartok et al) ` and :ref:`(PhD thesis of Bartok) `. 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: