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Merge branch 'DOI' of github.com:e-kwsm/lammps into doc-cleanup

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Axel Kohlmeyer
2020-03-12 05:43:44 -04:00
parent 23a402ddd3 8af9d40392
commit 1372c20d94
37 changed files with 89 additions and 94 deletions
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4
doc/src/Howto_tip4p.rst
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@ -41,7 +41,7 @@ coefficients.
|
For the TIP4/Ice model (J Chem Phys, 122, 234511 (2005);
http://dx.doi.org/10.1063/1.1931662) these values can be used:
https://doi.org/10.1063/1.1931662) these values can be used:
| O mass = 15.9994
| H mass = 1.008
@ -57,7 +57,7 @@ http://dx.doi.org/10.1063/1.1931662) these values can be used:
|
For the TIP4P/2005 model (J Chem Phys, 123, 234505 (2005);
http://dx.doi.org/10.1063/1.2121687), these values can be used:
https://doi.org/10.1063/1.2121687), these values can be used:
| O mass = 15.9994
| H mass = 1.008

4
doc/src/Packages_details.rst
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@ -2339,8 +2339,8 @@ The expressions and their use are discussed in the following papers
which discuss the `QuickFF <quickff_>`_ methodology.
.. _vanduyfhuys2015: http://dx.doi.org/10.1002/jcc.23877
.. _vanduyfhuys2018: http://dx.doi.org/10.1002/jcc.25173
.. _vanduyfhuys2015: https://doi.org/10.1002/jcc.23877
.. _vanduyfhuys2018: https://doi.org/10.1002/jcc.25173
.. _quickff: http://molmod.github.io/QuickFF
.. _yaff: https://github.com/molmod/yaff

2
doc/src/fix_orient.rst
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@ -193,7 +193,7 @@ Science, 117, 397-405 (2016).
.. _Wicaksono2:
**(Wicaksono2)** Wicaksono, figshare,
https://dx.doi.org/10.6084/m9.figshare.1488628.v1 (2015).
https://doi.org/10.6084/m9.figshare.1488628.v1 (2015).
----------

8
doc/src/fix_phonon.rst
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@ -203,19 +203,19 @@ the :doc:`dimension <dimension>` command, and nasr = 20.
**(Campana)** C. Campana and
M. H. Muser, *Practical Green's function approach to the
simulation of elastic semi-infinite solids*\ , `Phys. Rev. B [74], 075420 (2006) <http://dx.doi.org/10.1103/PhysRevB.74.075420>`_
simulation of elastic semi-infinite solids*\ , `Phys. Rev. B [74], 075420 (2006) <https://doi.org/10.1103/PhysRevB.74.075420>`_
.. _Kong:
**(Kong)** L.T. Kong, G. Bartels, C. Campana,
C. Denniston, and Martin H. Muser, *Implementation of Green's
function molecular dynamics: An extension to LAMMPS*\ , `Computer Physics Communications [180](6):1004-1010 (2009). <http://dx.doi.org/10.1016/j.cpc.2008.12.035>`_
function molecular dynamics: An extension to LAMMPS*\ , `Computer Physics Communications [180](6):1004-1010 (2009). <https://doi.org/10.1016/j.cpc.2008.12.035>`_
L.T. Kong, C. Denniston, and Martin H. Muser,
*An improved version of the Green's function molecular dynamics
method*\ , `Computer Physics Communications [182](2):540-541 (2011). <http://dx.doi.org/10.1016/j.cpc.2010.10.006>`_
method*\ , `Computer Physics Communications [182](2):540-541 (2011). <https://doi.org/10.1016/j.cpc.2010.10.006>`_
.. _Kong2011:
**(Kong2011)** L.T. Kong, *Phonon dispersion measured directly from
molecular dynamics simulations*\ , `Computer Physics Communications [182](10):2201-2207, (2011). <http://dx.doi.org/10.1016/j.cpc.2011.04.019>`_
molecular dynamics simulations*\ , `Computer Physics Communications [182](10):2201-2207, (2011). <https://doi.org/10.1016/j.cpc.2011.04.019>`_

2
doc/src/fix_poems.rst
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@ -140,4 +140,4 @@ Related commands
**(Anderson)** Anderson, Mukherjee, Critchley, Ziegler, and Lipton
"POEMS: Parallelizable Open-source Efficient Multibody Software ",
Engineering With Computers (2006). (`link to paper <http://dx.doi.org/10.1007/s00366-006-0026-x>`_)
Engineering With Computers (2006). (`link to paper <https://doi.org/10.1007/s00366-006-0026-x>`_)

9
doc/src/pair_dpd.rst
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@ -126,9 +126,14 @@ the work of :ref:`(Afshar) <Afshar>` and :ref:`(Phillips) <Phillips>`.
.. note::
The virial calculation for pressure when using this pair style
The virial calculation for pressure when using these pair styles
includes all the components of force listed above, including the
random force.
random force. Since the random force depends on random numbers,
everything that changes the order of atoms in the neighbor list
(e.g. different number of MPI ranks or a different neighbor list
skin distance) will also change the sequence in which the random
numbers are applied and thus the individual forces and therefore
also the virial/pressure.
----------

12
doc/src/pair_srp.rst
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@ -15,9 +15,9 @@ Syntax
* distance = *min* or *mid*
* zero or more keyword/value pairs may be appended
* keyword = *exclude*
.. parsed-literal::
*bptype* value = atom type for bond particles
*exclude* value = *yes* or *no*
@ -31,7 +31,7 @@ Examples
pair_coeff 1 2 none
pair_coeff 2 2 srp 100.0 0.8
pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 \* min exclude yes
pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 * min exclude yes
pair_coeff 1 1 dpd 60.0 50 1.0
pair_coeff 1 2 none
pair_coeff 2 2 srp 40.0
@ -57,7 +57,7 @@ bond-pairwise potential, such that the force on bond *i* due to bond
.. math::
F^{SRP}_{ij} & = C(1-r/r_c)\hat{r}_{ij} \qquad r < r_c
F^{\mathrm{SRP}}_{ij} = C(1-r/r_c)\hat{r}_{ij} \qquad r < r_c
where *r* and :math:`\hat{r}_{ij}` are the distance and unit vector
between the two bonds. Note that *btype* can be specified as an
@ -70,8 +70,8 @@ lever rule,
.. math::
F_{i1}^{SRP} & = F^{SRP}_{ij}(L) \\
F_{i2}^{SRP} & = F^{SRP}_{ij}(1-L)
F_{i1}^{\mathrm{SRP}} & = F^{\mathrm{SRP}}_{ij}(L) \\
F_{i2}^{\mathrm{SRP}} & = F^{\mathrm{SRP}}_{ij}(1-L)
where *L* is the normalized distance from the atom to the point of
closest approach of bond *i* and *j*\ . The *mid* option takes *L* as