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4
cmake/README.md
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@ -1383,8 +1383,8 @@ cmake -C ../cmake/presets/all_on.cmake -C ../cmake/presets/nolib.cmake -D PKG_GP
Some potentials that are also implemented in the Yet Another Force Field (YAFF) code.
The expressions and their use are discussed in the following papers:
<ul>
<li><a href="http://dx.doi.org/10.1002/jcc.23877" target="_blank">Vanduyfhuys et al., J. Comput. Chem., 36 (13), 1015-1027 (2015)</a></li>
<li><a href="http://dx.doi.org/10.1002/jcc.25173" target="_blank">Vanduyfhuys et al., J. Comput. Chem., 39 (16), 999-1011 (2018)</a></li>
<li><a href="https://doi.org/10.1002/jcc.23877" target="_blank">Vanduyfhuys et al., J. Comput. Chem., 36 (13), 1015-1027 (2015)</a></li>
<li><a href="https://doi.org/10.1002/jcc.25173" target="_blank">Vanduyfhuys et al., J. Comput. Chem., 39 (16), 999-1011 (2018)</a></li>
</ul>
</td>
<td>

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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

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doc/src/Packages_details.rst
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@ -2515,8 +2515,8 @@ 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

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doc/src/fix_orient.rst
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@ -205,7 +205,7 @@ Science, 117, 397-405 (2016).
**(Wicaksono2)** Wicaksono, figshare,
https://dx.doi.org/10.6084/m9.figshare.1488628.v1 (2015).
https://doi.org/10.6084/m9.figshare.1488628.v1 (2015).
----------

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doc/src/fix_phonon.rst
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@ -218,7 +218,7 @@ 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:
@ -226,15 +226,15 @@ simulation of elastic semi-infinite solids*\ , `Phys. Rev. B [74], 075420 (2006)
**(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>`_

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doc/src/fix_poems.rst
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@ -151,4 +151,4 @@ 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>`_)

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examples/HEAT/README
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@ -6,7 +6,7 @@ All input scripts are part of the supplementary (open access) material
supporting the publication of Wirnsberger et al. [J. Chem. Phys. 143,
124104 (2015)] and allow one to reproduce the key results reported in
that paper. The full article is available for download under
http://dx.doi.org/10.1063/1.4931597 or http://arxiv.org/pdf/1507.07081
https://doi.org/10.1063/1.4931597 or http://arxiv.org/pdf/1507.07081
and the supplementary material is available under
https://www.repository.cam.ac.uk/handle/1810/250539.

4
examples/USER/colvars/log.27Nov18.peptide-colvars.g++.1
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@ -101,7 +101,7 @@ colvars: Creating proxy instance
colvars: ----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 2018-11-16.
colvars: Please cite Fiorin et al, Mol Phys 2013:
colvars: http://dx.doi.org/10.1080/00268976.2013.813594
colvars: https://doi.org/10.1080/00268976.2013.813594
colvars: in any publication based on this calculation.
colvars: SMP parallelism is available.
colvars: Using LAMMPS interface, version 2018-08-29.
@ -405,7 +405,7 @@ colvars: Creating proxy instance
colvars: ----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 2018-11-16.
colvars: Please cite Fiorin et al, Mol Phys 2013:
colvars: http://dx.doi.org/10.1080/00268976.2013.813594
colvars: https://doi.org/10.1080/00268976.2013.813594
colvars: in any publication based on this calculation.
colvars: SMP parallelism is available.
colvars: Using LAMMPS interface, version 2018-08-29.

4
examples/USER/colvars/log.27Nov18.peptide-colvars.g++.4
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@ -101,7 +101,7 @@ colvars: Creating proxy instance
colvars: ----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 2018-11-16.
colvars: Please cite Fiorin et al, Mol Phys 2013:
colvars: http://dx.doi.org/10.1080/00268976.2013.813594
colvars: https://doi.org/10.1080/00268976.2013.813594
colvars: in any publication based on this calculation.
colvars: SMP parallelism is available.
colvars: Using LAMMPS interface, version 2018-08-29.
@ -405,7 +405,7 @@ colvars: Creating proxy instance
colvars: ----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 2018-11-16.
colvars: Please cite Fiorin et al, Mol Phys 2013:
colvars: http://dx.doi.org/10.1080/00268976.2013.813594
colvars: https://doi.org/10.1080/00268976.2013.813594
colvars: in any publication based on this calculation.
colvars: SMP parallelism is available.
colvars: Using LAMMPS interface, version 2018-08-29.

2
examples/USER/colvars/log.27Nov18.peptide-colvars2.g++.1
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@ -100,7 +100,7 @@ colvars: Creating proxy instance
colvars: ----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 2018-11-16.
colvars: Please cite Fiorin et al, Mol Phys 2013:
colvars: http://dx.doi.org/10.1080/00268976.2013.813594
colvars: https://doi.org/10.1080/00268976.2013.813594
colvars: in any publication based on this calculation.
colvars: SMP parallelism is available.
colvars: Using LAMMPS interface, version 2018-08-29.

2
examples/USER/colvars/log.27Nov18.peptide-colvars2.g++.4
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@ -100,7 +100,7 @@ colvars: Creating proxy instance
colvars: ----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 2018-11-16.
colvars: Please cite Fiorin et al, Mol Phys 2013:
colvars: http://dx.doi.org/10.1080/00268976.2013.813594
colvars: https://doi.org/10.1080/00268976.2013.813594
colvars: in any publication based on this calculation.
colvars: SMP parallelism is available.
colvars: Using LAMMPS interface, version 2018-08-29.

6
examples/USER/misc/rhok/README.md
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@ -19,7 +19,7 @@ For future reference we note that the structure factor S(k) is given by the vari
It is recommended to get familiar with the interface pinning method by reading:
[Ulf R. Pedersen, JCP 139, 104102 (2013)](http://dx.doi.org/10.1063/1.4818747)
[Ulf R. Pedersen, JCP 139, 104102 (2013)](https://doi.org/10.1063/1.4818747)
A detailed bibliography is provided at
@ -63,8 +63,8 @@ can be used to show this. The present directory contains the input files that we
the value fluctuates around the anchor point (a) -- showing that this is indeed a coexistence
state point.
The reference [JCP 139, 104102 (2013)](http://dx.doi.org/10.1063/1.4818747) gives details on using the method to find coexistence state points,
and the reference [JCP 142, 044104 (2015)](http://dx.doi.org/10.1063/1.4818747) show how the crystal growth rate can be computed from fluctuations.
The reference [JCP 139, 104102 (2013)](https://doi.org/10.1063/1.4818747) gives details on using the method to find coexistence state points,
and the reference [JCP 142, 044104 (2015)](https://doi.org/10.1063/1.4818747) show how the crystal growth rate can be computed from fluctuations.
That method have been experienced to be most effective in the slightly super-heated regime above the melting temperature.
## Contact

2
examples/USER/misc/ti/in.ti_spring
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@ -2,7 +2,7 @@
#
# Description: nonequilibrium thermodynamic integration. Further details in:
# R. Freitas, M. Asta, and M. de Koning, Computational Materials Science, (2016)
# http://dx.doi.org/10.1016/j.commatsci.2015.10.050
# https://doi.org/10.1016/j.commatsci.2015.10.050
#--------------------------- System setup -------------------------------------#

2
lib/colvars/README
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@ -27,7 +27,7 @@ Also available is a Doxygen-based developer documentation:
The reference article is:
G. Fiorin, M. L. Klein, and J. Hénin,
Molecular Physics 111, 3345 (2013).
http://dx.doi.org/10.1080/00268976.2013.813594
https://doi.org/10.1080/00268976.2013.813594
## Requirements

2
lib/colvars/colvarmodule.cpp
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@ -50,7 +50,7 @@ colvarmodule::colvarmodule(colvarproxy *proxy_in)
cvm::log("Initializing the collective variables module, version "+
cvm::to_str(COLVARS_VERSION)+".\n");
cvm::log("Please cite Fiorin et al, Mol Phys 2013:\n "
"https://dx.doi.org/10.1080/00268976.2013.813594\n"
"https://doi.org/10.1080/00268976.2013.813594\n"
"in any publication based on this calculation.\n");
if (proxy->smp_enabled() == COLVARS_OK) {

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lib/linalg/iparam2stage.F
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@ -130,7 +130,7 @@
*> of 2011 International Conference for High Performance Computing,
*> Networking, Storage and Analysis (SC '11), New York, NY, USA,
*> Article 8 , 11 pages.
*> http://doi.acm.org/10.1145/2063384.2063394
*> https://doi.acm.org/10.1145/2063384.2063394
*>
*> A. Haidar, J. Kurzak, P. Luszczek, 2013.
*> An improved parallel singular value algorithm and its implementation
@ -138,7 +138,7 @@
*> for High Performance Computing, Networking, Storage and Analysis (SC '13).
*> Denver, Colorado, USA, 2013.
*> Article 90, 12 pages.
*> http://doi.acm.org/10.1145/2503210.2503292
*> https://doi.acm.org/10.1145/2503210.2503292
*>
*> A. Haidar, R. Solca, S. Tomov, T. Schulthess and J. Dongarra.
*> A novel hybrid CPU-GPU generalized eigensolver for electronic structure

2
potentials/AlSiMgCuFe.meam
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@ -1,7 +1,7 @@
# DATE: 2012-06-29 CONTRIBUTOR: Greg Wagner, gjwagne@sandia.gov CITATION: Jelinek, Groh, Horstemeyer, Houze, Kim, Wagner, Moitra and Baskes, Phys Rev B, 85, 245102 (2012)
# MEAM Al, Si, Mg, Cu, Fe alloy potential
# use with AlS SiS MgS CuS FeS from library.meam
# http://dx.doi.org/10.1103/PhysRevB.85.245102
# https://doi.org/10.1103/PhysRevB.85.245102
Cmin(1,1,1) = 0.8
repuls(1,1) = 0.1

4
potentials/CH.airebo-m
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@ -1,8 +1,8 @@
# DATE: 2016-03-15 CONTRIBUTOR: T.C. O'Connor CITATION: O'Connor, Andzelm, Robbins, J. Chem. Phys. 142, 024903 (2015)
# AIREBO-M of T.C. O'Connor, J.W. Andzelm, M.O. Robbins (2015)
# Citation: J. Chem. Phys. 142, 024903 (2015); http://dx.doi.org/10.1063/1.4905549
# Citation: J. Chem. Phys. 142, 024903 (2015); https://doi.org/10.1063/1.4905549
# Based on AIREBO of S.J. Stuart, A.B. Tutein, J.A. Harrison (2000)
# Citation: J. Chem. Phys. 112, 6472 (2000); http://dx.doi.org/10.1063/1.481208
# Citation: J. Chem. Phys. 112, 6472 (2000); https://doi.org/10.1063/1.481208
1.7 rcmin_CC
1.3 rcmin_CH

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src/MISC/fix_orient_bcc.cpp
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@ -15,7 +15,7 @@
Contributing authors: Koenraad Janssens and David Olmsted (SNL)
Modification for bcc provided by: Tegar Wicaksono (UBC)
For a tutorial, please see "Order parameters of crystals in LAMMPS"
(https://dx.doi.org/10.6084/m9.figshare.1488628.v1
(https://doi.org/10.6084/m9.figshare.1488628.v1
------------------------------------------------------------------------- */
#include "fix_orient_bcc.h"

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src/USER-COLVARS/README
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@ -27,7 +27,7 @@ and in the reference article:
Using collective variables to drive molecular dynamics simulations,
G. Fiorin, M. L. Klein, and J. Henin,
Molecular Physics 111, 3345 (2013)
http://dx.doi.org/10.1080/00268976.2013.813594
https://doi.org/10.1080/00268976.2013.813594
A reference manual for the package and library is included with the
LAMMPS doc pages:

2
src/USER-MISC/compute_cnp_atom.cpp
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@ -12,7 +12,7 @@
Common Neighbor Parameter as proposed in:
Tsuzuki, Branicio, Rino, Comput Phys Comm, 177, 518 (2007)
Cite: http://dx.doi.org/10.1063/1.2197987
Cite: https://doi.org/10.1063/1.2197987
------------------------------------------------------------------------- */

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src/USER-MISC/compute_hma.cpp
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@ -31,16 +31,16 @@ More information about HMA is available in these publications:
A. J. Schultz, D. A. Kofke, “Comprehensive high-precision high-accuracy
equation of state and coexistence properties for classical Lennard-Jones
crystals and low-temperature fluid phases”, J. Chem. Phys. 149, 204508 (2018)
https://dx.doi.org/10.1063/1.5053714
https://doi.org/10.1063/1.5053714
S. G. Moustafa, A. J. Schultz, D. A. Kofke, “Harmonically Assisted Methods for
Computing the Free Energy of Classical Crystals by Molecular Simulation: A
Comparative Study”, J. Chem. Theory Comput. 13, 825-834 (2017)
https://dx.doi.org/10.1021/acs.jctc.6b01082
https://doi.org/10.1021/acs.jctc.6b01082
S. G. Moustafa, A. J. Schultz, D. A. Kofke, “Very fast averaging of thermal
properties of crystals by molecular simulation”, Phys. Rev. E 92, 043303 (2015)
https://dx.doi.org/10.1103/PhysRevE.92.043303
https://doi.org/10.1103/PhysRevE.92.043303
------------------------------------------------------------------------- */
#include <cmath>

2
src/USER-MISC/fix_filter_corotate.cpp
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@ -54,7 +54,7 @@ static const char cite_filter_corotate[] =
" Year = {2017},\n"
" Pages = {180 - 198},\n"
" Volume = {333},\n\n"
" Doi = {http://dx.doi.org/10.1016/j.jcp.2016.12.024},\n"
" Doi = {https://doi.org/10.1016/j.jcp.2016.12.024},\n"
" ISSN = {0021-9991},\n"
" Keywords = {Mollified impulse method},\n"
" Url = {http://www.sciencedirect.com/science/article/pii/S0021999116306787}\n"

2
src/USER-MISC/fix_flow_gauss.cpp
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@ -37,7 +37,7 @@ static const char cite_flow_gauss[] =
"title = {The Dynamics of Water in Porous Two-Dimensional Crystals},\n"
"volume = {121},\n"
"number = {1},\n"
"url = {http://dx.doi.org/10.1021/acs.jpcb.6b09387},\n"
"url = {https://doi.org/10.1021/acs.jpcb.6b09387},\n"
"doi = {10.1021/acs.jpcb.6b09387},\n"
"urldate = {2016-12-07},\n"
"journal = {J. Phys. Chem. B},\n"

4
src/USER-MISC/fix_grem.cpp
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@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
Force scaling fix for gREM.
Cite: http://dx.doi.org/10.1063/1.3432176
Cite: http://dx.doi.org/10.1021/acs.jpcb.5b07614
Cite: https://doi.org/10.1063/1.3432176
Cite: https://doi.org/10.1021/acs.jpcb.5b07614
------------------------------------------------------------------------- */

2
src/USER-MISC/pair_momb.cpp
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@ -37,7 +37,7 @@ static const char cite_momb[] =
" solution-phase synthesis of shape-selective Ag nanoparticles.},\n"
"volume = {118},\n"
"number = {6},\n"
"url = {http://dx.doi.org/10.1021/jp412098n},\n"
"url = {https://doi.org/10.1021/jp412098n},\n"
"doi = {10.1021/jp412098n},\n"
"journal = {J. Phys. Chem. C},\n"
"author = {Zhou, Ya, Wissam A. Saidi, and Kristen A. Fichthorn},\n"

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src/USER-YAFF/README
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@ -1,8 +1,8 @@
This package implements the styles that are needed to use typical force fields
generated by QuickFF for the simulation of metal-organic frameworks. The
QuickFF methodology is detailed in following papers:
Vanduyfhuys et al., J. Comput. Chem., 36 (13), 1015-1027 (2015) http://dx.doi.org/10.1002/jcc.23877
Vanduyfhuys et al., J. Comput. Chem., 39 (16), 999-1011 (2018) http://dx.doi.org/10.1002/jcc.25173
Vanduyfhuys et al., J. Comput. Chem., 36 (13), 1015-1027 (2015) https://doi.org/10.1002/jcc.23877
Vanduyfhuys et al., J. Comput. Chem., 39 (16), 999-1011 (2018) https://doi.org/10.1002/jcc.25173
The corresponding software package can be found on http://molmod.github.io/QuickFF