Update DOI resolver

https://www.doi.org/doi_handbook/2_Numbering.html#htmlencoding

cmake/README.md

@@ -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="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="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.25173" target="_blank">Vanduyfhuys et al., J. Comput. Chem., 39 (16), 999-1011 (2018)</a></li>
   </ul>
   </td>
   <td>

doc/src/Howto_tip4p.rst

@@ -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

doc/src/Packages_details.rst

@@ -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
+.. _vanduyfhuys2015: https://doi.org/10.1002/jcc.23877
-.. _vanduyfhuys2018: http://dx.doi.org/10.1002/jcc.25173
+.. _vanduyfhuys2018: https://doi.org/10.1002/jcc.25173
 .. _quickff: http://molmod.github.io/QuickFF
 .. _yaff: https://github.com/molmod/yaff
 

doc/src/fix_orient.rst

@@ -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).
 
 
 ----------

doc/src/fix_phonon.rst

@@ -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>`_

doc/src/fix_poems.rst

@@ -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>`_)

examples/HEAT/README

@@ -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.
 

examples/USER/colvars/log.27Nov18.peptide-colvars.g++.1

@@ -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.

examples/USER/colvars/log.27Nov18.peptide-colvars.g++.4

@@ -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.

examples/USER/colvars/log.27Nov18.peptide-colvars2.g++.1

@@ -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.

examples/USER/colvars/log.27Nov18.peptide-colvars2.g++.4

@@ -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.

examples/USER/misc/rhok/README.md

@@ -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,
+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)](http://dx.doi.org/10.1063/1.4818747) show how the crystal growth rate can be computed from fluctuations.
+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

examples/USER/misc/ti/in.ti_spring

@@ -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 -------------------------------------#

lib/colvars/README

@@ -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

lib/colvars/colvarmodule.cpp

@@ -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) {

lib/linalg/iparam2stage.F

@@ -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 

potentials/AlSiMgCuFe.meam

@@ -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

potentials/CH.airebo-m

@@ -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 

src/MISC/fix_orient_bcc.cpp

@@ -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"

src/USER-COLVARS/README

@@ -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:

src/USER-MISC/compute_cnp_atom.cpp

@@ -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
 
 ------------------------------------------------------------------------- */
 

src/USER-MISC/compute_hma.cpp

@@ -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>

src/USER-MISC/fix_filter_corotate.cpp

@@ -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"

src/USER-MISC/fix_flow_gauss.cpp

@@ -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"

src/USER-MISC/fix_grem.cpp

@@ -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: https://doi.org/10.1063/1.3432176
-   Cite: http://dx.doi.org/10.1021/acs.jpcb.5b07614
+   Cite: https://doi.org/10.1021/acs.jpcb.5b07614
 
 ------------------------------------------------------------------------- */
 

src/USER-MISC/pair_momb.cpp

@@ -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"

src/USER-YAFF/README

@@ -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., 36 (13), 1015-1027 (2015) https://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., 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