Update DOI URLs

See https://www.doi.org/doi_handbook/2_Numbering.html#htmlencoding
2021-11-10 02:19:44 +09:00 · 2021-11-10 02:19:44 +09:00 · fda20be88d
parent 8f5ff19603
commit fda20be88d
21 changed files with 42 additions and 42 deletions
--- a/Doc/release-notes
+++ b/Doc/release-notes
@ -652,7 +652,7 @@ Incompatible changes in 6.2 version:
 New in 6.1 version:

  * Hybrid functionals: Band parallelization over pair of bands, contributed
-    by Taylor Barnes et al, http://dx.doi.org/10.1016/j.cpc.2017.01.008
+    by Taylor Barnes et al, https://doi.org/10.1016/j.cpc.2017.01.008
  * Hybrid functionals with PAW now work
  * Optimized tetrahedron method, contributed by Mitsuaki Kawamura, U. Tokyo
  * PostProcessing: pp.x can now plot many bands in a single run.
--- a/EPW/examples/gan/pp/Ga_ONCV_LDA-1.0.upf
+++ b/EPW/examples/gan/pp/Ga_ONCV_LDA-1.0.upf
@ -29,7 +29,7 @@
 testing of the pseudopotential please refer to:
 
 M. Schlipf, F. Gygi, Comp. Phys. Comm. 196, 36 (2015)
- http://dx.doi.org/10.1016/j.cpc.2015.05.011
+ https://doi.org/10.1016/j.cpc.2015.05.011
 
 We kindly ask that you include this reference in all publications 
 associated to this pseudopotential.
--- a/EPW/examples/gan/pp/N_ONCV_LDA-1.0.upf
+++ b/EPW/examples/gan/pp/N_ONCV_LDA-1.0.upf
@ -29,7 +29,7 @@
 testing of the pseudopotential please refer to:
 
 M. Schlipf, F. Gygi, Comp. Phys. Comm. 196, 36 (2015)
- http://dx.doi.org/10.1016/j.cpc.2015.05.011
+ https://doi.org/10.1016/j.cpc.2015.05.011
 
 We kindly ask that you include this reference in all publications 
 associated to this pseudopotential.
--- a/EPW/src/stop_epw.f90
+++ b/EPW/src/stop_epw.f90
@ -62,7 +62,7 @@
    WRITE(epwbib, '(a)') "   Year    = {2016},                                                                     " 
    WRITE(epwbib, '(a)') "   Volume  = {209},                                                                      " 
    WRITE(epwbib, '(a)') "   Pages   = {116 - 133},                                                                "
-    WRITE(epwbib, '(a)') "   Doi     = {http://dx.doi.org/10.1016/j.cpc.2016.07.028}                               "  
+    WRITE(epwbib, '(a)') "   Doi     = {https://doi.org/10.1016/j.cpc.2016.07.028}                                 "
    WRITE(epwbib, '(a)') " }                                                                                       "
    ! 
    ! Specific functionalities
--- a/PHonon/Doc/INPUT_PH.html
+++ b/PHonon/Doc/INPUT_PH.html
@ -627,7 +627,7 @@ Electron-phonon coupling matrix elements are written
 to file prefix.epa.k for further processing by program
 epa.x which implements electron-phonon averaged (EPA)
 approximation as described in G. Samsonidze &amp; B. Kozinsky,
-Adv. Energy Mater. 2018, 1800246 <a href="http://dx.doi.org/10.1002/aenm.201800246">doi:10.1002/aenm.201800246</a>
+Adv. Energy Mater. 2018, 1800246 <a href="https://doi.org/10.1002/aenm.201800246">doi:10.1002/aenm.201800246</a>
 <a href="https://arxiv.org/abs/1511.08115">arXiv:1511.08115</a>
            </pre></dd>
 </dl>
--- a/PHonon/Doc/INPUT_PH.xml
+++ b/PHonon/Doc/INPUT_PH.xml
@ -291,7 +291,7 @@ Electron-phonon coupling matrix elements are written
 to file prefix.epa.k for further processing by program
 epa.x which implements electron-phonon averaged (EPA)
 approximation as described in G. Samsonidze &amp; B. Kozinsky,
-Adv. Energy Mater. 2018, 1800246 <a href="http://dx.doi.org/10.1002/aenm.201800246">doi:10.1002/aenm.201800246</a>
+Adv. Energy Mater. 2018, 1800246 <a href="https://doi.org/10.1002/aenm.201800246">doi:10.1002/aenm.201800246</a>
 <a href="https://arxiv.org/abs/1511.08115">arXiv:1511.08115</a>
            </opt>
            <opt val="'ahc'" >
--- a/PP/Doc/INPUT_PP.html
+++ b/PP/Doc/INPUT_PP.html
@ -201,7 +201,7 @@ Selects what to save in filplot:
   18 = The exchange and correlation magnetic field in the noncollinear case

   19 = Reduced density gradient
-        ( J. Chem. Theory Comput. 7, 625 (2011), <a href="http://dx.doi.org/10.1021/ct100641a">doi:10.1021/ct100641a</a> )
+        ( J. Chem. Theory Comput. 7, 625 (2011), <a href="https://doi.org/10.1021/ct100641a">doi:10.1021/ct100641a</a> )
        Set the isosurface between 0.3 and 0.6 to plot the
        non-covalent interactions (see also plot_num = 20)

@ -215,7 +215,7 @@ Selects what to save in filplot:
   22 = kinetic energy density (for meta-GGA and XDM only)

  123 = DORI: density overlap regions indicator
-        (<a href="http://dx.doi.org/10.1021/ct500490b">doi: 10.1021/ct500490b</a>) Implemented by D. Yang &amp; Q.Liu
+        (<a href="https://doi.org/10.1021/ct500490b">doi: 10.1021/ct500490b</a>) Implemented by D. Yang &amp; Q.Liu
         </pre></blockquote></td></tr>
 </table>
 <div align="right" style="margin-bottom: 5;">[<a href="#__top__">Back to Top</a>]</div>
--- a/PP/Doc/INPUT_PPACF.html
+++ b/PP/Doc/INPUT_PPACF.html
@ -69,7 +69,7 @@ ACF analysis and print files to track signatures of binding
 (<a href="https://journals.aps.org/prb/abstract/10.1103/PhysRevB.97.085115">PRB 97, 085115 (2018)</a>).

 For an illustration of how to use this code to set hybrid mixing
-value, please refer to JCP 148, 194115 (2018) <a href="http://dx.doi.org/10.1063/1.5012870">doi: 10.1063/1.5012870</a>.
+value, please refer to JCP 148, 194115 (2018) <a href="https://doi.org/10.1063/1.5012870">doi: 10.1063/1.5012870</a>.

 The code reads the output produced by <b>pw.x,</b> extracts and calculates
 $E_{c}^{nl}$, $T_{c}^{nl}$, $E_{c,\lambda}^{LDA}$, $E_{c,\lambda}^{nl}$,
@ -237,7 +237,7 @@ Option for Fock exchange (lfock=.True.):
 </tr>
 <tr><td align="left" valign="top" colspan="2"><blockquote><pre style="margin-bottom: -1em;">
 If .True. use Lin Lin's ACE (J. Chem. Theory Comput. 12(5), 2242-2249 (2016),
-<a href="http://dx.doi.org/10.1021/acs.jctc.6b00092">doi: 10.1021/acs.jctc.6b00092</a>).
+<a href="https://doi.org/10.1021/acs.jctc.6b00092">doi: 10.1021/acs.jctc.6b00092</a>).
               </pre></blockquote></td></tr>
 </table>
 <div align="right" style="margin-bottom: 5;">[<a href="#__top__">Back to Top</a>]</div>
--- a/PP/Doc/INPUT_molecularpdos.html
+++ b/PP/Doc/INPUT_molecularpdos.html
@ -80,7 +80,7 @@
 Reference:
    An explanation of the keywords and the implementation
    is provided in Scientific Reports | 6:24603 (2016)
-    <a href="http://dx.doi.org/10.1038/srep24603">DOI: 10.1038/srep24603</a> (Supp. Info).
+    <a href="https://doi.org/10.1038/srep24603">DOI: 10.1038/srep24603</a> (Supp. Info).


 <b>Structure of the input data:</b>
--- a/PP/Doc/INPUT_molecularpdos.xml
+++ b/PP/Doc/INPUT_molecularpdos.xml
@ -18,7 +18,7 @@
 Reference:
    An explanation of the keywords and the implementation
    is provided in Scientific Reports | 6:24603 (2016)
-    <a href="http://dx.doi.org/10.1038/srep24603">DOI: 10.1038/srep24603</a> (Supp. Info).
+    <a href="https://doi.org/10.1038/srep24603">DOI: 10.1038/srep24603</a> (Supp. Info).


 <b>Structure of the input data:</b>
--- a/PP/examples/W90_open_grid_example/reference/diamond.sa.wout
+++ b/PP/examples/W90_open_grid_example/reference/diamond.sa.wout
@ -49,7 +49,7 @@
             |        J. R. Yates, G. Pizzi, Y. S. Lee,          |
             |        I. Souza, D. Vanderbilt and N. Marzari,    |
             |        Comput. Phys. Commun. 185, 2309 (2014)     |
-             |        http://dx.doi.org/10.1016/j.cpc.2014.05.003|
+             |        https://doi.org/10.1016/j.cpc.2014.05.003  |
             |                                                   |
             |  in any publications arising from the use of      |
             |  this code. For the method please cite            |
--- a/PP/examples/WAN90_example/reference/diamond.sa.wout
+++ b/PP/examples/WAN90_example/reference/diamond.sa.wout
@ -32,7 +32,7 @@
             |        J. R. Yates, G. Pizzi, Y. S. Lee,          |
             |        I. Souza, D. Vanderbilt and N. Marzari,    |
             |        Comput. Phys. Commun. 185, 2309 (2014)     |
-             |        http://dx.doi.org/10.1016/j.cpc.2014.05.003|
+             |        https://doi.org/10.1016/j.cpc.2014.05.003  |
             |                                                   |
             |  in any publications arising from the use of      |
             |  this code. For the method please cite            |
--- a/PP/src/pw2critic.f90
+++ b/PP/src/pw2critic.f90
@ -8,7 +8,7 @@
 ! (with extension pwc) read by critic2. At present, this is used
 ! in combination with the output of wannier90 in the calculation of
 ! delocalization indices via maximally localized Wannier functions
-! (http://dx.doi.org/10.1021/acs.jctc.8b00549).
+! (https://doi.org/10.1021/acs.jctc.8b00549).
 !
 ! Preferred use: with norm-conserving pseudos, since critic2 will not
 ! know about the transformation near the atoms. Some notes:
--- a/PW/Doc/INPUT_PW.html
+++ b/PW/Doc/INPUT_PW.html
@ -731,7 +731,7 @@ external iteration on the charge density
 <tr><td align="left" valign="top" colspan="2"><blockquote><pre style="margin-bottom: -1em;">
 If <b>.TRUE.</b> perform orbital magnetization calculation.
 If finite electric field is applied (<a href="#lelfield">lelfield</a>==.true.) only Kubo terms are computed
-[for details see New J. Phys. 12, 053032 (2010), <a href="http://dx.doi.org/10.1088/1367-2630/12/5/053032">doi:10.1088/1367-2630/12/5/053032</a>].
+[for details see New J. Phys. 12, 053032 (2010), <a href="https://doi.org/10.1088/1367-2630/12/5/053032">doi:10.1088/1367-2630/12/5/053032</a>].

 The type of calculation is <b>'nscf'</b> and should be performed on an automatically
 generated uniform grid of k points.
@ -1692,7 +1692,7 @@ of the energy step for reciprocal vectors whose square modulus
 is greater than "ecfixed". In the kinetic energy, G^2 is
 replaced by G^2 + qcutz * (1 + erf ( (G^2 - ecfixed)/q2sigma) )
 See: M. Bernasconi et al, J. Phys. Chem. Solids 56, 501 (1995),
-<a href="http://dx.doi.org/10.1016/0022-3697(94)00228-2">doi:10.1016/0022-3697(94)00228-2</a>
+<a href="https://doi.org/10.1016/0022-3697(94)00228-2">doi:10.1016/0022-3697(94)00228-2</a>
         </pre></blockquote></td></tr>
 </table>
 <div align="right" style="margin-bottom: 5;">[<a href="#__top__">Back to Top</a>]</div>
@ -1726,7 +1726,7 @@ Use with care and if you know what you are doing!
 </tr>
 <tr><td align="left" valign="top" colspan="2"><blockquote><pre style="margin-bottom: -1em;">
 Use Adaptively Compressed Exchange operator as in
-Lin Lin, J. Chem. Theory Comput. 2016, 12, 2242--2249, <a href="http://dx.doi.org/10.1021/acs.jctc.6b00092">doi:10.1021/acs.jctc.6b00092</a>
+Lin Lin, J. Chem. Theory Comput. 2016, 12, 2242--2249, <a href="https://doi.org/10.1021/acs.jctc.6b00092">doi:10.1021/acs.jctc.6b00092</a>

 Set to false to use standard Exchange (much slower)
         </pre></blockquote></td></tr>
@ -1762,8 +1762,8 @@ the <a href="#exx_fraction">exx_fraction</a> default value is 0.20.
 <tr><td align="left" valign="top" colspan="2"><blockquote><pre style="margin-bottom: -1em;">
 screening_parameter for HSE like hybrid functionals.
 For more information, see:
-J. Chem. Phys. 118, 8207 (2003), <a href="http://dx.doi.org/10.1063/1.1564060">doi:10.1063/1.1564060</a>
-J. Chem. Phys. 124, 219906 (2006), <a href="http://dx.doi.org/10.1063/1.2204597">doi:10.1063/1.2204597</a>
+J. Chem. Phys. 118, 8207 (2003), <a href="https://doi.org/10.1063/1.1564060">doi:10.1063/1.1564060</a>
+J. Chem. Phys. 124, 219906 (2006), <a href="https://doi.org/10.1063/1.2204597">doi:10.1063/1.2204597</a>
         </pre></blockquote></td></tr>
 </table>
 <div align="right" style="margin-bottom: 5;">[<a href="#__top__">Back to Top</a>]</div>
@ -1939,7 +1939,7 @@ using <a href="#Hubbard_U">Hubbard_U</a> and <a href="#Hubbard_J">Hubbard_J</a>
 <dt><tt><span class="flag">lda_plus_u_kind = 2</span> :</tt></dt>
 <dd><pre style="margin-top: 0em; margin-bottom: -1em;">
 DFT+U+V simplified version of Campo Jr and Cococcioni,
-J. Phys.: Condens. Matter 22, 055602 (2010), <a href="http://dx.doi.org/10.1088/0953-8984/22/5/055602">doi:10.1088/0953-8984/22/5/055602</a>,
+J. Phys.: Condens. Matter 22, 055602 (2010), <a href="https://doi.org/10.1088/0953-8984/22/5/055602">doi:10.1088/0953-8984/22/5/055602</a>,
 using <a href="#Hubbard_V">Hubbard_V</a>
            </pre></dd>
 </dl>
@ -2533,7 +2533,7 @@ G.J. Martyna, and M.E. Tuckerman,
 "A reciprocal space based method for treating long
 range interactions in ab-initio and force-field-based
 calculation in clusters", J. Chem. Phys. 110, 2810 (1999),
-<a href="http://dx.doi.org/10.1063/1.477923">doi:10.1063/1.477923</a>.
+<a href="https://doi.org/10.1063/1.477923">doi:10.1063/1.477923</a>.
            </pre></dd>
 </dl>
 <dl style="margin-left: 1.5em;">
@ -2814,8 +2814,8 @@ Type of Van der Waals correction. Allowed values:
 <dd><pre style="margin-top: 0em; margin-bottom: -1em;">
 Semiempirical Grimme's DFT-D2. Optional variables:
 <a href="#london_s6">london_s6</a>, <a href="#london_rcut">london_rcut</a>, <a href="#london_c6">london_c6</a>, <a href="#london_rvdw">london_rvdw</a>
-S. Grimme, J. Comp. Chem. 27, 1787 (2006), <a href="http://dx.doi.org/10.1002/jcc.20495">doi:10.1002/jcc.20495</a>
-V. Barone et al., J. Comp. Chem. 30, 934 (2009), <a href="http://dx.doi.org/10.1002/jcc.21112">doi:10.1002/jcc.21112</a>
+S. Grimme, J. Comp. Chem. 27, 1787 (2006), <a href="https://doi.org/10.1002/jcc.20495">doi:10.1002/jcc.20495</a>
+V. Barone et al., J. Comp. Chem. 30, 934 (2009), <a href="https://doi.org/10.1002/jcc.21112">doi:10.1002/jcc.21112</a>
            </pre></dd>
 </dl>
 <dl style="margin-left: 1.5em;">
@ -2823,7 +2823,7 @@ V. Barone et al., J. Comp. Chem. 30, 934 (2009), <a href="http://dx.doi.org/10.1
 <dd><pre style="margin-top: 0em; margin-bottom: -1em;">
 Semiempirical Grimme's DFT-D3. Optional variables:
 <a href="#dftd3_version">dftd3_version</a>, <a href="#dftd3_threebody">dftd3_threebody</a>
-S. Grimme et al, J. Chem. Phys 132, 154104 (2010), <a href="http://dx.doi.org/10.1063/1.3382344">doi:10.1063/1.3382344</a>
+S. Grimme et al, J. Chem. Phys 132, 154104 (2010), <a href="https://doi.org/10.1063/1.3382344">doi:10.1063/1.3382344</a>
            </pre></dd>
 </dl>
 <dl style="margin-left: 1.5em;">
@ -2848,9 +2848,9 @@ A. Ambrosetti, A. M. Reilly, R. A. DiStasio, A. Tkatchenko, J. Chem. Phys. 140
 <dt><tt><span class="flag">'XDM'</span>, <span class="flag">'xdm'</span> :</tt></dt>
 <dd><pre style="margin-top: 0em; margin-bottom: -1em;">
 Exchange-hole dipole-moment model. Optional variables: <a href="#xdm_a1">xdm_a1</a>, <a href="#xdm_a2">xdm_a2</a>
-A. D. Becke et al., J. Chem. Phys. 127, 154108 (2007), <a href="http://dx.doi.org/10.1063/1.2795701">doi:10.1063/1.2795701</a>
+A. D. Becke et al., J. Chem. Phys. 127, 154108 (2007), <a href="https://doi.org/10.1063/1.2795701">doi:10.1063/1.2795701</a>
 A. Otero de la Roza et al., J. Chem. Phys. 136, 174109 (2012),
-<a href="http://dx.doi.org/10.1063/1.4705760">doi:10.1063/1.4705760</a>
+<a href="https://doi.org/10.1063/1.4705760">doi:10.1063/1.4705760</a>
            </pre></dd>
 </dl>
 <pre style="margin-bottom: -1em;"> Note that non-local functionals (eg vdw-DF) are NOT specified here but in <a href="#input_dft">input_dft</a>
@ -2905,7 +2905,7 @@ global scaling parameter for DFT-D. Default is good for PBE.
 atomic C6 coefficient of each atom type

 ( if not specified default values from S. Grimme, J. Comp. Chem. 27, 1787 (2006),
-  <a href="http://dx.doi.org/10.1002/jcc.20495">doi:10.1002/jcc.20495</a> are used; see file Modules/mm_dispersion.f90 )
+  <a href="https://doi.org/10.1002/jcc.20495">doi:10.1002/jcc.20495</a> are used; see file Modules/mm_dispersion.f90 )
         </pre></blockquote></td></tr>
 </table>
 <div align="right" style="margin-bottom: 5;">[<a href="#__top__">Back to Top</a>]</div>
@ -2923,7 +2923,7 @@ atomic C6 coefficient of each atom type
 atomic vdw radii of each atom type

 ( if not specified default values from S. Grimme, J. Comp. Chem. 27, 1787 (2006),
-  <a href="http://dx.doi.org/10.1002/jcc.20495">doi:10.1002/jcc.20495</a> are used; see file Modules/mm_dispersion.f90 )
+  <a href="https://doi.org/10.1002/jcc.20495">doi:10.1002/jcc.20495</a> are used; see file Modules/mm_dispersion.f90 )
         </pre></blockquote></td></tr>
 </table>
 <div align="right" style="margin-bottom: 5;">[<a href="#__top__">Back to Top</a>]</div>
@ -3075,7 +3075,7 @@ a value if the functional is one of B86bPBE, PW86PBE, PBE, BLYP. For functionals
 in this list, the coefficients are given in:
   <a href="http://schooner.chem.dal.ca/wiki/XDM">http://schooner.chem.dal.ca/wiki/XDM</a>
   A. Otero de la Roza, E. R. Johnson, J. Chem. Phys. 138, 204109 (2013),
-   <a href="http://dx.doi.org/10.1063/1.4705760">doi:10.1063/1.4705760</a>
+   <a href="https://doi.org/10.1063/1.4705760">doi:10.1063/1.4705760</a>
         </pre></blockquote></td></tr>
 </table>
 <div align="right" style="margin-bottom: 5;">[<a href="#__top__">Back to Top</a>]</div>
@ -3095,7 +3095,7 @@ a value if the functional is one of B86bPBE, PW86PBE, PBE, BLYP. For functionals
 in this list, the coefficients are given in:
   <a href="http://schooner.chem.dal.ca/wiki/XDM">http://schooner.chem.dal.ca/wiki/XDM</a>
   A. Otero de la Roza, E. R. Johnson, J. Chem. Phys. 138, 204109 (2013),
-   <a href="http://dx.doi.org/10.1063/1.4705760">doi:10.1063/1.4705760</a>
+   <a href="https://doi.org/10.1063/1.4705760">doi:10.1063/1.4705760</a>
         </pre></blockquote></td></tr>
 </table>
 <div align="right" style="margin-bottom: 5;">[<a href="#__top__">Back to Top</a>]</div>
@ -3904,7 +3904,7 @@ ion dynamics is over-damped Langevin
 <dt><tt><span class="flag">'langevin-smc'</span> :</tt></dt>
 <dd><pre style="margin-top: 0em; margin-bottom: -1em;">
 over-damped Langevin with Smart Monte Carlo:
-see R.J. Rossky, JCP, 69, 4628 (1978), <a href="http://dx.doi.org/10.1063/1.436415">doi:10.1063/1.436415</a>
+see R.J. Rossky, JCP, 69, 4628 (1978), <a href="https://doi.org/10.1063/1.436415">doi:10.1063/1.436415</a>
            </pre></dd>
 </dl>
 <pre style="margin-bottom: -1em;">
@ -5771,7 +5771,7 @@ constraint on the projection onto a given direction
 of the vector defined by the position of one atom
 minus the center of mass of the others.
 G. Roma, J.P. Crocombette: J. Nucl. Mater. 403, 32 (2010),
-<a href="http://dx.doi.org/10.1016/j.jnucmat.2010.06.001">doi:10.1016/j.jnucmat.2010.06.001</a>
+<a href="https://doi.org/10.1016/j.jnucmat.2010.06.001">doi:10.1016/j.jnucmat.2010.06.001</a>
                     </pre></dd>
 </dl>
 </blockquote></td></tr>
--- a/PW/src/exx.f90
+++ b/PW/src/exx.f90
@ -14,7 +14,7 @@ MODULE exx
  !! Implements ACE: Lin Lin, J. Chem. Theory Comput. 2016, 12, 2242.  
  !! Contains code for band parallelization over pairs of bands: see T. Barnes,
  !! T. Kurth, P. Carrier, N. Wichmann, D. Prendergast, P.R.C. Kent, J. Deslippe
-  !! Computer Physics Communications 2017, dx.doi.org/10.1016/j.cpc.2017.01.008.
+  !! Computer Physics Communications 2017, doi.org/10.1016/j.cpc.2017.01.008.
  !
  USE kinds,                ONLY : DP
  USE noncollin_module,     ONLY : noncolin, npol
--- a/PW/src/exx_band.f90
+++ b/PW/src/exx_band.f90
@ -12,7 +12,7 @@ MODULE exx_band
  !! See:  
  !! T. Barnes, T. Kurth, P. Carrier, N. Wichmann, D. Prendergast,
  !! P.R.C. Kent, J. Deslippe, Comp. Phys. Comm. (2017),  
-  !! dx.doi.org/10.1016/j.cpc.2017.01.008
+  !! doi.org/10.1016/j.cpc.2017.01.008
  !
  USE kinds,                ONLY : DP
  USE noncollin_module,     ONLY : npol
--- a/QEHeat/examples/pseudo/O_ONCV_PBE-1.0.upf
+++ b/QEHeat/examples/pseudo/O_ONCV_PBE-1.0.upf
@ -29,7 +29,7 @@
 testing of the pseudopotential please refer to:
 
 M. Schlipf, F. Gygi, Comp. Phys. Comm. 196, 36 (2015)
- http://dx.doi.org/10.1016/j.cpc.2015.05.011
+ https://doi.org/10.1016/j.cpc.2015.05.011
 
 We kindly ask that you include this reference in all publications 
 associated to this pseudopotential.
--- a/QEHeat/examples/pseudo/Si_ONCV_PBE-1.1.upf
+++ b/QEHeat/examples/pseudo/Si_ONCV_PBE-1.1.upf
@ -29,7 +29,7 @@
 testing of the pseudopotential please refer to:
 
 M. Schlipf, F. Gygi, Comp. Phys. Comm. 196, 36 (2015)
- http://dx.doi.org/10.1016/j.cpc.2015.05.011
+ https://doi.org/10.1016/j.cpc.2015.05.011
 
 We kindly ask that you include this reference in all publications 
 associated to this pseudopotential.
--- a/XSpectra/Doc/INPUT_MOLECULARNEXAFS
+++ b/XSpectra/Doc/INPUT_MOLECULARNEXAFS
@ -16,11 +16,11 @@
   Spectra of Planar Molecules
   Guido Fratesi, Valeria Lanzilotto, Luca Floreano, and Gian Paolo Brivio
   J. Phys. Chem. C 2013, 117, 6632−6638
-   http://dx.doi.org/10.1021/jp312569q
+   https://doi.org/10.1021/jp312569q

 Further examples are also described in:
   Phys. Chem. Chem. Phys., 2014, 16, 14834
-   http://dx.doi.org/10.1039/c4cp01625d
+   https://doi.org/10.1039/c4cp01625d

 The spectrum for each inequivalent atom of the same species sums up
 into a total spectrum, where the contributions from each atom (as
--- a/XSpectra/src/molecularnexafs.f90
+++ b/XSpectra/src/molecularnexafs.f90
@ -20,11 +20,11 @@
 !   Spectra of Planar Molecules
 !   Guido Fratesi, Valeria Lanzilotto, Luca Floreano, and Gian Paolo Brivio
 !   J. Phys. Chem. C 2013, 117, 6632−6638
-!   http://dx.doi.org/10.1021/jp312569q
+!   https://doi.org/10.1021/jp312569q
 !
 ! Further examples are also described in:
 !   Phys. Chem. Chem. Phys., 2014, 16, 14834
-!   http://dx.doi.org/10.1039/c4cp01625d
+!   https://doi.org/10.1039/c4cp01625d
 !
 ! The spectrum for each inequivalent atom of the same species sums up
 ! into a total spectrum, where the contributions from each atom (as
--- a/dev-tools/helpdoc.d/xml.tcl
+++ b/dev-tools/helpdoc.d/xml.tcl
@ -41,7 +41,7 @@ proc ::helpdoc::xml_doi {content} {
    set re {([dD][oO][iI]:?\s*)(10.[0-9]{4})(\.[0-9]+)?(/[-#%/=&@!,:\.\?\w\(\)]+[^\s\.,;:\)\]])}    
    #       1                  2            3          4

-    return [regsub -all $re $content  {<a href="http://dx.doi.org/\2\3\4">\0</a>}]
+    return [regsub -all $re $content  {<a href="https://doi.org/\2\3\4">\0</a>}]
 }

 proc ::helpdoc::xml_prb {content} {