Complete cleaning of tutorials base1, base2 and tddft.

abimkdocs/variables_abinit.py

@@ -6021,7 +6021,7 @@
 ABINIT knows the LibXC value from [[ixc]], that might not agree with the
 definitions from other codes. Usually, [[hyb_range_dft]] is the same as
 [[hyb_range_fock]], with one exception explained in [[hyb_range_dft]].
-The HSE06 value from LibCX is 0.11, the one of Espresso is 0.106, the one of
+The HSE06 value from LibCX is 0.11, the one of Quantum Espresso is 0.106, the one of
 VASP is 0.105835 (=0.2 $\AA^{-1}$).
 The HSE03 value from LibCX is 0.106066 ($=0.15/\sqrt{2})$), the one of VASP is
 0.1587531 (=0.3 $\AA^{-1}$).
@@ -7345,19 +7345,19 @@
 
   * 0 --> NO xc.
 
-  * 1 --> LDA or LSD, Teter Pade parametrization (4/93, published in [[cite:Goedecker1996]], which reproduces Perdew-Wang (which reproduces Ceperley-Alder!).
+  * 1 --> LDA or LSD, Teter Pade parametrization (4/93, published in [[cite:Goedecker1996]], which reproduces Perdew-Wang 92 [[cite:Perdew1992a]] (which reproduces Ceperley-Alder [[cite:Ceperley1980]]!).
   * 2 --> LDA, Perdew-Zunger-Ceperley-Alder (no spin-polarization) [[cite:Perdew1981]]
-  * 3 --> LDA, old Teter rational polynomial parametrization (4/91) fit to Ceperley-Alder data (no spin-polarization)
+  * 3 --> LDA, old Teter rational polynomial parametrization (4/91) fit to Ceperley-Alder data (no spin-polarization) [[cite:Ceperley1980]]
   * 4 --> LDA, Wigner functional (no spin-polarization)
-  * 5 --> LDA, Hedin-Lundqvist functional (no spin-polarization)
+  * 5 --> LDA, Hedin-Lundqvist functional (no spin-polarization) [[cite:Hedin1971]]
   * 6 --> LDA, "X-alpha" functional (no spin-polarization)
-  * 7 --> LDA or LSD, Perdew-Wang 92 functional
-  * 8 --> LDA or LSD, x-only part of the Perdew-Wang 92 functional
-  * 9 --> LDA or LSD, x- and RPA correlation part of the Perdew-Wang 92 functional
+  * 7 --> LDA or LSD, Perdew-Wang 92 functional [[cite:Perdew1992a]]
+  * 8 --> LDA or LSD, x-only part of the Perdew-Wang 92 functional [[cite:Perdew1992a]]
+  * 9 --> LDA or LSD, x- and RPA correlation part of the Perdew-Wang 92 functional [[cite:Perdew1992a]]
 
-  * 11 --> GGA, Perdew-Burke-Ernzerhof GGA functional
-  * 12 --> GGA, x-only part of Perdew-Burke-Ernzerhof GGA functional
-  * 13 --> GGA potential of van Leeuwen-Baerends, while for energy, Perdew-Wang 92 functional
+  * 11 --> GGA, Perdew-Burke-Ernzerhof GGA functional [[cite:Perdew1996]]
+  * 12 --> GGA, x-only part of Perdew-Burke-Ernzerhof GGA functional [[cite:Perdew1996]]
+  * 13 --> GGA potential of van Leeuwen-Baerends [[cite:VanLeeuwen1994]], while for energy, Perdew-Wang 92 functional [[cite:Perdew1992a]]
   * 14 --> GGA, revPBE of [[cite:Zhang1998]]
   * 15 --> GGA, RPBE of [[cite:Hammer1999]]
   * 16 --> GGA, HTCH93 of [[cite:Hamprecht1998]]
@@ -7546,7 +7546,7 @@
   * 183 -->  XC_GGA_X_OL2  Exchange form based on Ou-Yang and Levy v.2 [[cite:Fuentealba1995]]  [[cite:OuYang1991]]
   * 184 -->  XC_GGA_X_APBE  mu fixed from the semiclassical neutral atom [[cite:Constantin2011]]
   * 186 -->  XC_GGA_C_APBE  mu fixed from the semiclassical neutral atom [[cite:Constantin2011]]
-  * 191 -->  XC_GGA_X_HTBS! Haas, Tran, Blaha, and Schwarz [[cite:Haas2011]]
+  * 191 -->  XC_GGA_X_HTBS  Haas, Tran, Blaha, and Schwarz [[cite:Haas2011]]
   * 192 -->  XC_GGA_X_AIRY  Constantin et al based on the Airy gas [[cite:Constantin2009]]
   * 193 -->  XC_GGA_X_LAG  Local Airy Gas [[cite:Vitos2000]]
   * 194 -->  XC_GGA_XC_MOHLYP  Functional for organometallic chemistry [[cite:Schultz2005]]
@@ -7581,17 +7581,17 @@
   * 207 -->  XC_MGGA_X_BJ06  Becke & Johnson correction to Becke-Roussel 89 [[cite:Becke2006]]
 
 !!! warning
-    This Vxc-only mGGA can only be used with a LDA correlation, typically Perdew-Wang 92.
+    This Vxc-only mGGA can only be used with a LDA correlation, typically Perdew-Wang 92 [[cite:Perdew1992a]].
 
   * 208 -->  XC_MGGA_X_TB09  Tran-blaha - correction to Becke & Johnson correction to Becke-Roussel 89 [[cite:Tran2009]]
 
 !!! warning
-    This Vxc-only mGGA can only be used with a LDA correlation, typically Perdew-Wang 92.
+    This Vxc-only mGGA can only be used with a LDA correlation, typically Perdew-Wang 92 [[cite:Perdew1992a]].
 
   * 209 -->  XC_MGGA_X_RPP09  Rasanen, Pittalis, and Proetto correction to Becke & Johnson [[cite:Rasanen2010]]
 
 !!! warning
-    This Vxc-only mGGA can only be used with a LDA correlation, typically Perdew-Wang 92.
+    This Vxc-only mGGA can only be used with a LDA correlation, typically Perdew-Wang 92 [[cite:Perdew1992a]].
 
   * 232 -->  XC_MGGA_C_VSXC  VSxc from Van Voorhis and Scuseria (correlation part) [[cite:Voorhis1998]]
 
@@ -7614,9 +7614,9 @@
                                   to clarify the situation, and called HSE03 to the above choice of parameters,
                                   and called HSE06 to the functional where $\omega^{HF}=\omega^{PBE}$. By testing
                                   several properties for atoms they reached the conclusion that the best value
-                                  for $\omega=0.11$. Of course, codes are just as messy as the papers. In espresso
-                                  HSE06 has the value $\omega=0.106$. VASP, on the other hand, uses for HSE03 the
-                                  same value $\omega^{HF} = \omega^{PBE} = 0.3 (A^{-1}) \sim 0.1587$
+                                  for $\omega=0.11$. Of course, codes are just as messy as the papers. In Quantum Espresso
+                                  HSE06 has the value $\omega=0.106.$ VASP, on the other hand, uses for HSE03 the
+                                  same value $\omega^{HF} = \omega^{PBE} = 0.3 (A^{-1}) \sim 0.1587$,
                                   and for HSE06 $\omega^{HF} = \omega^{PBE} = 0.2 (A^{-1}) \sim 0.1058$.
                                   [[cite:Heyd2003]] [[cite:Heyd2006]] [[cite:Krukau2006]]
 

doc/abiref.bib

@@ -2209,22 +2209,6 @@ @article{Hybertsen1985
  year = {1985},
 }
 
-@article{Kolos1960,
- author = {Kolos, W. and Roothaan, C. C. J.},
- doi = {10.1103/revmodphys.32.219},
- issn = {0034-6861},
- journal = {Rev. Mod. Phys.},
- month = apr,
- number = {2},
- pages = {219-232},
- publisher = {American Physical Society (APS)},
- source = {Crossref},
- title = {Accurate Electronic Wave Functions for {theH2Molecule}},
- url = {https://doi.org/10.1103/revmodphys.32.219},
- volume = {32},
- year = {1960},
-}
-
 @article{Kohn1965,
  author = {Kohn, W. and Sham, L. J.},
  doi = {10.1103/physrev.140.a1133},
@@ -6699,7 +6683,7 @@ @article{Heyd2006
  author = {Heyd, Jochen and Scuseria, Gustavo E. and Ernzerhof, Matthias},
  publisher = {AIP Publishing},
  doi = {10.1063/1.2204597},
- title = {Erratum: {``hybrid} functionals based on a screened Coulomb potential'' {[J.} Chem. Phys. 118, 8207 (2003)]},
+ title = {Erratum: hybrid functionals based on a screened Coulomb potential - J. Chem. Phys. 118, 8207 (2003)},
  url = {http://dx.doi.org/10.1063/1.2204597},
  journal = {The Journal of Chemical Physics},
  issn = {0021-9606, 1089-7690},
@@ -6804,3 +6788,48 @@ @article{Bloch1929
 url = {https://doi.org/10.1007/BF01340281},
 doi = {10.1007/BF01340281},
 }
+
+@article{Kolos1960,
+  title = {Accurate Electronic Wave Functions for the H$_2$ Molecule},
+  author = {Kolos, W. and Roothaan, C. C. J.},
+  journal = {Rev. Mod. Phys.},
+  volume = {32},
+  issue = {2},
+  pages = {219--232},
+  numpages = {0},
+  year = {1960},
+  month = {Apr},
+  publisher = {American Physical Society},
+  doi = {10.1103/RevModPhys.32.219},
+  url = {https://link.aps.org/doi/10.1103/RevModPhys.32.219}
+}
+
+@article{Ceperley1980,
+  title = {Ground State of the Electron Gas by a Stochastic Method},
+  author = {Ceperley, D. M. and Alder, B. J.},
+  journal = {Phys. Rev. Lett.},
+  volume = {45},
+  issue = {7},
+  pages = {566--569},
+  numpages = {0},
+  year = {1980},
+  month = {Aug},
+  publisher = {American Physical Society},
+  doi = {10.1103/PhysRevLett.45.566},
+  url = {https://link.aps.org/doi/10.1103/PhysRevLett.45.566}
+}
+
+@article{VanLeeuwen1994,
+  title = {Exchange-correlation potential with correct asymptotic behavior},
+  author = {van Leeuwen, R. and Baerends, E. J.},
+  journal = {Phys. Rev. A},
+  volume = {49},
+  issue = {4},
+  pages = {2421--2431},
+  numpages = {0},
+  year = {1994},
+  month = {Apr},
+  publisher = {American Physical Society},
+  doi = {10.1103/PhysRevA.49.2421},
+  url = {https://link.aps.org/doi/10.1103/PhysRevA.49.2421}
+}

doc/tutorial/base1.md

@@ -122,7 +122,7 @@ tbase1_xo_DEN  tbase1_xo_EIG.nc  tbase1_xo_GSR.nc  tbase1_xo_OUT.nc  tbase1_xo_W
 
 Different output files have been created, including a `log` file and the output file `tbase1_1.out`. 
 To check that everything is correct, you can make a diff of
-`tbase1_1.out` with a reference file [[~abinit/tests/tutorial/Refs/tbase1_1.out]]
+`tbase1_1.out` with the reference file [[~abinit/tests/tutorial/Refs/tbase1_1.out]]
 
 ```sh
 diff tbase1_1.out ../../Refs/tbase1_1.out | less
@@ -136,15 +136,15 @@ files or timing differences, e.g.:
 
 ```diff
 2,3c2,3
-< .Version 8.0.8 of ABINIT
+< .Version 8.8.3 of ABINIT
 < .(MPI version, prepared for a x86_64_linux_gnu5.4 computer)
 ---
-> .Version 8.0.7  of ABINIT
+> .Version 8.8.0  of ABINIT
 > .(MPI version, prepared for a x86_64_linux_gnu5.3 computer)
 17c17
-< .Starting date : Fri 27 May 2016.
+< .Starting date : Fri 27 May 2018.
 ---
-> .Starting date : Thu 26 May 2016.
+> .Starting date : Thu 26 May 2018.
 27c27
 < - input  file    -> tbase1_1.in
 ---
@@ -357,7 +357,7 @@ Could you answer the following questions?
     On the first atom (located at -0.7 0 0 in cartesian coordinates, in Bohr), the
     force vector is pointing in the minus x direction, and in the plus x direction
     for the second atom located at +0.7 0 0 .  
-    The H2 molecule would like to expand...
+    The H$_2$ molecule would like to expand...
 
 ??? note "Q4. What is the difference of eigenenergies between the two electronic states?"
 
@@ -384,7 +384,7 @@ Could you answer the following questions?
 
 !!! tip
 
-    If |AbiPy| in installed on your machine, you can use the |abiopen| script
+    If |AbiPy| is installed on your machine, you can use the |abiopen| script
     with the `--expose` option to visualize the SCF cycle from the main output file:
 
         abiopen.py tbase1_1.out --expose --seaborn
@@ -604,7 +604,7 @@ as discussed in this [jupyter notebook](https://nbviewer.jupyter.org/github/abin
 The atomisation energy is the energy needed to separate a molecule in its constituent atoms, each being neutral.   
 In the present case, one must compute first the total energy of an isolated
 hydrogen atom. The atomisation energy will be the difference between the total
-energy of H2 and twice the total energy of H.  
+energy of H$_2 and twice the total energy of H.  
 There are some subtleties in the calculation of an isolated atom.
 
 * in many cases, the ground state of an isolated atom is spin-polarized, see the variables [[nsppol]] and [[spinat]] ; 
@@ -687,20 +687,20 @@ The total energy is
 
     etotal   -4.7010531489E-01
 
-while the total energy of the H2 molecule is (see test 13):
+while the total energy of the H$_2$ molecule is (see test 13):
 
     etotal   -1.1058360644E+00
 
 The atomisation energy is thus 0.1656 Ha (The difference between the total
-energy of the H2 molecule and twice the energy of an isolated Hydrogen atom).
+energy of the H$_2$ molecule and twice the energy of an isolated Hydrogen atom).
 
 At this stage, we can compare our results:
 
   * bond length: 1.522 Bohr 
   * atomisation energy at that bond length: 0.1656 Ha = 4.506 eV 
 
 with the experimental data as well as theoretical data using a much more
-accurate technique (see Kolos and Roothaan, Rev. Mod. Phys. 32, 219 (1960), especially p.225)
+accurate technique (see [[cite:Kolos1960]], especially p.225)
 
   * bond length: 1.401 Bohr 
   * atomisation energy: 4.747 eV 
@@ -724,7 +724,7 @@ These are:
 
 We used 10 Ha as cut-off energy, a 10x10x10 Bohr^3 supercell, the local-density approximation 
 (as well as the local-spin-density approximation) in the
-Teter parametrization, and a pseudopotential from the Goedecker-Hutter-Teter table (Phys. Rev. B 54, 1703 (1996)).
+Teter parametrization, and a pseudopotential from the Goedecker-Hutter-Teter table [[cite:Goedecker1996]].
 
 We will see in the [next tutorial](base2) how to address the choice
 of these parameters (except the pseudopotential).

doc/tutorial/base2.md

@@ -22,8 +22,8 @@ This tutorial should take about 1 hour.
 
 ## Summary of the previous tutorial
 
-We studied the H2 molecule in a big box. 
-We used 10 Ha as cut-off energy, a 10x10x10 Bohr^3 supercell, the local-density approximation 
+We studied the H$_2$ molecule in a big box. 
+We used 10 Ha as cut-off energy, a 10x10x10 Bohr$^3$ supercell, the local-density approximation 
 (as well as the local-spin-density approximation) in the Teter parametrization ([[ixc]]=1, the
 default), and a pseudopotential from the Goedecker-Hutter-Teter table.
 
@@ -50,7 +50,7 @@ Because we will compute many times the bond length and atomisation energy, it
 is worth to make a single input file that will do all the associated operations. 
 You should try to use 2 datasets (try to combine ~abinit/tests/tutorial/Input/tbase1_3.in with
 ~abinit/tests/tutorial/Input/tbase1_5.in!). 
-Do not try to have the same position of the H atom as one of the H2 atoms in the optimized geometry.
+Do not try to have the same position of the H atom as one of the H$_2$ atoms in the optimized geometry.
 
 The input file ~abinit/tests/tutorial/Input/tbase2_1.in is an example of file
 that will do the job, 
@@ -86,7 +86,7 @@ Convergence issues are discussed in [[help:abinit#7|section 7]] of the abinit he
 You should read it. 
 By the way, you have read many parts of the abinit_help file! 
 You are missing the sections
-[help:abinit#2|2]], [help:abinit#5|5]],  [help:abinit#7|7]].
+[[help:abinit#2|2]], [[help:abinit#5|5]],  [[help:abinit#7|7]].
 
 You are also missing the description of many input variables. 
 We suggest that you finish reading entirely the abinit_help file now, while 
@@ -232,15 +232,15 @@ We will use `acell 12 12 12` for the final run.
 
 For most solids the size of the unit cell will be smaller than that. 
 We are treating a lot of vacuum in this supercell! 
-So, the H2 study, with this pseudopotential, turns out to be not really easy. 
+So, the H$_2$ study, with this pseudopotential, turns out to be not really easy. 
 Of course, the number of states to be treated is minimal! 
 This allows to have reasonable CPU time still.
 
 ## 5 The final calculation in Local (Spin) Density Approximation
 
 We now use the correct values of both [[ecut]] and [[acell]]. 
 Well, you should modify the tbase2_3.in file to make a calculation with `acell 12 12 12` and `ecut 30`. 
-You can still use the double loop feature with `[[udtset]] 1 2`
+You can still use the double loop feature with `udtset 1 2`
 (which reduces to a single loop), to minimize the modifications to the file.
 The file ~abinit/tests/tutorial/Input/tbase2_4.in can be taken as an example
 of input file, and ~abinit/tests/tutorial/Refs/tbase2_4.out as an example of output file.
@@ -265,7 +265,7 @@ The output data are:
 * These are our final data for the local (spin) density approximation. 
 
 We have used [[ixc]]=1. 
-Other expressions for the local (spin) density approximation [2, 3 .. 7] are possible. 
+Other expressions for the local (spin) density approximation [2, 3 ... 7] are possible. 
 The values 1, 2, 3 and 7 should give about the same results, since they all start 
 from the XC energy of the homogeneous electron gas, as determined by Quantum Monte Carlo calculations.  
 Other possibilities (ixc = 4, 5, 6) are older local density functionals, that could not rely on these data.

doc/tutorial/index.md

@@ -39,8 +39,8 @@ The following schema should help you to understand these dependencies.
 <area shape="rect" coords="230  ,265 ,376 ,289 " href="rf2/index.html" />
 <area shape="rect" coords="230  ,290 ,376 ,309 " href="eph/index.html" /> 
 <area shape="rect" coords="230  ,310 ,376 ,334 " href="tdepes/index.html" /> 
-<area shape="rect" coords="230  ,335 ,327 ,365 " href="elastic/index.html" /> 
-<area shape="rect" coords="328  ,335 ,376 ,365 " href="nlo/index.html" /> 
+<area shape="rect" coords="230  ,335 ,376 ,365 " href="elastic/index.html" /> 
+<area shape="rect" coords="230  ,366 ,376 ,395 " href="nlo/index.html" /> 
 <area shape="rect" coords="360  ,420 ,456 ,465 " href="gw1/index.html" />
 <area shape="rect" coords="360  ,480 ,456 ,502 " href="gw2/index.html" /> 
 <area shape="rect" coords="360  ,503 ,456 ,525 " href="bse/index.html" /> 
@@ -52,7 +52,7 @@ The following schema should help you to understand these dependencies.
 <area shape="rect" coords="520  ,380 ,695 ,435 " href="paral_dfpt/index.html" />
 <area shape="rect" coords="520  ,445 ,695 ,500 " href="paral_mbt/index.html" />
 </map>
-<img style="height: 540px; width: 720px;" alt="Schema 1" src="index_assets/tutorial_flowchart_v6.png" usemap="#map1"/>
+<img style="height: 540px; width: 720px;" alt="Schema 1" src="index_assets/tutorial_flowchart_v7.png" usemap="#map1"/>
 </center>
 
 The "base" tutorials are presented at the top, in orange. The blocks in red represents additional tutorials related