small edit to citation generator

docs/pages/coupledcluster.md

@@ -54,7 +54,7 @@ taking advantage of the exponential form of the wavefunction. We could then proc
 
 ## Implementation of CCD and CCSD
 
-The derivation of the equations that are actually used to perform the calculations is quite lengthy and involves a lot of algebra. We will not go into the details here, but we will provide the final expressions for the Coupled Cluster Doubles and Coupled Cluster Singles and Doubles methods. The Coupled Cluster Doubles and Coupled Cluster Singles and Doubles methods are the most commonly used Coupled Cluster methods, and they are often used as benchmarks for other methods. All we need for the evaluation of the expressions below are the Coulomb integrals in the MS basis and physicists' notation, Fock matrix in the MS basis and the orbital energies obtained from the Hartree--Fock calculation. All these transformations are already explained [here](hartreefockmethod.html#the-integral-transforms) in the Hartree--Fock section. The expressions for the Coupled Cluster Doubles can be written as
+The derivation of the equations that are actually used to perform the calculations is quite lengthy and involves a lot of algebra. We will not go into the details here, but we will provide the final expressions for the Coupled Cluster Doubles and Coupled Cluster Singles and Doubles methods.<!--\cite{10.1063/1.460620}--> The Coupled Cluster Doubles and Coupled Cluster Singles and Doubles methods are the most commonly used Coupled Cluster methods, and they are often used as benchmarks for other methods. All we need for the evaluation of the expressions below are the Coulomb integrals in the MS basis and physicists' notation, Fock matrix in the MS basis and the orbital energies obtained from the Hartree--Fock calculation. All these transformations are already explained [here](hartreefockmethod.html#the-integral-transforms) in the Hartree--Fock section. The expressions for the Coupled Cluster Doubles can be written as
 
 \begin{equation}
 E\_{\text{CCD}}=\frac{1}{4}\braket{ij||ab}t\_{ij}^{ab}
@@ -109,7 +109,7 @@ t\_{ij}^{ab}=&\braket{ab||ij}+\hat{P}\_{(a/b)}\sum\_et\_{ij}^{ae}\left(\mathscr{
 &+\hat{P}\_{(i/j)}\sum\_et\_i^e\braket{ab||ej}-\hat{P}\_{(a/b)}\sum\_mt\_m^a\braket{mb||ij}
 \end{align}
 
-The Coupled Cluster Singles and Doubles amplitude equations are, again, nonlinear and require iterative solution methods to obtain the final amplitudes. The initial guess for the amplitudes is often set to zero, and the equations are solved iteratively until convergence is achieved.<!--\cite{10.1063/1.460620}-->
+The Coupled Cluster Singles and Doubles amplitude equations are, again, nonlinear and require iterative solution methods to obtain the final amplitudes. The initial guess for the amplitudes is often set to zero, and the equations are solved iteratively until convergence is achieved.
 
 {:.cite}
 > Stanton, John F., Jürgen Gauss, John D. Watts, and Rodney J. Bartlett. 1991. “A Direct Product Decomposition Approach for Symmetry Exploitation in Many-Body Methods. I. Energy Calculations.” *The Journal of Chemical Physics* 94: 4334–45. <https://doi.org/10.1063/1.460620>.

docs/pages/hartreefockmethod.md

@@ -65,7 +65,7 @@ and the two-electron Coulomb repulsion integrals
 J\_{\mu\nu\kappa\lambda}=\braket{\phi\_{\mu}\phi\_{\mu}|\hat{J}|\phi\_{\kappa}\phi\_{\lambda}},
 \end{equation}
 
-which play crucial roles in the Hartree--Fock calculation. The Hartree--Fock method revolves around solving the Roothaan equations \ref{eq:roothaan} iteratively. The Fock matrix is defined as
+which play crucial roles in the Hartree--Fock calculation.<!--\cite{10.1016/S0065-3276!08!60019-2}--> The Hartree--Fock method revolves around solving the Roothaan equations \ref{eq:roothaan} iteratively. The Fock matrix is defined as
 
 \begin{equation}\label{eq:fock}
 F\_{\mu\nu}=H\_{\mu\nu}^{core}+D\_{\kappa\lambda}(J\_{\mu\nu\kappa\lambda}-\frac{1}{2}J\_{\mu\lambda\kappa\nu})
@@ -148,3 +148,5 @@ A\_{pq}^{MS}=C\_{\mu p}^{MS}(\mathbf{I}\_{2}\otimes\_K\mathbf{A})\_{\mu\nu}C\_{\
 where $\mathbf{A}$ is an arbitrary one-electron integral.
 
 {:.cite}
+> Gill, Peter M. W. 1994. “Molecular Integrals over Gaussian Basis Functions.” In, edited by John R. Sabin and Michael C. Zerner, 25:141–205. Advances in Quantum Chemistry. Academic Press. <https://doi.org/10.1016/S0065-3276(08)60019-2>.
+>

docs/pages/mollerplessetperturbationtheory.md

@@ -41,15 +41,15 @@ where $s$ runs over all doubly excited determinants, $H\_{0s}^{'}$ is the matrix
 
 ## Implementation of 2nd and 3rd Order Corrections
 
-Having the antisymmetrized Coulomb integrals in the MS basis and physicists' notation defined [here](hartreefockmethod.html#the-integral-transforms), we can now proceed with the calculation of the correlation energy. We wil use the convention, that the indices $i$, $j$, $k$, and $l$ run over occupied spinorbitals, while the indices $a$, $b$, $c$, and $d$ run over virtual spinorbitals. The 2nd-order and 3rd-order correlation energies are given by the following expressions.
+Having the antisymmetrized Coulomb integrals in the MS basis and physicists' notation defined [here](hartreefockmethod.html#the-integral-transforms), we can now proceed with the calculation of the correlation energy. We wil use the convention, that the indices $i$, $j$, $k$, and $l$ run over occupied spinorbitals, while the indices $a$, $b$, $c$, and $d$ run over virtual spinorbitals. The 2nd-order and 3rd-order correlation energies are given by the following expressions.<!--\cite{10.1021/acs.jpclett.9b01641}-->
 
-The 2nd-order correlation energy:<!--\cite{10.1021/acs.jpclett.9b01641}-->
+The 2nd-order correlation energy:
 
 \begin{equation}
 E_{corr}^{MP2}=\frac{1}{4}\sum_{ijab}\frac{\braket{ab||ij}\braket{ij||ab}}{\varepsilon_i+\varepsilon_j-\varepsilon_a-\varepsilon_b}
 \end{equation}
 
-The 3rd-order correlation energy:<!--\cite{10.1021/acs.jpclett.9b01641}-->
+The 3rd-order correlation energy:
 
 \begin{align}
 E_{corr}^{MP3}=&\frac{1}{8}\sum_{ijab}\frac{\braket{ab||ij}\braket{cd||ab}\braket{ij||cd}}{(\varepsilon_i+\varepsilon_j-\varepsilon_a-\varepsilon_b)(\varepsilon_i+\varepsilon_j-\varepsilon_c-\varepsilon_d)}+\nonumber \\\\\

docs/tex/library.bib

@@ -28,7 +28,7 @@ @article{10.1021/acs.jpclett.9b01641
     doi = {10.1021/acs.jpclett.9b01641},
 }
 
-@incollection{molecular-integrals-over-gaussian-basis-functions,
+@incollection{10.1016/S0065-3276!08!60019-2,
     title = {Molecular integrals Over Gaussian Basis Functions},
     editor = {John R. Sabin and Michael C. Zerner},
     series = {Advances in Quantum Chemistry},

script/docstopdf.sh

@@ -20,20 +20,25 @@ ACRONYMS=(
 
 # create the main LaTeX document
 cat > docs/tex/main.tex << EOL
-\documentclass[open=any,parskip=half,11pt]{scrbook}
+\documentclass[,headsepline=true,parskip=half,open=any,11pt]{scrbook}
 
-\usepackage{amsmath}
-\usepackage{braket}
-\usepackage[left=2cm,top=2.5cm,right=2cm,bottom=2.5cm]{geometry}
-\usepackage[colorlinks=true,linkcolor=blue]{hyperref}
-\usepackage{mathrsfs}
+\usepackage{amsmath} % all the math environments and symbols
+\usepackage{braket} % braket notation
+\usepackage[left=2cm,top=2.5cm,right=2cm,bottom=2.5cm]{geometry} % page layout
+\usepackage[colorlinks=true,linkcolor=blue]{hyperref} % hyperlinks
+\usepackage{mathrsfs} % mathscr environment
 
-\usepackage[backend=biber,style=chem-acs]{biblatex}
+\usepackage[backend=biber,style=chem-acs]{biblatex} % bibliography
 \addbibresource{library.bib}
 
-\usepackage[acronym,automake,nogroupskip,toc]{glossaries}
+\usepackage[acronym,automake,nogroupskip,toc]{glossaries} % acronyms
 \makeglossaries
 
+\usepackage[automark]{scrlayer-scrpage} % page numbering in header
+\clearpairofpagestyles
+\ohead{\headmark}
+\ihead{\pagemark}
+
 \title{Algorithms of Quantum Chemistry}
 \author{Tom\'a\v s J\'ira}
 EOL
@@ -123,14 +128,14 @@ for PAGE in ${PAGES[@]}; do
     awk '/{:.cite}/ {exit} {print}' docs/pages/$PAGE.md > temp.md && mv temp.md docs/pages/$PAGE.md && echo "{:.cite}" >> docs/pages/$PAGE.md
 
     # get the citations
-    CITATIONS=($(grep -o "cite{.*}" docs/pages/$PAGE.md | sed 's/cite{// ; s/}//'))
+    CITATIONS=($(grep -o "cite{.*}--" docs/pages/$PAGE.md | sed 's/cite{// ; s/}--//'))
 
     # remove duplicates from the citations
     CITATIONS=($(echo "${CITATIONS[@]}" | tr " " "\n" | sort -u | tr "\n" " "))
 
     # find and append the citation
     for CITATION in ${CITATIONS[@]}; do
-        grep $CITATION docs/tex/library.md | awk '{print "> " $0 "\n>"}' >> docs/pages/$PAGE.md
+        grep $(echo "$CITATION" | sed 's/!/(/ ; s/!/)/') docs/tex/library.md | awk '{print "> " $0 "\n>"}' >> docs/pages/$PAGE.md
     done
 done