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Documentation in dist
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18
Makefile.am
18
Makefile.am
@ -87,6 +87,23 @@ tests_test_f_SOURCES = $(test_trexio_f) tests/test_f.f90
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tests_test_f_LDADD = src/libtrexio.la
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tests_test_f_LDFLAGS = -no-install
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HTML_FILES = docs/trexio.css \
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docs/index.html \
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docs/Sparse.html \
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docs/templator_hdf5.html \
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docs/trex.html \
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docs/README.html \
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docs/templator_front.html \
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docs/templator_text.html
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htmldir = $(docdir)
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dist_html_DATA = $(HTML_FILES)
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docs/index.html: $(SOURCES) src/README.org
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cd tools && ./build_doc.sh
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$(HTML_FILES): docs/index.html
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$(test_trexio_f): $(trexio_f)
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cp $(trexio_f) $(test_trexio_f)
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@ -99,6 +116,7 @@ CLEANFILES += $(SOURCES) $(trexio_f) $(trexio_h)
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BUILT_SOURCES = $(SOURCES) $(trexio_f) $(test_trexio_f)
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$(SOURCES): $(trexio_f)
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src/trexio.c: $(trexio_h)
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@ -2,7 +2,7 @@
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# Process this file with autoconf to produce a configure script.
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AC_PREREQ([2.69])
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AC_INIT([trexio], [0.2.0], [https://github.com/TREX-CoE/trexio/issues])
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AC_INIT([trexio], [0.3.0], [https://github.com/TREX-CoE/trexio/issues])
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AM_INIT_AUTOMAKE([subdir-objects color-tests parallel-tests silent-rules 1.11])
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AM_MAINTAINER_MODE()
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LT_INIT
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@ -4,6 +4,7 @@
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------------------
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- [[./trex.html][Data stored with TREXIO]]
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- [[./templator_front.html][Front end API]]
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- [[./templator_hdf5.html][HDF5 back end]]
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- [[./templator_text.html][TEXT back end]]
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@ -99,10 +99,11 @@ function main() {
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# Create documentation
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cd ${SRC}
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for dir in ${SRC}/templates_*/
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for dir in ${SRC}/templates_*/ ${TREXIO_ROOT}/
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do
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dir=${dir%*/}
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echo ${dir}
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OLDPWD=$PWD
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cd ${dir}
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for i in *.org
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do
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@ -110,7 +111,7 @@ function main() {
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echo "======= ${i} ======="
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extract_doc ${i} ${dir}
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done
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cd ..
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cd $OLDPWD
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done
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echo
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38
trex.org
38
trex.org
@ -11,12 +11,12 @@ In Fortran, the arrays are 1-based and in most other languages the
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arrays are 0-base. Hence, we introduce the ~index~ type which is an
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1-based ~int~ in the Fortran interface and 0-based otherwise.
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#+begin_src python :tangle trex.json
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#+begin_src python :tangle trex.json
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{
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#+end_src
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* Metadata
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As we expect our files to be archived in open-data repositories, we
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need to give the possibility to the users to store some metadata
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inside the files. We propose to store the list of names of the codes
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@ -175,7 +175,7 @@ arrays are 0-base. Hence, we introduce the ~index~ type which is an
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R_s(\mathbf{r}) = \mathcal{N}_s \vert\mathbf{r}-\mathbf{R}_A\vert^{n_s}
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\sum_{k=1}^{N_{\text{prim}}} a_{ks}\, f_{ks}(\gamma_{ks},p)\,
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\exp \left( - \gamma_{ks}
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\vert \mathbf{r}-\mathbf{R}_A \vert ^p \right).
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\vert \mathbf{r}-\mathbf{R}_A \vert ^p \right).
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\]
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In the case of Gaussian functions, $n_s$ is always zero.
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@ -190,7 +190,7 @@ arrays are 0-base. Hence, we introduce the ~index~ type which is an
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combination of /normalized/ primitives. This implies that a normalization
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constant for the primitive $ks$ needs to be computed and stored. If
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this normalization factor is not required, $f_{ks}=1$.
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Some codes assume that the basis function are normalized. This
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implies the computation of an extra normalization factor, $\mathcal{N}_s$.
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If the the basis function is not considered normalized, $\mathcal{N}_s=1$.
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@ -211,7 +211,7 @@ arrays are 0-base. Hence, we introduce the ~index~ type which is an
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| ~exponent~ | ~float~ | ~(basis.prim_num)~ | Exponents of the primitives ($\gamma_{ks}) |
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| ~coefficient~ | ~float~ | ~(basis.prim_num)~ | Coefficients of the primitives ($a_{ks}$) |
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| ~prim_factor~ | ~float~ | ~(basis.prim_num)~ | Normalization coefficients for the primitives ($f_{ks}$) |
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#+CALL: json(data=basis, title="basis")
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#+RESULTS:
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@ -221,12 +221,12 @@ arrays are 0-base. Hence, we introduce the ~index~ type which is an
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"type" : [ "str" , [] ]
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, "num" : [ "int" , [] ]
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, "prim_num" : [ "int" , [] ]
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, "nucleus_index" : [ "index" , [ "nucleus.num" ] ]
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, "nucleus_index" : [ "index", [ "nucleus.num" ] ]
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, "nucleus_shell_num" : [ "int" , [ "nucleus.num" ] ]
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, "shell_ang_mom" : [ "int" , [ "basis.num" ] ]
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, "shell_prim_num" : [ "int" , [ "basis.num" ] ]
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, "shell_factor" : [ "float", [ "basis.num" ] ]
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, "shell_prim_index" : [ "index" , [ "basis.num" ] ]
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, "shell_prim_index" : [ "index", [ "basis.num" ] ]
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, "exponent" : [ "float", [ "basis.prim_num" ] ]
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, "coefficient" : [ "float", [ "basis.prim_num" ] ]
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, "prim_factor" : [ "float", [ "basis.prim_num" ] ]
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@ -324,9 +324,9 @@ prim_factor =
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shell, as in the GAMESS convention where
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$\mathcal{N}_{x^2} \ne \mathcal{N}_{xy}$ because
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\[ \left[ \iiint \left(x-X_A \right)^2 R_{\theta(i)}
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(\mathbf{r}) dx\, dy\, dz \right]^{-1/2} \ne
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(\mathbf{r}) dx\, dy\, dz \right]^{-1/2} \ne
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\left[ \iiint \left( x-X_A \right) \left( y-Y_A \right) R_{\theta(i)}
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(\mathbf{r}) dx\, dy\, dz \right]^{-1/2}. \]
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(\mathbf{r}) dx\, dy\, dz \right]^{-1/2}. \]
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In such a case, one should set the normalization of the shell (in
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the [[Basis set][Basis set]] section) to $\mathcal{N}_{z^2}$, which is the
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@ -353,7 +353,7 @@ prim_factor =
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} ,
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#+end_src
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:end:
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** One-electron integrals
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:PROPERTIES:
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:CUSTOM_ID: ao_one_e
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@ -362,7 +362,7 @@ prim_factor =
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- \[ \hat{V}_{\text{ne}} = \sum_{A=1}^{N_\text{nucl}}
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\sum_{i=1}^{N_\text{elec}} \frac{-Z_A }{\vert \mathbf{R}_A -
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\mathbf{r}_i \vert} \] : electron-nucleus attractive potential,
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- \[ \hat{T}_{\text{e}} =
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- \[ \hat{T}_{\text{e}} =
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\sum_{i=1}^{N_\text{elec}} -\frac{1}{2}\hat{\Delta}_i \] : electronic kinetic energy
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- $\hat{h} = \hat{T}_\text{e} + \hat{V}_\text{ne} +
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\hat{V}_\text{ecp,l} + \hat{V}_\text{ecp,nl}$ : core electronic Hamiltonian
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@ -409,7 +409,7 @@ prim_factor =
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notation.
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# TODO: Physicist / Chemist functions
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- \[ \hat{W}_{\text{ee}} = \sum_{i=2}^{N_\text{elec}} \sum_{j=1}^{i-1} \frac{1}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron repulsive potential operator.
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- \[ \hat{W}^{lr}_{\text{ee}} = \sum_{i=2}^{N_\text{elec}}
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\sum_{j=1}^{i-1} \frac{\text{erf}(\vert \mathbf{r}_i -
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@ -460,9 +460,9 @@ prim_factor =
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** One-electron integrals
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The operators as the same as those defined in the
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[[ao_one_e][AO one-electron integrals section]]. Here, the integrals are given in
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[[#ao_one_e][AO one-electron integrals section]]. Here, the integrals are given in
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the basis of molecular orbitals.
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#+NAME: mo_1e_int
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| ~overlap~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert j \rangle$ |
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| ~kinetic~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{T}_e \vert j \rangle$ |
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@ -490,7 +490,7 @@ prim_factor =
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** Two-electron integrals
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The operators as the same as those defined in the
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[[ao_two_e][AO two-electron integrals section]]. Here, the integrals are given in
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[[#ao_one_e][AO one-electron integrals section]]. Here, the integrals are given in
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the basis of molecular orbitals.
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#+NAME: mo_2e_int
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@ -511,7 +511,7 @@ prim_factor =
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* TODO Slater determinants
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* TODO Reduced density matrices
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#+NAME: rdm
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| ~one_e~ | ~float~ | ~(mo.num, mo.num)~ |
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| ~one_e_up~ | ~float~ | ~(mo.num, mo.num)~ |
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@ -532,12 +532,12 @@ prim_factor =
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#+end_src
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:end:
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* Appendix :noexport:
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* Appendix
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** Python script from table to json
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#+NAME: json
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#+begin_src python :var data=nucleus title="nucleus" last=0 :results output drawer
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print("""#+begin_src python :tangle trex.json""")
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#+begin_src python :var data=nucleus title="nucleus" last=0 :results output drawer
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print("""#+begin_src python :tangle trex.json""")
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print(""" "%s": {"""%(title))
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indent = " "
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f1 = 0 ; f2 = 0 ; f3 = 0
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