mirror of
https://github.com/TREX-CoE/trexio.git
synced 2024-08-24 22:21:43 +02:00
Merge branch 'master' into unit-testing
This commit is contained in:
commit
411334e2ee
34
Makefile.am
34
Makefile.am
@ -55,13 +55,13 @@ lib_LTLIBRARIES = src/libtrexio.la
|
||||
|
||||
SOURCES = \
|
||||
$(trexio_h) \
|
||||
$(srcdir)/src/trexio.c \
|
||||
$(srcdir)/src/trexio_private.h \
|
||||
$(srcdir)/src/trexio_s.h \
|
||||
$(srcdir)/src/trexio_hdf5.c \
|
||||
$(srcdir)/src/trexio_hdf5.h \
|
||||
$(srcdir)/src/trexio_text.c \
|
||||
$(srcdir)/src/trexio_text.h
|
||||
src/trexio.c \
|
||||
src/trexio_private.h \
|
||||
src/trexio_s.h \
|
||||
src/trexio_hdf5.c \
|
||||
src/trexio_hdf5.h \
|
||||
src/trexio_text.c \
|
||||
src/trexio_text.h
|
||||
|
||||
ORG_FILES = \
|
||||
src/templates_front/templator_front.org \
|
||||
@ -99,6 +99,7 @@ check_PROGRAMS = $(TESTS)
|
||||
|
||||
# specify common options for all tests
|
||||
LDADD = src/libtrexio.la
|
||||
|
||||
# in principal, specifying -no-install (see example below) is not mandatory
|
||||
# for the tests to compile and pass, but the compilations itself differs
|
||||
tests_io_num_hdf5_LDFLAGS = -no-install
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||||
@ -124,18 +125,37 @@ tests_test_f_SOURCES = $(test_trexio_f) tests/test_f.f90
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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 \
|
||||
docs/README.html \
|
||||
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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||||
|
||||
$(HTML_FILES): docs/index.html
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||||
|
||||
|
||||
if TREXIO_DEVEL
|
||||
|
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CLEANFILES += $(SOURCES) $(trexio_f) $(trexio_h)
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|
||||
BUILT_SOURCES = $(SOURCES) $(trexio_f) $(test_trexio_f)
|
||||
|
||||
|
||||
$(SOURCES): $(trexio_f)
|
||||
src/trexio.c: $(trexio_h)
|
||||
|
||||
$(trexio_f): $(ORG_FILES)
|
||||
cd $(srcdir)/tools && ./build_trexio.sh
|
||||
|
||||
docs/index.html: $(SOURCES) $(srcdir)/src/README.org
|
||||
cd $(srcdir)/tools && ./build_doc.sh
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||||
|
||||
cppcheck: cppcheck.out
|
||||
cat cppcheck.out
|
||||
|
||||
|
@ -2,7 +2,7 @@
|
||||
# Process this file with autoconf to produce a configure script.
|
||||
|
||||
AC_PREREQ([2.69])
|
||||
AC_INIT([trexio], [0.2.0], [https://github.com/TREX-CoE/trexio/issues])
|
||||
AC_INIT([trexio], [0.3.0], [https://github.com/TREX-CoE/trexio/issues])
|
||||
AM_INIT_AUTOMAKE([subdir-objects color-tests parallel-tests silent-rules 1.11])
|
||||
AM_MAINTAINER_MODE()
|
||||
LT_INIT
|
||||
@ -72,7 +72,7 @@ AC_CHECK_HEADERS([fcntl.h inttypes.h stdint.h stdbool.h stdlib.h string.h unistd
|
||||
|
||||
|
||||
PKG_HDF5=""
|
||||
AX_LIB_HDF5([serial])
|
||||
AX_LIB_HDF5()
|
||||
|
||||
if test "x${with_hdf5}" = xno; then
|
||||
AC_MSG_WARN([
|
||||
|
@ -4,6 +4,7 @@
|
||||
|
||||
------------------
|
||||
|
||||
- [[./trex.html][Data stored with TREXIO]]
|
||||
- [[./templator_front.html][Front end API]]
|
||||
- [[./templator_hdf5.html][HDF5 back end]]
|
||||
- [[./templator_text.html][TEXT back end]]
|
||||
|
@ -1643,6 +1643,7 @@ trexio_read_$group_dset$_low (trexio_t* const file, char* dset, const uint32_t m
|
||||
,*/
|
||||
}
|
||||
|
||||
return TREXIO_FAILURE;
|
||||
}
|
||||
|
||||
trexio_exit_code
|
||||
@ -1803,7 +1804,6 @@ trexio_write_$group_dset$ (trexio_t* const file, const char** dset, const uint32
|
||||
FREE(str_compiled);
|
||||
|
||||
return rc;
|
||||
|
||||
}
|
||||
#+end_src
|
||||
|
||||
@ -1831,6 +1831,7 @@ trexio_has_$group_dset$ (trexio_t* const file)
|
||||
break;
|
||||
,*/
|
||||
}
|
||||
|
||||
return TREXIO_FAILURE;
|
||||
}
|
||||
#+end_src
|
||||
@ -1968,6 +1969,7 @@ trexio_read_$group_str$ (trexio_t* const file, char* const str, const uint32_t m
|
||||
,*/
|
||||
}
|
||||
|
||||
return TREXIO_FAILURE;
|
||||
}
|
||||
#+end_src
|
||||
|
||||
@ -2000,6 +2002,7 @@ trexio_write_$group_str$ (trexio_t* const file, const char* str, const uint32_t
|
||||
,*/
|
||||
}
|
||||
|
||||
return TREXIO_FAILURE;
|
||||
}
|
||||
#+end_src
|
||||
|
||||
|
@ -289,15 +289,6 @@ trexio_hdf5_read_$group_dset$ (trexio_t* const file, $group_dset_dtype$* const $
|
||||
|
||||
const trexio_hdf5_t* f = (const trexio_hdf5_t*) file;
|
||||
|
||||
herr_t status;
|
||||
int rrank;
|
||||
// get the rank of the dataset in a file
|
||||
status = H5LTget_dataset_ndims (f->$group$_group, $GROUP_DSET$_NAME, &rrank);
|
||||
|
||||
if (status < 0) return TREXIO_FAILURE;
|
||||
|
||||
if (rrank != (int) rank) return TREXIO_INVALID_ARG_3;
|
||||
|
||||
// open the dataset to get its dimensions
|
||||
hid_t dset_id = H5Dopen(f->$group$_group, $GROUP_DSET$_NAME, H5P_DEFAULT);
|
||||
if (dset_id <= 0) return TREXIO_INVALID_ID;
|
||||
@ -306,28 +297,37 @@ trexio_hdf5_read_$group_dset$ (trexio_t* const file, $group_dset_dtype$* const $
|
||||
hsize_t* ddims = CALLOC( (int) rank, hsize_t);
|
||||
if (ddims == NULL) return TREXIO_FAILURE;
|
||||
|
||||
// read dimensions from the existing dataset
|
||||
status = H5LDget_dset_dims(dset_id, ddims);
|
||||
// get the dataspace of the dataset
|
||||
hid_t dspace_id = H5Dget_space(dset_id);
|
||||
// get the rank and dimensions of the dataset
|
||||
int rrank = H5Sget_simple_extent_dims(dspace_id, ddims, NULL);
|
||||
|
||||
H5Dclose(dset_id);
|
||||
if (status < 0) {
|
||||
// check that dimensions are consistent
|
||||
if (rrank != (int) rank) {
|
||||
FREE(ddims);
|
||||
return TREXIO_FAILURE;
|
||||
H5Sclose(dspace_id);
|
||||
H5Dclose(dset_id);
|
||||
return TREXIO_INVALID_ARG_3;
|
||||
}
|
||||
|
||||
for (uint32_t i=0; i<rank; ++i){
|
||||
if (ddims[i] != dims[i]) {
|
||||
FREE(ddims);
|
||||
H5Sclose(dspace_id);
|
||||
H5Dclose(dset_id);
|
||||
return TREXIO_INVALID_ARG_4;
|
||||
}
|
||||
}
|
||||
|
||||
FREE(ddims);
|
||||
H5Sclose(dspace_id);
|
||||
H5Dclose(dset_id);
|
||||
|
||||
/* High-level H5LT API. No need to deal with dataspaces and datatypes */
|
||||
status = H5LTread_dataset(f->$group$_group,
|
||||
$GROUP_DSET$_NAME,
|
||||
H5T_$GROUP_DSET_H5_DTYPE$,
|
||||
$group_dset$);
|
||||
herr_t status = H5LTread_dataset(f->$group$_group,
|
||||
$GROUP_DSET$_NAME,
|
||||
H5T_$GROUP_DSET_H5_DTYPE$,
|
||||
$group_dset$);
|
||||
if (status < 0) return TREXIO_FAILURE;
|
||||
|
||||
return TREXIO_SUCCESS;
|
||||
|
@ -99,10 +99,11 @@ function main() {
|
||||
# Create documentation
|
||||
cd ${SRC}
|
||||
|
||||
for dir in ${SRC}/templates_*/
|
||||
for dir in ${SRC}/templates_*/ ${TREXIO_ROOT}/
|
||||
do
|
||||
dir=${dir%*/}
|
||||
echo ${dir}
|
||||
OLDPWD=$PWD
|
||||
cd ${dir}
|
||||
for i in *.org
|
||||
do
|
||||
@ -110,7 +111,7 @@ function main() {
|
||||
echo "======= ${i} ======="
|
||||
extract_doc ${i} ${dir}
|
||||
done
|
||||
cd ..
|
||||
cd $OLDPWD
|
||||
done
|
||||
|
||||
echo
|
||||
|
50
trex.org
50
trex.org
@ -1,5 +1,7 @@
|
||||
#+TITLE: TREX Configuration file
|
||||
#+STARTUP: latexpreview
|
||||
#+SETUPFILE: docs/theme.setup
|
||||
|
||||
|
||||
All the quantities are saved in atomic units.
|
||||
The dimensions of the arrays in the tables below are given in
|
||||
@ -11,12 +13,12 @@ In Fortran, the arrays are 1-based and in most other languages the
|
||||
arrays are 0-base. Hence, we introduce the ~index~ type which is an
|
||||
1-based ~int~ in the Fortran interface and 0-based otherwise.
|
||||
|
||||
#+begin_src python :tangle trex.json
|
||||
#+begin_src python :tangle trex.json
|
||||
{
|
||||
#+end_src
|
||||
|
||||
* Metadata
|
||||
|
||||
|
||||
As we expect our files to be archived in open-data repositories, we
|
||||
need to give the possibility to the users to store some metadata
|
||||
inside the files. We propose to store the list of names of the codes
|
||||
@ -175,7 +177,7 @@ arrays are 0-base. Hence, we introduce the ~index~ type which is an
|
||||
R_s(\mathbf{r}) = \mathcal{N}_s \vert\mathbf{r}-\mathbf{R}_A\vert^{n_s}
|
||||
\sum_{k=1}^{N_{\text{prim}}} a_{ks}\, f_{ks}(\gamma_{ks},p)\,
|
||||
\exp \left( - \gamma_{ks}
|
||||
\vert \mathbf{r}-\mathbf{R}_A \vert ^p \right).
|
||||
\vert \mathbf{r}-\mathbf{R}_A \vert ^p \right).
|
||||
\]
|
||||
|
||||
In the case of Gaussian functions, $n_s$ is always zero.
|
||||
@ -190,7 +192,7 @@ arrays are 0-base. Hence, we introduce the ~index~ type which is an
|
||||
combination of /normalized/ primitives. This implies that a normalization
|
||||
constant for the primitive $ks$ needs to be computed and stored. If
|
||||
this normalization factor is not required, $f_{ks}=1$.
|
||||
|
||||
|
||||
Some codes assume that the basis function are normalized. This
|
||||
implies the computation of an extra normalization factor, $\mathcal{N}_s$.
|
||||
If the the basis function is not considered normalized, $\mathcal{N}_s=1$.
|
||||
@ -208,10 +210,10 @@ arrays are 0-base. Hence, we introduce the ~index~ type which is an
|
||||
| ~shell_prim_num~ | ~int~ | ~(basis.num)~ | Number of primitives in the shell ($N_{\text{prim}}$) |
|
||||
| ~shell_factor~ | ~float~ | ~(basis.num)~ | Normalization factor of the shell ($\mathcal{N}_s$) |
|
||||
| ~shell_prim_index~ | ~index~ | ~(basis.num)~ | Index of the first primitive in the complete list |
|
||||
| ~exponent~ | ~float~ | ~(basis.prim_num)~ | Exponents of the primitives ($\gamma_{ks}) |
|
||||
| ~exponent~ | ~float~ | ~(basis.prim_num)~ | Exponents of the primitives ($\gamma_{ks}$) |
|
||||
| ~coefficient~ | ~float~ | ~(basis.prim_num)~ | Coefficients of the primitives ($a_{ks}$) |
|
||||
| ~prim_factor~ | ~float~ | ~(basis.prim_num)~ | Normalization coefficients for the primitives ($f_{ks}$) |
|
||||
|
||||
|
||||
#+CALL: json(data=basis, title="basis")
|
||||
|
||||
#+RESULTS:
|
||||
@ -221,12 +223,12 @@ arrays are 0-base. Hence, we introduce the ~index~ type which is an
|
||||
"type" : [ "str" , [] ]
|
||||
, "num" : [ "int" , [] ]
|
||||
, "prim_num" : [ "int" , [] ]
|
||||
, "nucleus_index" : [ "index" , [ "nucleus.num" ] ]
|
||||
, "nucleus_index" : [ "index", [ "nucleus.num" ] ]
|
||||
, "nucleus_shell_num" : [ "int" , [ "nucleus.num" ] ]
|
||||
, "shell_ang_mom" : [ "int" , [ "basis.num" ] ]
|
||||
, "shell_prim_num" : [ "int" , [ "basis.num" ] ]
|
||||
, "shell_factor" : [ "float", [ "basis.num" ] ]
|
||||
, "shell_prim_index" : [ "index" , [ "basis.num" ] ]
|
||||
, "shell_prim_index" : [ "index", [ "basis.num" ] ]
|
||||
, "exponent" : [ "float", [ "basis.prim_num" ] ]
|
||||
, "coefficient" : [ "float", [ "basis.prim_num" ] ]
|
||||
, "prim_factor" : [ "float", [ "basis.prim_num" ] ]
|
||||
@ -324,9 +326,9 @@ prim_factor =
|
||||
shell, as in the GAMESS convention where
|
||||
$\mathcal{N}_{x^2} \ne \mathcal{N}_{xy}$ because
|
||||
\[ \left[ \iiint \left(x-X_A \right)^2 R_{\theta(i)}
|
||||
(\mathbf{r}) dx\, dy\, dz \right]^{-1/2} \ne
|
||||
(\mathbf{r}) dx\, dy\, dz \right]^{-1/2} \ne
|
||||
\left[ \iiint \left( x-X_A \right) \left( y-Y_A \right) R_{\theta(i)}
|
||||
(\mathbf{r}) dx\, dy\, dz \right]^{-1/2}. \]
|
||||
(\mathbf{r}) dx\, dy\, dz \right]^{-1/2}. \]
|
||||
|
||||
In such a case, one should set the normalization of the shell (in
|
||||
the [[Basis set][Basis set]] section) to $\mathcal{N}_{z^2}$, which is the
|
||||
@ -353,7 +355,7 @@ prim_factor =
|
||||
} ,
|
||||
#+end_src
|
||||
:end:
|
||||
|
||||
|
||||
** One-electron integrals
|
||||
:PROPERTIES:
|
||||
:CUSTOM_ID: ao_one_e
|
||||
@ -362,7 +364,7 @@ prim_factor =
|
||||
- \[ \hat{V}_{\text{ne}} = \sum_{A=1}^{N_\text{nucl}}
|
||||
\sum_{i=1}^{N_\text{elec}} \frac{-Z_A }{\vert \mathbf{R}_A -
|
||||
\mathbf{r}_i \vert} \] : electron-nucleus attractive potential,
|
||||
- \[ \hat{T}_{\text{e}} =
|
||||
- \[ \hat{T}_{\text{e}} =
|
||||
\sum_{i=1}^{N_\text{elec}} -\frac{1}{2}\hat{\Delta}_i \] : electronic kinetic energy
|
||||
- $\hat{h} = \hat{T}_\text{e} + \hat{V}_\text{ne} +
|
||||
\hat{V}_\text{ecp,l} + \hat{V}_\text{ecp,nl}$ : core electronic Hamiltonian
|
||||
@ -375,8 +377,8 @@ prim_factor =
|
||||
| ~overlap~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert q \rangle$ |
|
||||
| ~kinetic~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{T}_e \vert q \rangle$ |
|
||||
| ~potential_n_e~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ne}} \vert q \rangle$ |
|
||||
| ~ecp_local~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ecp,l} \vert q \rangle$ |
|
||||
| ~ecp_non_local~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ecp,nl} \vert q \rangle$ |
|
||||
| ~ecp_local~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ecp,l}} \vert q \rangle$ |
|
||||
| ~ecp_non_local~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ecp,nl}} \vert q \rangle$ |
|
||||
| ~core_hamiltonian~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{h} \vert q \rangle$ |
|
||||
|
||||
#+CALL: json(data=ao_1e_int, title="ao_1e_int")
|
||||
@ -409,7 +411,7 @@ prim_factor =
|
||||
notation.
|
||||
|
||||
# TODO: Physicist / Chemist functions
|
||||
|
||||
|
||||
- \[ \hat{W}_{\text{ee}} = \sum_{i=2}^{N_\text{elec}} \sum_{j=1}^{i-1} \frac{1}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron repulsive potential operator.
|
||||
- \[ \hat{W}^{lr}_{\text{ee}} = \sum_{i=2}^{N_\text{elec}}
|
||||
\sum_{j=1}^{i-1} \frac{\text{erf}(\vert \mathbf{r}_i -
|
||||
@ -460,15 +462,15 @@ prim_factor =
|
||||
** One-electron integrals
|
||||
|
||||
The operators as the same as those defined in the
|
||||
[[ao_one_e][AO one-electron integrals section]]. Here, the integrals are given in
|
||||
[[#ao_one_e][AO one-electron integrals section]]. Here, the integrals are given in
|
||||
the basis of molecular orbitals.
|
||||
|
||||
|
||||
#+NAME: mo_1e_int
|
||||
| ~overlap~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert j \rangle$ |
|
||||
| ~kinetic~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{T}_e \vert j \rangle$ |
|
||||
| ~potential_n_e~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{V}_{\text{ne}} \vert j \rangle$ |
|
||||
| ~ecp_local~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{V}_{\text{ecp,l} \vert j \rangle$ |
|
||||
| ~ecp_non_local~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{V}_{\text{ecp,nl} \vert j \rangle$ |
|
||||
| ~ecp_local~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{V}_{\text{ecp,l}} \vert j \rangle$ |
|
||||
| ~ecp_non_local~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{V}_{\text{ecp,nl}} \vert j \rangle$ |
|
||||
| ~core_hamiltonian~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{h} \vert j \rangle$ |
|
||||
|
||||
#+CALL: json(data=mo_1e_int, title="mo_1e_int")
|
||||
@ -490,7 +492,7 @@ prim_factor =
|
||||
** Two-electron integrals
|
||||
|
||||
The operators as the same as those defined in the
|
||||
[[ao_two_e][AO two-electron integrals section]]. Here, the integrals are given in
|
||||
[[#ao_one_e][AO one-electron integrals section]]. Here, the integrals are given in
|
||||
the basis of molecular orbitals.
|
||||
|
||||
#+NAME: mo_2e_int
|
||||
@ -511,7 +513,7 @@ prim_factor =
|
||||
|
||||
* TODO Slater determinants
|
||||
* TODO Reduced density matrices
|
||||
|
||||
|
||||
#+NAME: rdm
|
||||
| ~one_e~ | ~float~ | ~(mo.num, mo.num)~ |
|
||||
| ~one_e_up~ | ~float~ | ~(mo.num, mo.num)~ |
|
||||
@ -532,12 +534,12 @@ prim_factor =
|
||||
#+end_src
|
||||
:end:
|
||||
|
||||
* Appendix :noexport:
|
||||
* Appendix
|
||||
** Python script from table to json
|
||||
|
||||
#+NAME: json
|
||||
#+begin_src python :var data=nucleus title="nucleus" last=0 :results output drawer
|
||||
print("""#+begin_src python :tangle trex.json""")
|
||||
#+begin_src python :var data=nucleus title="nucleus" last=0 :results output drawer
|
||||
print("""#+begin_src python :tangle trex.json""")
|
||||
print(""" "%s": {"""%(title))
|
||||
indent = " "
|
||||
f1 = 0 ; f2 = 0 ; f3 = 0
|
||||
|
Loading…
Reference in New Issue
Block a user