mirror of
https://github.com/TREX-CoE/trexio.git
synced 2024-12-23 04:43:57 +01:00
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 = \
|
SOURCES = \
|
||||||
$(trexio_h) \
|
$(trexio_h) \
|
||||||
$(srcdir)/src/trexio.c \
|
src/trexio.c \
|
||||||
$(srcdir)/src/trexio_private.h \
|
src/trexio_private.h \
|
||||||
$(srcdir)/src/trexio_s.h \
|
src/trexio_s.h \
|
||||||
$(srcdir)/src/trexio_hdf5.c \
|
src/trexio_hdf5.c \
|
||||||
$(srcdir)/src/trexio_hdf5.h \
|
src/trexio_hdf5.h \
|
||||||
$(srcdir)/src/trexio_text.c \
|
src/trexio_text.c \
|
||||||
$(srcdir)/src/trexio_text.h
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src/trexio_text.h
|
||||||
|
|
||||||
ORG_FILES = \
|
ORG_FILES = \
|
||||||
src/templates_front/templator_front.org \
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src/templates_front/templator_front.org \
|
||||||
@ -99,6 +99,7 @@ check_PROGRAMS = $(TESTS)
|
|||||||
|
|
||||||
# specify common options for all tests
|
# specify common options for all tests
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||||||
LDADD = src/libtrexio.la
|
LDADD = src/libtrexio.la
|
||||||
|
|
||||||
# in principal, specifying -no-install (see example below) is not mandatory
|
# in principal, specifying -no-install (see example below) is not mandatory
|
||||||
# for the tests to compile and pass, but the compilations itself differs
|
# for the tests to compile and pass, but the compilations itself differs
|
||||||
tests_io_num_hdf5_LDFLAGS = -no-install
|
tests_io_num_hdf5_LDFLAGS = -no-install
|
||||||
@ -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
|
tests_test_f_LDFLAGS = -no-install
|
||||||
|
|
||||||
|
|
||||||
|
HTML_FILES = docs/trexio.css \
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||||||
|
docs/index.html \
|
||||||
|
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 \
|
||||||
|
docs/templator_front.html \
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||||||
|
docs/templator_text.html
|
||||||
|
|
||||||
|
htmldir = $(docdir)
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||||||
|
dist_html_DATA = $(HTML_FILES)
|
||||||
|
|
||||||
|
$(HTML_FILES): docs/index.html
|
||||||
|
|
||||||
|
|
||||||
if TREXIO_DEVEL
|
if TREXIO_DEVEL
|
||||||
|
|
||||||
CLEANFILES += $(SOURCES) $(trexio_f) $(trexio_h)
|
CLEANFILES += $(SOURCES) $(trexio_f) $(trexio_h)
|
||||||
|
|
||||||
BUILT_SOURCES = $(SOURCES) $(trexio_f) $(test_trexio_f)
|
BUILT_SOURCES = $(SOURCES) $(trexio_f) $(test_trexio_f)
|
||||||
|
|
||||||
|
|
||||||
$(SOURCES): $(trexio_f)
|
$(SOURCES): $(trexio_f)
|
||||||
src/trexio.c: $(trexio_h)
|
src/trexio.c: $(trexio_h)
|
||||||
|
|
||||||
$(trexio_f): $(ORG_FILES)
|
$(trexio_f): $(ORG_FILES)
|
||||||
cd $(srcdir)/tools && ./build_trexio.sh
|
cd $(srcdir)/tools && ./build_trexio.sh
|
||||||
|
|
||||||
|
docs/index.html: $(SOURCES) $(srcdir)/src/README.org
|
||||||
|
cd $(srcdir)/tools && ./build_doc.sh
|
||||||
|
|
||||||
cppcheck: cppcheck.out
|
cppcheck: cppcheck.out
|
||||||
cat cppcheck.out
|
cat cppcheck.out
|
||||||
|
|
||||||
|
@ -2,7 +2,7 @@
|
|||||||
# Process this file with autoconf to produce a configure script.
|
# Process this file with autoconf to produce a configure script.
|
||||||
|
|
||||||
AC_PREREQ([2.69])
|
AC_PREREQ([2.69])
|
||||||
AC_INIT([trexio], [0.2.0], [https://github.com/TREX-CoE/trexio/issues])
|
AC_INIT([trexio], [0.3.0], [https://github.com/TREX-CoE/trexio/issues])
|
||||||
AM_INIT_AUTOMAKE([subdir-objects color-tests parallel-tests silent-rules 1.11])
|
AM_INIT_AUTOMAKE([subdir-objects color-tests parallel-tests silent-rules 1.11])
|
||||||
AM_MAINTAINER_MODE()
|
AM_MAINTAINER_MODE()
|
||||||
LT_INIT
|
LT_INIT
|
||||||
@ -72,7 +72,7 @@ AC_CHECK_HEADERS([fcntl.h inttypes.h stdint.h stdbool.h stdlib.h string.h unistd
|
|||||||
|
|
||||||
|
|
||||||
PKG_HDF5=""
|
PKG_HDF5=""
|
||||||
AX_LIB_HDF5([serial])
|
AX_LIB_HDF5()
|
||||||
|
|
||||||
if test "x${with_hdf5}" = xno; then
|
if test "x${with_hdf5}" = xno; then
|
||||||
AC_MSG_WARN([
|
AC_MSG_WARN([
|
||||||
|
@ -4,6 +4,7 @@
|
|||||||
|
|
||||||
------------------
|
------------------
|
||||||
|
|
||||||
|
- [[./trex.html][Data stored with TREXIO]]
|
||||||
- [[./templator_front.html][Front end API]]
|
- [[./templator_front.html][Front end API]]
|
||||||
- [[./templator_hdf5.html][HDF5 back end]]
|
- [[./templator_hdf5.html][HDF5 back end]]
|
||||||
- [[./templator_text.html][TEXT back end]]
|
- [[./templator_text.html][TEXT back end]]
|
||||||
|
@ -1643,6 +1643,7 @@ trexio_read_$group_dset$_low (trexio_t* const file, char* dset, const uint32_t m
|
|||||||
,*/
|
,*/
|
||||||
}
|
}
|
||||||
|
|
||||||
|
return TREXIO_FAILURE;
|
||||||
}
|
}
|
||||||
|
|
||||||
trexio_exit_code
|
trexio_exit_code
|
||||||
@ -1803,7 +1804,6 @@ trexio_write_$group_dset$ (trexio_t* const file, const char** dset, const uint32
|
|||||||
FREE(str_compiled);
|
FREE(str_compiled);
|
||||||
|
|
||||||
return rc;
|
return rc;
|
||||||
|
|
||||||
}
|
}
|
||||||
#+end_src
|
#+end_src
|
||||||
|
|
||||||
@ -1831,6 +1831,7 @@ trexio_has_$group_dset$ (trexio_t* const file)
|
|||||||
break;
|
break;
|
||||||
,*/
|
,*/
|
||||||
}
|
}
|
||||||
|
|
||||||
return TREXIO_FAILURE;
|
return TREXIO_FAILURE;
|
||||||
}
|
}
|
||||||
#+end_src
|
#+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
|
#+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
|
#+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;
|
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
|
// open the dataset to get its dimensions
|
||||||
hid_t dset_id = H5Dopen(f->$group$_group, $GROUP_DSET$_NAME, H5P_DEFAULT);
|
hid_t dset_id = H5Dopen(f->$group$_group, $GROUP_DSET$_NAME, H5P_DEFAULT);
|
||||||
if (dset_id <= 0) return TREXIO_INVALID_ID;
|
if (dset_id <= 0) return TREXIO_INVALID_ID;
|
||||||
@ -306,25 +297,34 @@ trexio_hdf5_read_$group_dset$ (trexio_t* const file, $group_dset_dtype$* const $
|
|||||||
hsize_t* ddims = CALLOC( (int) rank, hsize_t);
|
hsize_t* ddims = CALLOC( (int) rank, hsize_t);
|
||||||
if (ddims == NULL) return TREXIO_FAILURE;
|
if (ddims == NULL) return TREXIO_FAILURE;
|
||||||
|
|
||||||
// read dimensions from the existing dataset
|
// get the dataspace of the dataset
|
||||||
status = H5LDget_dset_dims(dset_id, ddims);
|
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);
|
// check that dimensions are consistent
|
||||||
if (status < 0) {
|
if (rrank != (int) rank) {
|
||||||
FREE(ddims);
|
FREE(ddims);
|
||||||
return TREXIO_FAILURE;
|
H5Sclose(dspace_id);
|
||||||
|
H5Dclose(dset_id);
|
||||||
|
return TREXIO_INVALID_ARG_3;
|
||||||
}
|
}
|
||||||
|
|
||||||
for (uint32_t i=0; i<rank; ++i){
|
for (uint32_t i=0; i<rank; ++i){
|
||||||
if (ddims[i] != dims[i]) {
|
if (ddims[i] != dims[i]) {
|
||||||
FREE(ddims);
|
FREE(ddims);
|
||||||
|
H5Sclose(dspace_id);
|
||||||
|
H5Dclose(dset_id);
|
||||||
return TREXIO_INVALID_ARG_4;
|
return TREXIO_INVALID_ARG_4;
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
FREE(ddims);
|
FREE(ddims);
|
||||||
|
H5Sclose(dspace_id);
|
||||||
|
H5Dclose(dset_id);
|
||||||
|
|
||||||
/* High-level H5LT API. No need to deal with dataspaces and datatypes */
|
/* High-level H5LT API. No need to deal with dataspaces and datatypes */
|
||||||
status = H5LTread_dataset(f->$group$_group,
|
herr_t status = H5LTread_dataset(f->$group$_group,
|
||||||
$GROUP_DSET$_NAME,
|
$GROUP_DSET$_NAME,
|
||||||
H5T_$GROUP_DSET_H5_DTYPE$,
|
H5T_$GROUP_DSET_H5_DTYPE$,
|
||||||
$group_dset$);
|
$group_dset$);
|
||||||
|
@ -99,10 +99,11 @@ function main() {
|
|||||||
# Create documentation
|
# Create documentation
|
||||||
cd ${SRC}
|
cd ${SRC}
|
||||||
|
|
||||||
for dir in ${SRC}/templates_*/
|
for dir in ${SRC}/templates_*/ ${TREXIO_ROOT}/
|
||||||
do
|
do
|
||||||
dir=${dir%*/}
|
dir=${dir%*/}
|
||||||
echo ${dir}
|
echo ${dir}
|
||||||
|
OLDPWD=$PWD
|
||||||
cd ${dir}
|
cd ${dir}
|
||||||
for i in *.org
|
for i in *.org
|
||||||
do
|
do
|
||||||
@ -110,7 +111,7 @@ function main() {
|
|||||||
echo "======= ${i} ======="
|
echo "======= ${i} ======="
|
||||||
extract_doc ${i} ${dir}
|
extract_doc ${i} ${dir}
|
||||||
done
|
done
|
||||||
cd ..
|
cd $OLDPWD
|
||||||
done
|
done
|
||||||
|
|
||||||
echo
|
echo
|
||||||
|
18
trex.org
18
trex.org
@ -1,5 +1,7 @@
|
|||||||
#+TITLE: TREX Configuration file
|
#+TITLE: TREX Configuration file
|
||||||
#+STARTUP: latexpreview
|
#+STARTUP: latexpreview
|
||||||
|
#+SETUPFILE: docs/theme.setup
|
||||||
|
|
||||||
|
|
||||||
All the quantities are saved in atomic units.
|
All the quantities are saved in atomic units.
|
||||||
The dimensions of the arrays in the tables below are given in
|
The dimensions of the arrays in the tables below are given in
|
||||||
@ -208,7 +210,7 @@ arrays are 0-base. Hence, we introduce the ~index~ type which is an
|
|||||||
| ~shell_prim_num~ | ~int~ | ~(basis.num)~ | Number of primitives in the shell ($N_{\text{prim}}$) |
|
| ~shell_prim_num~ | ~int~ | ~(basis.num)~ | Number of primitives in the shell ($N_{\text{prim}}$) |
|
||||||
| ~shell_factor~ | ~float~ | ~(basis.num)~ | Normalization factor of the shell ($\mathcal{N}_s$) |
|
| ~shell_factor~ | ~float~ | ~(basis.num)~ | Normalization factor of the shell ($\mathcal{N}_s$) |
|
||||||
| ~shell_prim_index~ | ~index~ | ~(basis.num)~ | Index of the first primitive in the complete list |
|
| ~shell_prim_index~ | ~index~ | ~(basis.num)~ | Index of the first primitive in the complete list |
|
||||||
| ~exponent~ | ~float~ | ~(basis.prim_num)~ | Exponents of the primitives ($\gamma_{ks}) |
|
| ~exponent~ | ~float~ | ~(basis.prim_num)~ | Exponents of the primitives ($\gamma_{ks}$) |
|
||||||
| ~coefficient~ | ~float~ | ~(basis.prim_num)~ | Coefficients of the primitives ($a_{ks}$) |
|
| ~coefficient~ | ~float~ | ~(basis.prim_num)~ | Coefficients of the primitives ($a_{ks}$) |
|
||||||
| ~prim_factor~ | ~float~ | ~(basis.prim_num)~ | Normalization coefficients for the primitives ($f_{ks}$) |
|
| ~prim_factor~ | ~float~ | ~(basis.prim_num)~ | Normalization coefficients for the primitives ($f_{ks}$) |
|
||||||
|
|
||||||
@ -375,8 +377,8 @@ prim_factor =
|
|||||||
| ~overlap~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert q \rangle$ |
|
| ~overlap~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert q \rangle$ |
|
||||||
| ~kinetic~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{T}_e \vert q \rangle$ |
|
| ~kinetic~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{T}_e \vert q \rangle$ |
|
||||||
| ~potential_n_e~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ne}} \vert q \rangle$ |
|
| ~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_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_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)~ | $\langle p \vert \hat{h} \vert q \rangle$ |
|
| ~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")
|
#+CALL: json(data=ao_1e_int, title="ao_1e_int")
|
||||||
@ -460,15 +462,15 @@ prim_factor =
|
|||||||
** One-electron integrals
|
** One-electron integrals
|
||||||
|
|
||||||
The operators as the same as those defined in the
|
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.
|
the basis of molecular orbitals.
|
||||||
|
|
||||||
#+NAME: mo_1e_int
|
#+NAME: mo_1e_int
|
||||||
| ~overlap~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert j \rangle$ |
|
| ~overlap~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert j \rangle$ |
|
||||||
| ~kinetic~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{T}_e \vert j \rangle$ |
|
| ~kinetic~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{T}_e \vert j \rangle$ |
|
||||||
| ~potential_n_e~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{V}_{\text{ne}} \vert j \rangle$ |
|
| ~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_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_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)~ | $\langle i \vert \hat{h} \vert j \rangle$ |
|
| ~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")
|
#+CALL: json(data=mo_1e_int, title="mo_1e_int")
|
||||||
@ -490,7 +492,7 @@ prim_factor =
|
|||||||
** Two-electron integrals
|
** Two-electron integrals
|
||||||
|
|
||||||
The operators as the same as those defined in the
|
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.
|
the basis of molecular orbitals.
|
||||||
|
|
||||||
#+NAME: mo_2e_int
|
#+NAME: mo_2e_int
|
||||||
@ -532,7 +534,7 @@ prim_factor =
|
|||||||
#+end_src
|
#+end_src
|
||||||
:end:
|
:end:
|
||||||
|
|
||||||
* Appendix :noexport:
|
* Appendix
|
||||||
** Python script from table to json
|
** Python script from table to json
|
||||||
|
|
||||||
#+NAME: json
|
#+NAME: json
|
||||||
|
Loading…
Reference in New Issue
Block a user