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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
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SOURCES = \
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$(trexio_h) \
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$(srcdir)/src/trexio.c \
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$(srcdir)/src/trexio_private.h \
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$(srcdir)/src/trexio_s.h \
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$(srcdir)/src/trexio_hdf5.c \
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$(srcdir)/src/trexio_hdf5.h \
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$(srcdir)/src/trexio_text.c \
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$(srcdir)/src/trexio_text.h
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src/trexio.c \
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src/trexio_private.h \
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src/trexio_s.h \
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src/trexio_hdf5.c \
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src/trexio_hdf5.h \
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src/trexio_text.c \
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src/trexio_text.h
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ORG_FILES = \
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src/templates_front/templator_front.org \
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@ -99,6 +99,7 @@ check_PROGRAMS = $(TESTS)
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# specify common options for all tests
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LDADD = src/libtrexio.la
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# in principal, specifying -no-install (see example below) is not mandatory
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# for the tests to compile and pass, but the compilations itself differs
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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 \
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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 = $(HTML_FILES)
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$(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) $(test_trexio_f)
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$(SOURCES): $(trexio_f)
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src/trexio.c: $(trexio_h)
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$(trexio_f): $(ORG_FILES)
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cd $(srcdir)/tools && ./build_trexio.sh
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docs/index.html: $(SOURCES) $(srcdir)/src/README.org
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cd $(srcdir)/tools && ./build_doc.sh
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cppcheck: cppcheck.out
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cat cppcheck.out
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@ -2,7 +2,7 @@
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# Process this file with autoconf to produce a configure script.
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AC_PREREQ([2.69])
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AC_INIT([trexio], [0.2.0], [https://github.com/TREX-CoE/trexio/issues])
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AC_INIT([trexio], [0.3.0], [https://github.com/TREX-CoE/trexio/issues])
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AM_INIT_AUTOMAKE([subdir-objects color-tests parallel-tests silent-rules 1.11])
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AM_MAINTAINER_MODE()
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LT_INIT
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@ -72,7 +72,7 @@ AC_CHECK_HEADERS([fcntl.h inttypes.h stdint.h stdbool.h stdlib.h string.h unistd
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PKG_HDF5=""
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AX_LIB_HDF5([serial])
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AX_LIB_HDF5()
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if test "x${with_hdf5}" = xno; then
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AC_MSG_WARN([
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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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@ -1643,6 +1643,7 @@ trexio_read_$group_dset$_low (trexio_t* const file, char* dset, const uint32_t m
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,*/
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}
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return TREXIO_FAILURE;
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}
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trexio_exit_code
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@ -1803,7 +1804,6 @@ trexio_write_$group_dset$ (trexio_t* const file, const char** dset, const uint32
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FREE(str_compiled);
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return rc;
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}
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#+end_src
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@ -1831,6 +1831,7 @@ trexio_has_$group_dset$ (trexio_t* const file)
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break;
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,*/
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}
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return TREXIO_FAILURE;
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}
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#+end_src
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@ -1968,6 +1969,7 @@ trexio_read_$group_str$ (trexio_t* const file, char* const str, const uint32_t m
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,*/
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}
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return TREXIO_FAILURE;
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}
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#+end_src
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@ -2000,6 +2002,7 @@ trexio_write_$group_str$ (trexio_t* const file, const char* str, const uint32_t
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,*/
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}
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return TREXIO_FAILURE;
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}
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#+end_src
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@ -289,15 +289,6 @@ trexio_hdf5_read_$group_dset$ (trexio_t* const file, $group_dset_dtype$* const $
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const trexio_hdf5_t* f = (const trexio_hdf5_t*) file;
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herr_t status;
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int rrank;
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// get the rank of the dataset in a file
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status = H5LTget_dataset_ndims (f->$group$_group, $GROUP_DSET$_NAME, &rrank);
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if (status < 0) return TREXIO_FAILURE;
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if (rrank != (int) rank) return TREXIO_INVALID_ARG_3;
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// open the dataset to get its dimensions
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hid_t dset_id = H5Dopen(f->$group$_group, $GROUP_DSET$_NAME, H5P_DEFAULT);
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if (dset_id <= 0) return TREXIO_INVALID_ID;
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@ -306,25 +297,34 @@ trexio_hdf5_read_$group_dset$ (trexio_t* const file, $group_dset_dtype$* const $
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hsize_t* ddims = CALLOC( (int) rank, hsize_t);
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if (ddims == NULL) return TREXIO_FAILURE;
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// read dimensions from the existing dataset
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status = H5LDget_dset_dims(dset_id, ddims);
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// get the dataspace of the dataset
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hid_t dspace_id = H5Dget_space(dset_id);
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// get the rank and dimensions of the dataset
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int rrank = H5Sget_simple_extent_dims(dspace_id, ddims, NULL);
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H5Dclose(dset_id);
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if (status < 0) {
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// check that dimensions are consistent
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if (rrank != (int) rank) {
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FREE(ddims);
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return TREXIO_FAILURE;
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H5Sclose(dspace_id);
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H5Dclose(dset_id);
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return TREXIO_INVALID_ARG_3;
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}
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for (uint32_t i=0; i<rank; ++i){
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if (ddims[i] != dims[i]) {
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FREE(ddims);
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H5Sclose(dspace_id);
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H5Dclose(dset_id);
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return TREXIO_INVALID_ARG_4;
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}
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}
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FREE(ddims);
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H5Sclose(dspace_id);
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H5Dclose(dset_id);
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/* High-level H5LT API. No need to deal with dataspaces and datatypes */
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status = H5LTread_dataset(f->$group$_group,
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herr_t status = H5LTread_dataset(f->$group$_group,
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$GROUP_DSET$_NAME,
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H5T_$GROUP_DSET_H5_DTYPE$,
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$group_dset$);
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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 $OLDPWD
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done
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echo
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22
trex.org
22
trex.org
@ -1,5 +1,7 @@
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#+TITLE: TREX Configuration file
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#+STARTUP: latexpreview
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#+SETUPFILE: docs/theme.setup
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All the quantities are saved in atomic units.
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The dimensions of the arrays in the tables below are given in
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@ -208,7 +210,7 @@ arrays are 0-base. Hence, we introduce the ~index~ type which is an
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| ~shell_prim_num~ | ~int~ | ~(basis.num)~ | Number of primitives in the shell ($N_{\text{prim}}$) |
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| ~shell_factor~ | ~float~ | ~(basis.num)~ | Normalization factor of the shell ($\mathcal{N}_s$) |
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| ~shell_prim_index~ | ~index~ | ~(basis.num)~ | Index of the first primitive in the complete list |
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| ~exponent~ | ~float~ | ~(basis.prim_num)~ | Exponents of the primitives ($\gamma_{ks}) |
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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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@ -221,12 +223,12 @@ 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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@ -375,8 +377,8 @@ prim_factor =
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| ~overlap~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert q \rangle$ |
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| ~kinetic~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{T}_e \vert q \rangle$ |
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| ~potential_n_e~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ne}} \vert q \rangle$ |
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| ~ecp_local~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ecp,l} \vert q \rangle$ |
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| ~ecp_non_local~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ecp,nl} \vert q \rangle$ |
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| ~ecp_local~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ecp,l}} \vert q \rangle$ |
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| ~ecp_non_local~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ecp,nl}} \vert q \rangle$ |
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| ~core_hamiltonian~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{h} \vert q \rangle$ |
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#+CALL: json(data=ao_1e_int, title="ao_1e_int")
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@ -460,15 +462,15 @@ 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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| ~potential_n_e~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{V}_{\text{ne}} \vert j \rangle$ |
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| ~ecp_local~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{V}_{\text{ecp,l} \vert j \rangle$ |
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| ~ecp_non_local~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{V}_{\text{ecp,nl} \vert j \rangle$ |
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| ~ecp_local~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{V}_{\text{ecp,l}} \vert j \rangle$ |
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| ~ecp_non_local~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{V}_{\text{ecp,nl}} \vert j \rangle$ |
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| ~core_hamiltonian~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{h} \vert j \rangle$ |
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#+CALL: json(data=mo_1e_int, title="mo_1e_int")
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@ -490,7 +492,7 @@ 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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@ -532,7 +534,7 @@ 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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