Merge branch 'master' into unit-testing

Makefile.am

@@ -55,13 +55,13 @@ lib_LTLIBRARIES = src/libtrexio.la
 
 SOURCES = \
  $(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
+ 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
@@ -124,18 +125,37 @@ tests_test_f_SOURCES = $(test_trexio_f) tests/test_f.f90
 tests_test_f_LDFLAGS = -no-install
 
 
+HTML_FILES =  docs/trexio.css            \
+              docs/index.html            \
+              docs/Sparse.html           \
+              docs/templator_hdf5.html   \
+              docs/trex.html             \
+              docs/README.html           \
+              docs/templator_front.html  \
+              docs/templator_text.html
+
+htmldir = $(docdir)
+dist_html_DATA = $(HTML_FILES)
+
+$(HTML_FILES): docs/index.html
+
+
 if TREXIO_DEVEL
 
 CLEANFILES += $(SOURCES) $(trexio_f) $(trexio_h)
 
 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
+
 cppcheck: cppcheck.out
 	cat cppcheck.out
 

configure.ac

@@ -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([

src/README.org

@@ -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]]

src/templates_front/templator_front.org

@@ -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
    

src/templates_hdf5/templator_hdf5.org

@@ -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
+  // 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);
-    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,
+  herr_t status = H5LTread_dataset(f->$group$_group,
-			    $GROUP_DSET$_NAME,
+			           $GROUP_DSET$_NAME,
-			    H5T_$GROUP_DSET_H5_DTYPE$,
+			           H5T_$GROUP_DSET_H5_DTYPE$,
-			    $group_dset$);
+			           $group_dset$);
   if (status < 0) return TREXIO_FAILURE;
 
   return TREXIO_SUCCESS;

tools/build_doc.sh

@@ -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

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
@@ -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_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}$) |
 
@@ -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" ] ]
@@ -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_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)~ | $\langle p \vert \hat{h} \vert q \rangle$                |
 
    #+CALL: json(data=ao_1e_int, title="ao_1e_int")
@@ -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_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)~ | $\langle i \vert \hat{h} \vert j \rangle$                |
 
    #+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
@@ -532,7 +534,7 @@ prim_factor =
   #+end_src
   :end:
 
-* Appendix                                                         :noexport:
+* Appendix
 ** Python script from table to json
 
  #+NAME: json