Merge pull request #119 from TREX-CoE/state

Improvement on state

CMakeLists.txt

@@ -4,7 +4,7 @@ cmake_minimum_required(VERSION 3.16)
 
 # Initialize the CMake project.
 project(Trexio
-	VERSION 2.3.2
+	VERSION 2.4.0
 	DESCRIPTION "TREX I/O library"
 	LANGUAGES C Fortran
 	)

ChangeLog

@@ -1,6 +1,12 @@
 CHANGES
 =======
 
+2.4
+---
+
+- Added state/energy
+- Made state/id an index instead of an int
+
 2.3
 ---
 

configure.ac

@@ -2,7 +2,7 @@
 # Process this file with autoconf to produce a configure script.
 
 AC_PREREQ([2.69])
-AC_INIT([trexio],[2.3.2],[https://github.com/TREX-CoE/trexio/issues])
+AC_INIT([trexio],[2.4.0],[https://github.com/TREX-CoE/trexio/issues])
 
 AC_CONFIG_SRCDIR([Makefile.in])
 AC_CONFIG_HEADERS([include/config.h])

python/pytrexio/_version.py

@@ -1 +1 @@
-__version__ = "1.3.2"
+__version__ = "2.4.0"

src/templates_front/templator_front.org

@@ -1732,6 +1732,12 @@ def _cp(source: str, destination: str):
     and write it as ~state_id~ attribute.
  ~trexio_get_state~ returns current state of the ~trexio_t~ file handle.
 
+    **Warning:** The ~trexio_set_state~ and ~trexio_get_state~ functions still
+    use the old convention where the ground state was state ~0~. From version 2.4.0,
+    the ~state_id~ variable has changed to ~index~ type, so using the more recent
+ ~trexio_write_state_id~ and ~trexio_read_state_id~ will give different results
+    in Fortran.
+
     input parameters:
  ~file~  -- TREXIO file handle.
  ~state~ -- ~int32_t~ ID of a state (0 for ground state).
@@ -2132,24 +2138,35 @@ trexio_read_$group_num$_64 (trexio_t* const file, $group_num_dtype_double$* cons
   if (num  == NULL) return TREXIO_INVALID_ARG_2;
   if (trexio_has_$group_num$(file) != TREXIO_SUCCESS) return TREXIO_ATTR_MISSING;
 
+  trexio_exit_code rc = TREXIO_GROUP_READ_ERROR;
+    
   switch (file->back_end) {
 
   case TREXIO_TEXT:
-    return trexio_text_read_$group_num$(file, num);
+    rc = trexio_text_read_$group_num$(file, num);
+    break;
 
   case TREXIO_HDF5:
 #ifdef HAVE_HDF5
-    return trexio_hdf5_read_$group_num$(file, num);
+    rc = trexio_hdf5_read_$group_num$(file, num);
 #else
-    return TREXIO_BACK_END_MISSING;
+    rc = TREXIO_BACK_END_MISSING;
 #endif
+    break;
 /*
   case TREXIO_JSON:
-    return trexio_json_read_$group_num$(file, num);
+    rc = trexio_json_read_$group_num$(file, num);
+    break;
 ,*/
   }
 
-  return TREXIO_FAILURE;
+  if (rc != TREXIO_SUCCESS) return rc;
+
+ /* Handle index type */
+  if ($is_index$) {
+    ,*num += ($group_num_dtype_double$) 1;
+  }
+  return rc;
 }
      #+end_src
 
@@ -2161,20 +2178,26 @@ trexio_write_$group_num$_64 (trexio_t* const file, const $group_num_dtype_double
   //if (num <= 0L) return TREXIO_INVALID_NUM; /* this line is uncommented by the generator for dimensioning variables; do NOT remove! */
   if (trexio_has_$group_num$(file) == TREXIO_SUCCESS && file->mode != 'u') return TREXIO_ATTR_ALREADY_EXISTS;
 
+ /* Handle index type */
+  $group_num_dtype_double$ num_write = num;
+  if ($is_index$) {
+    num_write -= ($group_num_dtype_double$) 1;
+  }
+
   switch (file->back_end) {
 
   case TREXIO_TEXT:
-    return trexio_text_write_$group_num$(file, num);
+    return trexio_text_write_$group_num$(file, num_write);
 
   case TREXIO_HDF5:
 #ifdef HAVE_HDF5
-    return trexio_hdf5_write_$group_num$(file, num);
+    return trexio_hdf5_write_$group_num$(file, num_write);
 #else
     return TREXIO_BACK_END_MISSING;
 #endif
 /*
   case TREXIO_JSON:
-    return trexio_json_write_$group_num$(file, num);
+    return trexio_json_write_$group_num$(file, num_write);
 ,*/
   }
 
@@ -2219,6 +2242,12 @@ trexio_read_$group_num$_32 (trexio_t* const file, $group_num_dtype_single$* cons
   if (rc != TREXIO_SUCCESS) return rc;
 
   ,*num = ($group_num_dtype_single$) num_64;
+
+ /* Handle index type */
+  if ($is_index$) {
+    ,*num += ($group_num_dtype_single$) 1;
+  }
+
   return TREXIO_SUCCESS;
 }
      #+end_src
@@ -2232,20 +2261,26 @@ trexio_write_$group_num$_32 (trexio_t* const file, const $group_num_dtype_single
   //if (num <= 0) return TREXIO_INVALID_NUM; /* this line is uncommented by the generator for dimensioning variables; do NOT remove! */
   if (trexio_has_$group_num$(file) == TREXIO_SUCCESS && file->mode != 'u') return TREXIO_ATTR_ALREADY_EXISTS;
 
+ /* Handle index type */
+  $group_num_dtype_single$ num_write = num;
+  if ($is_index$) {
+    num_write -= ($group_num_dtype_single$) 1;
+  }
+
   switch (file->back_end) {
 
   case TREXIO_TEXT:
-    return trexio_text_write_$group_num$(file, ($group_num_dtype_double$) num);
+    return trexio_text_write_$group_num$(file, ($group_num_dtype_double$) num_write);
 
   case TREXIO_HDF5:
 #ifdef HAVE_HDF5
-    return trexio_hdf5_write_$group_num$(file, ($group_num_dtype_double$) num);
+    return trexio_hdf5_write_$group_num$(file, ($group_num_dtype_double$) num_write);
 #else
     return TREXIO_BACK_END_MISSING;
 #endif
 /*
   case TREXIO_JSON:
-    return trexio_json_write_$group_num$(file, ($group_num_dtype_double$) num);
+    return trexio_json_write_$group_num$(file, ($group_num_dtype_double$) num_write);
     break;
 ,*/
   }

tests/io_dset_int_hdf5.c

@@ -17,6 +17,7 @@ static int test_write_dset (const char* file_name, const back_end_t backend) {
   // parameters to be written
   int num = 12;
   int nucl_index[12] = {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11};
+  int state_id = 2;
 
 /*================= START OF TEST ==================*/
 
@@ -32,6 +33,10 @@ static int test_write_dset (const char* file_name, const back_end_t backend) {
   rc = trexio_write_basis_nucleus_index(file, nucl_index);
   assert (rc == TREXIO_SUCCESS);
 
+  // write index attribute in a file
+  rc = trexio_write_state_id(file, state_id);
+  assert (rc == TREXIO_SUCCESS);
+
   // close current session
   rc = trexio_close(file);
   assert (rc == TREXIO_SUCCESS);
@@ -89,8 +94,9 @@ static int test_read_dset (const char* file_name, const back_end_t backend) {
   trexio_exit_code rc;
 
   // parameters to be read
-  int num;
+  int num = 0;
-  int* nucl_index;
+  int* nucl_index = NULL;
+  int state_id = 0;
 
 /*================= START OF TEST ==================*/
 
@@ -103,6 +109,11 @@ static int test_read_dset (const char* file_name, const back_end_t backend) {
   assert (rc == TREXIO_SUCCESS);
   assert (num == 12);
 
+  // read index attribute from the file
+  rc = trexio_read_state_id(file, &state_id);
+  assert (rc == TREXIO_SUCCESS);
+  assert (state_id == 2);
+
   // read numerical dataset from the file
   nucl_index = (int*) calloc(num, sizeof(int));
   rc = trexio_read_basis_nucleus_index(file, nucl_index);

tests/io_dset_int_text.c

@@ -17,6 +17,7 @@ static int test_write_dset (const char* file_name, const back_end_t backend) {
   // parameters to be written
   int num = 12;
   int nucl_index[12] = {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11};
+  int state_id = 2;
 
 /*================= START OF TEST ==================*/
 
@@ -32,6 +33,10 @@ static int test_write_dset (const char* file_name, const back_end_t backend) {
   rc = trexio_write_basis_nucleus_index(file, nucl_index);
   assert (rc == TREXIO_SUCCESS);
 
+  // write index attribute in a file
+  rc = trexio_write_state_id(file, state_id);
+  assert (rc == TREXIO_SUCCESS);
+
   // close current session
   rc = trexio_close(file);
   assert (rc == TREXIO_SUCCESS);
@@ -89,8 +94,9 @@ static int test_read_dset (const char* file_name, const back_end_t backend) {
   trexio_exit_code rc;
 
   // parameters to be read
-  int num;
+  int num = 0;
-  int* nucl_index;
+  int* nucl_index = NULL;
+  int state_id = 0;
 
 /*================= START OF TEST ==================*/
 
@@ -103,6 +109,11 @@ static int test_read_dset (const char* file_name, const back_end_t backend) {
   assert (rc == TREXIO_SUCCESS);
   assert (num == 12);
 
+  // read index attribute from the file
+  rc = trexio_read_state_id(file, &state_id);
+  assert (rc == TREXIO_SUCCESS);
+  assert (state_id == 2);
+
   // read numerical dataset from the file
   nucl_index = (int*) calloc(num, sizeof(int));
   rc = trexio_read_basis_nucleus_index(file, nucl_index);

tests/test_f.f90

@@ -85,6 +85,7 @@ subroutine test_write(file_name, back_end)
 
   integer :: i, j, n_buffers = 5
   integer(8) :: buf_size_sparse, buf_size_det, offset
+  integer   :: state_id
 
   buf_size_sparse = 100/n_buffers
   buf_size_det    = 50/n_buffers
@@ -107,6 +108,7 @@ subroutine test_write(file_name, back_end)
 
   ! parameters to be written
   nucleus_num = 12
+  state_id = 2
   charge = (/ 6., 6., 6., 6., 6., 6., 1., 1., 1., 1., 1., 1.  /)
   coord  = reshape( (/ 0.00000000d0,  1.39250319d0 ,  0.00000000d0 , &
                       -1.20594314d0,  0.69625160d0 ,  0.00000000d0 , &
@@ -182,6 +184,9 @@ subroutine test_write(file_name, back_end)
   rc = trexio_write_basis_nucleus_index(trex_file, basis_nucleus_index)
   call trexio_assert(rc, TREXIO_SUCCESS, 'SUCCESS WRITE INDEX')
 
+  rc = trexio_write_state_id(trex_file, state_id)
+  call trexio_assert(rc, TREXIO_SUCCESS, 'SUCCESS WRITE INDEX TYPE')
+
   ! write ao_num which will be used to determine the optimal size of int indices
   if (trexio_has_ao_num(trex_file) == TREXIO_HAS_NOT) then
     rc = trexio_write_ao_num(trex_file, ao_num)
@@ -302,6 +307,7 @@ subroutine test_read(file_name, back_end)
   integer*8 :: offset_det_data_read = 5
   integer*8 :: determinant_num
   integer   :: int_num
+  integer   :: state_id
 
   ! orbital lists
   integer*4 :: orb_list_up(150)
@@ -312,6 +318,7 @@ subroutine test_read(file_name, back_end)
 
   num = 12
   basis_shell_num = 24
+  state_id = 0
 
   index_sparse_ao_2e_int_eri = 0
   value_sparse_ao_2e_int_eri = 0.0d0
@@ -379,6 +386,15 @@ subroutine test_read(file_name, back_end)
     call exit(-1)
   endif
 
+  rc = trexio_read_state_id(trex_file, state_id)
+  call trexio_assert(rc, TREXIO_SUCCESS)
+  if (state_id == 2) then
+    write(*,*) 'SUCCESS READ INDEX TYPE'
+  else
+    print *, 'FAILURE INDEX TYPE CHECK'
+    call exit(-1)
+  endif
+
 
   rc = trexio_read_nucleus_point_group(trex_file, sym_str, 10)
   call trexio_assert(rc, TREXIO_SUCCESS)

tools/generator_tools.py

@@ -611,8 +611,13 @@ def get_detailed_num_dict (configuration: dict) -> dict:
                     tmp_dict.update(get_dtype_dict(v2[0], 'num'))
                     if v2[0] in ['int', 'dim', 'dim readonly']:
                         tmp_dict['trex_json_int_type'] = v2[0]
+                        tmp_dict['is_index'] = 'false'
+                    elif v2[0] in ['index']:
+                        tmp_dict['trex_json_int_type'] = v2[0]
+                        tmp_dict['is_index'] = 'file->one_based'
                     else:
                         tmp_dict['trex_json_int_type'] = ''
+                        tmp_dict['is_index'] = 'false'
 
                     num_dict[tmp_num] = tmp_dict
 

trex.org

@@ -190,13 +190,14 @@
    The ~id~ and ~current_label~ attributes need to be specified for each file.
 
    #+NAME: state
-   | Variable        | Type  | Dimensions    | Description                                                                                 |
+   | Variable        | Type    | Dimensions    | Description                                                                                 |
-   |-----------------+-------+---------------+---------------------------------------------------------------------------------------------|
+   |-----------------+---------+---------------+---------------------------------------------------------------------------------------------|
-   | ~num~           | ~dim~ |               | Number of states (including the ground state)                                               |
+   | ~num~           | ~dim~   |               | Number of states (including the ground state)                                               |
-   | ~id~            | ~int~ |               | Index of the current state (0 is ground state)                                              |
+   | ~id~            | ~index~ |               | Index of the current state (0 is ground state)                                              |
-   | ~current_label~ | ~str~ |               | Label of the current state                                                                  |
+   | ~energy~        | ~float~ |               | Energy of the current state                                                                 |
-   | ~label~         | ~str~ | ~(state.num)~ | Labels of all states                                                                        |
+   | ~current_label~ | ~str~   |               | Label of the current state                                                                  |
-   | ~file_name~     | ~str~ | ~(state.num)~ | Names of the TREXIO files linked to the current one (i.e. containing data for other states) |
+   | ~label~         | ~str~   | ~(state.num)~ | Labels of all states                                                                        |
+   | ~file_name~     | ~str~   | ~(state.num)~ | Names of the TREXIO files linked to the current one (i.e. containing data for other states) |
 
    #+CALL: json(data=state, title="state")
 
@@ -204,11 +205,12 @@
    :results:
    #+begin_src python :tangle trex.json
        "state": {
-                     "num" : [ "dim", []              ]
+                     "num" : [ "dim"  , []              ]
-         ,            "id" : [ "int", []              ]
+         ,            "id" : [ "index", []              ]
-         , "current_label" : [ "str", []              ]
+         ,        "energy" : [ "float", []              ]
-         ,         "label" : [ "str", [ "state.num" ] ]
+         , "current_label" : [ "str"  , []              ]
-         ,     "file_name" : [ "str", [ "state.num" ] ]
+         ,         "label" : [ "str"  , [ "state.num" ] ]
+         ,     "file_name" : [ "str"  , [ "state.num" ] ]
        } ,
    #+end_src
    :end: