From 886a3d2162845797041ff988f9c389ab0a9630f3 Mon Sep 17 00:00:00 2001
From: q-posev <posenitskiy@irsamc.ups-tlse.fr>
Date: Wed, 3 Mar 2021 11:49:21 +0100
Subject: [PATCH] working append mode for hdf5

---
 src/trexio_hdf5.org | 64 +++++++++++++++++++++++++++++++++------------
 1 file changed, 48 insertions(+), 16 deletions(-)

diff --git a/src/trexio_hdf5.org b/src/trexio_hdf5.org
index 06e8df2..97d2b91 100644
--- a/src/trexio_hdf5.org
+++ b/src/trexio_hdf5.org
@@ -159,26 +159,59 @@ trexio_exit_code trexio_hdf5_init(trexio_t* file) {
   trexio_hdf5_t* f = (trexio_hdf5_t*) file;
 
   /* If file doesn't exist, create it */
-  int f_ishere = 0;
+  int f_exists = 0;
   struct stat st;
   
-  if (stat(file->file_name, &st) == 0) {
-    printf("%s \n","HDF5 file already exists");
-   // RDWR OR RDONLY ???
-    f->file_id = H5Fopen(file->file_name, H5F_ACC_RDWR, H5P_DEFAULT);
-    f_ishere = 1;
+  if (stat(file->file_name, &st) == 0) f_exists = 1;
+  
+  if (f_exists == 1) {
+
+    switch (file->mode) {
+    case 'r': 
+      // reading the existing file -> open as RDONLY
+      f->file_id = H5Fopen(file->file_name, H5F_ACC_RDONLY, H5P_DEFAULT);
+      break;
+    case 'a': 
+      // appending the existing file -> open as RDWR
+      f->file_id = H5Fopen(file->file_name, H5F_ACC_RDWR, H5P_DEFAULT);
+      break;
+    case 'w': 
+      // writing the existing file -> overwrite it (_TRUNC) [_EXCL | H5F_ACC_DEBUG as an alternative]
+      f->file_id = H5Fcreate(file->file_name, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+      break;
+    }  
+
   } else {
-    f->file_id = H5Fcreate(file->file_name, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
-    f_ishere = 0;
+
+    switch (file->mode) {
+    case 'r': 
+      // reading non-existing file -> error
+      return TREXIO_FAILURE;
+    case 'a': 
+    case 'w': 
+      // appending or writing non-existing file -> create it
+      f->file_id = H5Fcreate(file->file_name, H5F_ACC_EXCL, H5P_DEFAULT, H5P_DEFAULT);
+      break;
+    }  
+
   }  
 
-  /* Create groups in the hdf5 file */
-  if (f_ishere == 0){
-    f->nucleus_group = H5Gcreate(f->file_id, NUCLEUS_GROUP_NAME, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
-    //f->electron_group = H5Gcreate(f->file_id, ELECTRON_GROUP_NAME, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
-  } else { 
-    f->nucleus_group = H5Gopen(f->file_id, NUCLEUS_GROUP_NAME, H5P_DEFAULT);
-    //f->electron_group = H5Gopen(f->file_id, ELECTRON_GROUP_NAME, H5P_DEFAULT);   
+  /* Create or open groups in the hdf5 file assuming that they exist if file exists */    
+  switch (file->mode) {
+    case 'r':
+    case 'a': 
+      if (f_exists == 1) {
+        f->nucleus_group = H5Gopen(f->file_id, NUCLEUS_GROUP_NAME, H5P_DEFAULT);
+      //f->electron_group = H5Gopen(f->file_id, ELECTRON_GROUP_NAME, H5P_DEFAULT);   
+      } else {
+        f->nucleus_group = H5Gcreate(f->file_id, NUCLEUS_GROUP_NAME, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+      //f->electron_group = H5Gcreate(f->file_id, ELECTRON_GROUP_NAME, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+      }
+      break;
+    case 'w':
+      f->nucleus_group = H5Gcreate(f->file_id, NUCLEUS_GROUP_NAME, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+      //f->electron_group = H5Gcreate(f->file_id, ELECTRON_GROUP_NAME, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+      break;
   }
   assert (f->nucleus_group > 0L);
   //assert (f->electron_group > 0L);
@@ -578,7 +611,6 @@ trexio_exit_code trexio_hdf5_write_nucleus_coord(const trexio_t* file, const dou
 }
 
     #+end_src
-** TODO Read/Write the charge attribute
 
 * File suffixes                                                     :noxport: