From 6eb2366a6f5603ee7e2df67ff782ccf9f5285d1d Mon Sep 17 00:00:00 2001 From: scemama Date: Wed, 19 Jan 2022 14:14:51 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20TREX-CoE?= =?UTF-8?q?/trexio@51c43fe1ac79ead3e5aeb89f919b5e50363df139=20=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- README.html | 4 +- examples.html | 82 +++--- index.html | 4 +- templator_front.html | 593 ++++++++++++++++++++++++++----------------- templator_hdf5.html | 87 ++++--- templator_text.html | 138 +++++----- trex.html | 116 ++++----- 7 files changed, 589 insertions(+), 435 deletions(-) diff --git a/README.html b/README.html index 46f1b7a..74b7df0 100644 --- a/README.html +++ b/README.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> - + TREXIO source code documentation @@ -347,7 +347,7 @@ and bug reports should be submitted at

Author: TREX-CoE

-

Created: 2022-01-17 Mon 18:16

+

Created: 2022-01-19 Wed 14:14

Validate

diff --git a/examples.html b/examples.html index 9e179db..ad3ff4c 100644 --- a/examples.html +++ b/examples.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> - + Examples @@ -333,24 +333,24 @@ for the JavaScript code in this tag.

Table of Contents

-
-

1 Accessing sparse quantities

+
+

1 Accessing sparse quantities

-
-

1.1 Fortran

+
+

1.1 Fortran

program print_energy
@@ -411,8 +411,8 @@ One needs to read from the TREXIO file:
-
-

1.1.1 Declare Temporary variables

+
+

1.1.1 Declare Temporary variables

integer                       :: i, j, k, l, m
@@ -427,8 +427,8 @@ One needs to read from the TREXIO file:
-
-

1.1.2 Obtain the name of the TREXIO file from the command line, and open it for reading

+
+

1.1.2 Obtain the name of the TREXIO file from the command line, and open it for reading

call getarg(1, filename)
@@ -444,8 +444,8 @@ f = trexio_open (filename, 'r', TREXIO_HDF5
-
-

1.1.3 Read the nuclear repulsion energy

+
+

1.1.3 Read the nuclear repulsion energy

rc = trexio_read_nucleus_repulsion(f, E_nn)
@@ -459,8 +459,8 @@ f = trexio_open (filename, 'r', TREXIO_HDF5
-
-

1.1.4 Read the number of molecular orbitals

+
+

1.1.4 Read the number of molecular orbitals

rc = trexio_read_mo_num(f, n)
@@ -474,8 +474,8 @@ f = trexio_open (filename, 'r', TREXIO_HDF5
-
-

1.1.5 Allocate memory

+
+

1.1.5 Allocate memory

allocate( D(n,n), h0(n,n) )
@@ -487,8 +487,8 @@ W(:,:,:,:) = 0.d0
-
-

1.1.6 Read one-electron quantities

+
+

1.1.6 Read one-electron quantities

rc = trexio_has_mo_1e_int_core_hamiltonian(f)
@@ -520,8 +520,8 @@ rc = trexio_read_rdm_1e(f, D)
-
-

1.1.7 Read two-electron quantities

+
+

1.1.7 Read two-electron quantities

Reading is done with OpenMP. Each thread reads its own buffer, and @@ -537,8 +537,8 @@ to be protected in the critical section when modified.

-
-
1.1.7.1 Electron repulsion integrals
+
+
1.1.7.1 Electron repulsion integrals
rc = trexio_has_mo_2e_int_eri(f)
@@ -587,8 +587,8 @@ icount = BUFSIZE
-
-
1.1.7.2 Reduced density matrix
+
+
1.1.7.2 Reduced density matrix
rc = trexio_has_rdm_2e(f)
@@ -632,8 +632,8 @@ icount = bufsize
-
-

1.1.8 Compute the energy

+
+

1.1.8 Compute the energy

When the orbitals are real, we can use @@ -679,8 +679,8 @@ E = E + E_nn

-
-

1.1.9 Terminate

+
+

1.1.9 Terminate

  deallocate( D, h0, G, W )
@@ -695,7 +695,7 @@ E = E + E_nn

Author: TREX-CoE

-

Created: 2022-01-17 Mon 18:16

+

Created: 2022-01-19 Wed 14:14

Validate

diff --git a/index.html b/index.html index 46f1b7a..74b7df0 100644 --- a/index.html +++ b/index.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> - + TREXIO source code documentation @@ -347,7 +347,7 @@ and bug reports should be submitted at

Author: TREX-CoE

-

Created: 2022-01-17 Mon 18:16

+

Created: 2022-01-19 Wed 14:14

Validate

diff --git a/templator_front.html b/templator_front.html index e3fb8d7..e207a7f 100644 --- a/templator_front.html +++ b/templator_front.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> - + Front end API @@ -333,140 +333,144 @@ for the JavaScript code in this tag.

Table of Contents

+ +
  • 3. Templates for front end -
    • -
  • 3.3. Templates for front end has/read/write a dataset of numerical data +
  • 3.2.1. Introduction
    • +
  • 3.2.2. C templates for front end +
    • +
  • 3.2.3. Fortran templates for front end
    • +
  • 3.2.4. Python templates for front end
    • + + +
  • 3.3. Templates for front end has/read/write a dataset of numerical data -
    • -
  • 3.3.3. Fortran templates for front end
    • -
  • 3.3.4. Python templates for front end
    • - - -
  • 3.4. Templates for front end has/read/write a dataset of sparse data +
  • 3.3.1. Introduction
    • +
  • 3.3.2. C templates for front end +
    • +
  • 3.3.3. Fortran templates for front end
    • +
  • 3.3.4. Python templates for front end
    • + + +
  • 3.4. Templates for front end has/read/write a dataset of sparse data -
    • -
  • 3.4.3. Fortran templates for front end
    • -
  • 3.4.4. Python templates for front end
    • - - -
  • 3.5. Templates for front end has/read/write a dataset of strings +
  • 3.4.1. Introduction
    • +
  • 3.4.2. C templates for front end +
    • +
  • 3.4.3. Fortran templates for front end
    • +
  • 3.4.4. Python templates for front end
    • + + +
  • 3.5. Templates for front end has/read/write a dataset of strings -
    • -
  • 3.5.3. Fortran templates for front end
    • -
  • 3.5.4. Python templates for front end
    • - - -
  • 3.6. Templates for front end has/read/write a single string attribute +
  • 3.5.1. Introduction
    • +
  • 3.5.2. C templates for front end +
    • +
  • 3.5.3. Fortran templates for front end
    • +
  • 3.5.4. Python templates for front end
    • + + +
  • 3.6. Templates for front end has/read/write a single string attribute
    • -
  • 4. Fortran helper/wrapper functions
    • +
  • 4. Fortran helper/wrapper functions
    • -

    -break; -

    -
    -

    1 Coding conventions

    +
    +

    1 Coding conventions

    • integer types will be defined using types given in stdint.h
      • @@ -481,8 +485,8 @@ break;
    -
    -

    1.1 Memory allocation

    +
    +

    1.1 Memory allocation

    Memory allocation of structures can be facilitated by using the @@ -517,8 +521,8 @@ The maximum string size for the filenames is 4096 characters.

    -
    -

    2 Front end

    +
    +

    2 Front end

    All calls to TREXIO are thread-safe. @@ -526,10 +530,10 @@ TREXIO front end is modular, which simplifies implementation of new back ends.

    -
    -

    2.1 Error handling

    +
    +

    2.1 Error handling

    - +
    @@ -770,8 +774,8 @@ and the corresponding message are not propagated to the source code. -
    -

    2.1.1 Decoding errors

    +
    +

    2.1.1 Decoding errors

    The trexio_string_of_error converts an exit code into a string. The @@ -797,8 +801,8 @@ and the corresponding message are not propagated to the source code.

    -
    -
    2.1.1.1 C source code
    +
    +
    2.1.1.1 C source code
    const char*
@@ -909,8 +913,8 @@ and the corresponding message are not propagated to the source code.
    -
    -
    2.1.1.2 Fortran interface
    +
    +
    2.1.1.2 Fortran interface
    interface
@@ -926,8 +930,8 @@ and the corresponding message are not propagated to the source code.
    -
    -
    2.1.1.3 Python interface
    +
    +
    2.1.1.3 Python interface
    class Error(Exception):
@@ -966,8 +970,8 @@ and the corresponding message are not propagated to the source code.
    -
    -

    2.2 Back ends

    +
    +

    2.2 Back ends

    TREXIO has several back ends: @@ -991,8 +995,8 @@ lines that correspond to the TREXIO_JSON back end (not implemented

    -
    -

    2.2.1 C

    +
    +

    2.2.1 C

    typedef int32_t back_end_t;
@@ -1035,8 +1039,8 @@ This is useful due to the fact that HDF5 back end can be disabled at configure s
    -
    -

    2.2.2 Fortran

    +
    +

    2.2.2 Fortran

      integer(trexio_backend), parameter :: TREXIO_HDF5 = 0
@@ -1062,8 +1066,8 @@ The function below is a Fortran interface for the aforementioned C-compatible
    -
    -

    2.2.3 Python

    +
    +

    2.2.3 Python

    # define TREXIO back ends
@@ -1077,8 +1081,8 @@ The function below is a Fortran interface for the aforementioned C-compatible
    -
    -

    2.3 Read/write behavior

    +
    +

    2.3 Read/write behavior

    Every time a reading function is called, the data is read from the @@ -1106,8 +1110,8 @@ concurrent programs, the behavior is not specified.

    -
    -

    2.4 TREXIO file type

    +
    +

    2.4 TREXIO file type

    trexio_s is the the main type for TREXIO files, visible to the users @@ -1141,8 +1145,8 @@ TREXIO files will have as a first argument the TREXIO file handle.

    -
    -

    2.4.1 TREXIOFile Python class

    +
    +

    2.4.1 TREXIOFile Python class

    class File:
@@ -1180,12 +1184,15 @@ TREXIO files will have as a first argument the TREXIO file handle.
         self.back_end = back_end
 
         self.isOpen = False
+        self.exists = False
         if pytrexio_s is None:
-            self.pytrexio_s = open(filename, mode, back_end)
+            self.pytrexio_s = _open(filename, mode, back_end)
             self.isOpen = True
+            self.exists = True
         else:
             self.pytrexio_s = pytrexio_s
             self.isOpen = None
+            self.exists = None
 
         self.info = info
 
@@ -1194,17 +1201,23 @@ TREXIO files will have as a first argument the TREXIO file handle.
         """Close a TREXIO File."""
 
         if self.isOpen:
-            close(self.pytrexio_s)
+            _close(self.pytrexio_s)
             self.isOpen = False
         else:
             raise Exception("TREXIO File object has not been opened.")
 
 
+    def inquire(self):
+        """Inquire whether a TREXIO file exists."""
+
+        self.exists = _inquire(self.filename)
+
+
     def __del__(self):
         """This is a TREXIO File destructor."""
 
         if self.isOpen:
-            close(self.pytrexio_s)
+            _close(self.pytrexio_s)
         elif self.isOpen is None:
             raise Exception("[WIP]: TREXIO file handle provided but what if the file is already closed?")
         else:
@@ -1215,8 +1228,8 @@ TREXIO files will have as a first argument the TREXIO file handle.
    -
    -

    2.5 Polymorphism of the file handle

    +
    +

    2.5 Polymorphism of the file handle

    Polymorphism of the trexio_t type is handled by ensuring that the @@ -1235,8 +1248,8 @@ corresponding types for all back ends can be safely casted to

    -
    -

    2.6 File opening

    +
    +

    2.6 File opening

    trexio_open creates a new TREXIO file or opens existing one. @@ -1275,8 +1288,8 @@ renaming the .txt data files.

    -
    -

    2.6.1 C

    +
    +

    2.6.1 C

    trexio_t*
@@ -1463,8 +1476,8 @@ renaming the .txt data files.
    -
    -

    2.6.2 Fortran

    +
    +

    2.6.2 Fortran

    interface
@@ -1482,11 +1495,11 @@ renaming the .txt data files.
    -
    -

    2.6.3 Python

    +
    +

    2.6.3 Python

    -
    def open(file_name: str, mode: str, back_end: int):
+
    def _open(file_name: str, mode: str, back_end: int):
     """Create TREXIO file or open existing one.
 
     Parameters:
@@ -1531,8 +1544,8 @@ renaming the .txt data files.
    -
    -

    2.6.4 Zero-based versus one-based arrays of indices

    +
    +

    2.6.4 Zero-based versus one-based arrays of indices

    Because arrays are zero-based in Fortran, we need to set a flag to @@ -1565,8 +1578,8 @@ know if we need to shift by 1 arrays of indices.

    -
    -

    2.7 File closing

    +
    +

    2.7 File closing

    trexio_close closes an existing trexio_t file. @@ -1583,8 +1596,8 @@ output:

    -
    -

    2.7.1 C

    +
    +

    2.7.1 C

    trexio_exit_code
@@ -1665,8 +1678,8 @@ output:
    -
    -

    2.7.2 Fortran

    +
    +

    2.7.2 Fortran

    interface
@@ -1680,11 +1693,11 @@ output:
    -
    -

    2.7.3 Python

    +
    +

    2.7.3 Python

    -
    def close(trexio_file):
+
    def _close(trexio_file):
     """Close TREXIO file.
 
     Parameter is a ~trexio_file~ object that has been created by a call to ~open~ function.
@@ -1701,14 +1714,104 @@ output:
    + +
    +

    2.8 File existence

    +
    +

    +trexio_inquire check whether TREXIO file exists. +

    + +

    +input parameters: + file_name - string containing file name +

    + +

    +output: + trexio_exit_code exit code. +

    -
    -

    3 Templates for front end

    +
    +

    2.8.1 C

    +
    +
    +
    trexio_exit_code
+trexio_inquire (const char* file_name)
+{
+
+  if (file_name == NULL || file_name[0] == '\0') return TREXIO_INVALID_ARG_1;
+
+  /* First check if the TREXIO file exists and if it is a directory */
+  trexio_exit_code rc_text = trexio_text_inquire(file_name);
+
+#ifdef HAVE_HDF5
+  /* FILE_ERROR here means that the file exists but it is not a directory -> check with HDF5 */
+  if (rc_text == TREXIO_FILE_ERROR) {
+    trexio_exit_code rc_hdf5 = trexio_hdf5_inquire(file_name);
+    return rc_hdf5;
+  /* If rc_text is TREXIO_SUCCESS -> file is a TREXIO directory; TREXIO_FAILURE -> file/directory does not exist */
+  } else {
+    return rc_text;
+  }
+#else
+  return rc_text;
+#endif
+}
+
    +
    +
    +
    + +
    +

    2.8.2 Fortran

    +
    +

    +The function below is a C binding. +The front end Fortran function for trexio_inquire can be found in the Fortran helper/wrapper functions. +

    + +
    +
    interface
+   integer function trexio_inquire_c (filename) bind(C, name="trexio_inquire")
+     use, intrinsic :: iso_c_binding
+     import
+     character(kind=c_char), dimension(*)       :: filename
+   end function trexio_inquire_c
+end interface
+
    +
    +
    +
    + +
    +

    2.8.3 Python

    +
    +
    +
    def _inquire(file_name: str) -> bool:
+    """Check whether ~file_name~ TREXIO file exists.
+    """
+    rc = pytr.trexio_inquire(trexio_file_name)
+    if rc == TREXIO_SUCCESS:
+        return True
+    elif rc == TREXIO_FAILURE:
+        return False
+    else:
+        raise Error(rc)
+
    +
    +
    +
    +
    +
    + +
    +

    3 Templates for front end

    -
    -

    3.1 Description

    +
    +

    3.1 Description

    Consider the following block of trex.json: @@ -1929,12 +2032,12 @@ value will result in TREXIO_INVALID_ARG_2 exit code.

    -
    -

    3.2 Templates for front end has/read/write a single numerical attribute

    +
    +

    3.2 Templates for front end has/read/write a single numerical attribute

    -
    -

    3.2.1 Introduction

    +
    +

    3.2.1 Introduction

    This section concerns API calls related to numerical attributes, @@ -2005,8 +2108,8 @@ namely single value of int/float types.

    -
    -

    3.2.2 C templates for front end

    +
    +

    3.2.2 C templates for front end

    The C templates that correspond to each of the abovementioned @@ -2020,12 +2123,12 @@ precision (see Table above).

    -
    -
    3.2.2.1 Function declarations
    +
    +
    3.2.2.1 Function declarations
    -
    -
    3.2.2.2 Source code for double precision functions
    +
    +
    3.2.2.2 Source code for double precision functions
    trexio_exit_code
@@ -2088,8 +2191,8 @@ precision (see Table above).
    -
    -
    3.2.2.3 Source code for single precision functions
    +
    +
    3.2.2.3 Source code for single precision functions
    trexio_exit_code
@@ -2164,8 +2267,8 @@ precision (see Table above).
    -
    -
    3.2.2.4 Source code for default functions
    +
    +
    3.2.2.4 Source code for default functions
    trexio_exit_code
@@ -2220,8 +2323,8 @@ precision (see Table above).
    -
    -

    3.2.3 Fortran templates for front end

    +
    +

    3.2.3 Fortran templates for front end

    The Fortran templates that provide an access to the C API calls from Fortran. @@ -2306,8 +2409,8 @@ These templates are based on the use of iso_c_binding. Pointers hav

    -
    -

    3.2.4 Python templates for front end

    +
    +

    3.2.4 Python templates for front end

    def write_$group_num$(trexio_file, num_w: $group_num_py_dtype$) -> None:
@@ -2392,12 +2495,12 @@ These templates are based on the use of iso_c_binding. Pointers hav
    -
    -

    3.3 Templates for front end has/read/write a dataset of numerical data

    +
    +

    3.3 Templates for front end has/read/write a dataset of numerical data

    -
    -

    3.3.1 Introduction

    +
    +

    3.3.1 Introduction

    This section concerns API calls related to datasets. @@ -2479,8 +2582,8 @@ This section concerns API calls related to datasets.

    -
    -

    3.3.2 C templates for front end

    +
    +

    3.3.2 C templates for front end

    The C templates that correspond to each of the abovementioned functions can be found below. @@ -2491,12 +2594,12 @@ The basic (non-suffixed) API call on datasets deals with double precision (see T

    -
    -
    3.3.2.1 Function declarations
    +
    +
    3.3.2.1 Function declarations
    -
    -
    3.3.2.2 Source code for double precision functions
    +
    +
    3.3.2.2 Source code for double precision functions
    trexio_exit_code
@@ -2610,7 +2713,7 @@ The basic (non-suffixed) API call on datasets deals with double precision (see T
 
     case TREXIO_HDF5:
 #ifdef HAVE_HDF5
-      rc = trexio_hdf5_write_$group_dset$(file, 
+      rc = trexio_hdf5_write_$group_dset$(file,
                                           (const $group_dset_dtype_double$*) $group_dset$_p,
                                           rank, dims);
       break;
@@ -2659,8 +2762,8 @@ The basic (non-suffixed) API call on datasets deals with double precision (see T
    -
    -
    3.3.2.3 Source code for single precision functions
    +
    +
    3.3.2.3 Source code for single precision functions
    trexio_exit_code
@@ -2811,11 +2914,11 @@ The basic (non-suffixed) API call on datasets deals with double precision (see T
    -
    -
    3.3.2.4 Source code for memory-safe functions
    +
    +
    3.3.2.4 Source code for memory-safe functions
    -
    trexio_exit_code rc;
+
    trexio_exit_code rc;
 int64_t $group_dset_dim$ = 0;
 
 /* Error handling for this call is added by the generator */
@@ -2971,8 +3074,8 @@ rc = trexio_read_$group_dset_dim$_64(file, &($group_dset_dim$));
    -
    -
    3.3.2.5 Source code for default functions
    +
    +
    3.3.2.5 Source code for default functions
    trexio_exit_code
@@ -3047,8 +3150,8 @@ rc = trexio_read_$group_dset_dim$_64(file, &($group_dset_dim$));
    -
    -

    3.3.3 Fortran templates for front end

    +
    +

    3.3.3 Fortran templates for front end

    The Fortran templates that provide an access to the C API calls from Fortran. @@ -3133,8 +3236,8 @@ These templates are based on the use of iso_c_binding. Pointers hav

    -
    -

    3.3.4 Python templates for front end

    +
    +

    3.3.4 Python templates for front end

    def write_$group_dset$(trexio_file, dset_w) -> None:
@@ -3329,12 +3432,12 @@ These templates are based on the use of iso_c_binding. Pointers hav
    -
    -

    3.4 Templates for front end has/read/write a dataset of sparse data

    +
    +

    3.4 Templates for front end has/read/write a dataset of sparse data

    -
    -

    3.4.1 Introduction

    +
    +

    3.4.1 Introduction

    Sparse data structures are used typically for large tensors such as @@ -3495,16 +3598,16 @@ This section concerns API calls related to sparse data structures.

    -
    -

    3.4.2 C templates for front end

    +
    +

    3.4.2 C templates for front end

    -
    -
    3.4.2.1 Function declarations
    +
    +
    3.4.2.1 Function declarations
    -
    -
    3.4.2.2 Source code for default functions
    +
    +
    3.4.2.2 Source code for default functions
    trexio_exit_code trexio_read_safe_$group_dset$(trexio_t* const file,
@@ -3779,8 +3882,8 @@ This section concerns API calls related to sparse data structures.
    -
    -

    3.4.3 Fortran templates for front end

    +
    +

    3.4.3 Fortran templates for front end

    The Fortran templates that provide an access to the C API calls from Fortran. @@ -3875,8 +3978,8 @@ These templates are based on the use of iso_c_binding. Pointers hav

    -
    -

    3.4.4 Python templates for front end

    +
    +

    3.4.4 Python templates for front end

    def write_$group_dset$(trexio_file: File, offset_file: int, buffer_size: int, indices: list, values: list) -> None:
@@ -4097,12 +4200,12 @@ These templates are based on the use of iso_c_binding. Pointers hav
    -
    -

    3.5 Templates for front end has/read/write a dataset of strings

    +
    +

    3.5 Templates for front end has/read/write a dataset of strings

    -
    -

    3.5.1 Introduction

    +
    +

    3.5.1 Introduction

    This section concerns API calls related to datasets of strings. @@ -4142,8 +4245,8 @@ This section concerns API calls related to datasets of strings.

    -
    -

    3.5.2 C templates for front end

    +
    +

    3.5.2 C templates for front end

    First parameter is the TREXIO file handle. Second parameter is the variable to be written/read @@ -4151,12 +4254,12 @@ to/from the TREXIO file (except for trexio_has_ functi

    -
    -
    3.5.2.1 Function declarations
    +
    +
    3.5.2.1 Function declarations
    -
    -
    3.5.2.2 Source code for default functions
    +
    +
    3.5.2.2 Source code for default functions
    trexio_exit_code
@@ -4406,8 +4509,8 @@ to/from the TREXIO file (except for trexio_has_ functi
    -
    -

    3.5.3 Fortran templates for front end

    +
    +

    3.5.3 Fortran templates for front end

    The Fortran templates that provide an access to the C API calls from Fortran. @@ -4503,8 +4606,8 @@ These templates are based on the use of iso_c_binding. Pointers hav

    -
    -

    3.5.4 Python templates for front end

    +
    +

    3.5.4 Python templates for front end

    def write_$group_dset$(trexio_file, dset_w: list) -> None:
@@ -4620,12 +4723,12 @@ These templates are based on the use of iso_c_binding. Pointers hav
    -
    -

    3.6 Templates for front end has/read/write a single string attribute

    +
    +

    3.6 Templates for front end has/read/write a single string attribute

    -
    -

    3.6.1 Introduction

    +
    +

    3.6.1 Introduction

    This section concerns API calls related to string attributes. @@ -4665,16 +4768,16 @@ This section concerns API calls related to string attributes.

    -
    -

    3.6.2 C templates for front end

    +
    +

    3.6.2 C templates for front end

    -
    -
    3.6.2.1 Function declarations
    +
    +
    3.6.2.1 Function declarations
    -
    -
    3.6.2.2 Source code for default functions
    +
    +
    3.6.2.2 Source code for default functions
    trexio_exit_code
@@ -4778,8 +4881,8 @@ This section concerns API calls related to string attributes.
    -
    -

    3.6.3 Fortran templates for front end

    +
    +

    3.6.3 Fortran templates for front end

    The Fortran templates that provide an access to the C API calls from Fortran. @@ -4856,8 +4959,8 @@ These templates are based on the use of iso_c_binding. Pointers hav

    -
    -

    3.6.4 Python templates for front end

    +
    +

    3.6.4 Python templates for front end

    def write_$group_str$(trexio_file, str_w: str) -> None:
@@ -4947,8 +5050,8 @@ These templates are based on the use of iso_c_binding. Pointers hav
    -
    -

    4 Fortran helper/wrapper functions

    +
    +

    4 Fortran helper/wrapper functions

    The function below adapts the original C-based trexio_open for Fortran. @@ -4983,6 +5086,26 @@ Note, that Fortran interface calls the main TREXIO API, which is wr

    +

    +The function below adapts the original C-based trexio_inquire for Fortran. +This is needed due to the same reasons as for trexio_open function. +Note, that Fortran interface calls the main TREXIO API, which is written in C. +

    + +
    +
    integer function trexio_inquire (filename)
+  use, intrinsic :: iso_c_binding
+  implicit none
+  character(len=*), intent(in)        :: filename
+  character(len=len_trim(filename)+1) :: filename_c
+
+  filename_c = trim(filename) // c_null_char
+  trexio_inquire = trexio_inquire_c(filename_c)
+end function trexio_inquire
+
+
    +
    +

    The subroutine below transforms an array of Fortran strings into one big string using TREXIO_DELIM symbol as a delimeter and adds NULL character in the end in order to properly pass the desired string to @@ -5083,7 +5206,7 @@ two code are identical, i.e. if the assert statement pass.

    Author: TREX-CoE

    -

    Created: 2022-01-17 Mon 18:15

    +

    Created: 2022-01-19 Wed 14:14

    Validate

    diff --git a/templator_hdf5.html b/templator_hdf5.html index 8f2a1b3..780ce3e 100644 --- a/templator_hdf5.html +++ b/templator_hdf5.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> - + HDF5 back end @@ -311,29 +311,29 @@ for the JavaScript code in this tag.

    Table of Contents

    -
    -

    1 HDF5 back end

    +
    +

    1 HDF5 back end

    -
    -

    1.1 Template for HDF5 definitions

    +
    +

    1.1 Template for HDF5 definitions

    #define $GROUP$_GROUP_NAME          "$group$"
@@ -345,8 +345,8 @@ for the JavaScript code in this tag.
    -
    -

    1.2 Template for HDF5 structures

    +
    +

    1.2 Template for HDF5 structures

    typedef struct trexio_hdf5_s {
@@ -359,10 +359,26 @@ for the JavaScript code in this tag.
    - -
    -

    1.3 Template for HDF5 init/deinit

    +
    +

    1.3 Template for HDF5 init/deinit

    +
    +
    trexio_exit_code
+trexio_hdf5_inquire(const char* file_name)
+{
+  /* H5Fis_hdf5 determines whether file is in HDF5 format */
+  htri_t rc = H5Fis_hdf5(file_name);
+  if (rc > 0 ) {
+    return TREXIO_SUCCESS;    //exists and HDF5
+  } else if (rc == 0) {
+    return TREXIO_FILE_ERROR; //exists but not HDF5
+  } else {
+    return TREXIO_FAILURE;    //does not exist or function fails
+  }
+}
+
    +
    + 
    trexio_exit_code
 trexio_hdf5_init (trexio_t* const file)
@@ -420,8 +436,11 @@ for the JavaScript code in this tag.
 
   return TREXIO_SUCCESS;
 }
+
    +
    -trexio_exit_code +
    +
    trexio_exit_code
 trexio_hdf5_deinit (trexio_t* const file)
 {
 
@@ -441,8 +460,8 @@ for the JavaScript code in this tag.
    -
    -

    1.4 Template for HDF5 has/read/write the numerical attribute

    +
    +

    1.4 Template for HDF5 has/read/write the numerical attribute

    trexio_exit_code
@@ -536,8 +555,8 @@ for the JavaScript code in this tag.
    -
    -

    1.5 Template for HDF5 has/read/write the dataset of numerical data

    +
    +

    1.5 Template for HDF5 has/read/write the dataset of numerical data

    trexio_exit_code
@@ -659,8 +678,8 @@ for the JavaScript code in this tag.
    -
    -

    1.6 Template for HDF5 has/read/write the dataset of sparse data

    +
    +

    1.6 Template for HDF5 has/read/write the dataset of sparse data

    Sparse data is stored using extensible datasets of HDF5. Extensibility is required @@ -861,8 +880,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s

    -
    -

    1.7 Template for HDF5 has/read/write the dataset of strings

    +
    +

    1.7 Template for HDF5 has/read/write the dataset of strings

    trexio_exit_code
@@ -1066,8 +1085,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
    -
    -

    1.8 Template for HDF5 has/read/write the string attribute

    +
    +

    1.8 Template for HDF5 has/read/write the string attribute

    trexio_exit_code
@@ -1189,8 +1208,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
    -
    -

    1.9 Helper functions

    +
    +

    1.9 Helper functions

    trexio_exit_code
@@ -1452,7 +1471,7 @@ due to the fact that the sparse data will be written in chunks of user-defined s

    Author: TREX-CoE

    -

    Created: 2022-01-17 Mon 18:15

    +

    Created: 2022-01-19 Wed 14:14

    Validate

    diff --git a/templator_text.html b/templator_text.html index 084bd2f..4bac26b 100644 --- a/templator_text.html +++ b/templator_text.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> - + TEXT back end @@ -311,28 +311,28 @@ for the JavaScript code in this tag.

    Table of Contents

    -
    -

    1 TEXT back end

    +
    +

    1 TEXT back end

    The "file" produced by the text back end is a directory with one @@ -353,8 +353,8 @@ The file is written when closed, or when the flush function is called.

    -
    -

    1.1 Template for group-related structures in text back end

    +
    +

    1.1 Template for group-related structures in text back end

    typedef struct $group$_s {
@@ -373,8 +373,8 @@ The file is written when closed, or when the flush function is called.
    -
    -

    1.2 Template for general structure in text back end

    +
    +

    1.2 Template for general structure in text back end

    typedef struct trexio_text_s {
@@ -387,9 +387,33 @@ The file is written when closed, or when the flush function is called.
    -
    -

    1.3 Initialize function (constant part)

    +
    +

    1.3 Initialize function (constant part)

    +
    +
    trexio_exit_code
+trexio_text_inquire (const char* file_name)
+{
+  /* Check if the file with "file_name" exists and that it is a directory */
+  struct stat st;
+
+  int rc = stat(file_name, &st);
+
+  bool file_exists = rc == 0;
+
+  if (file_exists) {
+
+    bool is_a_directory = st.st_mode & S_IFDIR;
+    if (!is_a_directory) return TREXIO_FILE_ERROR;
+
+    return TREXIO_SUCCESS;
+  } else {
+    return TREXIO_FAILURE;
+  }
+}
+
    +
    + 
    trexio_exit_code
 trexio_text_init (trexio_t* const file)
@@ -402,30 +426,19 @@ The file is written when closed, or when the flush function is called.
   /* Put all pointers to NULL but leave parent untouched */
   memset(&(f->parent)+1,0,sizeof(trexio_text_t)-sizeof(trexio_t));
 
-  /* If directory doesn't exist, create it in write mode */
-  struct stat st;
+  /* Check if directory exists */
+  trexio_exit_code rc;
+  rc = trexio_text_inquire(file->file_name);
+  /* TREXIO file exists but is not  a directory */
+  if (rc == TREXIO_FILE_ERROR) return rc;
+  /* If directory does not exist - create it in write mode */
+  if (rc == TREXIO_FAILURE) {
 
-  int rc = stat(file->file_name, &st);
+    if (file->mode == 'r') return TREXIO_READONLY;
 
-  bool file_exists = rc == 0;
+    int rc_dir = mkdir(file->file_name, 0777);
+    if (rc_dir != 0) return TREXIO_ERRNO;
 
-  if (file_exists) {
-
-    bool is_a_directory = st.st_mode & S_IFDIR;
-    if (!is_a_directory) {
-      return TREXIO_FILE_ERROR;
-    }
-
-  } else {
-
-    if (file->mode == 'r') {
-      return TREXIO_READONLY;
-    }
-
-    rc = mkdir(file->file_name, 0777);
-    if (rc != 0) {
-      return TREXIO_ERRNO;
-    }
   }
 
   /* Create the lock file in the directory */
@@ -491,7 +504,6 @@ The file is written when closed, or when the flush function is called.
    - 
    trexio_exit_code
 trexio_text_unlock (trexio_t* const file)
@@ -519,8 +531,8 @@ The file is written when closed, or when the flush function is called.
    -
    -

    1.4 Deinitialize function (templated part)

    +
    +

    1.4 Deinitialize function (templated part)

    trexio_exit_code
@@ -542,8 +554,8 @@ The file is written when closed, or when the flush function is called.
    -
    -

    1.5 Template for text read struct

    +
    +

    1.5 Template for text read struct

    $group$_t*
@@ -835,8 +847,8 @@ trexio_text_read_$group$ (trexio_text_t*
    -
    -

    1.6 Template for text flush struct

    +
    +

    1.6 Template for text flush struct

    trexio_exit_code
@@ -901,8 +913,8 @@ trexio_text_read_$group$ (trexio_text_t*
    -
    -

    1.7 Template for text free memory

    +
    +

    1.7 Template for text free memory

    Memory is allocated when reading. The following function frees memory. @@ -947,8 +959,8 @@ Memory is allocated when reading. The following function frees memory.

    -
    -

    1.8 Template for has/read/write the numerical attribute

    +
    +

    1.8 Template for has/read/write the numerical attribute

    trexio_exit_code
@@ -1011,8 +1023,8 @@ Memory is allocated when reading. The following function frees memory.
    -
    -

    1.9 Template for has/read/write the dataset of numerical data

    +
    +

    1.9 Template for has/read/write the dataset of numerical data

    The group_dset array is assumed allocated with the appropriate size. @@ -1108,8 +1120,8 @@ The group_dset array is assumed allocated with the appropriate size

    -
    -

    1.10 Template for has/read/write the dataset of strings

    +
    +

    1.10 Template for has/read/write the dataset of strings

    The group_dset array is assumed allocated with the appropriate size. @@ -1210,8 +1222,8 @@ The group_dset array is assumed allocated with the appropriate size

    -
    -

    1.11 Template for has/read/write the string attribute

    +
    +

    1.11 Template for has/read/write the string attribute

    trexio_exit_code
@@ -1285,8 +1297,8 @@ The group_dset array is assumed allocated with the appropriate size
    -
    -

    1.12 Template for has/read/write the dataset of sparse data

    +
    +

    1.12 Template for has/read/write the dataset of sparse data

    Each sparse array is stored in a separate .txt file due to the fact that sparse I/O has to be decoupled @@ -1563,7 +1575,7 @@ User provides indices and values of the sparse array as two separate variables.

    Author: TREX-CoE

    -

    Created: 2022-01-17 Mon 18:15

    +

    Created: 2022-01-19 Wed 14:14

    Validate

    diff --git a/trex.html b/trex.html index 6211a1d..f2b2377 100644 --- a/trex.html +++ b/trex.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> - + TREX Configuration file @@ -333,33 +333,33 @@ for the JavaScript code in this tag.

    Table of Contents

    @@ -409,8 +409,8 @@ fetched using multiple function calls to perform I/O on buffers.

    -
    -

    1 Metadata (metadata group)

    +
    +

    1 Metadata (metadata group)

    As we expect our files to be archived in open-data repositories, we @@ -420,7 +420,7 @@ which have participated to the creation of the file, a list of authors of the file, and a textual description.

    -
    +
    @@ -487,15 +487,15 @@ authors of the file, and a textual description. -
    -

    2 Electron (electron group)

    +
    +

    2 Electron (electron group)

    We consider wave functions expressed in the spin-free formalism, where the number of ↑ and ↓ electrons is fixed.

    -
    +
    @@ -534,15 +534,15 @@ the number of ↑ and ↓ electrons is fixed. -
    -

    3 Nucleus (nucleus group)

    +
    +

    3 Nucleus (nucleus group)

    The nuclei are considered as fixed point charges. Coordinates are given in Cartesian \((x,y,z)\) format.

    -
    +
    @@ -609,8 +609,8 @@ given in Cartesian \((x,y,z)\) format. -
    -

    4 Effective core potentials (ecp group)

    +
    +

    4 Effective core potentials (ecp group)

    An effective core potential (ECP) \(V_A^{\text{ECP}}\) replacing the @@ -643,7 +643,7 @@ The functions \(V_{A\ell}\) are parameterized as: See http://dx.doi.org/10.1063/1.4984046 or https://doi.org/10.1063/1.5121006 for more info.

    -
    +
    @@ -741,8 +741,8 @@ The latter causes issues when written before ang_mom in the TREXIO

    -
    -

    4.1 Example

    +
    +

    4.1 Example

    For example, consider H2 molecule with the following @@ -805,8 +805,8 @@ power = [

    -
    -

    5 Basis set (basis group)

    +
    +

    5 Basis set (basis group)

    We consider here basis functions centered on nuclei. Hence, we enable @@ -859,7 +859,7 @@ If the the basis function is not considered normalized, \(\mathcal{N}_s=1\). All the basis set parameters are stored in one-dimensional arrays:

    -
    +
    @@ -953,8 +953,8 @@ All the basis set parameters are stored in one-dimensional arrays:
    -
    -

    5.1 Example

    +
    +

    5.1 Example

    For example, consider H2 with the following basis set (in GAMESS @@ -1032,8 +1032,8 @@ prim_factor =

    -
    -

    6 Atomic orbitals (ao group)

    +
    +

    6 Atomic orbitals (ao group)

    Going from the atomic basis set to AOs implies a systematic @@ -1085,13 +1085,13 @@ shell, as in the GAMESS convention where

    In such a case, one should set the normalization of the shell (in -the Basis set section) to \(\mathcal{N}_{z^2}\), which is the +the Basis set section) to \(\mathcal{N}_{z^2}\), which is the normalization factor of the atomic orbitals in spherical coordinates. The normalization factor of the \(xy\) function which should be introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).

    - +
    @@ -1143,8 +1143,8 @@ introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
    -
    -

    6.1 One-electron integrals (ao_1e_int group)

    +
    +

    6.1 One-electron integrals (ao_1e_int group)

    • \[ \hat{V}_{\text{ne}} = \sum_{A=1}^{N_\text{nucl}} @@ -1162,7 +1162,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are over atomic orbitals.

      - +
      @@ -1229,8 +1229,8 @@ over atomic orbitals. -
      -

      6.2 Two-electron integrals (ao_2e_int group)

      +
      +

      6.2 Two-electron integrals (ao_2e_int group)

      The two-electron integrals for a two-electron operator \(\hat{O}\) are @@ -1251,7 +1251,7 @@ notation. \mathbf{r}_j \vert)}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron long range potential -

      +
      @@ -1291,10 +1291,10 @@ notation. -
      -

      7 Molecular orbitals (mo group)

      +
      +

      7 Molecular orbitals (mo group)

      -
      +
      @@ -1360,8 +1360,8 @@ notation.
    -
    -

    7.1 One-electron integrals (mo_1e_int group)

    +
    +

    7.1 One-electron integrals (mo_1e_int group)

    The operators as the same as those defined in the @@ -1369,7 +1369,7 @@ The operators as the same as those defined in the the basis of molecular orbitals.

    - +
    @@ -1436,8 +1436,8 @@ the basis of molecular orbitals. -
    -

    7.2 Two-electron integrals (mo_2e_int group)

    +
    +

    7.2 Two-electron integrals (mo_2e_int group)

    The operators as the same as those defined in the @@ -1445,7 +1445,7 @@ The operators as the same as those defined in the the basis of molecular orbitals.

    -
    +
    @@ -1485,11 +1485,11 @@ the basis of molecular orbitals. -
    -

    8 TODO Slater determinants

    +
    +

    8 TODO Slater determinants

    -
    -

    9 Reduced density matrices (rdm group)

    +
    +

    9 Reduced density matrices (rdm group)

    The reduced density matrices are defined in the basis of molecular @@ -1542,7 +1542,7 @@ The total energy can be computed as: \]

    -
    +
    @@ -1625,7 +1625,7 @@ The total energy can be computed as:

    Author: TREX-CoE

    -

    Created: 2022-01-17 Mon 18:16

    +

    Created: 2022-01-19 Wed 14:14

    Validate