diff --git a/README.html b/README.html index e979e39..171f712 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: 2022-04-13 Wed 14:40

+

Created: 2022-04-14 Thu 14:11

Validate

diff --git a/examples.html b/examples.html index 1f990b8..ede8889 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: 2022-04-13 Wed 14:40

+

Created: 2022-04-14 Thu 14:11

Validate

diff --git a/index.html b/index.html index e979e39..171f712 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: 2022-04-13 Wed 14:40

+

Created: 2022-04-14 Thu 14:11

Validate

diff --git a/templator_front.html b/templator_front.html index 16a0680..fd09eec 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 @@ -333,160 +333,160 @@ for the JavaScript code in this tag.

Table of Contents

-
-

1 Coding conventions

+
+

1 Coding conventions

  • integer types will be defined using types given in stdint.h
    • @@ -501,8 +501,8 @@ for the JavaScript code in this tag.
-
-

1.1 Memory allocation

+
+

1.1 Memory allocation

Memory allocation of structures can be facilitated by using the @@ -537,8 +537,8 @@ The maximum string size for the filenames is 4096 characters.

-
-

2 Front end

+
+

2 Front end

All calls to TREXIO are thread-safe. @@ -546,10 +546,10 @@ TREXIO front end is modular, which simplifies implementation of new back ends.

-
-

2.1 Error handling

+
+

2.1 Error handling

- +
@@ -752,6 +752,12 @@ TREXIO front end is modular, which simplifies implementation of new back ends. + + + + + +
32 'Unsafe operation in safe mode'
TREXIO_INVALID_ELECTRON_NUM33'Inconsistent value of electron num'
@@ -796,8 +802,8 @@ 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 @@ -823,8 +829,8 @@ 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*
@@ -924,6 +930,9 @@ and the corresponding message are not propagated to the source code.
   case TREXIO_SAFE_MODE:
     return "Unsafe operation in safe mode";
     break;
+  case TREXIO_INVALID_ELECTRON_NUM:
+    return "Inconsistent value of electron num";
+    break;
   }
   return "Unknown error";
 }
@@ -938,8 +947,8 @@ and the corresponding message are not propagated to the source code.
-
-
2.1.1.2 Fortran interface
+
+
2.1.1.2 Fortran interface
interface
@@ -955,8 +964,8 @@ 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):
@@ -995,8 +1004,8 @@ and the corresponding message are not propagated to the source code.
-
-

2.2 Back ends

+
+

2.2 Back ends

TREXIO has several back ends: @@ -1025,8 +1034,8 @@ 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;
@@ -1075,8 +1084,8 @@ 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_back_end_t), parameter :: TREXIO_HDF5 = 0
@@ -1117,8 +1126,8 @@ consistency, in version 2.2 it was renamed trexio_has_back_end.
-
-

2.2.3 Python

+
+

2.2.3 Python

# define TREXIO back ends
@@ -1133,8 +1142,8 @@ consistency, in version 2.2 it was renamed trexio_has_back_end.
-
-

2.3 Read/write behavior

+
+

2.3 Read/write behavior

Every time a reading function is called, the data is read from the @@ -1163,8 +1172,8 @@ 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 @@ -1198,8 +1207,8 @@ 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:
@@ -1288,8 +1297,8 @@ 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 @@ -1308,8 +1317,8 @@ 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 the existing one. @@ -1365,8 +1374,8 @@ renaming the .txt data files.

-
-

2.6.1 C

+
+

2.6.1 C

trexio_t*
@@ -1634,8 +1643,8 @@ renaming the .txt data files.
-
-

2.6.2 Fortran

+
+

2.6.2 Fortran

interface
@@ -1653,8 +1662,8 @@ renaming the .txt data files.
-
-

2.6.3 Python

+
+

2.6.3 Python

def _open(file_name: str, mode: str, back_end: int):
@@ -1702,8 +1711,8 @@ 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 @@ -1736,8 +1745,8 @@ 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. @@ -1754,8 +1763,8 @@ output:

-
-

2.7.1 C

+
+

2.7.1 C

trexio_exit_code
@@ -1768,7 +1777,7 @@ output:
 
   assert(file->back_end < TREXIO_INVALID_BACK_END);
 
-  /* Things to be done before the closing the file in the back-end */
+  /* Things to be done before closing the file in the back-end */
   rc = trexio_pre_close(file);
   if (rc != TREXIO_SUCCESS) {
     return rc;
@@ -1842,8 +1851,8 @@ output:
-
-

2.7.2 Fortran

+
+

2.7.2 Fortran

interface
@@ -1858,8 +1867,8 @@ output:
-
-

2.7.3 Python

+
+

2.7.3 Python

def _close(trexio_file):
@@ -1880,8 +1889,8 @@ output:
-
-

2.8 File existence

+
+

2.8 File existence

trexio_inquire check whether TREXIO file exists. @@ -1918,8 +1927,8 @@ You can see examples of both functionalities in test_f.f90 (search

-
-

2.8.1 C

+
+

2.8.1 C

trexio_exit_code
@@ -1949,8 +1958,8 @@ You can see examples of both functionalities in test_f.f90  (search
-
-

2.8.2 Fortran

+
+

2.8.2 Fortran

The function below is a C binding. @@ -1970,8 +1979,8 @@ The front end Fortran function for trexio_inquire can be found in t

-
-

2.8.3 Python

+
+

2.8.3 Python

def _inquire(file_name: str) -> bool:
@@ -1990,8 +1999,8 @@ The front end Fortran function for trexio_inquire can be found in t
-
-

2.9 Tasks to be done before closing

+
+

2.9 Tasks to be done before closing

trexio_exit_code
@@ -2008,55 +2017,60 @@ The front end Fortran function for trexio_inquire can be found in t
     bool has_dn   = (trexio_has_electron_dn_num(file) == TREXIO_SUCCESS);
     bool has_updn = (trexio_has_electron_num(file) == TREXIO_SUCCESS);
 
-    if (has_updn && has_up && has_dn) {
-      rc = trexio_read_electron_up_num(file, &nup);
-      if (rc != TREXIO_SUCCESS) return rc;
+    if (file->mode != 'r') {
+      if (has_updn && has_up && has_dn) {
+        rc = trexio_read_electron_up_num(file, &nup);
+        if (rc != TREXIO_SUCCESS) return rc;
 
-      rc = trexio_read_electron_dn_num(file, &ndn);
-      if (rc != TREXIO_SUCCESS) return rc;
+        rc = trexio_read_electron_dn_num(file, &ndn);
+        if (rc != TREXIO_SUCCESS) return rc;
 
-      rc = trexio_read_electron_num(file, &nelec);
-      if (rc != TREXIO_SUCCESS) return rc;
+        rc = trexio_read_electron_num(file, &nelec);
+        if (rc != TREXIO_SUCCESS) return rc;
+
+        if (nelec != nup + ndn) {
+          if (file->mode == 'u') {
+            nelec = nup + ndn;
+            rc = trexio_write_electron_num(file, nelec);
+            if (rc != TREXIO_SUCCESS) return rc;
+          } else {
+            return TREXIO_INVALID_ELECTRON_NUM;
+          }
+        }
+      } else if (has_up && has_dn) {
+        rc = trexio_read_electron_up_num(file, &nup);
+        if (rc != TREXIO_SUCCESS) return rc;
+
+        rc = trexio_read_electron_dn_num(file, &ndn);
+        if (rc != TREXIO_SUCCESS) return rc;
 
-      if (nelec != nup + ndn) {
         nelec = nup + ndn;
         rc = trexio_write_electron_num(file, nelec);
         if (rc != TREXIO_SUCCESS) return rc;
+      } else if (has_up) {
+        rc = trexio_read_electron_up_num(file, &nup);
+        if (rc != TREXIO_SUCCESS) return rc;
+
+        ndn = 0;
+        rc = trexio_write_electron_dn_num(file, ndn);
+        if (rc != TREXIO_SUCCESS) return rc;
+
+        nelec = nup;
+        rc = trexio_write_electron_num(file, nelec);
+        if (rc != TREXIO_SUCCESS) return rc;
+      } else if (has_dn) {
+        rc = trexio_read_electron_dn_num(file, &ndn);
+        if (rc != TREXIO_SUCCESS) return rc;
+
+        nup = 0;
+        rc = trexio_write_electron_up_num(file, nup);
+        if (rc != TREXIO_SUCCESS) return rc;
+
+        nelec = ndn;
+        rc = trexio_write_electron_num(file, nelec);
+        if (rc != TREXIO_SUCCESS) return rc;
       }
-    } else if (has_up && has_dn) {
-      rc = trexio_read_electron_up_num(file, &nup);
-      if (rc != TREXIO_SUCCESS) return rc;
-
-      rc = trexio_read_electron_dn_num(file, &ndn);
-      if (rc != TREXIO_SUCCESS) return rc;
-
-      nelec = nup + ndn;
-      rc = trexio_write_electron_num(file, nelec);
-      if (rc != TREXIO_SUCCESS) return rc;
-    } else if (has_up) {
-      rc = trexio_read_electron_up_num(file, &nup);
-      if (rc != TREXIO_SUCCESS) return rc;
-
-      ndn = 0;
-      rc = trexio_write_electron_dn_num(file, ndn);
-      if (rc != TREXIO_SUCCESS) return rc;
-
-      nelec = nup;
-      rc = trexio_write_electron_num(file, nelec);
-      if (rc != TREXIO_SUCCESS) return rc;
-    } else if (has_dn) {
-      rc = trexio_read_electron_dn_num(file, &ndn);
-      if (rc != TREXIO_SUCCESS) return rc;
-
-      nup = 0;
-      rc = trexio_write_electron_up_num(file, nup);
-      if (rc != TREXIO_SUCCESS) return rc;
-
-      nelec = ndn;
-      rc = trexio_write_electron_num(file, nelec);
-      if (rc != TREXIO_SUCCESS) return rc;
     }
-
   }
 
   return TREXIO_SUCCESS;
@@ -2067,12 +2081,12 @@ The front end Fortran function for trexio_inquire can be found in t
-
-

3 Templates for front end

+
+

3 Templates for front end

-
-

3.1 Description

+
+

3.1 Description

Consider the following block of trex.json: @@ -2293,12 +2307,12 @@ 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, @@ -2369,8 +2383,8 @@ 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 @@ -2384,12 +2398,12 @@ 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
@@ -2453,8 +2467,8 @@ 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
@@ -2530,8 +2544,8 @@ 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
@@ -2586,8 +2600,8 @@ 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. @@ -2679,8 +2693,8 @@ 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:
@@ -2765,12 +2779,12 @@ 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. @@ -2852,8 +2866,8 @@ 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. @@ -2864,12 +2878,12 @@ The basic (non-suffixed) API call on datasets deals with real(cdouble

-
-
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
@@ -3032,8 +3046,8 @@ The basic (non-suffixed) API call on datasets deals with real(cdouble
-
-
3.3.2.3 Source code for single precision functions
+
+
3.3.2.3 Source code for single precision functions
trexio_exit_code
@@ -3184,11 +3198,11 @@ The basic (non-suffixed) API call on datasets deals with real(cdouble
-
-
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 */
@@ -3344,8 +3358,8 @@ 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
@@ -3420,8 +3434,8 @@ 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. @@ -3513,8 +3527,8 @@ 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:
@@ -3709,12 +3723,12 @@ 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 @@ -3875,16 +3889,16 @@ 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,
@@ -4160,8 +4174,8 @@ 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. @@ -4262,8 +4276,8 @@ 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:
@@ -4484,12 +4498,12 @@ 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. @@ -4529,8 +4543,8 @@ 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 @@ -4538,12 +4552,12 @@ 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
@@ -4793,8 +4807,8 @@ 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. @@ -4893,8 +4907,8 @@ 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:
@@ -5010,12 +5024,12 @@ 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. @@ -5055,16 +5069,16 @@ 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
@@ -5168,8 +5182,8 @@ 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. @@ -5249,8 +5263,8 @@ 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:
@@ -5339,12 +5353,12 @@ These templates are based on the use of iso_c_binding. Pointers hav
-
-

3.7 Templates for front end delete an entire group (UNSAFE MODE)

+
+

3.7 Templates for front end delete an entire group (UNSAFE MODE)

-
-

3.7.1 Introduction

+
+

3.7.1 Introduction

This section concerns API calls related to string attributes. @@ -5374,8 +5388,8 @@ This section concerns API calls related to string attributes.

-
-

3.7.2 C templates for front end

+
+

3.7.2 C templates for front end

trexio_exit_code
@@ -5410,8 +5424,8 @@ This section concerns API calls related to string attributes.
-
-

3.7.3 Fortran templates for front end

+
+

3.7.3 Fortran templates for front end

The Fortran templates that provide an access to the C API calls from Fortran. @@ -5431,8 +5445,8 @@ These templates are based on the use of iso_c_binding. Pointers hav

-
-

3.7.4 Python templates for front end

+
+

3.7.4 Python templates for front end

def delete_$group$(trexio_file) -> None:
@@ -5457,8 +5471,8 @@ These templates are based on the use of iso_c_binding. Pointers hav
-
-

4 General helper functions

+
+

4 General helper functions

This section contains general helper functions like trexio_info. @@ -5485,8 +5499,8 @@ then value of the metadata_unsafe attribute can be changed using th

-
-

4.1 C

+
+

4.1 C

trexio_exit_code
@@ -5531,8 +5545,8 @@ then value of the metadata_unsafe attribute can be changed using th
-
-

4.2 Fortran

+
+

4.2 Fortran

interface
@@ -5545,8 +5559,8 @@ then value of the metadata_unsafe attribute can be changed using th
-
-

4.3 Python

+
+

4.3 Python

def info():
@@ -5562,8 +5576,8 @@ then value of the metadata_unsafe attribute can be changed using th
-
-

5 Fortran helper/wrapper functions

+
+

5 Fortran helper/wrapper functions

The function below adapts the original C-based trexio_open for Fortran. @@ -5715,7 +5729,7 @@ two code are identical, i.e. if the assert statement pass.

Author: TREX-CoE

-

Created: 2022-04-13 Wed 14:40

+

Created: 2022-04-14 Thu 14:11

Validate

diff --git a/templator_hdf5.html b/templator_hdf5.html index 17fce5c..f4b16f4 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 @@ -311,22 +311,22 @@ for the JavaScript code in this tag.

Table of Contents

-
-

1 Template for HDF5 definitions

+
+

1 Template for HDF5 definitions

#define $GROUP$_GROUP_NAME          "$group$"
@@ -338,8 +338,8 @@ for the JavaScript code in this tag.
-
-

2 Template for HDF5 structures

+
+

2 Template for HDF5 structures

typedef struct trexio_hdf5_s {
@@ -352,8 +352,8 @@ for the JavaScript code in this tag.
-
-

3 Template for HDF5 init/deinit

+
+

3 Template for HDF5 init/deinit

trexio_exit_code
@@ -417,18 +417,20 @@ for the JavaScript code in this tag.
   /* Create or open groups in the hdf5 file assuming that they exist if file exists */
   switch (file->mode) {
     case 'r':
-      f->$group$_group = H5Gopen(f->file_id, $GROUP$_GROUP_NAME, H5P_DEFAULT);
+      if (H5Lexists(f->file_id, $GROUP$_GROUP_NAME, H5P_DEFAULT) > 0) f->$group$_group = H5Gopen(f->file_id, $GROUP$_GROUP_NAME, H5P_DEFAULT);
+      if (H5Lexists(f->file_id, $GROUP$_GROUP_NAME, H5P_DEFAULT) == 0) f->$group$_group = (hid_t) 0;
       break;
     case 'u':
     case 'w':
       if (f_exists == 1) {
-        f->$group$_group = H5Gopen(f->file_id, $GROUP$_GROUP_NAME, H5P_DEFAULT);
+        if (H5Lexists(f->file_id, $GROUP$_GROUP_NAME, H5P_DEFAULT) >  0) f->$group$_group = H5Gopen(f->file_id, $GROUP$_GROUP_NAME, H5P_DEFAULT);
+        if (H5Lexists(f->file_id, $GROUP$_GROUP_NAME, H5P_DEFAULT) == 0) f->$group$_group = H5Gcreate(f->file_id, $GROUP$_GROUP_NAME, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
       } else {
         f->$group$_group = H5Gcreate(f->file_id, $GROUP$_GROUP_NAME, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
       }
       break;
   }
-  if (f->$group$_group <= 0L) return TREXIO_INVALID_ID;
+  if (f->$group$_group < (hid_t) 0) return TREXIO_INVALID_ID;
 
   return TREXIO_SUCCESS;
 }
@@ -442,7 +444,7 @@ for the JavaScript code in this tag.
 
   trexio_hdf5_t* f = (trexio_hdf5_t*) file;
 
-  H5Gclose(f->$group$_group);
+  if (f->$group$_group != (hid_t) 0) H5Gclose(f->$group$_group);
   f->$group$_group = 0;
 
   H5Fclose(f->file_id);
@@ -456,8 +458,8 @@ for the JavaScript code in this tag.
-
-

4 Template for HDF5 has/read/write a numerical attribute

+
+

4 Template for HDF5 has/read/write a numerical attribute

trexio_exit_code
@@ -560,8 +562,8 @@ for the JavaScript code in this tag.
-
-

5 Template for HDF5 has/read/write a dataset of numerical data

+
+

5 Template for HDF5 has/read/write a dataset of numerical data

trexio_exit_code
@@ -694,8 +696,8 @@ for the JavaScript code in this tag.
-
-

6 Template for HDF5 has/read/write a dataset of sparse data

+
+

6 Template for HDF5 has/read/write a dataset of sparse data

Sparse data is stored using extensible datasets of HDF5. Extensibility is required @@ -896,8 +898,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s

-
-

7 Template for HDF5 has/read/write a dataset of strings

+
+

7 Template for HDF5 has/read/write a dataset of strings

trexio_exit_code
@@ -1094,8 +1096,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
-
-

8 Template for HDF5 has/read/write a string attribute

+
+

8 Template for HDF5 has/read/write a string attribute

trexio_exit_code
@@ -1221,8 +1223,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
-
-

9 Template for HDF5 delete a group (UNSAFE mode)

+
+

9 Template for HDF5 delete a group (UNSAFE mode)

Note: in early versions of the HDF5 library (v < 1.10) unlinking an object was not working as expected @@ -1262,8 +1264,8 @@ Thus, any corrupted/lost file space will remain in the first file. The use of

-
-

10 Helper functions

+
+

10 Helper functions

trexio_exit_code
@@ -1524,7 +1526,7 @@ Thus, any corrupted/lost file space will remain in the first file. The use of 
 

 
Author: TREX-CoE

-
Created: 2022-04-13 Wed 14:40

+
Created: 2022-04-14 Thu 14:11

 
Validate

 

 
diff --git a/templator_text.html b/templator_text.html
index 5b2a567..7d6a93e 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
@@ -311,29 +311,29 @@ 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 @@ -354,8 +354,8 @@ 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 {
@@ -374,8 +374,8 @@ 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 {
@@ -388,8 +388,8 @@ 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
@@ -532,8 +532,8 @@ 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
@@ -555,8 +555,8 @@ The file is written when closed, or when the flush function is called.
-
-

1.5 Template for text read a group

+
+

1.5 Template for text read a group

$group$_t*
@@ -857,8 +857,8 @@ trexio_text_read_$group$ (trexio_text_t*
-
-

1.6 Template for text flush a group

+
+

1.6 Template for text flush a group

trexio_exit_code
@@ -922,8 +922,8 @@ 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. @@ -970,8 +970,8 @@ Memory is allocated when reading. The following function frees memory.

-
-

1.8 Template for has/read/write a numerical attribute

+
+

1.8 Template for has/read/write a numerical attribute

trexio_exit_code
@@ -1034,8 +1034,8 @@ Memory is allocated when reading. The following function frees memory.
-
-

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

+
+

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

The group_dset array is assumed allocated with the appropriate size. @@ -1131,8 +1131,8 @@ The group_dset array is assumed allocated with the appropriate size

-
-

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

+
+

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

The group_dset array is assumed allocated with the appropriate size. @@ -1233,8 +1233,8 @@ The group_dset array is assumed allocated with the appropriate size

-
-

1.11 Template for has/read/write a string attribute

+
+

1.11 Template for has/read/write a string attribute

trexio_exit_code
@@ -1308,8 +1308,8 @@ 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 @@ -1583,8 +1583,8 @@ User provides indices and values of the sparse array as two separate variables.

-
-

1.13 Template for text delete a group (UNSAFE mode)

+
+

1.13 Template for text delete a group (UNSAFE mode)

trexio_exit_code
@@ -1615,7 +1615,7 @@ User provides indices and values of the sparse array as two separate variables.

Author: TREX-CoE

-

Created: 2022-04-13 Wed 14:40

+

Created: 2022-04-14 Thu 14:11

Validate

diff --git a/trex.html b/trex.html index 28be10e..6468e7c 100644 --- a/trex.html +++ b/trex.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> - + TREX Configuration file @@ -333,34 +333,34 @@ for the JavaScript code in this tag.

Table of Contents

@@ -406,8 +406,8 @@ the examples.

-
-

1 Metadata (metadata group)

+
+

1 Metadata (metadata group)

As we expect our files to be archived in open-data repositories, we @@ -417,7 +417,7 @@ which have participated to the creation of the file, a list of authors of the file, and a textual description.

- +
@@ -498,15 +498,15 @@ then the unsafe attribute value can be manually overwritten (in uns -
-

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.

-
+
@@ -552,15 +552,15 @@ 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.

-
+
@@ -627,8 +627,8 @@ 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 @@ -661,7 +661,7 @@ 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.

-
+
@@ -763,8 +763,8 @@ If you encounter the aforementioned issue, please report it to our -

4.1 Example

+
+

4.1 Example

For example, consider H2 molecule with the following @@ -827,8 +827,8 @@ power = [

-
-

5 Basis set (basis group)

+
+

5 Basis set (basis group)

We consider here basis functions centered on nuclei. Hence, we enable @@ -881,7 +881,7 @@ If the the basis function is not considered normalized, \(\mathcal{N}_s=1\). All the basis set parameters are stored in one-dimensional arrays:

-
+
@@ -975,8 +975,8 @@ 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 @@ -1054,8 +1054,8 @@ prim_factor =

-
-

6 Atomic orbitals (ao group)

+
+

6 Atomic orbitals (ao group)

Going from the atomic basis set to AOs implies a systematic @@ -1108,13 +1108,13 @@ 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 \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).

- +
@@ -1166,8 +1166,8 @@ 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}} @@ -1184,7 +1184,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are over atomic orbitals.

    - +
    @@ -1244,8 +1244,8 @@ 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 @@ -1266,7 +1266,7 @@ notation. \mathbf{r}_j \vert)}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron long range potential -

    +
    @@ -1306,10 +1306,10 @@ notation. -
    -

    7 Molecular orbitals (mo group)

    +
    +

    7 Molecular orbitals (mo group)

    -
    +
    @@ -1375,8 +1375,8 @@ 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 @@ -1384,7 +1384,7 @@ The operators as the same as those defined in the the basis of molecular orbitals.

- +
@@ -1444,8 +1444,8 @@ 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 @@ -1453,7 +1453,7 @@ The operators as the same as those defined in the the basis of molecular orbitals.

-
+
@@ -1493,11 +1493,11 @@ 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 @@ -1550,7 +1550,7 @@ The total energy can be computed as: \]

-
+
@@ -1631,8 +1631,8 @@ The total energy can be computed as: -
-

10 Quantum Monte Carlo data (qmc group)

+
+

10 Quantum Monte Carlo data (qmc group)

In quantum Monte Carlo calculations, the wave function is evaluated @@ -1646,7 +1646,7 @@ By convention, the electron coordinates contain first all the electrons of $↑$-spin and then all the $↓$-spin.

-
+
@@ -1701,7 +1701,7 @@ of $↑$-spin and then all the $↓$-spin.

Author: TREX-CoE

-

Created: 2022-04-13 Wed 14:40

+

Created: 2022-04-14 Thu 14:11

Validate