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Moved sparse documentation in src/templates_front/templator_front.org
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Sparse.org
111
Sparse.org
@ -1,113 +1,4 @@
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* JSON
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"ao_2e_int" : {
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"eri_num" : [ "int", [ ] ]
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"eri" : [ "float sparse", [ "ao.num", "ao.num", "ao.num", "ao.num" ] ]
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},
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* Front end
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For example, the integral $\langle ij | kl \rangle = x$ can be
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represented represented as
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- a quartet of integers $(i,j,k,l)$
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- a floating point value $x$
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To store $N$ integrals in the file, we can store
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- An array of quartets of integers
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- An array of values (floats)
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These two arrays have the same size, $N$.
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As the number of integrals to store can be prohibitively large, it
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is important to be able to read/write the integrals in chunks. So we
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need to give two extra parameters to the functions:
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- ~offset~ : the index of the 1st integral we want to read. An
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offset of zero implies to read the first integral
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- ~num~ : the number of integrals to read
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We need to provide one function to read a chunk of indices, and one
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function to read a chunk of values, because some users might want to
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read only the values of the integrals, or only the indices.
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Here is an example for the indices:
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#+BEGIN_SRC c
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trexio_exit_code
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trexio_read_chunk_ao_2e_int_eri_index_32(trexio_t* const file,
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const int64_t offset,
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const int64_t num,
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int32_t* buffer)
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{
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if (file == NULL) return TREXIO_INVALID_ARG_1;
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if (offset < 0L) return TREXIO_INVALID_ARG_2;
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if (num < 0L) return TREXIO_INVALID_ARG_3;
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const uint32_t rank = 4; // To be set by generator : number of indices
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int64_t nmax; // Max number of integrals
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trexio_exit_code rc;
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rc = trexio_read_ao_2e_int_eri_num(const file, &nmax);
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if (rc != TREXIO_SUCCESS) return rc;
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switch (file->back_end) {
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case TREXIO_TEXT:
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return trexio_text_read_chunk_ao_2e_int_eri_index(file, buffer, offset, num, rank, nmax);
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break;
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case TREXIO_HDF5:
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return trexio_hdf5_read_chunk_ao_2e_int_eri_index(file, buffer, offset, num, rank, nmax);
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break;
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/*
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case TREXIO_JSON:
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return trexio_json_read_chunk_ao_2e_int_eri_index(file, buffer, offset, num, rank, nmax);
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break;
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,*/
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default:
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return TREXIO_FAILURE; /* Impossible case */
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}
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}
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#+END_SRC
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For the values,
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#+BEGIN_SRC c
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trexio_exit_code
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trexio_read_chunk_ao_2e_int_eri_value_64(trexio_t* const file,
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const int64_t offset,
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const int64_t num,
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double* buffer)
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{
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if (file == NULL) return TREXIO_INVALID_ARG_1;
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if (offset < 0L) return TREXIO_INVALID_ARG_2;
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if (num < 0L) return TREXIO_INVALID_ARG_3;
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int64_t nmax; // Max number of integrals
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trexio_exit_code rc;
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rc = trexio_read_ao_2e_int_eri_num(const file, &nmax);
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if (rc != TREXIO_SUCCESS) return rc;
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switch (file->back_end) {
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case TREXIO_TEXT:
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return trexio_text_read_chunk_ao_2e_int_eri_value(file, buffer, offset, num, nmax);
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break;
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case TREXIO_HDF5:
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return trexio_hdf5_read_chunk_ao_2e_int_eri_index(file, buffer, offset, num, nmax);
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break;
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/*
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case TREXIO_JSON:
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return trexio_json_read_chunk_ao_2e_int_eri_index(file, buffer, offset, num, nmax);
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break;
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,*/
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default:
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return TREXIO_FAILURE; /* Impossible case */
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}
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}
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#+END_SRC
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See templator_front.org
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* Text back end
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As the size of the dataset should be extensible, the simplest
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@ -1405,7 +1405,7 @@ end interface
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Sparse data structures are used typically for large tensors such as
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two-electron integrals. For example, in the =trex.json= file sparse
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arrays appear as the ~eri~ array:
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arrays appear as for the ~eri~ :
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#+begin_src python
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"ao_2e_int" : {
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@ -1413,6 +1413,108 @@ end interface
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"eri" : [ "float sparse", [ "ao.num", "ao.num", "ao.num", "ao.num" ] ]
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}
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#+end_src
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The electron repulsion integral $\langle ij | kl \rangle$ is
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represented as a quartet of integers $(i,j,k,l)$ and a floating
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point value.
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To store $N$ integrals in the file, we store
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- An array of quartets of integers
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- An array of values (floats)
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Both arrays have the same size, $N$, the number of non-zero integrals.
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Knowing the maximum dimensions allows to check that the integers are
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in a valid range, and also lets the library choose the smallest
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integer representation to compress the storage.
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Fortran uses 1-based array indexing, while C uses 0-based indexing.
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Internally, we use a 0-based representation but the Fortran binding
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does the appropriate conversion when reading or writing.
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As the number of integrals to store can be prohibitively large, we
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provide the possibility to read/write the integrals in chunks. So the
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functions take two extra parameters:
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- ~offset~ : the index of the 1st integral we want to read. An
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offset of zero implies to read the first integral.
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- ~num~ : the number of integrals to read.
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We provide a function to read a chunk of indices, and a function to
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read a chunk of values, because some users might want to read only
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the values of the integrals, or only the indices.
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Here is an example for the indices:
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#+BEGIN_SRC c
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trexio_exit_code
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trexio_read_chunk_ao_2e_int_eri_index_32(trexio_t* const file,
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const int64_t offset,
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const int64_t num,
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int32_t* buffer)
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{
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if (file == NULL) return TREXIO_INVALID_ARG_1;
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if (offset < 0L) return TREXIO_INVALID_ARG_2;
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if (num < 0L) return TREXIO_INVALID_ARG_3;
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const uint32_t rank = 4; // To be set by generator : number of indices
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int64_t nmax; // Max number of integrals
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trexio_exit_code rc;
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rc = trexio_read_ao_2e_int_eri_num(const file, &nmax);
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if (rc != TREXIO_SUCCESS) return rc;
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switch (file->back_end) {
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case TREXIO_TEXT:
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return trexio_text_read_chunk_ao_2e_int_eri_index(file, buffer, offset, num, rank, nmax);
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break;
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case TREXIO_HDF5:
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return trexio_hdf5_read_chunk_ao_2e_int_eri_index(file, buffer, offset, num, rank, nmax);
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break;
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default:
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return TREXIO_FAILURE; /* Impossible case */
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}
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}
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#+END_SRC
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For the values,
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#+BEGIN_SRC c
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trexio_exit_code
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trexio_read_chunk_ao_2e_int_eri_value_64(trexio_t* const file,
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const int64_t offset,
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const int64_t num,
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double* buffer)
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{
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if (file == NULL) return TREXIO_INVALID_ARG_1;
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if (offset < 0L) return TREXIO_INVALID_ARG_2;
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if (num < 0L) return TREXIO_INVALID_ARG_3;
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int64_t nmax; // Max number of integrals
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trexio_exit_code rc;
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rc = trexio_read_ao_2e_int_eri_num(const file, &nmax);
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if (rc != TREXIO_SUCCESS) return rc;
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switch (file->back_end) {
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case TREXIO_TEXT:
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return trexio_text_read_chunk_ao_2e_int_eri_value(file, buffer, offset, num, nmax);
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break;
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case TREXIO_HDF5:
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return trexio_hdf5_read_chunk_ao_2e_int_eri_index(file, buffer, offset, num, nmax);
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break;
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default:
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return TREXIO_FAILURE; /* Impossible case */
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}
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}
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#+END_SRC
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* Fortran helper/wrapper functions
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The function below adapts the original C-based ~trexio_open~ for Fortran.
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