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https://github.com/TREX-CoE/trexio.git
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Add I/O for coefficient_size
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17ea14f648
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@ -4238,14 +4238,15 @@ def delete_$group$(trexio_file) -> None:
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This section concerns API calls related to Slater determinants.
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| Function name | Description |
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|----------------------------------------+----------------------------------------|
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| ~trexio_has_determinant_coefficient~ | Check if an attribute exists in a file |
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| ~trexio_has_determinant_list~ | Check if an attribute exists in a file |
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| ~trexio_write_determinant_coefficient~ | Write an attribute |
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| ~trexio_write_determinant_list~ | Write an attribute |
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| ~trexio_read_determinant_coefficient~ | Read an attribute |
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| ~trexio_read_determinant_list~ | Read an attribute |
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| Function name | Description |
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|--------------------------------------------+----------------------------------------|
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| ~trexio_has_determinant_coefficient~ | Check if an attribute exists in a file |
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| ~trexio_has_determinant_list~ | Check if an attribute exists in a file |
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| ~trexio_write_determinant_coefficient~ | Write an attribute |
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| ~trexio_write_determinant_list~ | Write an attribute |
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| ~trexio_read_determinant_coefficient~ | Read an attribute |
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| ~trexio_read_determinant_list~ | Read an attribute |
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| ~trexio_read_determinant_coefficient_size~ | Get the number of the coefficients |
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*** C source code
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@ -4260,6 +4261,7 @@ trexio_exit_code trexio_write_determinant_list(trexio_t* const file, const int64
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trexio_exit_code trexio_write_safe_determinant_list(trexio_t* const file, const int64_t offset_file, const int64_t buffer_size, const int64_t* dset_in, const int64_t dim_in);
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trexio_exit_code trexio_write_determinant_coefficient(trexio_t* const file, const int64_t offset_file, const int64_t buffer_size, const double* dset);
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trexio_exit_code trexio_write_safe_determinant_coefficient(trexio_t* const file, const int64_t offset_file, const int64_t buffer_size, const double* dset_in, const int64_t dim_in);
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trexio_exit_code trexio_read_determinant_coefficient_size(trexio_t* const file, int64_t* const size_max);
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#+end_src
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#+begin_src c :tangle read_determinant_front.c
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@ -4370,7 +4372,37 @@ trexio_read_determinant_coefficient (trexio_t* const file, const int64_t offset_
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return rc;
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}
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trexio_exit_code
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trexio_read_determinant_coefficient_size(trexio_t* const file, int64_t* const size_max)
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{
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if (file == NULL) return TREXIO_INVALID_ARG_1;
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if (size_max == NULL) return TREXIO_INVALID_ARG_2;
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if (trexio_has_determinant_coefficient(file) != TREXIO_SUCCESS) return TREXIO_DSET_MISSING;
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switch (file->back_end) {
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case TREXIO_TEXT:
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return trexio_text_read_determinant_coefficient_size(file, size_max);
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break;
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case TREXIO_HDF5:
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#ifdef HAVE_HDF5
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return trexio_hdf5_read_determinant_coefficient_size(file, size_max);
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break;
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#else
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return TREXIO_BACK_END_MISSING;
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#endif
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/*
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case TREXIO_JSON:
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return trexio_json_read_
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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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trexio_exit_code
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@ -4490,6 +4522,8 @@ trexio_write_determinant_coefficient (trexio_t* const file, const int64_t offset
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break;
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,*/
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}
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return TREXIO_FAILURE;
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}
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trexio_exit_code
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@ -4596,6 +4630,32 @@ interface
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integer(c_int64_t), intent(in), value :: list_size
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end function trexio_write_safe_determinant_list
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end interface
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interface
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integer(trexio_exit_code) function trexio_write_determinant_coefficient(trex_file, &
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offset_file, buffer_size, coefficient) bind(C)
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use, intrinsic :: iso_c_binding
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import
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integer(c_int64_t), intent(in), value :: trex_file
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integer(c_int64_t), intent(in), value :: offset_file
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integer(c_int64_t), intent(in), value :: buffer_size
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real(c_double), intent(in) :: coefficient(*)
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end function trexio_write_determinant_coefficient
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end interface
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interface
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integer(trexio_exit_code) function trexio_write_safe_determinant_coefficient (trex_file, &
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offset_file, buffer_size, &
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coefficient, coefficient_size) bind(C)
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use, intrinsic :: iso_c_binding
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import
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integer(c_int64_t), intent(in), value :: trex_file
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integer(c_int64_t), intent(in), value :: offset_file
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integer(c_int64_t), intent(in), value :: buffer_size
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real(c_double), intent(in) :: coefficient(*)
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integer(c_int64_t), intent(in), value :: coefficient_size
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end function trexio_write_safe_determinant_coefficient
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end interface
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#+end_src
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#+begin_src f90 :tangle read_determinant_front_fortran.f90
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@ -4624,6 +4684,42 @@ interface
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integer(c_int64_t), intent(in), value :: list_size
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end function trexio_read_safe_determinant_list
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end interface
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interface
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integer(trexio_exit_code) function trexio_read_safe_determinant_coefficient (trex_file, &
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offset_file, buffer_size, &
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coefficient, coefficient_size) bind(C)
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use, intrinsic :: iso_c_binding
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import
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integer(c_int64_t), intent(in), value :: trex_file
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integer(c_int64_t), intent(in), value :: offset_file
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integer(c_int64_t), intent(inout) :: buffer_size
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real(c_double), intent(out) :: coefficient(*)
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integer(c_int64_t), intent(in), value :: coefficient_size
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end function trexio_read_safe_determinant_coefficient
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end interface
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interface
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integer(trexio_exit_code) function trexio_read_determinant_coefficient(trex_file, &
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offset_file, buffer_size, coefficient) bind(C)
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use, intrinsic :: iso_c_binding
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import
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integer(c_int64_t), intent(in), value :: trex_file
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integer(c_int64_t), intent(in), value :: offset_file
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integer(c_int64_t), intent(inout) :: buffer_size
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real(c_double), intent(out) :: coefficient(*)
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end function trexio_read_determinant_coefficient
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end interface
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interface
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integer(trexio_exit_code) function trexio_read_determinant_coefficient_size (trex_file, &
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size_max) bind(C)
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use, intrinsic :: iso_c_binding
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import
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integer(c_int64_t), intent(in), value :: trex_file
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integer(c_int64_t), intent(out) :: size_max
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end function trexio_read_determinant_coefficient_size
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end interface
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#+end_src
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#+begin_src f90 :tangle has_determinant_front_fortran.f90
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@ -4634,6 +4730,14 @@ interface
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integer(c_int64_t), intent(in), value :: trex_file
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end function trexio_has_determinant_list
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end interface
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interface
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integer(trexio_exit_code) function trexio_has_determinant_coefficient (trex_file) bind(C)
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use, intrinsic :: iso_c_binding
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import
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integer(c_int64_t), intent(in), value :: trex_file
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end function trexio_has_determinant_coefficient
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end interface
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#+end_src
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*** Python interface
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@ -4706,6 +4810,50 @@ def write_determinant_list(trexio_file: File, offset_file: int, buffer_size: int
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if rc != TREXIO_SUCCESS:
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raise Error(rc)
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def write_determinant_coefficient(trexio_file: File, offset_file: int, buffer_size: int, coefficients: list) -> None:
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"""Write the determinant coefficients in the TREXIO file.
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Parameters:
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trexio_file:
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TREXIO File object.
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offset_file: int
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The number of coefficients to be skipped in the file when writing.
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buffer_size: int
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The number of coefficients to write in the file.
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coefficients: list OR numpy.ndarray
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Array of determinant_coefficient to be written. If array data type does not correspond to int64, the conversion is performed.
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Raises:
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- trexio.Error if TREXIO return code ~rc~ is different from TREXIO_SUCCESS and prints the error message.
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- Exception from some other error (e.g. RuntimeError).
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"""
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try:
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import numpy as np
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except ImportError:
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raise Exception("NumPy cannot be imported.")
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if not isinstance(offset_file, int):
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raise TypeError("offset_file argument has to be an integer.")
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if not isinstance(buffer_size, int):
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raise TypeError("buffer_size argument has to be an integer.")
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if not isinstance(coefficients, (list, tuple, np.ndarray)):
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raise TypeError("coefficients argument has to be an array (list, tuple or NumPy ndarray).")
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if isinstance(coefficients, np.ndarray) and not coefficients.dtype==np.float64:
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# convert to float64 if input is in a different precision
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coefficients_64 = np.float64(coefficients)
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rc = pytr.trexio_write_safe_determinant_coefficient(trexio_file.pytrexio_s, offset_file, buffer_size, coefficients_64)
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else:
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rc = pytr.trexio_write_safe_determinant_coefficient(trexio_file.pytrexio_s, offset_file, buffer_size, coefficients)
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if rc != TREXIO_SUCCESS:
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raise Error(rc)
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#+end_src
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#+begin_src python :tangle read_determinant_front.py
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@ -4718,10 +4866,10 @@ def read_determinant_list(trexio_file: File, offset_file: int, buffer_size: int)
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TREXIO File object.
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offset_file: int
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The number of integrals to be skipped in the file when reading.
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The number of determinants to be skipped in the file when reading.
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buffer_size: int
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The number of integrals to read from the file.
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The number of determinants to read from the file.
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Returns:
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(determinants, n_int_read, eof_flag) tuple where
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@ -4749,7 +4897,7 @@ def read_determinant_list(trexio_file: File, offset_file: int, buffer_size: int)
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# read the number of determinants already in the file
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det_num = read_determinant_num(trexio_file)
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# TODO: calculate the rank (number of int bit fields per determinant)
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# calculate the int_num (number of int bit fields per determinant)
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mo_num = read_mo_num(trexio_file)
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int_num = 2*int((mo_num-1)/64+1)
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@ -4779,6 +4927,94 @@ def read_determinant_list(trexio_file: File, offset_file: int, buffer_size: int)
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dets_reshaped = np.reshape(determinants, (verified_size, int_num), order='C')
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return (dets_reshaped, n_int_read, eof_flag)
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def read_determinant_coefficient(trexio_file: File, offset_file: int, buffer_size: int) -> tuple:
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"""Read determinant_coefficient from the TREXIO file.
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Parameters:
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trexio_file:
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TREXIO File object.
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offset_file: int
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The number of coefficient to be skipped in the file when reading.
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buffer_size: int
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The number of coefficients to read from the file.
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Returns:
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(coefficients, n_int_read, eof_flag) tuple where
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- coefficients are NumPy arrays [numpy.ndarray] with the default int64 precision;
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- n_int_read [int] is the number of coefficients read from the trexio_file
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(either strictly equal to buffer_size or less than buffer_size if EOF has been reached);
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- eof_flag [bool] is True when EOF has been reached (i.e. when call to low-level pytrexio API returns TREXIO_END)
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False otherwise.
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Raises:
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- trexio.Error if TREXIO return code ~rc~ is different from TREXIO_SUCCESS and prints the error message.
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- Exception from some other error (e.g. RuntimeError).
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"""
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try:
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import numpy as np
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except ImportError:
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raise Exception("NumPy cannot be imported.")
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if not isinstance(offset_file, int):
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raise TypeError("offset_file argument has to be an integer.")
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if not isinstance(buffer_size, int):
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raise TypeError("buffer_size argument has to be an integer.")
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# read the number of determinants already in the file
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det_num = read_determinant_coefficient_size(trexio_file)
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# additional modification needed to avoid allocating more memory than needed if EOF will be reached during read
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overflow = offset_file + buffer_size - det_num
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eof_flag = False
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if overflow > 0:
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verified_size = buffer_size - overflow
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eof_flag = True
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else:
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verified_size = buffer_size
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# main call to the low-level (SWIG-wrapped) trexio_read function, which also requires the sizes of the output to be provided
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# read_buf_size contains the number of elements being read from the file, useful when EOF has been reached
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rc, n_int_read, coefficients = pytr.trexio_read_safe_determinant_coefficient(trexio_file.pytrexio_s,
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offset_file,
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verified_size,
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verified_size)
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if rc != TREXIO_SUCCESS:
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raise Error(rc)
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if n_int_read == 0:
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raise ValueError("No integrals have been read from the file.")
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if coefficients is None:
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raise ValueError("Returned NULL array from the low-level pytrexio API.")
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return (coefficients, n_int_read, eof_flag)
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def read_determinant_coefficient_size(trexio_file) -> int:
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"""Read the number of determinant coefficients stored in the TREXIO file.
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Parameter is a ~TREXIO File~ object that has been created by a call to ~open~ function.
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Returns:
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~num~: int
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Integer value of corresponding to the size of the determinant_coefficient array from ~trexio_file~.
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Raises:
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- Exception from AssertionError if TREXIO return code ~rc~ is different from TREXIO_SUCCESS and prints the error message using trexio_string_of_error.
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- Exception from some other error (e.g. RuntimeError).
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"""
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rc, num = pytr.trexio_read_determinant_coefficient_size(trexio_file.pytrexio_s)
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if rc != TREXIO_SUCCESS:
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raise Error(rc)
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return num
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#+end_src
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#+end_src
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#+begin_src python :tangle has_determinant_front.py
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@ -4800,6 +5036,25 @@ def has_determinant_list(trexio_file) -> bool:
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raise Error(rc)
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return rc == TREXIO_SUCCESS
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def has_determinant_coefficient(trexio_file) -> bool:
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"""Check that determinant_coefficient exists in the TREXIO file.
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Parameter is a ~TREXIO File~ object that has been created by a call to ~open~ function.
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Returns:
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True if the variable exists, False otherwise
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Raises:
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- trexio.Error if TREXIO return code ~rc~ is TREXIO_FAILURE and prints the error message using string_of_error.
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- Exception from some other error (e.g. RuntimeError).
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"""
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rc = pytr.trexio_has_determinant_coefficient(trexio_file.pytrexio_s)
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if rc == TREXIO_FAILURE:
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raise Error(rc)
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return rc == TREXIO_SUCCESS
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#+end_src
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* TODO General helper functions
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@ -562,6 +562,7 @@ trexio_hdf5_read_$group_dset$_size (trexio_t* const file, int64_t* const size_ma
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{
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if (file == NULL) return TREXIO_INVALID_ARG_1;
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if (size_max == NULL) return TREXIO_INVALID_ARG_2;
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const trexio_hdf5_t* f = (const trexio_hdf5_t*) file;
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@ -988,6 +989,7 @@ trexio_exit_code trexio_hdf5_write_determinant_list(trexio_t* const file, const
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trexio_exit_code trexio_hdf5_has_determinant_coefficient(trexio_t* const file);
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trexio_exit_code trexio_hdf5_read_determinant_coefficient(trexio_t* const file, const int64_t offset_file, const uint32_t rank, const uint64_t* dims, int64_t* const eof_read_size, double* const coeff);
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trexio_exit_code trexio_hdf5_write_determinant_coefficient(trexio_t* const file, const int64_t offset_file, const uint32_t rank, const uint64_t* dims, const double* coeff);
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trexio_exit_code trexio_hdf5_read_determinant_coefficient_size(trexio_t* const file, int64_t* const size_max);
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#+end_src
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#+begin_src c :tangle read_determinant_hdf5.c
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@ -1138,6 +1140,48 @@ trexio_exit_code trexio_hdf5_write_determinant_coefficient(trexio_t* const file,
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return TREXIO_SUCCESS;
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}
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trexio_exit_code
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trexio_hdf5_read_determinant_coefficient_size (trexio_t* const file, int64_t* const size_max)
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{
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if (file == NULL) return TREXIO_INVALID_ARG_1;
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if (size_max == NULL) return TREXIO_INVALID_ARG_2;
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char dset_coeff_name[128];
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memset(dset_coeff_name, 0, sizeof(dset_coeff_name));
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const int32_t trexio_state = file->state;
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if (trexio_state != 0) {
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sprintf(dset_coeff_name, "determinant_coefficient_state_%" PRId32, trexio_state);
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} else {
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strncpy(dset_coeff_name, "determinant_coefficient", 24);
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}
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const trexio_hdf5_t* f = (const trexio_hdf5_t*) file;
|
||||
|
||||
hid_t dset_id = H5Dopen(f->determinant_group, dset_coeff_name, H5P_DEFAULT);
|
||||
if (dset_id <= 0) return TREXIO_INVALID_ID;
|
||||
|
||||
hid_t fspace_id = H5Dget_space(dset_id);
|
||||
if (fspace_id < 0) {
|
||||
H5Dclose(dset_id);
|
||||
return TREXIO_INVALID_ID;
|
||||
}
|
||||
|
||||
// allocate space for the dimensions to be read
|
||||
hsize_t ddims[1] = {0};
|
||||
|
||||
// get the rank and dimensions of the dataset
|
||||
H5Sget_simple_extent_dims(fspace_id, ddims, NULL);
|
||||
|
||||
H5Dclose(dset_id);
|
||||
H5Sclose(fspace_id);
|
||||
|
||||
*size_max = (int64_t) ddims[0];
|
||||
|
||||
return TREXIO_SUCCESS;
|
||||
}
|
||||
#+end_src
|
||||
|
||||
#+begin_src c :tangle has_determinant_hdf5.c
|
||||
|
||||
@ -1326,6 +1326,7 @@ trexio_exit_code trexio_text_write_determinant_list(trexio_t* const file, const
|
||||
trexio_exit_code trexio_text_has_determinant_coefficient(trexio_t* const file);
|
||||
trexio_exit_code trexio_text_read_determinant_coefficient(trexio_t* const file, const int64_t offset_file, const uint32_t rank, const uint64_t* dims, int64_t* const eof_read_size, double* const coeff);
|
||||
trexio_exit_code trexio_text_write_determinant_coefficient(trexio_t* const file, const int64_t offset_file, const uint32_t rank, const uint64_t* dims, const double* coeff);
|
||||
trexio_exit_code trexio_text_read_determinant_coefficient_size(trexio_t* const file, int64_t* const size_max);
|
||||
#+end_src
|
||||
|
||||
#+begin_src c :tangle read_determinant_text.c
|
||||
@ -1429,7 +1430,7 @@ trexio_exit_code trexio_text_read_determinant_coefficient(trexio_t* const file,
|
||||
if (trexio_state != 0) {
|
||||
sprintf(coeff_file_name, "/determinant_coefficient_state_%" PRId32 ".txt", trexio_state);
|
||||
} else {
|
||||
strncpy(coeff_file_name, "/determinant_coefficient.txt", 28);
|
||||
strncpy(coeff_file_name, "/determinant_coefficient.txt", 32);
|
||||
}
|
||||
|
||||
/* The full path to the destination TXT file with sparse data. This will include TREXIO directory name. */
|
||||
@ -1487,6 +1488,59 @@ trexio_exit_code trexio_text_read_determinant_coefficient(trexio_t* const file,
|
||||
|
||||
return TREXIO_SUCCESS;
|
||||
}
|
||||
|
||||
trexio_exit_code
|
||||
trexio_text_read_determinant_coefficient_size(trexio_t* const file, int64_t* const size_max)
|
||||
{
|
||||
if (file == NULL) return TREXIO_INVALID_ARG_1;
|
||||
if (size_max == NULL) return TREXIO_INVALID_ARG_2;
|
||||
|
||||
char coeff_file_name[256];
|
||||
memset(coeff_file_name, 0, sizeof(coeff_file_name));
|
||||
const int32_t trexio_state = file->state;
|
||||
|
||||
if (trexio_state != 0) {
|
||||
sprintf(coeff_file_name, "/determinant_coefficient_state_%" PRId32 ".txt.size", trexio_state);
|
||||
} else {
|
||||
strncpy(coeff_file_name, "/determinant_coefficient.txt.size", 64);
|
||||
}
|
||||
|
||||
/* The full path to the destination TXT file with sparse data. This will include TREXIO directory name. */
|
||||
char file_full_path[TREXIO_MAX_FILENAME_LENGTH];
|
||||
/* Copy directory name in file_full_path */
|
||||
strncpy (file_full_path, file->file_name, TREXIO_MAX_FILENAME_LENGTH);
|
||||
/* Append name of the file with sparse data */
|
||||
strncat (file_full_path, coeff_file_name,
|
||||
TREXIO_MAX_FILENAME_LENGTH-strlen(coeff_file_name));
|
||||
|
||||
/* Open the file in "r" (read) mode to guarantee that no truncation happens upon consecutive reads */
|
||||
FILE* f = fopen(file_full_path, "r");
|
||||
if(f == NULL) return TREXIO_FILE_ERROR;
|
||||
|
||||
/* Read the data from the file and check the return code of fprintf to verify that > 0 bytes have been read or reached EOF */
|
||||
int rc;
|
||||
int64_t size_item, size_accum=0L;
|
||||
|
||||
/* Read the values from the file. BEWARE OF POSSIBLE MAX_INT64 OVERFLOW ! */
|
||||
while(fscanf(f, "%" SCNd64, &size_item) != EOF) {
|
||||
/* Check that summation will not overflow the int64_t value */
|
||||
if (INT64_MAX - size_accum > size_item) {
|
||||
size_accum += size_item;
|
||||
} else {
|
||||
fclose(f);
|
||||
,*size_max = -1L;
|
||||
return TREXIO_INT_SIZE_OVERFLOW;
|
||||
}
|
||||
}
|
||||
|
||||
/* Close the TXT file */
|
||||
rc = fclose(f);
|
||||
if(rc != 0) return TREXIO_FILE_ERROR;
|
||||
|
||||
/* Overwrite the value at the input address and return TREXIO_SUCCESS */
|
||||
,*size_max = size_accum;
|
||||
return TREXIO_SUCCESS;
|
||||
}
|
||||
#+end_src
|
||||
|
||||
#+begin_src c :tangle write_determinant_text.c
|
||||
@ -1553,7 +1607,7 @@ trexio_exit_code trexio_text_write_determinant_coefficient(trexio_t* const file,
|
||||
if (trexio_state != 0) {
|
||||
sprintf(coeff_file_name, "/determinant_coefficient_state_%" PRId32 ".txt", trexio_state);
|
||||
} else {
|
||||
strncpy(coeff_file_name, "/determinant_coefficient.txt", 28);
|
||||
strncpy(coeff_file_name, "/determinant_coefficient.txt", 32);
|
||||
}
|
||||
|
||||
/* The full path to the destination TXT file with sparse data. This will include TREXIO directory name. */
|
||||
@ -1584,6 +1638,24 @@ trexio_exit_code trexio_text_write_determinant_coefficient(trexio_t* const file,
|
||||
rc = fclose(f);
|
||||
if (rc != 0) return TREXIO_FILE_ERROR;
|
||||
|
||||
/* Append .size to the file_full_path in order to write additional info about the written buffer of data */
|
||||
strncat(file_full_path, ".size", 6);
|
||||
|
||||
/* Open the new file in "a" (append) mode to append info about the buffer that has been just written */
|
||||
FILE *f_wSize = fopen(file_full_path, "a");
|
||||
if (f_wSize == NULL) return TREXIO_FILE_ERROR;
|
||||
|
||||
/* Write the buffer_size */
|
||||
rc = fprintf(f_wSize, "%" PRIu64 "\n", dims[0]);
|
||||
if (rc <= 0) {
|
||||
fclose(f_wSize);
|
||||
return TREXIO_FAILURE;
|
||||
}
|
||||
|
||||
/* Close the TXT file */
|
||||
rc = fclose(f_wSize);
|
||||
if (rc != 0) return TREXIO_FILE_ERROR;
|
||||
|
||||
/* Exit upon success */
|
||||
return TREXIO_SUCCESS;
|
||||
}
|
||||
@ -1624,7 +1696,7 @@ trexio_exit_code trexio_text_has_determinant_coefficient(trexio_t* const file)
|
||||
if (trexio_state != 0) {
|
||||
sprintf(coeff_file_name, "/determinant_coefficient_state_%" PRId32 ".txt", trexio_state);
|
||||
} else {
|
||||
strncpy(coeff_file_name, "/determinant_coefficient.txt", 28);
|
||||
strncpy(coeff_file_name, "/determinant_coefficient.txt", 32);
|
||||
}
|
||||
|
||||
/* The full path to the destination TXT file with sparse data. This will include TREXIO directory name. */
|
||||
|
||||
Loading…
Reference in New Issue
Block a user