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https://github.com/TREX-CoE/trexio.git
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Helper functions to convert bit-wise determinants into lists of orbitals
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114cbf3081
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@ -36,6 +36,10 @@
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/* Return num variables as part of the output tuple */
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%apply int *OUTPUT { int32_t* const num};
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%apply int *OUTPUT { int64_t* const num};
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%apply int *OUTPUT { int32_t* const num_up};
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%apply int *OUTPUT { int32_t* const num_dn};
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%apply int *OUTPUT { int64_t* const num_up};
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%apply int *OUTPUT { int64_t* const num_dn};
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%apply float *OUTPUT { float* const num};
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%apply float *OUTPUT { double* const num};
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/* Return TREXIO exit code from trexio_open as part of the output tuple */
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@ -45,6 +49,10 @@
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/* Return number of sparse data points read from the file as part of the output tuple */
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%apply int *INOUT { int64_t* const buffer_size_read};
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/*
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%apply int { bitfield_t };
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*/
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/* Does not work for arrays (SIGSEGV) */
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/* This enables access to trexio_[...]_read_dset_str_low set of functions
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@ -93,6 +101,11 @@ import_array();
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%apply (double* ARGOUT_ARRAY1, int64_t DIM1) {(double* const value_sparse_read, const int64_t size_value_read)};
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%apply (int32_t* ARGOUT_ARRAY1, int64_t DIM1) {(int32_t* const index_sparse_read, const int64_t size_index_read)};
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/* Enable write|read_safe functions to convert numpy arrays from orbital list arrays */
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%apply (int32_t* ARGOUT_ARRAY1, int64_t DIM1) {(int32_t* const dset_up_out, const int64_t dim_up_out)};
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%apply (int32_t* ARGOUT_ARRAY1, int64_t DIM1) {(int32_t* const dset_dn_out, const int64_t dim_dn_out)};
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%apply (int64_t* ARGOUT_ARRAY1, int64_t DIM1) {(int64_t* const dset_up_out, const int64_t dim_up_out)};
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%apply (int64_t* ARGOUT_ARRAY1, int64_t DIM1) {(int64_t* const dset_dn_out, const int64_t dim_dn_out)};
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/* This tells SWIG to treat char ** dset_in pattern as a special case
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Enables access to trexio_[...]_write_dset_str set of functions directly, i.e.
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@ -43,6 +43,7 @@ typedef int32_t trexio_exit_code;
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#include <stdlib.h>
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#include <stdbool.h>
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#include <string.h>
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#include <err.h>
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#include "trexio.h"
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#include "trexio_private.h"
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@ -5154,7 +5155,7 @@ def has_determinant_coefficient(trexio_file) -> bool:
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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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* General helper functions
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This section contains general helper functions like ~trexio_info~.
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@ -5172,56 +5173,196 @@ def has_determinant_coefficient(trexio_file) -> bool:
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However, if the user validated that the file is correct (e.g. using ~trexio-tools~),
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then value of the ~metadata_unsafe~ attribute can be changed using the aforementioned function.
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TODO:
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~trexio_bitfield_to_list~ functions converts the bit field representation of a
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given determinants into a list of ~mo.num~ occupation numbers.
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(adapt from slaterlib or QP)
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~trexio_to_orbital_list~ function converts the list of integer bit fields of a
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given determinant into a list of indices of the occupied orbitals (for one spin component).
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~trexio_to_orbital_list_up_dn~ function does the same but for both up- and down-spin components
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of the determinant and returns two list of orbitals each corresponding to a different component.
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** C
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#+begin_src c :tangle prefix_front.h :exports none
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trexio_exit_code trexio_info(void);
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trexio_exit_code trexio_mark_safety(trexio_t* const file, const int32_t safety_flag);
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#+begin_src c :tangle prefix_front.h
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trexio_exit_code trexio_info(void);
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trexio_exit_code trexio_mark_safety(trexio_t* const file, const int32_t safety_flag);
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#+end_src
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#+begin_src c :tangle prefix_front.h
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typedef int64_t bitfield_t;
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#define ORBITAL_SHIFT 1
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#define INT_SIZE 64
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#define NORB_PER_INT ( 8*sizeof(bitfield_t) )
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/* Popcount and trailz */
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#if INT_SIZE == 64
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extern int __builtin_popcountll (unsigned long long x_0);
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#define popcnt(X) __builtin_popcountll((unsigned long long) X)
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extern int __builtin_ctzll (unsigned long long x_0);
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#define trailz(X) __builtin_ctzll((unsigned long long) X)
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#elif INT_SIZE == 32
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extern int __builtin_popcountl (unsigned long x_0);
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#define popcnt(X) __builtin_popcountl((unsigned long) X)
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extern int __builtin_ctzl(unsigned long x_0);
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#define trailz(X) __builtin_ctzl((unsigned long) X)
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#elif INT_SIZE == 16
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extern int __builtin_popcount (unsigned int x_0);
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#define popcnt(X) __builtin_popcount((unsigned int) X)
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extern int __builtin_ctz (unsigned int x_0);
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#define trailz(X) __builtin_ctz((unsigned int) X)
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#else
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#error("Invalid INT_SIZE")
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#endif
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trexio_exit_code trexio_to_orbital_list (const int32_t N_int, const bitfield_t* d1, int32_t* const list, int32_t* const occupied_num);
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trexio_exit_code trexio_to_orbital_list_up_dn (const int32_t N_int, const bitfield_t* d1, int32_t* const list_up, int32_t* const list_dn, int32_t* const occ_num_up, int32_t* const occ_num_dn);
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trexio_exit_code trexio_safe_to_orbital_list (const int32_t N_int, const int64_t* dset_in, const int64_t dim_in, int32_t* const dset_out, const int64_t dim_out, int32_t* const num);
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trexio_exit_code trexio_safe_to_orbital_list_up_dn (const int32_t N_int, const int64_t* dset_in, const int64_t dim_in, int32_t* const dset_up_out, const int64_t dim_up_out, int32_t* const dset_dn_out, const int64_t dim_dn_out, int32_t* const num_up, int32_t* const num_dn);
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#+end_src
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#+begin_src c :tangle prefix_front.c
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trexio_exit_code
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trexio_info (void)
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{
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printf("TREXIO_PACKAGE_VERSION : %s\n", TREXIO_PACKAGE_VERSION);
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trexio_exit_code trexio_to_orbital_list(const int32_t N_int,
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const bitfield_t* d1,
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int32_t* const list,
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int32_t* const occupied_num)
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{
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if (N_int <= 0) return TREXIO_INVALID_ARG_1;
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if (d1 == NULL) return TREXIO_INVALID_ARG_2;
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if (list == NULL) return TREXIO_INVALID_ARG_3;
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if (occupied_num == NULL) return TREXIO_INVALID_ARG_4;
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#ifdef TREXIO_GIT_HASH
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printf("TREXIO_GIT_HASH : %s\n", TREXIO_GIT_HASH);
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#else
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printf("GIT_HASH is stored in the config.h file, which is missing.");
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#endif
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bitfield_t tmp;
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int32_t shift;
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int32_t k;
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int32_t pos;
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#ifdef HAVE_HDF5
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printf("HAVE_HDF5 : true\n");
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printf("%s\n", H5_VERS_INFO);
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#else
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printf("HAVE_HDF5 : false\n");
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printf("TREXIO configured without the HDF5 library\n");
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#endif
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k = 0;
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shift = ORBITAL_SHIFT;
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return TREXIO_SUCCESS;
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}
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#+end_src
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for (int32_t i=0 ; i<N_int ; i++)
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{
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tmp = d1[i];
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#+begin_src c :tangle prefix_front.c
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trexio_exit_code
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trexio_mark_safety (trexio_t* const file, const int32_t safety_flag)
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{
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while (tmp != (bitfield_t) 0)
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{
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pos = trailz(tmp);
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if (pos < 0) return TREXIO_FAILURE;
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if (file == NULL) return TREXIO_INVALID_ARG_1;
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/* 1 for true ; 0 for false */
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if (safety_flag != 0 && safety_flag != 1) return TREXIO_INVALID_ARG_2;
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/* Cannot mark the file in safe mode */
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if (file->mode != 'u') return TREXIO_FAILURE;
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list[k] = ( (int32_t) pos) + shift;
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tmp ^= ( ((bitfield_t) 1) << pos);
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k++;
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}
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shift += NORB_PER_INT;
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}
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return trexio_write_metadata_unsafe(file, safety_flag);
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}
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#+end_src
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,*occupied_num = (int32_t) k;
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return TREXIO_SUCCESS;
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}
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#+end_src
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#+begin_src c :tangle prefix_front.c
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trexio_exit_code trexio_to_orbital_list_up_dn(const int32_t N_int,
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const bitfield_t* d1,
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int32_t* const list_up,
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int32_t* const list_dn,
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int32_t* const occ_num_up,
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int32_t* const occ_num_dn)
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{
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if (N_int <= 0) return TREXIO_INVALID_ARG_1;
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if (d1 == NULL) return TREXIO_INVALID_ARG_2;
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if (list_up == NULL) return TREXIO_INVALID_ARG_3;
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if (list_dn == NULL) return TREXIO_INVALID_ARG_4;
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if (occ_num_up == NULL) return TREXIO_INVALID_ARG_5;
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if (occ_num_dn == NULL) return TREXIO_INVALID_ARG_6;
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trexio_exit_code rc;
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/* First process up-spin electrons */
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rc = trexio_to_orbital_list(N_int, &d1[0], list_up, occ_num_up);
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if (rc != TREXIO_SUCCESS) return rc;
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/* Now process down-spin electrons */
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rc = trexio_to_orbital_list(N_int, &d1[N_int], list_dn, occ_num_dn);
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if (rc != TREXIO_SUCCESS) return rc;
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return TREXIO_SUCCESS;
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}
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#+end_src
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#+begin_src c :tangle prefix_front.c
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trexio_exit_code
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trexio_safe_to_orbital_list (const int32_t N_int,
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const int64_t* dset_in,
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const int64_t dim_in,
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int32_t* const dset_out,
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const int64_t dim_out,
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int32_t* const num)
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{
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return trexio_to_orbital_list(N_int, dset_in, dset_out, num);
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}
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trexio_exit_code
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trexio_safe_to_orbital_list_up_dn (const int32_t N_int,
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const int64_t* dset_in,
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const int64_t dim_in,
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int32_t* const dset_up_out,
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const int64_t dim_up_out,
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int32_t* const dset_dn_out,
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const int64_t dim_dn_out,
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int32_t* const num_up,
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int32_t* const num_dn)
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{
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return trexio_to_orbital_list_up_dn(N_int, dset_in, dset_up_out, dset_dn_out, num_up, num_dn);
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}
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#+end_src
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#+begin_src c :tangle prefix_front.c
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trexio_exit_code
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trexio_info (void)
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{
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printf("TREXIO_PACKAGE_VERSION : %s\n", TREXIO_PACKAGE_VERSION);
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#ifdef TREXIO_GIT_HASH
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printf("TREXIO_GIT_HASH : %s\n", TREXIO_GIT_HASH);
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#else
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printf("GIT_HASH is stored in the config.h file, which is missing.");
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#endif
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#ifdef HAVE_HDF5
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printf("HAVE_HDF5 : true\n");
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printf("%s\n", H5_VERS_INFO);
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#else
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printf("HAVE_HDF5 : false\n");
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printf("TREXIO configured without the HDF5 library\n");
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#endif
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return TREXIO_SUCCESS;
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}
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#+end_src
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#+begin_src c :tangle prefix_front.c
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trexio_exit_code
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trexio_mark_safety (trexio_t* const file, const int32_t safety_flag)
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{
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if (file == NULL) return TREXIO_INVALID_ARG_1;
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/* 1 for true ; 0 for false */
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if (safety_flag != 0 && safety_flag != 1) return TREXIO_INVALID_ARG_2;
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/* Cannot mark the file in safe mode */
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if (file->mode != 'u') return TREXIO_FAILURE;
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return trexio_write_metadata_unsafe(file, safety_flag);
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}
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#+end_src
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** Fortran
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@ -5233,18 +5374,104 @@ interface
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end interface
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#+end_src
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#+begin_src f90 :tangle prefix_fortran.f90
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interface
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integer(trexio_exit_code) function trexio_to_orbital_list(N_int, d1, list, occupied_num) bind(C)
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use, intrinsic :: iso_c_binding
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import
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integer(c_int32_t), intent(in), value :: N_int
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integer(c_int64_t), intent(in) :: d1(*)
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integer(c_int32_t), intent(out) :: list(*)
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integer(c_int32_t), intent(inout) :: occupied_num
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end function trexio_to_orbital_list
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end interface
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interface
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integer(trexio_exit_code) function trexio_to_orbital_list_up_dn(N_int, d1, list_up, list_dn, occ_num_up, occ_num_dn) bind(C)
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use, intrinsic :: iso_c_binding
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import
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integer(c_int32_t), intent(in), value :: N_int
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integer(c_int64_t), intent(in) :: d1(*)
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integer(c_int32_t), intent(out) :: list_up(*)
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integer(c_int32_t), intent(out) :: list_dn(*)
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integer(c_int32_t), intent(inout) :: occ_num_up
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integer(c_int32_t), intent(inout) :: occ_num_dn
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end function trexio_to_orbital_list_up_dn
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end interface
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#+end_src
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** Python
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#+begin_src python :tangle basic_python.py
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def info():
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"""Print the info about the installed TREXIO library.
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"""
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"""Print the info about the installed TREXIO library."""
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rc = pytr.trexio_info()
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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 basic_python.py
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def to_orbital_list(n_int: int, determinant: list) -> list:
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"""Convert a given determinant into a list of occupied orbitals.
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Input:
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~determinant~ - list of bit fields (integers)
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~n_int~ - number of bit fields per determinant of a given spin
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Returns:
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~orbital_list~: list
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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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# max possible size of the orbital list per spin component (upper limit on the number of MOs)
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size_max = n_int * 64
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rc, orbital_list, occ_num = pytr.trexio_safe_to_orbital_list(n_int, determinant, size_max)
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if rc != TREXIO_SUCCESS:
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raise Error(rc)
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if len(orbital_list) < occ_num:
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raise Exception("Inconsistent size of the orbital_list.")
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return orbital_list
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def to_orbital_list_up_dn(n_int: int, determinant: list) -> tuple:
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"""Convert a given determinant into two lists of occupied orbitals.
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Input:
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~determinant~ - list of bit fields (integers)
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~n_int~ - number of bit fields per determinant of a given spin
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Returns:
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result: tuple with the following items:
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~orbital_list_up~: list of orbitals occupied by up-spin electrons
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~orbital_list_dn~: list of orbitals occupied by down-spin electrons
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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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# max possible size of the orbital list per spin component (upper limit on the number of MOs)
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size_max = n_int * 64
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rc, orbital_list_up, orbital_list_dn, occ_num_up, occ_num_dn = pytr.trexio_safe_to_orbital_list_up_dn(n_int, determinant, size_max, size_max)
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if rc != TREXIO_SUCCESS:
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raise Error(rc)
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if len(orbital_list_up) < occ_num_up:
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raise Exception("Inconsistent size of the orbital_list for up-spin electrons.")
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if len(orbital_list_dn) < occ_num_dn:
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raise Exception("Inconsistent size of the orbital_list for down-spin electrons.")
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return (orbital_list_up[0:occ_num_up], orbital_list_dn[0:occ_num_dn])
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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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