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mirror of https://github.com/TREX-CoE/trexio.git synced 2024-12-23 04:43:57 +01:00

Helper functions to convert bit-wise determinants into lists of orbitals

This commit is contained in:
q-posev 2022-04-22 13:15:32 +02:00
parent 114cbf3081
commit 32cb2255c4
2 changed files with 281 additions and 41 deletions

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