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Added documentation
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# =============== DOCUMENTATION =============== #
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HTML_TANGLED = docs/index.html \
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docs/Sparse.html \
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docs/examples.html \
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docs/templator_hdf5.html \
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docs/trex.html \
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docs/README.html \
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22
Sparse.org
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Sparse.org
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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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solution is to use one file for each sparse data set, and store a
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the name of this file in the group.
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Each integral can be a line in the file:
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i j k l x
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which can be read with "%10ld %10ld %10ld %10ld %24.16e".
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The offset can be used with ~fseek(69L*offset, SEEK_SET)~
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* HDF5 Back end
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We need to declare the number of rows of the dataset as
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~UNLIMITED~. This requires to use the ~Chunked~ storage, and the
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chunks should absolutely not be larger than 1MB.
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To extend the storage, see :
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https://support.hdfgroup.org/HDF5/doc1.6/UG/10_Datasets.html
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(figure 17)
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If the offset+num > nmax, we need to extend the dataset.
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examples.org
Normal file
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examples.org
Normal file
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#+TITLE: Examples
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#+STARTUP: latexpreview
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#+SETUPFILE: docs/theme.setup
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* Accessing sparse quantities
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** Fortran
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:PROPERTIES:
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:header-args: :tangle print_energy.f90
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:END:
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#+begin_src f90
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program print_energy
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use trexio
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implicit none
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character*(128) :: filename ! Name of the input file
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integer :: rc ! Return code for error checking
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integer(8) :: f ! TREXIO file handle
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character*(128) :: err_msg ! Error message
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#+end_src
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This program computes the energy as:
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\[
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E = E_{\text{NN}} + \sum_{ij} D_{ij}\, \langle i | h | j \rangle\,
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+\, \frac{1}{2} \sum_{ijkl} \Gamma_{ijkl}\, \langle i j | k l
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\rangle\; \textrm{ with } \; 0 < i,j,k,l \le n
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\]
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One needs to read from the TREXIO file:
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- $n$ :: The number of molecular orbitals
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- $E_{\text{NN}}$ :: The nuclear repulsion energy
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- $D_{ij}$ :: The one-body reduced density matrix
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- $\langle i |h| j \rangle$ :: The one-electron Hamiltonian integrals
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- $\Gamma_{ijkl}$ :: The two-body reduced density matrix
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- $\langle i j | k l \rangle$ :: The electron repulsion integrals
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#+begin_src f90
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integer :: n
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double precision :: E, E_nn
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double precision, allocatable :: D(:,:), h0(:,:)
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double precision, allocatable :: G(:,:,:,:), W(:,:,:,:)
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#+end_src
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*** Declare Temporary variables
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#+begin_src f90
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integer :: i, j, k, l, m
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integer(8), parameter :: BUFSIZE = 10000_8
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integer(8) :: offset, icount, size_max
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integer :: buffer_index(4,BUFSIZE)
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double precision :: buffer_values(BUFSIZE)
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double precision, external :: ddot ! BLAS dot product
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#+end_src
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*** Obtain the name of the TREXIO file from the command line, and open it for reading
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#+begin_src f90
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call getarg(1, filename)
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f = trexio_open (filename, 'r', TREXIO_HDF5, rc)
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if (rc /= TREXIO_SUCCESS) then
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call trexio_string_of_error(rc, err_msg)
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print *, 'Error opening TREXIO file: '//trim(err_msg)
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stop
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end if
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#+end_src
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*** Read the nuclear repulsion energy
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#+begin_src f90
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rc = trexio_read_nucleus_repulsion(f, E_nn)
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if (rc /= TREXIO_SUCCESS) then
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call trexio_string_of_error(rc, err_msg)
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print *, 'Error reading nuclear repulsion: '//trim(err_msg)
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stop
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end if
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#+end_src
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*** Read the number of molecular orbitals
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#+begin_src f90
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rc = trexio_read_mo_num(f, n)
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if (rc /= TREXIO_SUCCESS) then
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call trexio_string_of_error(rc, err_msg)
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print *, 'Error reading number of MOs: '//trim(err_msg)
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stop
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end if
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#+end_src
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*** Allocate memory
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#+begin_src f90
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allocate( D(n,n), h0(n,n) )
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allocate( G(n,n,n,n), W(n,n,n,n) )
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#+end_src
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*** Read one-electron quantities
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#+begin_src f90
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rc = trexio_has_mo_1e_int_core_hamiltonian(f)
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if (rc /= TREXIO_SUCCESS) then
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stop 'No core hamiltonian in file'
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end if
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rc = trexio_read_mo_1e_int_core_hamiltonian(f, h0)
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if (rc /= TREXIO_SUCCESS) then
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call trexio_string_of_error(rc, err_msg)
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print *, 'Error reading core Hamiltonian: '//trim(err_msg)
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stop
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end if
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rc = trexio_has_rdm_1e(f)
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if (rc /= TREXIO_SUCCESS) then
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stop 'No 1e RDM in file'
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end if
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rc = trexio_read_rdm_1e(f, D)
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if (rc /= TREXIO_SUCCESS) then
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call trexio_string_of_error(rc, err_msg)
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print *, 'Error reading one-body RDM: '//trim(err_msg)
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stop
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end if
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#+end_src
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*** Read two-electron quantities
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#+begin_src f90
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rc = trexio_has_mo_2e_int_eri(f)
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if (rc /= TREXIO_SUCCESS) then
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stop 'No electron repulsion integrals in file'
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end if
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rc = trexio_read_mo_2e_int_eri_size (f, size_max)
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if (rc /= TREXIO_SUCCESS) then
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call trexio_string_of_error(rc, err_msg)
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print *, 'Error reading number of ERIs: '//trim(err_msg)
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stop
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end if
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W(:,:,:,:) = 0.d0
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icount = BUFSIZE
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offset = 0_8
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do while (offset < size_max)
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rc = trexio_read_mo_2e_int_eri(f, offset, icount, buffer_index, buffer_values)
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if (rc /= TREXIO_SUCCESS) exit
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do m=1,min(icount, size_max-offset)
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i = buffer_index(1,m)
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j = buffer_index(2,m)
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k = buffer_index(3,m)
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l = buffer_index(4,m)
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W(i,j,k,l) = buffer_values(m)
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W(k,j,i,l) = buffer_values(m)
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W(i,l,k,j) = buffer_values(m)
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W(k,l,i,j) = buffer_values(m)
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W(j,i,l,k) = buffer_values(m)
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W(j,k,l,i) = buffer_values(m)
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W(l,i,j,k) = buffer_values(m)
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W(l,k,j,i) = buffer_values(m)
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end do
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offset = offset + icount
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end do
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rc = trexio_has_rdm_2e(f)
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if (rc /= TREXIO_SUCCESS) then
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stop 'No two-body density matrix in file'
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end if
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rc = trexio_read_rdm_2e_size (f, size_max)
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if (rc /= TREXIO_SUCCESS) then
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call trexio_string_of_error(rc, err_msg)
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print *, 'Error reading number of 2-RDM elements: '//trim(err_msg)
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stop
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end if
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G(:,:,:,:) = 0.d0
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icount = BUFSIZE
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offset = 0_8
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do while (offset < size_max)
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rc = trexio_read_rdm_2e(f, offset, icount, buffer_index, buffer_values)
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if (rc /= TREXIO_SUCCESS) exit
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do m=1,min(icount, size_max-offset)
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i = buffer_index(1,m)
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j = buffer_index(2,m)
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k = buffer_index(3,m)
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l = buffer_index(4,m)
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G(i,j,k,l) = buffer_values(m)
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end do
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offset = offset + icount
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end do
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#+end_src
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*** Compute the energy
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#+begin_src f90
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E = E_nn + &
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ddot( n**2, D, 1, h0, 1 ) + &
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0.5d0 * ddot( n**4, G, 1, W, 1 )
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print *, 'Energy: ', E
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#+end_src
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*** Terminate
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#+begin_src f90
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deallocate( D, h0, G, W )
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end program
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#+end_src
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trex.org
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trex.org
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#+STARTUP: latexpreview
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#+SETUPFILE: docs/theme.setup
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This page contains information about the general structure of the
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TREXIO library. The source code of the library can be automatically
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generated based on the contents of the ~trex.json~ configuration file,
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which itself is compiled from different sections (groups) presented below.
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This page contains information about the general structure of the
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TREXIO library. The source code of the library can be automatically
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generated based on the contents of the ~trex.json~ configuration file,
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which itself is compiled from different sections (groups) presented
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below.
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For more information about the automatic generation on the source code
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or regarding possible modifications, please contact the TREXIO developers.
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For more information about the automatic generation on the source code
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or regarding possible modifications, please contact the TREXIO
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developers.
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All quantities are saved in TREXIO file in atomic units.
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The dimensions of the arrays in the tables below are given in
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column-major order (as in Fortran), and the ordering of the dimensions
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is reversed in the produced ~trex.json~ configuration file as the library is
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All quantities are saved in TREXIO file in atomic units. The
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dimensions of the arrays in the tables below are given in column-major
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order (as in Fortran), and the ordering of the dimensions is reversed
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in the produced ~trex.json~ configuration file as the library is
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written in C.
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TREXIO currently supports ~int~, ~float~ and ~str~ types for both single attributes and arrays.
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Note, that some attributes might have ~dim~ type (e.g. ~num~ of the ~nucleus~ group).
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This type is treated exactly the same as ~int~ with the only difference that ~dim~ variables
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cannot be negative or zero. This additional constraint is required because ~dim~ attributes
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are used internally to allocate memory and to check array boundaries in the memory-safe API.
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Most of the times, the ~dim~ variables contain ~num~ suffix.
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TREXIO currently supports ~int~, ~float~ and ~str~ types for both
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single attributes and arrays. Note, that some attributes might have
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~dim~ type (e.g. ~num~ of the ~nucleus~ group). This type is treated
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exactly the same as ~int~ with the only difference that ~dim~
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variables cannot be negative. This additional constraint is required
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because ~dim~ attributes are used internally to allocate memory and to
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check array boundaries in the memory-safe API. Most of the times, the
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~dim~ variables contain the ~num~ suffix.
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In Fortran, the arrays are 1-based and in most other languages the
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arrays are 0-based. Hence, we introduce the ~index~ type which is an
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1-based ~int~ in the Fortran interface and 0-based otherwise.
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For sparse data structures such as electron replusion integrals,
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the data can be too large to fit in memory and the data needs to be
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fetched using multiple function calls to perform I/O on buffers.
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#+begin_src python :tangle trex.json :exports none
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{
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#+end_src
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