LCPQ/quantum_package
10
0
Fork 0
mirror of https://github.com/LCPQ/quantum_package synced 2024-06-02 11:25:26 +02:00
Code Issues Releases Wiki Activity

minor modifs in README.rst

Browse Source
This commit is contained in:
Emmanuel Giner 2018-12-22 14:44:19 +01:00
parent 4f60b423bf
commit 9dc1408907
13 changed files with 168 additions and 108 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

3
data/module_gitignore
View File

@ -5,7 +5,9 @@
/vortex/u/eginer/qp_toto/quantum_package/src/tools/fcidump
/vortex/u/eginer/qp_toto/quantum_package/src/tools/four_idx_transform
/vortex/u/eginer/qp_toto/quantum_package/src/tools/molden
/vortex/u/eginer/qp_toto/quantum_package/src/tools/print_wf
/vortex/u/eginer/qp_toto/quantum_package/src/tools/save_natorb
/vortex/u/eginer/qp_toto/quantum_package/src/tools/save_one_body_dm
/vortex/u/eginer/qp_toto/quantum_package/src/tools/save_ortho_mos
/vortex/u/eginer/qp_toto/quantum_package/src/tools/write_integrals_erf
IRPF90_man
@ -16,6 +18,7 @@ ao_basis
ao_one_e_integrals
ao_two_e_erf_integrals
ao_two_e_integrals
aux_quantities
bitmask
davidson
davidson_undressed

2
src/becke_numerical_grid/README.rst
View File

@ -6,7 +6,7 @@ This module contains all quantities needed to build the Becke's grid used in gen
This grid is built as the reunion of a spherical grid around each atom. Each spherical grid contains a certain number of radial and angular points.
For a simple example of how to use the grid, see example.irp.f.
For a simple example of how to use the grid, see :file:`example.irp.f`.
The spherical integration uses Lebedev-Laikov grids, which was used from the code distributed through CCL (http://www.ccl.net/).
See next section for explanations and citation policies.

2
src/bitmask/README.rst
View File

@ -25,4 +25,4 @@ transforming a bit string to a list of integers for example.
bit_kind = bit_kind_size / 8
For an example of how to use the bitmaks, see the file :file:`example.irp.f`.

9
src/hartree_fock/README.rst
View File

@ -6,13 +6,20 @@ Hartree-Fock
The Hartree-Fock module performs *Restricted* Hartree-Fock calculations (the
spatial part of the |MOs| is common for alpha and beta spinorbitals).
The Hartree-Fock program does the following:
The Hartree-Fock in an SCF and therefore is based on the ``scf_utils`` structure.
It performs the following actions:
#. Compute/Read all the one- and two-electron integrals, and store them in memory
#. Check in the |EZFIO| database if there is a set of |MOs|. If there is, it
will read them as initial guess. Otherwise, it will create a guess.
#. Perform the |SCF| iterations
The definition of the Fock matrix is in :file:`hartree_fock fock_matrix_hf.irp.f`
For the keywords related to the |SCF| procedure, see the ``scf_utils`` directory where you will find all options.
The main are:
# :option:`scf_utils thresh_scf`
# :option:`scf_utils level_shift`
At each iteration, the |MOs| are saved in the |EZFIO| database. Hence, if the calculation
crashes for any unexpected reason, the calculation can be restarted by running again
the |SCF| with the same |EZFIO| database.

14
src/hartree_fock/hf_energy.irp.f
View File

@ -1,6 +1,13 @@
BEGIN_PROVIDER [double precision, extra_energy_contrib_from_density]
BEGIN_PROVIDER [double precision, extra_e_contrib_density]
implicit none
extra_energy_contrib_from_density = 0.D0
BEGIN_DOC
! Extra contribution to the SCF energy coming from the density.
!
! For a Hartree-Fock calculation: extra_e_contrib_density = 0
!
! For a Kohn-Sham or Range-separated Kohn-Sham: the exchange/correlation - trace of the V_xc potential
END_DOC
extra_e_contrib_density = 0.D0
END_PROVIDER
@ -8,6 +15,9 @@ END_PROVIDER
&BEGIN_PROVIDER [ double precision, HF_two_electron_energy]
&BEGIN_PROVIDER [ double precision, HF_one_electron_energy]
implicit none
BEGIN_DOC
! Hartree-Fock energy containing the nuclear repulsion, and its one- and two-body components.
END_DOC
integer :: i,j
HF_energy = nuclear_repulsion
do j=1,ao_num

13
src/kohn_sham/README.rst
View File

@ -1,18 +1,25 @@
============
Hartree-Fock
Kohn-Sham
============
The Hartree-Fock module performs *Restricted* Hartree-Fock calculations (the
The Kohn-Sham module performs *Restricted* Kohn-Sham calculations (the
spatial part of the |MOs| is common for alpha and beta spinorbitals).
The Hartree-Fock program does the following:
The Kohn-Sham in an SCF and therefore is based on the ``scf_utils`` structure.
It performs the following actions:
#. Compute/Read all the one- and two-electron integrals, and store them in memory
#. Check in the |EZFIO| database if there is a set of |MOs|. If there is, it
will read them as initial guess. Otherwise, it will create a guess.
#. Perform the |SCF| iterations
The definition of the Fock matrix is in :file:`kohn_sham fock_matrix_ks.irp.f`
For the keywords related to the |SCF| procedure, see the ``scf_utils`` directory where you will find all options.
The main are:
# :option:`scf_utils thresh_scf`
# :option:`scf_utils level_shift`
At each iteration, the |MOs| are saved in the |EZFIO| database. Hence, if the calculation
crashes for any unexpected reason, the calculation can be restarted by running again
the |SCF| with the same |EZFIO| database.

43
src/kohn_sham/fock_matrix_ks.irp.f
View File

@ -199,46 +199,3 @@ END_PROVIDER
END_PROVIDER
BEGIN_PROVIDER [ double precision, KS_energy]
&BEGIN_PROVIDER [ double precision, two_electron_energy]
&BEGIN_PROVIDER [ double precision, one_electron_energy]
&BEGIN_PROVIDER [ double precision, Fock_matrix_energy]
&BEGIN_PROVIDER [ double precision, trace_potential_xc ]
implicit none
BEGIN_DOC
! Hartree-Fock energy
END_DOC
integer :: i,j
double precision :: accu_mono,accu_fock
KS_energy = nuclear_repulsion
one_electron_energy = 0.d0
two_electron_energy = 0.d0
Fock_matrix_energy = 0.d0
trace_potential_xc = 0.d0
do j=1,ao_num
do i=1,ao_num
Fock_matrix_energy += Fock_matrix_ao_alpha(i,j) * SCF_density_matrix_ao_alpha(i,j) + &
Fock_matrix_ao_beta(i,j) * SCF_density_matrix_ao_beta(i,j)
two_electron_energy += 0.5d0 * ( ao_bi_elec_integral_alpha(i,j) * SCF_density_matrix_ao_alpha(i,j) &
+ao_bi_elec_integral_beta(i,j) * SCF_density_matrix_ao_beta(i,j) )
one_electron_energy += ao_mono_elec_integral(i,j) * (SCF_density_matrix_ao_alpha(i,j) + SCF_density_matrix_ao_beta (i,j) )
! possible bug fix for open-shell
! trace_potential_xc += (ao_potential_alpha_xc(i,j) + ao_potential_beta_xc(i,j) ) * (SCF_density_matrix_ao_alpha(i,j) + SCF_density_matrix_ao_beta (i,j) )
trace_potential_xc += ao_potential_alpha_xc(i,j) * SCF_density_matrix_ao_alpha(i,j) + ao_potential_beta_xc(i,j) * SCF_density_matrix_ao_beta (i,j)
enddo
enddo
KS_energy += e_exchange_dft + e_correlation_dft + one_electron_energy + two_electron_energy
END_PROVIDER
BEGIN_PROVIDER [double precision, extra_energy_contrib_from_density]
implicit none
! possible bug fix for open-shell:
! extra_energy_contrib_from_density = e_exchange_dft + e_correlation_dft - 0.25d0 * trace_potential_xc
extra_energy_contrib_from_density = e_exchange_dft + e_correlation_dft - 0.5d0 * trace_potential_xc
END_PROVIDER

43
src/kohn_sham/ks_enery.irp.f Normal file
View File

@ -0,0 +1,43 @@
BEGIN_PROVIDER [ double precision, KS_energy]
&BEGIN_PROVIDER [ double precision, two_electron_energy]
&BEGIN_PROVIDER [ double precision, one_electron_energy]
&BEGIN_PROVIDER [ double precision, Fock_matrix_energy]
&BEGIN_PROVIDER [ double precision, trace_potential_xc ]
implicit none
BEGIN_DOC
! Kohn-Sham energy containing the nuclear repulsion energy, and the various components of this quantity.
END_DOC
integer :: i,j
double precision :: accu_mono,accu_fock
KS_energy = nuclear_repulsion
one_electron_energy = 0.d0
two_electron_energy = 0.d0
Fock_matrix_energy = 0.d0
trace_potential_xc = 0.d0
do j=1,ao_num
do i=1,ao_num
Fock_matrix_energy += Fock_matrix_ao_alpha(i,j) * SCF_density_matrix_ao_alpha(i,j) + &
Fock_matrix_ao_beta(i,j) * SCF_density_matrix_ao_beta(i,j)
two_electron_energy += 0.5d0 * ( ao_bi_elec_integral_alpha(i,j) * SCF_density_matrix_ao_alpha(i,j) &
+ao_bi_elec_integral_beta(i,j) * SCF_density_matrix_ao_beta(i,j) )
one_electron_energy += ao_mono_elec_integral(i,j) * (SCF_density_matrix_ao_alpha(i,j) + SCF_density_matrix_ao_beta (i,j) )
trace_potential_xc += ao_potential_alpha_xc(i,j) * SCF_density_matrix_ao_alpha(i,j) + ao_potential_beta_xc(i,j) * SCF_density_matrix_ao_beta (i,j)
enddo
enddo
KS_energy += e_exchange_dft + e_correlation_dft + one_electron_energy + two_electron_energy
END_PROVIDER
BEGIN_PROVIDER [double precision, extra_e_contrib_density]
implicit none
BEGIN_DOC
! Extra contribution to the SCF energy coming from the density.
!
! For a Hartree-Fock calculation: extra_e_contrib_density = 0
!
! For a Kohn-Sham or Range-separated Kohn-Sham: the exchange/correlation - 1/2 trace of the V_xc potential
END_DOC
extra_e_contrib_density = e_exchange_dft + e_correlation_dft - 0.5d0 * trace_potential_xc
END_PROVIDER

23
src/kohn_sham_rs/README.rst
View File

@ -1,18 +1,27 @@
============
Hartree-Fock
============
=========================
Range-separated Kohn-Sham
=========================
The Hartree-Fock module performs *Restricted* Hartree-Fock calculations (the
spatial part of the |MOs| is common for alpha and beta spinorbitals).
The Range-separated Kohn-Sham module performs *Restricted* Kohn-Sham calculations (the
spatial part of the |MOs| is common for alpha and beta spinorbitals) where the coulomb interaction is partially treated using exact exchange.
The splitting of the interaction between long- and short-range is determined by the range-separation parameter :option:`ao_two_e_erf_integrals mu_erf`. The long-range part of the interaction is explicitly treated with exact exchange, and the short-range part of the interaction is treated with appropriate DFT functionals.
The Hartree-Fock program does the following:
The Range-separated Kohn-Sham in an SCF and therefore is based on the ``scf_utils`` structure.
It performs the following actions:
#. Compute/Read all the one- and two-electron integrals, and store them in memory
#. Check in the |EZFIO| database if there is a set of |MOs|. If there is, it
will read them as initial guess. Otherwise, it will create a guess.
#. Perform the |SCF| iterations
The definition of the Fock matrix is in :file:`kohn_sham_rs fock_matrix_rs_ks.irp.f`
For the keywords related to the |SCF| procedure, see the ``scf_utils`` directory where you will find all options.
The main are:
# :option:`scf_utils thresh_scf`
# :option:`scf_utils level_shift`
At each iteration, the |MOs| are saved in the |EZFIO| database. Hence, if the calculation
crashes for any unexpected reason, the calculation can be restarted by running again
the |SCF| with the same |EZFIO| database.
@ -24,8 +33,6 @@ To start a calculation from scratch, the simplest way is to remove the
``mo_basis`` directory from the |EZFIO| database, and run the |SCF| again.
.. _DIIS: https://en.wikipedia.org/w/index.php?title=DIIS
.. _level-shifting: https://doi.org/10.1002/qua.560070407

47
src/kohn_sham_rs/fock_matrix_rs_ks.irp.f
View File

@ -245,50 +245,3 @@ END_PROVIDER
END_PROVIDER
BEGIN_PROVIDER [ double precision, RS_KS_energy ]
!BEGIN_PROVIDER [ double precision, SCF_energy ]
&BEGIN_PROVIDER [ double precision, two_electron_energy]
&BEGIN_PROVIDER [ double precision, one_electron_energy]
&BEGIN_PROVIDER [ double precision, Fock_matrix_energy]
&BEGIN_PROVIDER [ double precision, trace_potential_xc ]
implicit none
BEGIN_DOC
! Range-separated Kohn-Sham energy
END_DOC
RS_KS_energy = nuclear_repulsion
integer :: i,j
double precision :: accu_mono,accu_fock
one_electron_energy = 0.d0
two_electron_energy = 0.d0
Fock_matrix_energy = 0.d0
trace_potential_xc = 0.d0
do j=1,ao_num
do i=1,ao_num
Fock_matrix_energy += Fock_matrix_ao_alpha(i,j) * SCF_density_matrix_ao_alpha(i,j) + &
Fock_matrix_ao_beta(i,j) * SCF_density_matrix_ao_beta(i,j)
two_electron_energy += 0.5d0 * ( ao_bi_elec_integral_alpha(i,j) * SCF_density_matrix_ao_alpha(i,j) &
+ao_bi_elec_integral_beta(i,j) * SCF_density_matrix_ao_beta(i,j) )
one_electron_energy += ao_mono_elec_integral(i,j) * (SCF_density_matrix_ao_alpha(i,j) + SCF_density_matrix_ao_beta (i,j) )
! possible bug fix for open-shell
! trace_potential_xc += (ao_potential_alpha_xc(i,j) + ao_potential_beta_xc(i,j) ) * (SCF_density_matrix_ao_alpha(i,j) + SCF_density_matrix_ao_beta (i,j) )
trace_potential_xc += ao_potential_alpha_xc(i,j) * SCF_density_matrix_ao_alpha(i,j) + ao_potential_beta_xc(i,j) * SCF_density_matrix_ao_beta (i,j)
enddo
enddo
RS_KS_energy += e_exchange_dft + e_correlation_dft + one_electron_energy + two_electron_energy
!SCF_energy = RS_KS_energy
END_PROVIDER
BEGIN_PROVIDER [double precision, extra_energy_contrib_from_density]
implicit none
! possible bug fix for open-shell:
! extra_energy_contrib_from_density = e_exchange_dft + e_correlation_dft - 0.25d0 * trace_potential_xc
extra_energy_contrib_from_density = e_exchange_dft + e_correlation_dft - 0.5d0 * trace_potential_xc
END_PROVIDER
!BEGIN_PROVIDER [ double precision, SCF_energy ]
! implicit none
! SCF_energy = RS_KS_energy
!END_PROVIDER

42
src/kohn_sham_rs/rs_ks_energy.irp.f Normal file
View File

@ -0,0 +1,42 @@
BEGIN_PROVIDER [ double precision, RS_KS_energy ]
&BEGIN_PROVIDER [ double precision, two_electron_energy]
&BEGIN_PROVIDER [ double precision, one_electron_energy]
&BEGIN_PROVIDER [ double precision, Fock_matrix_energy]
&BEGIN_PROVIDER [ double precision, trace_potential_xc ]
implicit none
BEGIN_DOC
! Range-separated Kohn-Sham energy containing the nuclear repulsion energy, and the various components of this quantity.
END_DOC
RS_KS_energy = nuclear_repulsion
integer :: i,j
double precision :: accu_mono,accu_fock
one_electron_energy = 0.d0
two_electron_energy = 0.d0
Fock_matrix_energy = 0.d0
trace_potential_xc = 0.d0
do j=1,ao_num
do i=1,ao_num
Fock_matrix_energy += Fock_matrix_ao_alpha(i,j) * SCF_density_matrix_ao_alpha(i,j) + &
Fock_matrix_ao_beta(i,j) * SCF_density_matrix_ao_beta(i,j)
two_electron_energy += 0.5d0 * ( ao_bi_elec_integral_alpha(i,j) * SCF_density_matrix_ao_alpha(i,j) &
+ao_bi_elec_integral_beta(i,j) * SCF_density_matrix_ao_beta(i,j) )
one_electron_energy += ao_mono_elec_integral(i,j) * (SCF_density_matrix_ao_alpha(i,j) + SCF_density_matrix_ao_beta (i,j) )
trace_potential_xc += ao_potential_alpha_xc(i,j) * SCF_density_matrix_ao_alpha(i,j) + ao_potential_beta_xc(i,j) * SCF_density_matrix_ao_beta (i,j)
enddo
enddo
RS_KS_energy += e_exchange_dft + e_correlation_dft + one_electron_energy + two_electron_energy
END_PROVIDER
BEGIN_PROVIDER [double precision, extra_e_contrib_density]
implicit none
BEGIN_DOC
! Extra contribution to the SCF energy coming from the density.
!
! For a Hartree-Fock calculation: extra_e_contrib_density = 0
!
! For a Kohn-Sham or Range-separated Kohn-Sham: the exchange/correlation - 1/2 trace of the V_xc potential
END_DOC
extra_e_contrib_density = e_exchange_dft + e_correlation_dft - 0.5d0 * trace_potential_xc
END_PROVIDER

33
src/scf_utils/README.rst
View File

@ -3,4 +3,35 @@ scf_utils
=========
TODO
The scf_utils module performs *Restricted* SCF calculations (the
spatial part of the |MOs| is common for alpha and beta spinorbitals) based on a single-determinant wave function.
This module does not produce any executable *and must not do*, but instead it contains everything one needs to perform an orbital optimization based on an Fock matrix.
The ``scf_utils`` module is included in the :file:`NEED` of the various single determinant SCF procedures, such as ``hartree_fock`` or ``kohn_sham``, where a specific definition of the Fock matrix is given (see :file:`hartree_fock fock_matrix_hf.irp.f` for an example).
All SCF programs perform the following actions:
#. Compute/Read all the one- and two-electron integrals, and store them in memory
#. Check in the |EZFIO| database if there is a set of |MOs|. If there is, it
will read them as initial guess. Otherwise, it will create a guess.
#. Perform the |SCF| iterations based on the definition of the Fock matrix
The main keywords/options are:
# :option:`scf_utils thresh_scf`
# :option:`scf_utils level_shift`
At each iteration, the |MOs| are saved in the |EZFIO| database. Hence, if the calculation
crashes for any unexpected reason, the calculation can be restarted by running again
the |SCF| with the same |EZFIO| database.
The `DIIS`_ algorithm is implemented, as well as the `level-shifting`_ method.
If the |SCF| does not converge, try again with a higher value of :option:`level_shift`.
To start a calculation from scratch, the simplest way is to remove the
``mo_basis`` directory from the |EZFIO| database, and run the |SCF| again.
.. _DIIS: https://en.wikipedia.org/w/index.php?title=DIIS
.. _level-shifting: https://doi.org/10.1002/qua.560070407

2
src/scf_utils/fock_matrix.irp.f
View File

@ -138,7 +138,7 @@ BEGIN_PROVIDER [ double precision, SCF_energy ]
(ao_mono_elec_integral(i,j) + Fock_matrix_ao_beta (i,j) ) * SCF_density_matrix_ao_beta (i,j) )
enddo
enddo
SCF_energy += extra_energy_contrib_from_density
SCF_energy += extra_e_contrib_density
END_PROVIDER