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Updated documentation

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This commit is contained in:
Anthony Scemama 2019-06-15 00:28:29 +02:00
parent 51f81843a6
commit 6479c294e8
16 changed files with 467 additions and 57 deletions
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26
docs/source/modules/cipsi.rst
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@ -1213,6 +1213,7 @@ Subroutines / functions
:columns: 3
* :c:data:`generators_bitmask`
* :c:data:`selection_weight`
* :c:data:`pt2_stoch_istate`
* :c:data:`psi_selectors`
* :c:data:`psi_det`
@ -1235,6 +1236,7 @@ Subroutines / functions
* :c:data:`n_det_generators`
* :c:data:`psi_det_generators`
* :c:data:`n_int`
* :c:data:`pseudo_sym`
* :c:data:`psi_det_generators`
Called by:
@ -1590,6 +1592,7 @@ Subroutines / functions
* :c:data:`h_apply_buffer_allocated`
* :c:data:`n_det`
* :c:data:`s2_eig`
* :c:data:`variance_max`
* :c:data:`do_pt2`
* :c:data:`psi_energy`
* :c:data:`pt2_relative_error`
@ -1810,16 +1813,18 @@ Subroutines / functions
* :c:data:`psi_bilinear_matrix_values`
* :c:data:`psi_bilinear_matrix_transp_values`
* :c:data:`mo_num`
* :c:data:`psi_det_sorted`
* :c:data:`psi_bilinear_matrix_transp_rows_loc`
* :c:data:`n_states`
* :c:data:`pt2_f`
* :c:data:`psi_bilinear_matrix_values`
* :c:data:`elec_alpha_num`
* :c:data:`psi_bilinear_matrix_values`
* :c:data:`weight_selection`
* :c:data:`psi_bilinear_matrix_transp_values`
* :c:data:`n_int`
* :c:data:`psi_det_alpha_unique`
* :c:data:`psi_det_sorted`
* :c:data:`psi_det_sorted`
* :c:data:`pseudo_sym`
* :c:data:`psi_bilinear_matrix_columns_loc`
* :c:data:`psi_selectors_coef_transp`
@ -1893,6 +1898,7 @@ Subroutines / functions
* :c:data:`pt2_e0_denominator`
* :c:data:`pt2_stoch_istate`
* :c:data:`read_wf`
* :c:data:`selection_weight`
* :c:data:`state_average_weight`
* :c:data:`threshold_generators`
@ -1913,6 +1919,7 @@ Subroutines / functions
.. hlist::
:columns: 3
* :c:data:`selection_weight`
* :c:data:`pt2_stoch_istate`
* :c:data:`psi_det`
* :c:data:`zmq_state`
@ -1969,6 +1976,7 @@ Subroutines / functions
* :c:data:`pt2_e0_denominator`
* :c:data:`pt2_stoch_istate`
* :c:data:`selection_weight`
* :c:data:`state_average_weight`
* :c:data:`threshold_generators`
@ -2413,6 +2421,7 @@ Subroutines / functions
:columns: 3
* :c:func:`zmq_pt2`
* :c:func:`zmq_selection`
Touches:
@ -2440,6 +2449,7 @@ Subroutines / functions
:columns: 3
* :c:data:`psi_det_sorted`
* :c:data:`selection_weight`
* :c:data:`pt2_stoch_istate`
* :c:data:`psi_selectors`
* :c:data:`psi_bilinear_matrix_values`
@ -2450,6 +2460,7 @@ Subroutines / functions
* :c:data:`state_average_weight`
* :c:data:`n_det`
* :c:data:`s2_eig`
* :c:data:`psi_det_sorted`
* :c:data:`pt2_j`
* :c:data:`mo_two_e_integrals_in_map`
* :c:data:`psi_bilinear_matrix_transp_values`
@ -2467,7 +2478,7 @@ Subroutines / functions
* :c:data:`threshold_generators`
* :c:data:`psi_det_beta_unique`
* :c:data:`det_to_occ_pattern`
* :c:data:`psi_det_sorted`
* :c:data:`global_selection_buffer`
* :c:data:`psi_bilinear_matrix_transp_rows_loc`
* :c:data:`n_states`
* :c:data:`pt2_f`
@ -2476,7 +2487,7 @@ Subroutines / functions
* :c:data:`n_int`
* :c:data:`psi_det_hii`
* :c:data:`pt2_j`
* :c:data:`global_selection_buffer`
* :c:data:`pseudo_sym`
* :c:data:`pt2_w`
* :c:data:`pt2_u`
@ -2545,12 +2556,12 @@ Subroutines / functions
:columns: 3
* :c:data:`psi_det_sorted`
* :c:data:`selection_weight`
* :c:data:`psi_selectors`
* :c:data:`psi_bilinear_matrix_values`
* :c:data:`n_det`
* :c:data:`psi_bilinear_matrix_columns_loc`
* :c:data:`n_det_selectors`
* :c:data:`psi_bilinear_matrix_transp_values`
* :c:data:`psi_det_alpha_unique`
* :c:data:`psi_bilinear_matrix_transp_values`
* :c:data:`state_average_weight`
@ -2566,8 +2577,9 @@ Subroutines / functions
* :c:data:`n_states`
* :c:data:`pt2_f`
* :c:data:`n_det_generators`
* :c:data:`pt2_match_weight`
* :c:data:`psi_bilinear_matrix_transp_values`
* :c:data:`n_int`
* :c:data:`pseudo_sym`
Called by:
@ -2592,6 +2604,7 @@ Subroutines / functions
* :c:func:`save_wavefunction`
* :c:func:`selection_collector`
* :c:func:`selection_slave_inproc`
* :c:func:`update_pt2_and_variance_weights`
* :c:func:`write_double`
Touches:
@ -2607,4 +2620,5 @@ Subroutines / functions
* :c:data:`psi_det_size`
* :c:data:`psi_det_sorted_bit`
* :c:data:`pt2_match_weight`
* :c:data:`variance_match_weight`

7
docs/source/modules/iterations.rst
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@ -160,6 +160,13 @@ Subroutines / functions
* :c:func:`run_cipsi`
* :c:func:`run_stochastic_cipsi`
Calls:
.. hlist::
:columns: 3
* :c:func:`print_energy_components`
.. c:function:: save_iterations:

1
docs/source/programs/fci.rst
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@ -89,6 +89,7 @@ fci
* :c:data:`pt2_match_weight`
* :c:data:`pt2_stoch_istate`
* :c:data:`read_wf`
* :c:data:`selection_weight`
* :c:data:`state_average_weight`
* :c:data:`threshold_generators`
* :c:data:`variance_match_weight`

1
docs/source/programs/pt2.rst
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@ -55,5 +55,6 @@ pt2
* :c:data:`pt2_e0_denominator`
* :c:data:`pt2_stoch_istate`
* :c:data:`read_wf`
* :c:data:`selection_weight`
* :c:data:`state_average_weight`
* :c:data:`threshold_generators`

37
docs/source/programs/rotate_mos.rst Normal file
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@ -0,0 +1,37 @@
.. _rotate_mos:
.. program:: rotate_mos
==========
rotate_mos
==========
Rotates molecular orbitals i and j by combining them as
$1/\sqrt{2} ( \phi_i + \phi_j )$ and
$1/\sqrt{2} ( \phi_i - \phi_j )$.
Needs:
.. hlist::
:columns: 3
* :c:data:`ao_num`
* :c:data:`mo_num`
* :c:data:`mo_coef`
Calls:
.. hlist::
:columns: 3
* :c:func:`save_mos`
Touches:
.. hlist::
:columns: 3
* :c:data:`mo_coef`

39
docs/source/programs/sort_by_fock_energies.rst Normal file
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@ -0,0 +1,39 @@
.. _sort_by_fock_energies:
.. program:: sort_by_fock_energies
=====================
sort_by_fock_energies
=====================
Program that saves the current |MOs| ordered by diagonal element of the Fock operator.
Warning : the Fock operator, and therefore its matrix elements, depends on the occupancy.
Needs:
.. hlist::
:columns: 3
* :c:data:`fock_matrix_mo`
* :c:data:`ao_num`
* :c:data:`mo_num`
* :c:data:`mo_coef`
Calls:
.. hlist::
:columns: 3
* :c:func:`dsort`
* :c:func:`save_mos`
Touches:
.. hlist::
:columns: 3
* :c:data:`mo_coef`

27
docs/source/programs/swap_mos.rst Normal file
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@ -0,0 +1,27 @@
.. _swap_mos:
.. program:: swap_mos
========
swap_mos
========
Swaps the indices of two molecular orbitals
Needs:
.. hlist::
:columns: 3
* :c:data:`ao_num`
* :c:data:`mo_coef`
Calls:
.. hlist::
:columns: 3
* :c:func:`save_mos`

19
docs/source/programs/test.rst Normal file
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@ -0,0 +1,19 @@
.. _test:
.. program:: test
====
test
====
Calls:
.. hlist::
:columns: 3
* :c:func:`two_e_integrals_index`
* :c:func:`two_e_integrals_index_reverse`

10
man/fci.1
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@ -125,10 +125,10 @@ Touches:
\fBpsi_occ_pattern\fP
.IP \(bu 2
\fBc0_weight\fP
.UNINDENT
.INDENT 2.0
.IP \(bu 2
\fBdistributed_davidson\fP
.UNINDENT
.INDENT 2.0
.IP \(bu 2
\fBpsi_coef\fP
.IP \(bu 2
@ -143,10 +143,10 @@ Touches:
\fBpsi_energy\fP
.IP \(bu 2
\fBpsi_occ_pattern\fP
.UNINDENT
.INDENT 2.0
.IP \(bu 2
\fBpsi_energy\fP
.UNINDENT
.INDENT 2.0
.IP \(bu 2
\fBpt2_e0_denominator\fP
.IP \(bu 2
@ -156,6 +156,8 @@ Touches:
.IP \(bu 2
\fBread_wf\fP
.IP \(bu 2
\fBselection_weight\fP
.IP \(bu 2
\fBstate_average_weight\fP
.IP \(bu 2
\fBthreshold_generators\fP

2
man/pt2.1
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@ -104,6 +104,8 @@ Touches:
.IP \(bu 2
\fBread_wf\fP
.IP \(bu 2
\fBselection_weight\fP
.IP \(bu 2
\fBstate_average_weight\fP
.IP \(bu 2
\fBthreshold_generators\fP

85
man/rotate_mos.1 Normal file
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@ -0,0 +1,85 @@
.\" Man page generated from reStructuredText.
.
.TH "ROTATE_MOS" "1" "Jun 15, 2019" "2.0" "Quantum Package"
.SH NAME
rotate_mos \- | Quantum Package >
.
.nr rst2man-indent-level 0
.
.de1 rstReportMargin
\\$1 \\n[an-margin]
level \\n[rst2man-indent-level]
level margin: \\n[rst2man-indent\\n[rst2man-indent-level]]
-
\\n[rst2man-indent0]
\\n[rst2man-indent1]
\\n[rst2man-indent2]
..
.de1 INDENT
.\" .rstReportMargin pre:
. RS \\$1
. nr rst2man-indent\\n[rst2man-indent-level] \\n[an-margin]
. nr rst2man-indent-level +1
.\" .rstReportMargin post:
..
.de UNINDENT
. RE
.\" indent \\n[an-margin]
.\" old: \\n[rst2man-indent\\n[rst2man-indent-level]]
.nr rst2man-indent-level -1
.\" new: \\n[rst2man-indent\\n[rst2man-indent-level]]
.in \\n[rst2man-indent\\n[rst2man-indent-level]]u
..
.INDENT 0.0
.INDENT 3.5
Rotates molecular orbitals i and j by combining them as
$1/sqrt{2} ( phi_i + phi_j )$ and
$1/sqrt{2} ( phi_i \- phi_j )$.
.sp
Needs:
.INDENT 0.0
.INDENT 2.0
.IP \(bu 2
\fBao_num\fP
.UNINDENT
.INDENT 2.0
.IP \(bu 2
\fBmo_num\fP
.UNINDENT
.INDENT 2.0
.IP \(bu 2
\fBmo_coef\fP
.UNINDENT
.UNINDENT
.sp
Calls:
.INDENT 0.0
.INDENT 2.0
.IP \(bu 2
\fBsave_mos()\fP
.UNINDENT
.INDENT 2.0
.UNINDENT
.INDENT 2.0
.UNINDENT
.UNINDENT
.sp
Touches:
.INDENT 0.0
.INDENT 2.0
.IP \(bu 2
\fBmo_coef\fP
.UNINDENT
.INDENT 2.0
.UNINDENT
.INDENT 2.0
.UNINDENT
.UNINDENT
.UNINDENT
.UNINDENT
.SH AUTHOR
A. Scemama, E. Giner
.SH COPYRIGHT
2019, A. Scemama, E. Giner
.\" Generated by docutils manpage writer.
.

89
man/sort_by_fock_energies.1 Normal file
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@ -0,0 +1,89 @@
.\" Man page generated from reStructuredText.
.
.TH "SORT_BY_FOCK_ENERGIES" "1" "Jun 15, 2019" "2.0" "Quantum Package"
.SH NAME
sort_by_fock_energies \- | Quantum Package >
.
.nr rst2man-indent-level 0
.
.de1 rstReportMargin
\\$1 \\n[an-margin]
level \\n[rst2man-indent-level]
level margin: \\n[rst2man-indent\\n[rst2man-indent-level]]
-
\\n[rst2man-indent0]
\\n[rst2man-indent1]
\\n[rst2man-indent2]
..
.de1 INDENT
.\" .rstReportMargin pre:
. RS \\$1
. nr rst2man-indent\\n[rst2man-indent-level] \\n[an-margin]
. nr rst2man-indent-level +1
.\" .rstReportMargin post:
..
.de UNINDENT
. RE
.\" indent \\n[an-margin]
.\" old: \\n[rst2man-indent\\n[rst2man-indent-level]]
.nr rst2man-indent-level -1
.\" new: \\n[rst2man-indent\\n[rst2man-indent-level]]
.in \\n[rst2man-indent\\n[rst2man-indent-level]]u
..
.INDENT 0.0
.INDENT 3.5
Program that saves the current MOs ordered by diagonal element of the Fock operator.
.sp
Warning : the Fock operator, and therefore its matrix elements, depends on the occupancy.
.sp
Needs:
.INDENT 0.0
.INDENT 2.0
.IP \(bu 2
\fBfock_matrix_mo\fP
.IP \(bu 2
\fBao_num\fP
.UNINDENT
.INDENT 2.0
.IP \(bu 2
\fBmo_num\fP
.UNINDENT
.INDENT 2.0
.IP \(bu 2
\fBmo_coef\fP
.UNINDENT
.UNINDENT
.sp
Calls:
.INDENT 0.0
.INDENT 2.0
.IP \(bu 2
\fBdsort()\fP
.UNINDENT
.INDENT 2.0
.IP \(bu 2
\fBsave_mos()\fP
.UNINDENT
.INDENT 2.0
.UNINDENT
.UNINDENT
.sp
Touches:
.INDENT 0.0
.INDENT 2.0
.IP \(bu 2
\fBmo_coef\fP
.UNINDENT
.INDENT 2.0
.UNINDENT
.INDENT 2.0
.UNINDENT
.UNINDENT
.UNINDENT
.UNINDENT
.SH AUTHOR
A. Scemama, E. Giner
.SH COPYRIGHT
2019, A. Scemama, E. Giner
.\" Generated by docutils manpage writer.
.

69
man/swap_mos.1 Normal file
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@ -0,0 +1,69 @@
.\" Man page generated from reStructuredText.
.
.TH "SWAP_MOS" "1" "Jun 15, 2019" "2.0" "Quantum Package"
.SH NAME
swap_mos \- | Quantum Package >
.
.nr rst2man-indent-level 0
.
.de1 rstReportMargin
\\$1 \\n[an-margin]
level \\n[rst2man-indent-level]
level margin: \\n[rst2man-indent\\n[rst2man-indent-level]]
-
\\n[rst2man-indent0]
\\n[rst2man-indent1]
\\n[rst2man-indent2]
..
.de1 INDENT
.\" .rstReportMargin pre:
. RS \\$1
. nr rst2man-indent\\n[rst2man-indent-level] \\n[an-margin]
. nr rst2man-indent-level +1
.\" .rstReportMargin post:
..
.de UNINDENT
. RE
.\" indent \\n[an-margin]
.\" old: \\n[rst2man-indent\\n[rst2man-indent-level]]
.nr rst2man-indent-level -1
.\" new: \\n[rst2man-indent\\n[rst2man-indent-level]]
.in \\n[rst2man-indent\\n[rst2man-indent-level]]u
..
.INDENT 0.0
.INDENT 3.5
Swaps the indices of two molecular orbitals
.sp
Needs:
.INDENT 0.0
.INDENT 2.0
.IP \(bu 2
\fBao_num\fP
.UNINDENT
.INDENT 2.0
.IP \(bu 2
\fBmo_coef\fP
.UNINDENT
.INDENT 2.0
.UNINDENT
.UNINDENT
.sp
Calls:
.INDENT 0.0
.INDENT 2.0
.IP \(bu 2
\fBsave_mos()\fP
.UNINDENT
.INDENT 2.0
.UNINDENT
.INDENT 2.0
.UNINDENT
.UNINDENT
.UNINDENT
.UNINDENT
.SH AUTHOR
A. Scemama, E. Giner
.SH COPYRIGHT
2019, A. Scemama, E. Giner
.\" Generated by docutils manpage writer.
.

17
src/tools/rotate_mos.irp.f
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@ -1,17 +1,26 @@
program rotate_mos
implicit none
BEGIN_DOC
! Rotates molecular orbitals i and j by combining them as
! $1/\sqrt{2} ( \phi_i + \phi_j )$ and
! $1/\sqrt{2} ( \phi_i - \phi_j )$.
END_DOC
integer :: iorb,jorb
read(5,*)iorb,jorb
double precision, allocatable :: mo_coef_tmp(:,:)
allocate(mo_coef_tmp(ao_num,mo_num))
mo_coef_tmp = mo_coef
integer :: i,j
double precision :: dsqrt2_inv
double precision, allocatable :: mo_coef_tmp(:,:)
read(5,*)iorb,jorb
allocate(mo_coef_tmp(ao_num,mo_num))
mo_coef_tmp = mo_coef
dsqrt2_inv = 1.d0/dsqrt(2.d0)
do i = 1, ao_num
mo_coef(i,iorb) = dsqrt2_inv * ( mo_coef_tmp(i,iorb) + mo_coef_tmp(i,jorb) )
mo_coef(i,jorb) = dsqrt2_inv * ( mo_coef_tmp(i,iorb) - mo_coef_tmp(i,jorb) )
enddo
touch mo_coef
call save_mos

12
src/tools/sort_by_fock_energies.irp.f
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@ -1,23 +1,28 @@
program sort_by_fock_energies
BEGIN_DOC
! programs that save the current mos ordered by Diagonal element of the Fock operator.
!
! Warning : the Fock operator, and therefore its matrix elements, depends on the occupancy.
! Program that saves the current |MOs| ordered by diagonal element of the Fock operator.
!
! Warning : the Fock operator, and therefore its matrix elements, depends on the occupancy.
END_DOC
implicit none
integer :: i,j,k
integer, allocatable :: iorder(:)
double precision, allocatable :: fock_energies_tmp(:), new_mo_coef(:,:)
allocate(iorder(mo_num), fock_energies_tmp(mo_num),new_mo_coef(ao_num,mo_num))
do i = 1, mo_num
fock_energies_tmp(i) = Fock_matrix_diag_mo(i)
print*,'fock_energies_tmp(i) = ',fock_energies_tmp(i)
iorder(i) = i
enddo
print*,''
print*,'Sorting by Fock energies'
print*,''
call dsort(fock_energies_tmp,iorder,mo_num)
do i = 1, mo_num
k = iorder(i)
print*,'fock_energies_new(i) = ',fock_energies_tmp(i)
@ -25,6 +30,7 @@ program sort_by_fock_energies
new_mo_coef(j,i) = mo_coef(j,k)
enddo
enddo
mo_coef = new_mo_coef
touch mo_coef
call save_mos

3
src/tools/swap_mos.irp.f
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@ -1,5 +1,8 @@
program swap_mos
implicit none
BEGIN_DOC
! Swaps the indices of two molecular orbitals
END_DOC
integer :: i,j, i1, i2
double precision :: x
print *, 'MOs to swap?'