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Merge branch 'toto' of git://github.com/eginer/quantum_package

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Anthony Scemama 2019-01-07 01:43:56 +01:00
commit c48b0fa6f7
19 changed files with 273 additions and 90 deletions
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2
TODO
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@ -21,6 +21,8 @@
# User doc:
* Videos:
+) RHF
* Renvoyer a la doc des modules : c'est pour les programmeurs au depart!
* Mettre le mp2 comme exercice

1
docs/source/Makefile
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@ -3,3 +3,4 @@ default:
make -C ../ html
clean:
make -C ../ clean
rm modules/*.rst

1
docs/source/_static/links.rst
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@ -39,6 +39,7 @@
.. |OPAM| replace:: `OPAM`_
.. |Python| replace:: `Python`_
.. |qp| replace:: *Quantum Package*
.. |resultsFile| replace:: `resultsFile`_
.. |SLURM| replace:: `SLURM`_
.. |ZeroMQ| replace:: `ZeroMQ`_

2
docs/source/index.rst
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@ -12,8 +12,8 @@
:caption: Introduction
:hidden:
intro/selected_ci
intro/install
intro/selected_ci
.. toctree::
:maxdepth: 1

14
docs/source/intro/intro.rst
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@ -11,8 +11,18 @@ The |qp|
What it is
==========
The |qp| is an open-source programming environment for quantum chemistry,
especially for `wave function theory <https://en.wikipedia.org/wiki/Ab_initio_quantum_chemistry_methods>`_ (|WFT|).
The |qp| is an open-source **programming environment** for quantum chemistry.
It has been built from the **developper** point of view in order to help
the design of new quantum chemistry methods,
especially for `wave function theory <https://en.wikipedia.org/wiki/Ab_initio_quantum_chemistry_methods>`_ (|WFT|).
From the **user** point of view, the |qp| proposes a stand-alone path
to use optimized selected configuration interaction |sCI| based on the
|CIPSI| algorithm that can efficiently reach near-full configuration interaction
|FCI| quality for relatively large systems (see for instance :cite:`Caffarel_2016,Caffarel_2016.2,Loos_2018,Scemama_2018,Dash_2018,Garniron_2017.2,Loos_2018,Garniron_2018,Giner2018Oct`).
To have a simple example of how to use the |CIPSI| program, go to the `users_guide/quickstart`.
The main goal is the development of selected configuration interaction |sCI|
methods and multi-reference perturbation theory |MRPT| in the
determinant-driven paradigm. It also contains the very basics of Kohn-Sham `density functional theory <https://en.wikipedia.org/wiki/Density_functional_theory>`_ |KS-DFT| and `range-separated hybrids <https://aip.scitation.org/doi/10.1063/1.1383587>`_ |RSH|.

62
docs/source/modules/perturbation.rst
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@ -245,6 +245,20 @@ Subroutines / functions
.. c:function:: perturb_buffer_by_mono_epstein_nesbet_2x2_no_ci_diag
.. code:: text
subroutine perturb_buffer_by_mono_epstein_nesbet_2x2_no_ci_diag(i_generator,buffer,buffer_size,e_2_pert_buffer,coef_pert_buffer,sum_e_2_pert,sum_norm_pert,sum_H_pert_diag,N_st,Nint,key_mask,fock_diag_tmp,electronic_energy)
File: :file:`perturbation.irp.f_shell_13`
Applly pertubration ``epstein_nesbet_2x2_no_ci_diag`` to the buffer of determinants generated in the H_apply routine.
.. c:function:: perturb_buffer_by_mono_h_core
.. code:: text
@ -343,6 +357,20 @@ Subroutines / functions
.. c:function:: perturb_buffer_epstein_nesbet_2x2_no_ci_diag
.. code:: text
subroutine perturb_buffer_epstein_nesbet_2x2_no_ci_diag(i_generator,buffer,buffer_size,e_2_pert_buffer,coef_pert_buffer,sum_e_2_pert,sum_norm_pert,sum_H_pert_diag,N_st,Nint,key_mask,fock_diag_tmp,electronic_energy)
File: :file:`perturbation.irp.f_shell_13`
Applly pertubration ``epstein_nesbet_2x2_no_ci_diag`` to the buffer of determinants generated in the H_apply routine.
.. c:function:: perturb_buffer_h_core
.. code:: text
@ -405,7 +433,7 @@ Subroutines / functions
subroutine pt2_dummy (electronic_energy,det_ref,det_pert,fock_diag_tmp,c_pert,e_2_pert,H_pert_diag,Nint,ndet,N_st,minilist,idx_minilist,N_minilist)
File: :file:`pt2_equations.irp.f_template_309`
File: :file:`pt2_equations.irp.f_template_360`
Dummy perturbation to add all connected determinants.
@ -419,7 +447,7 @@ Subroutines / functions
subroutine pt2_epstein_nesbet (electronic_energy,det_ref,det_pert,fock_diag_tmp,c_pert,e_2_pert,H_pert_diag,Nint,ndet,N_st,minilist,idx_minilist,N_minilist)
File: :file:`pt2_equations.irp.f_template_309`
File: :file:`pt2_equations.irp.f_template_360`
Compute the standard Epstein-Nesbet perturbative first order coefficient and second order energetic contribution for the various N_st states.
@ -439,7 +467,7 @@ Subroutines / functions
subroutine pt2_epstein_nesbet_2x2 (electronic_energy,det_ref,det_pert,fock_diag_tmp,c_pert,e_2_pert,H_pert_diag,Nint,ndet,N_st,minilist,idx_minilist,N_minilist)
File: :file:`pt2_equations.irp.f_template_309`
File: :file:`pt2_equations.irp.f_template_360`
Computes the Epstein-Nesbet 2x2 diagonalization coefficient and energetic contribution for the various N_st states.
@ -453,6 +481,28 @@ Subroutines / functions
.. c:function:: pt2_epstein_nesbet_2x2_no_ci_diag
.. code:: text
subroutine pt2_epstein_nesbet_2x2_no_ci_diag(electronic_energy,det_ref,det_pert,fock_diag_tmp,c_pert,e_2_pert,H_pert_diag,Nint,ndet,N_st,minilist,idx_minilist,N_minilist)
File: :file:`pt2_equations.irp.f_template_360`
compute the Epstein-Nesbet 2x2 diagonalization coefficient and energetic contribution
for the various N_st states.
e_2_pert(i) = 0.5 * (( <det_pert|H|det_pert> - E(i) ) - sqrt( ( <det_pert|H|det_pert> - E(i)) ^2 + 4 <psi(i)|H|det_pert>^2 )
c_pert(i) = e_2_pert(i)/ <psi(i)|H|det_pert>
.. c:function:: pt2_h_core
.. code:: text
@ -481,7 +531,7 @@ Subroutines / functions
subroutine pt2_moller_plesset (electronic_energy,det_ref,det_pert,fock_diag_tmp,c_pert,e_2_pert,H_pert_diag,Nint,ndet,N_st,minilist,idx_minilist,N_minilist)
File: :file:`pt2_equations.irp.f_template_309`
File: :file:`pt2_equations.irp.f_template_360`
Computes the standard Moller-Plesset perturbative first order coefficient and second order energetic contribution for the various N_st states.
@ -501,7 +551,7 @@ Subroutines / functions
subroutine pt2_moller_plesset_general (electronic_energy,det_ref,det_pert,fock_diag_tmp,c_pert,e_2_pert,H_pert_diag,Nint,ndet,N_st,minilist,idx_minilist,N_minilist)
File: :file:`pt2_equations.irp.f_template_309`
File: :file:`pt2_equations.irp.f_template_360`
Computes the standard Moller-Plesset perturbative first order coefficient and second order energetic contribution for the various N_st states.
@ -521,7 +571,7 @@ Subroutines / functions
subroutine pt2_qdpt (electronic_energy,det_ref,det_pert,fock_diag_tmp,c_pert,e_2_pert,H_pert_diag,Nint,ndet,N_st,minilist,idx_minilist,N_minilist)
File: :file:`pt2_equations.irp.f_template_309`
File: :file:`pt2_equations.irp.f_template_360`
Computes the QDPT first order coefficient and second order energetic contribution for the various N_st states.

14
docs/source/modules/tools.rst
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@ -73,6 +73,20 @@ Subroutines / functions
.. c:function:: print_e_conv
.. code:: text
subroutine print_e_conv
File: :file:`print_e_conv.irp.f`
program that prints in a human readable format the convergence of the CIPSI algorithm
.. c:function:: print_wf
.. code:: text

4
docs/source/programmers_guide/index_providers.rst
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@ -1156,6 +1156,7 @@ Index of Subroutines/Functions
* :c:func:`perturb_buffer_by_mono_dummy`
* :c:func:`perturb_buffer_by_mono_epstein_nesbet`
* :c:func:`perturb_buffer_by_mono_epstein_nesbet_2x2`
* :c:func:`perturb_buffer_by_mono_epstein_nesbet_2x2_no_ci_diag`
* :c:func:`perturb_buffer_by_mono_h_core`
* :c:func:`perturb_buffer_by_mono_moller_plesset`
* :c:func:`perturb_buffer_by_mono_moller_plesset_general`
@ -1163,12 +1164,14 @@ Index of Subroutines/Functions
* :c:func:`perturb_buffer_dummy`
* :c:func:`perturb_buffer_epstein_nesbet`
* :c:func:`perturb_buffer_epstein_nesbet_2x2`
* :c:func:`perturb_buffer_epstein_nesbet_2x2_no_ci_diag`
* :c:func:`perturb_buffer_h_core`
* :c:func:`perturb_buffer_moller_plesset`
* :c:func:`perturb_buffer_moller_plesset_general`
* :c:func:`perturb_buffer_qdpt`
* :c:func:`primitive_value`
* :c:func:`print_det`
* :c:func:`print_e_conv`
* :c:func:`print_extrapolated_energy`
* :c:func:`print_generators_bitmasks_holes`
* :c:func:`print_generators_bitmasks_holes_for_one_generator`
@ -1184,6 +1187,7 @@ Index of Subroutines/Functions
* :c:func:`pt2_dummy`
* :c:func:`pt2_epstein_nesbet`
* :c:func:`pt2_epstein_nesbet_2x2`
* :c:func:`pt2_epstein_nesbet_2x2_no_ci_diag`
* :c:func:`pt2_find_sample`
* :c:func:`pt2_find_sample_lr`
* :c:func:`pt2_h_core`

2
docs/source/programmers_guide/programming.rst
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@ -11,7 +11,7 @@ in order to write a new program is the name of the required |IRPF90| entities
which may already exist in other modules. For example, writing a program which
prints the Hartree-Fock energy is as simple as:
.. code:: irpf90
.. code:: fortran
program print_hf_energy
implicit none

14
docs/source/users_guide/qp_plugins.rst
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@ -25,15 +25,15 @@ Usage
List all the available plugins.
.. option:: list -i
.. option:: -i
List all the *installed* plugins.
.. option:: list -u
.. option:: -u
List all the *uninstalled* plugins.
.. option:: list -q
.. option:: -q
List all the downloaded repositories.
@ -53,12 +53,12 @@ Usage
Uninstall the plugin ``plugin_name``.
.. option:: create -n <plugin_name>
.. option:: -n <plugin_name>
Create a new plugin named ``plugin_name`` in local repository.
Create a new plugin named ``plugin_name`` (in local repository by default).
.. option:: create -n <plugin_name> -r <repository>
.. option:: -r <repository>
Create a new plugin named ``plugin_name`` in the specified repository.
Specify in which repository the new plugin will be created.

5
docs/source/users_guide/quickstart.rst
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@ -2,8 +2,9 @@
Quick-start guide
=================
This tutorial should talk you through everything you need to get started with
the |qp|. As an example, we will run a |CIPSI| calculation on the HCN molecule.
This tutorial should teach you everything you need to get started with
the the basics of the |qp|.
As an example, we will run a frozen core |CIPSI| calculation on the HCN molecule in the 631-G basis set.
Demo video

85
scripts/qp_e_conv_fci
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@ -1,67 +1,46 @@
#!/bin/bash
file=$1
out=${file}.conv
Ndet=`grep "N_det =" $file | cut -d "=" -f 2`
Evar=`grep "E =" $file | cut -d "=" -f 2`
EPT2=`grep "E+rPT2 =" $file | cut -d "=" -f 2 | cut -d "+" -f 1`
err=`grep "E+rPT2 =" $file | cut -d "=" -f 2 | cut -d "+" -f 2 | cut -d "/" -f 2 | cut -d " " -f 5`
qp=$QP_ROOT
source ${qp}/quantum_package.rc
Ndetarray=[]
j=0
for i in $Ndet
qp_run print_e_conv $1
nstates=`cat ${1}/determinants/n_states`
echo $nstates
for i in `seq 1 $nstates`
do
Ndetarray[$j]=$i
let "j=j+1"
done
Nmax=${#Ndetarray[*]}
let "Nmax-=1"
Evararray=[]
j=0
for i in $Evar
do
Evararray[$j]=$i
let "j=j+1"
done
EPT2array=[]
j=0
for i in $EPT2
do
EPT2array[$j]=$i
let "j=j+1"
done
errarray=[]
j=0
for i in $err
do
errarray[$j]=$i
let "j=j+1"
done
echo "#Ndet E_var E+PT2 statistical error " > $out
for i in `seq 0 $Nmax`
do
echo ${Ndetarray[$i]} ${Evararray[$i]} ${EPT2array[$i]} ${errarray[$i]} >> $out
done
out=${1}.${i}.conv
cat << EOF > ${out}.plt
set term eps
set output "$out.eps"
set term pdf
set output "$out.pdf"
set log x
set xlabel "Number of determinants"
set ylabel "Total Energy (a.u.)"
plot "$out" w lp title "E_{var}", "$out" u 1:3:4 w errorlines title "E_{var} + PT2"
plot "$out" w lp title "E_{var} state $i", "$out" u 1:3 w lp title "E_{var} + PT2 state $i"
EOF
gnuplot ${out}.plt
rm ${out}.plt
done
for i in `seq 2 $nstates`
do
out=${1}.${i}.delta_e.conv
cat << EOF > ${out}.plt
set term pdf
set output "$out.pdf"
set log x
set xlabel "Number of determinants"
set ylabel "Energy difference (a.u.)"
plot "$out" w lp title "Delta E_{var} state $i", "$out" u 1:3 w lp title "Delta E_{var} + PT2 state $i"
EOF
gnuplot ${out}.plt
rm ${out}.plt
done

2
src/ao_one_e_ints/pot_ao_erf_ints.irp.f
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@ -43,7 +43,7 @@ double precision function NAI_pol_mult_erf_ao(i_ao,j_ao,mu_in,C_center)
NAI_pol_mult_erf_ao += integral * ao_coef_normalized_ordered_transp(j,j_ao)*ao_coef_normalized_ordered_transp(i,i_ao)
enddo
enddo
end

1
src/iterations/NEED
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@ -1 +0,0 @@

26
src/kohn_sham_rs/61.rsks.bats
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@ -6,33 +6,33 @@ source $QP_ROOT/tests/bats/common.bats.sh
function run() {
thresh=1.e-8
qp_edit -c $1
functional=$2
ezfio set_file $1
ezfio set scf_utils thresh_scf 1.e-10
ezfio set dft_keywords exchange_functional "short_range_PBE"
ezfio set dft_keywords correlation_functional "short_range_PBE"
ezfio set ao_two_e_erf_ints mu_erf 0.5
ezfio set dft_keywords exchange_functional $functional
ezfio set dft_keywords correlation_functional $functional
ezfio set ao_two_e_erf_ints mu_erf 0.5
ezfio set becke_numerical_grid grid_type_sgn 1
qp_run rs_ks_scf $1
energy="$(ezfio get kohn_sham_rs energy)"
eq $energy $2 $thresh
eq $energy $3 $thresh
}
@test "H3COH" { # 11.4566s
run h3coh.ezfio -115.50238225208
@test "H3COH" {
run h3coh.ezfio short_range_PBE -115.50238225208
}
@test "N2" { # 18.2364s
run n2.ezfio -109.404692225719
@test "HCN" {
run hcn.ezfio short_range_PBE -93.26674673761752
}
@test "HCN" { # 28.801s
run hcn.ezfio -93.26674673761752
@test "N2" {
run n2.ezfio short_range_PBE -109.404692225719
}
@test "SiH2_3B1" { # 82.3904s
[[ -n $TRAVIS ]] && skip
run sih2_3b1.ezfio -290.372258160809
@test "SiH2_3B1" {
run sih2_3b1.ezfio short_range_LDA -289.4398733527755
}

2
src/mo_basis/track_orb.irp.f
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@ -47,11 +47,9 @@ subroutine reorder_active_orb
double precision :: x
integer :: i1,i2
print*, 'swapping the active MOs'
do j = 1, n_act_orb
i1 = list_act(j)
i2 = index_active_orb(j)
print*, i1,i2
do i=1,ao_num
x = mo_coef(i,i1)
mo_coef(i,i1) = mo_coef(i,i2)

51
src/perturbation/pt2_equations.irp.f
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@ -146,6 +146,57 @@ end
subroutine pt2_epstein_nesbet_2x2_no_ci_diag($arguments)
use bitmasks
implicit none
$declarations
BEGIN_DOC
! compute the Epstein-Nesbet 2x2 diagonalization coefficient and energetic contribution
!
! for the various N_st states.
!
! e_2_pert(i) = 0.5 * (( <det_pert|H|det_pert> - E(i) ) - sqrt( ( <det_pert|H|det_pert> - E(i)) ^2 + 4 <psi(i)|H|det_pert>^2 )
!
! c_pert(i) = e_2_pert(i)/ <psi(i)|H|det_pert>
!
END_DOC
integer :: i,j
double precision :: diag_H_mat_elem_fock,delta_e, h
double precision :: i_H_psi_array(N_st)
ASSERT (Nint == N_int)
ASSERT (Nint > 0)
PROVIDE psi_energy
call i_H_psi(det_pert,psi_selectors,psi_selectors_coef,Nint,N_det_selectors,psi_selectors_size,N_st,i_H_psi_array)
h = diag_H_mat_elem_fock(det_ref,det_pert,fock_diag_tmp,Nint)
do i =1,N_st
if (i_H_psi_array(i) /= 0.d0) then
delta_e = h - psi_energy(i)
if (delta_e > 0.d0) then
e_2_pert(i) = 0.5d0 * (delta_e - dsqrt(delta_e * delta_e + 4.d0 * i_H_psi_array(i) * i_H_psi_array(i)))
else
e_2_pert(i) = 0.5d0 * (delta_e + dsqrt(delta_e * delta_e + 4.d0 * i_H_psi_array(i) * i_H_psi_array(i)))
endif
if (dabs(i_H_psi_array(i)) > 1.d-6) then
c_pert(i) = e_2_pert(i)/i_H_psi_array(i)
else
c_pert(i) = 0.d0
endif
H_pert_diag(i) = h*c_pert(i)*c_pert(i)
else
e_2_pert(i) = 0.d0
c_pert(i) = 0.d0
H_pert_diag(i) = 0.d0
endif
enddo
end
subroutine pt2_moller_plesset ($arguments)
use bitmasks
implicit none

71
src/tools/print_e_conv.irp.f Normal file
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@ -0,0 +1,71 @@
program print_e_conv
implicit none
BEGIN_DOC
! program that prints in a human readable format the convergence of the CIPSI algorithm
END_DOC
provide ezfio_filename
call routine
end
subroutine routine
implicit none
integer :: N_iter_tmp
integer :: i,istate
character*(128) :: output
integer :: i_unit_output,getUnitAndOpen
character*(128) :: filename
integer, allocatable :: n_det_tmp(:)
call ezfio_get_iterations_N_iter(N_iter_tmp)
print*,'N_iter_tmp = ',N_iter_tmp
double precision, allocatable :: e(:,:),pt2(:,:)
allocate(e(N_states, 100),pt2(N_states, 100),n_det_tmp(100))
call ezfio_get_iterations_energy_iterations(e)
call ezfio_get_iterations_pt2_iterations(pt2)
call ezfio_get_iterations_n_det_iterations(n_det_tmp)
do istate = 1, N_states
if (istate.lt.10)then
write (filename, "(I1)")istate
else
write (filename, "(I2)")istate
endif
print*,filename
output=trim(ezfio_filename)//'.'//trim(filename)//'.conv'
output=trim(output)
print*,'output = ',trim(output)
i_unit_output = getUnitAndOpen(output,'w')
write(i_unit_output,*)'# N_det E_var E_var + PT2'
do i = 1, N_iter_tmp
write(i_unit_output,'(I9,X,3(F16.10,X))')n_det_tmp(i),e(istate,i),e(istate,i) + pt2(istate,i)
enddo
enddo
if(N_states.gt.1)then
double precision, allocatable :: deltae(:,:),deltae_pt2(:,:)
allocate(deltae(N_states,100),deltae_pt2(N_states,100))
do i = 1, N_iter_tmp
do istate = 1, N_states
deltae(istate,i) = e(istate,i) - e(1,i)
deltae_pt2(istate,i) = e(istate,i) + pt2(istate,i) - (e(1,i) + pt2(1,i))
enddo
enddo
do istate = 2, N_states
if (istate.lt.10)then
write (filename, "(I1)")istate
else
write (filename, "(I2)")istate
endif
output=trim(ezfio_filename)//'.'//trim(filename)//'.delta_e.conv'
print*,'output = ',trim(output)
i_unit_output = getUnitAndOpen(output,'w')
write(i_unit_output,*)'# N_det Delta E_var Delta (E_var + PT2)'
do i = 1, N_iter_tmp
write(i_unit_output,'(I9,X,100(F16.10,X))')n_det_tmp(i),deltae(istate,i),deltae_pt2(istate,i)
enddo
enddo
endif
end

4
src/tools/print_wf.irp.f
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@ -59,6 +59,8 @@ subroutine routine
else
coef_2_2 = 0.5d0 * (delta_e + dsqrt(delta_e * delta_e + 4.d0 * hij * hij )) /hij
endif
else
coef_2_2 = 0.d0
endif
call get_excitation(psi_det(1,1,1),psi_det(1,1,i),exc,degree,phase,N_int)
call decode_exc(exc,degree,h1,p1,h2,p2,s1,s2)
@ -83,7 +85,7 @@ subroutine routine
print*,'hdouble = ',hdouble
print*,'hmono+hdouble = ',hmono+hdouble
print*,'hij = ',hij
else
else if(degree ==2)then
print*,'s1',s1
print*,'h1,p1 = ',h1,p1
print*,'s2',s2