added some providers and the first tutorial for plugins
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@ -22,6 +22,8 @@ we will go through a series of examples that allow you to do the following thing
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IV) print out the one- and two-electron rdms,
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V) obtain the AOs and MOs on the DFT grid, together with the density,
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How the tutorial will be done
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-----------------------------
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This tuto is as follows:
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i) you READ THIS FILE UNTIL THE END in order to get the big picture and vocabulary,
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ii) you go to the directory qp2/plugins/tuto_plugins/ and you will find detailed tuto there for each of the 5 examples.
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@ -32,7 +34,7 @@ The first thing to do is to be in the QPSH mode: you execute the qp2/bin/qpsh sc
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the environement variables and allows for the completion of command lines in bash (that is an AMAZING feature :)
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Then, you need to known where you want to create your plugin, and what is the name of the plugin.
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!!!! WARINING: The plugins are NECESSARILY located in qp2/plugins/ !!!!
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!!!! WARNING: The plugins are NECESSARILY located in qp2/plugins/ !!!!
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Ex: If you want to create a plugin named "my_fancy_plugin" in the directory plugins/plugins_test/,
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this goes with the command
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qp plugins create -n my_fancy_plugin -r plugins_test/
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@ -0,0 +1,24 @@
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program my_program
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implicit none
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BEGIN_DOC
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! This program is there essentially to show how one can use providers in programs
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END_DOC
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integer :: i,j
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double precision :: accu
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print*,'Trace on the AO basis '
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print*,trace_ao_one_e_ints
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print*,'Trace on the AO basis after projection on the MO basis'
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print*,trace_ao_one_e_ints_from_mo
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print*,'Trace of MO integrals '
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print*,trace_mo_one_e_ints
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print*,'ao_num = ',ao_num
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print*,'mo_num = ',mo_num
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if(ao_num .ne. mo_num)then
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print*,'The AO basis and MO basis are different ...'
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print*,'Trace on the AO basis should not be the same as Trace of MO integrals'
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print*,'Only the second one must be equal to the trace on the MO integrals'
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else
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print*,'The AO basis and MO basis are the same !'
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print*,'All traces should coincide '
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endif
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end
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@ -0,0 +1,32 @@
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program my_program_to_print_stuffs
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implicit none
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BEGIN_DOC
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! TODO : Put the documentation of the program here
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END_DOC
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integer :: i,j,k,l
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double precision :: integral
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double precision :: get_ao_two_e_integral, get_two_e_integral ! declaration of the functions
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print*,'AO integrals, physicist notations : <i j|k l>'
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do i = 1, ao_num
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do j = 1, ao_num
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do k = 1, ao_num
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do l = 1, ao_num
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integral = get_ao_two_e_integral(i, j, k, l, ao_integrals_map)
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print*,i,j,k,l,integral
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enddo
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enddo
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enddo
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enddo
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print*,'MO integrals, physicist notations : <i j|k l>'
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do i = 1, mo_num
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do j = 1, mo_num
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do k = 1, mo_num
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do l = 1, mo_num
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integral = get_two_e_integral(i, j, k, l, mo_integrals_map)
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print*,i,j,k,l,integral
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enddo
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enddo
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enddo
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enddo
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end
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@ -0,0 +1,111 @@
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! This file is an example of the kind of manipulations that you can do with providers
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!
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!!!!!!!!!!!!!!!!!!!!!!!!!! Main providers useful for the program !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
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!!! type name
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BEGIN_PROVIDER [ double precision, trace_mo_one_e_ints]
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implicit none
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BEGIN_DOC
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! trace_mo_one_e_ints = Trace of the one-electron integrals on the MO basis
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!
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! = sum_i mo_one_e_integrals(i,i)
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END_DOC
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integer :: i
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trace_mo_one_e_ints = 0.d0
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do i = 1, mo_num
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trace_mo_one_e_ints += mo_one_e_integrals(i,i)
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enddo
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END_PROVIDER
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BEGIN_PROVIDER [ double precision, trace_ao_one_e_ints]
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implicit none
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BEGIN_DOC
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! trace_ao_one_e_ints = Trace of the one-electron integrals on the AO basis taking into account the non orthogonality
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!
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! Be aware that the trace of an operator in a non orthonormal basis is Tr(A S^{-1}) = \sum_{m,n}(A_mn S^{-1}_mn)
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!
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! WARNING: it is equal to the trace on the MO basis if and only if the AO basis and MO basis
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! have the same number of functions
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END_DOC
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integer :: i,j
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double precision, allocatable :: inv_overlap_times_integrals(:,:) ! = h S^{-1}
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allocate(inv_overlap_times_integrals(ao_num,ao_num))
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! routine that computes the product of two matrices, you can check it with
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! irpman get_AB_prod
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call get_AB_prod(ao_one_e_integrals,ao_num,ao_num,s_inv,ao_num,inv_overlap_times_integrals)
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! Tr(inv_overlap_times_integrals) = Tr(h S^{-1})
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trace_ao_one_e_ints = 0.d0
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do i = 1, ao_num
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trace_ao_one_e_ints += inv_overlap_times_integrals(i,i)
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enddo
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!
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! testing the formula Tr(A S^{-1}) = \sum_{m,n}(A_mn S^{-1}_mn)
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double precision :: test
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test = 0.d0
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do i = 1, ao_num
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do j = 1, ao_num
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test += ao_one_e_integrals(j,i) * s_inv(i,j)
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enddo
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enddo
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if(dabs(accu - trace_ao_one_e_ints).gt.1.d-12)then
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print*,'Warning ! '
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print*,'Something is wrong because Tr(AB) \ne sum_{mn}A_mn B_nm'
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endif
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END_PROVIDER
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BEGIN_PROVIDER [ double precision, trace_ao_one_e_ints_from_mo]
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implicit none
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BEGIN_DOC
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! trace_ao_one_e_ints_from_mo = Trace of the one-electron integrals on the AO basis after projection on the MO basis
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!
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! = Tr([SC h {SC}^+] S^{-1})
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!
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! = Be aware that the trace of an operator in a non orthonormal basis is = Tr(A S^{-1}) where S is the metric
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! Must be equal to the trace_mo_one_e_ints
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END_DOC
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integer :: i
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double precision, allocatable :: inv_overlap_times_integrals(:,:)
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allocate(inv_overlap_times_integrals(ao_num,ao_num))
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! Using the provider ao_one_e_integrals_from_mo = [SC h {SC}^+]
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call get_AB_prod(ao_one_e_integrals_from_mo,ao_num,ao_num,s_inv,ao_num,inv_overlap_times_integrals)
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! inv_overlap_times_integrals = [SC h {SC}^+] S^{-1}
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trace_ao_one_e_ints_from_mo = 0.d0
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! Computing the trace
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do i = 1, ao_num
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trace_ao_one_e_ints_from_mo += inv_overlap_times_integrals(i,i)
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enddo
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END_PROVIDER
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!!!!!!!!!!!!!!!!!!!!!!!!!!! Additional providers to check some stuffs !!!!!!!!!!!!!!!!!!!!!!!!!
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BEGIN_PROVIDER [ double precision, ao_one_e_int_no_ov_from_mo, (ao_num, ao_num) ]
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BEGIN_DOC
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! ao_one_e_int_no_ov_from_mo = C mo_one_e_integrals C^T
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!
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! WARNING : NON EQUAL TO ao_one_e_integrals due to the non orthogonality
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END_DOC
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call mo_to_ao_no_overlap(mo_one_e_integrals,mo_num,ao_one_e_int_no_ov_from_mo,ao_num)
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END_PROVIDER
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BEGIN_PROVIDER [ double precision, ao_one_e_int_no_ov_from_mo_ov_ov, (ao_num, ao_num)]
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BEGIN_DOC
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! ao_one_e_int_no_ov_from_mo_ov_ov = S ao_one_e_int_no_ov_from_mo S = SC mo_one_e_integrals (SC)^T
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!
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! EQUAL TO ao_one_e_integrals ONLY IF ao_num = mo_num
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END_DOC
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double precision, allocatable :: tmp(:,:)
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allocate(tmp(ao_num, ao_num))
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call get_AB_prod(ao_overlap,ao_num,ao_num,ao_one_e_int_no_ov_from_mo,ao_num,tmp)
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call get_AB_prod(tmp,ao_num,ao_num,ao_overlap,ao_num,ao_one_e_int_no_ov_from_mo_ov_ov)
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END_PROVIDER
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BEGIN_PROVIDER [ double precision, c_t_s_c, (mo_num, mo_num)]
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implicit none
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BEGIN_DOC
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! C^T S C = should be the identity
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END_DOC
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call get_AB_prod(mo_coef_transp,mo_num,ao_num,S_mo_coef,mo_num,c_t_s_c)
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END_PROVIDER
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@ -1,14 +1,15 @@
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======================================
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Tutorial for plugin I: One-e integrals
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======================================
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=====================================================================
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Tutorial for plugin I: One-e integrals (duration: 20 minutes at most)
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=====================================================================
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!!! Requirements:
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a) you know how to create an EZFIO file and run calculations with QP
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Requirements
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------------
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a) You know how to create an EZFIO file and run calculations with QP
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(check the tuto: `<https://quantumpackage.github.io/qp2/post/hartree-fock/>`),
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b) you have an EZFIO file in the sto-3g from the file H2.xyz in plugins/tuto_plugins,
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and you have run an HF calculation giving an energy of -1.116759 a.u.,
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c) you made an qp set_file YOUR_EZFIO_FILE_FOR_H2 in order to be,
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d) you have READ the ../README.rst file to HAVE THE VOCABULARY.
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b) You have an EZFIO file with MOs created (with the 'scf' executable for instance).
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As we are going to print out some integrals, don't take a too large system/basis (Ex: H2, cc-pVDZ is ok :)
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c) You made an qp set_file YOUR_EZFIO_FILE_FOR_H2 in order to work on that ezfio folder,
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d) You have READ the ../README.rst file to HAVE THE VOCABULARY.
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Our goals:
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----------
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@ -22,14 +23,14 @@ I) Starting: creating the plugin
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We will go step-by-step through these plugins.
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The name of the plugin will be "plugin_I", and its location is in "tuto_plugins".
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Therefore to create the plugin, we do
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Therefore to create the plugin, we do:
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$ qp plugins create -n plugin_I -r tuto_plugins
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Then to an "ls" in qp2/plugins/tuto_plugins/
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and you will find a directory called "plugin_I".
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qp plugins create -n plugin_I -r tuto_plugins
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Then do an "ls" in qp2/plugins/tuto_plugins/ and you will find a directory called "plugin_I".
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In that directory you will find:
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i) a "NEED" file that will eventually contain all the other modules/plugins needed by our "plugin_I"
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ii) a "README.rst" file that you can AND SHOULD modify in order to document what is doing the plugin.
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i) a "NEED" file that will eventually contain all the other modules/plugins needed by our "plugin_I"
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ii) a "README.rst" file that you can AND SHOULD modify in order to document what is doing the plugin.
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iii) a "plugin_I.irp.f" file that is a program to be compiled and just printing "Hello world"
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II) Specifying the dependencies
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@ -78,8 +79,8 @@ The variables that we need are
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ao_one_e_integrals
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mo_one_e_integrals
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You can check them with
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irpman ao_one_e_integral
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irpman mo_one_e_integral
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irpman ao_one_e_integrals
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irpman mo_one_e_integrals
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in order to get some information on where they are created, and many more information.
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We will modify the executable such that it prints out the integrals.
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@ -87,7 +88,7 @@ We will modify the executable such that it prints out the integrals.
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IV) Printing out the one-electron integrals
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--------------------------------------------
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We will create a program that will print out the one-electron integrals on the AO and MO basis.
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You can then copy the file "print_one_e_h.irp.f" in your plugin.
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You can then copy the file "print_one_e_h.irp.f" located in "plugins/tuto_plugins/tuto_I" in your plugin.
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In the file you will see that we simply browse the two arrays "ao_one_e_integrals" and "mo_one_e_integrals", which are global variables (providers) and we browse them until either "ao_num" or "mo_num" which are also providers representing the number of AOs or MOs.
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You can check these variables with irpman !
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If you recompile using "ninja" as before, and another executable has been created "print_one_e_h".
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@ -95,3 +96,31 @@ Then, you can run the program on the ezfio file by doing
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qp run print_one_e_h
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and will print out the data you need :)
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By the way, as the file "plugin_I.irp.f" contains nothing but a "Hello world" print, you can simply remove it if you want.
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V) Printing out the two-electron integrals
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------------------------------------------
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We will now create a file that prints out the two-electron integrals in the AO and MO basis.
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These can be accessed with the following subroutines :
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+) get_ao_two_e_integral for the AO basis
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+) get_two_e_integral for the MO basis
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check them with irpman !
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To print the two-electron integrals, you can copy the file "print_two_e_h.irp.f" in your plugin and recompile.
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Then just run the program
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qp run print_two_e_h
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and it will print all the things you want :)
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VI) Creating new providers and a program to print them
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------------------------------------------------------
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We will now create new providers that manipulates the objects that we just printed.
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As an example, we will compute the trace of the one electron integrals in the AO and MO basis.
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In the file "traces_one_e.irp.f" you will find the several new providers among which
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a) trace_mo_one_e_ints : simply the sum of the diagonal matrix element of the one-electron integrals
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b) trace_ao_one_e_ints : the corresponding trace on the AO basis : Sum(m,n) S^{-1}_{mn} h_{mn}
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c) trace_ao_one_e_ints_from_mo : the trace on the AO basis with the integrals obtained first from the MO basis
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As explained in these files, "trace_mo_one_e_ints" is equal to "trace_ao_one_e_ints" only if the number of AO basis functions is equal to the number of MO basis functions, which means if you work with cartesian functions.
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(You can check with "qp create_ezfio -h" for the option to create an EZFIO with cartesian basis functions)
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In the file "print_traces_on_e.irp.f" you will find an example of executable that prints out the various providers.
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Copy these two files in your plugin and recompile to execute it.
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Execute the program print_traces_on_e and check for the results !
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@ -45,3 +45,13 @@ BEGIN_PROVIDER [ double precision, ao_one_e_integrals_imag,(ao_num,ao_num)]
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END_PROVIDER
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BEGIN_PROVIDER [ double precision, ao_one_e_integrals_from_mo, (ao_num, ao_num)]
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implicit none
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BEGIN_DOC
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! Integrals of the one e hamiltonian obtained from the integrals on the MO basis
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!
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! WARNING : this is equal to ao_one_e_integrals only if the AO and MO basis have the same number of functions
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END_DOC
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call mo_to_ao(mo_one_e_integrals,mo_num,ao_one_e_integrals_from_mo,ao_num)
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END_PROVIDER
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@ -166,6 +166,10 @@
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if(frozen_orb_scf)then
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integer :: iorb,jorb
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! active|core|active
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!active | | 0 |
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!core | 0 | | 0
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!active | | 0 |
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do i = 1, n_core_orb
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iorb = list_core(i)
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do j = 1, n_act_orb
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@ -2041,3 +2041,22 @@ subroutine get_A_squared(A,n,A2)
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double precision, intent(out):: A2(n,n)
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call dgemm('N','N',n,n,n,1.d0,A,size(A,1),A,size(A,1),0.d0,A2,size(A2,1))
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end
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subroutine get_AB_prod(A,n,m,B,l,AB)
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implicit none
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BEGIN_DOC
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! AB = A B where A is n x m, B is m x l. Use the dgemm routine
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END_DOC
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double precision, intent(in) :: A(n,m),B(m,l)
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integer, intent(in) :: n,m,l
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double precision, intent(out):: AB(n,l)
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if(size(A,2).ne.m.or.size(B,1).ne.m)then
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print*,'error in get_AB_prod ! '
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print*,'matrices do not have the good dimension '
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print*,'size(A,2) = ',size(A,2)
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print*,'size(B,1) = ',size(B,1)
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print*,'m = ',m
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stop
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endif
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call dgemm('N','N',n,l,m,1.d0,A,size(A,1),B,size(B,1),0.d0,AB,size(AB,1))
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end
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