From 1fd93d76b6ad7d7733834bae2da0b9dbbea8d49f Mon Sep 17 00:00:00 2001 From: eginer Date: Thu, 21 Mar 2024 15:31:06 +0100 Subject: [PATCH 1/8] working on the tuto --- plugins/README.rst | 76 +++++++++++++++ plugins/tuto_plugins/n2.xyz | 4 + .../tuto_plugins/tuto_I/print_one_e_h.irp.f | 20 ++++ plugins/tuto_plugins/tuto_I/tuto_I.rst | 97 +++++++++++++++++++ 4 files changed, 197 insertions(+) create mode 100644 plugins/README.rst create mode 100644 plugins/tuto_plugins/n2.xyz create mode 100644 plugins/tuto_plugins/tuto_I/print_one_e_h.irp.f create mode 100644 plugins/tuto_plugins/tuto_I/tuto_I.rst diff --git a/plugins/README.rst b/plugins/README.rst new file mode 100644 index 00000000..7f3f3c75 --- /dev/null +++ b/plugins/README.rst @@ -0,0 +1,76 @@ +============================== +Tutorial for creating a plugin +============================== + +Introduction: what is a plugin, and what this tuto will be about ? +============================================================ +The QP is split into two kinds of routines/global variables (i.e. providers): + i) the core modules locatedin qp2/src/, which contains all the bulk of a quantum chemistry software (integrals, matrix elements between Slater determinants, linear algebra routines, DFT stuffs etc..) + ii) the plugins which are external stuffs connected to the qp2/src/ stuffs. + +More precisely, a plugin of the QP is a directory where you can create routines, +providers and executables that use all the global variables/functions/routines already created +in the modules ofqp2/src or in other plugins. + +Instead of giving a theoretical lecture on what is a plugin, +we will go through a series of examples that allow you to do the following thing: + I) print out one- and two-electron integrals on the AO/MO basis, + creates two providers which manipulate these objects, + print out these providers, + II) browse the Slater determinants stored in the EZFIO wave function and compute their matrix elements, + III) build the Hamiltonian matrix and diagonalize it either with Lapck or Davidson, + IV) print out the one- and two-electron rdms, + V) obtain the AOs and MOs on the DFT grid, together with the density, + +This tuto is as follows: + i) you READ THIS FILE UNTIL THE END in order to get the big picture and vocabulary, + ii) you go to the directory qp2/plugins/tuto_plugins/ and you will find detailed tuto there for each of the 5 examples. + +Creating a plugin: the basic +---------------------------- +The first thing to do is to be in the QPSH mode: you execute the qp2/bin/qpsh script that essentially loads all +the environement variables and allows for the completion of command lines in bash (that is an AMAZING feature :) + +Then, you need to known where you want to create your plugin, and what is the name of the plugin. +!!!! WARINING: The plugins are NECESSARILY located in qp2/plugins/ !!!! +Ex: If you want to create a plugin named "my_fancy_plugin" in the directory plugins/plugins_test/, +this goes with the command +qp plugins create -n my_fancy_plugin -r plugins_test/ + +Then, to create plugin of your dreams, the two questions you need to answer are the following: +a) What do I need to compute what I want, which means what are the objects that I need ? + There are two kind of objects: + + the routines/functions + Ex: Linear algebra routines, integration routines etc ... + + the global variables which are called the PROVIDERS + Ex: one-electron integrals, Slater determinants, density matrices etc ... +b) Where do I find these objects ? + The objects (routines/functions/providers) are necessarily created in other modules/plugins + Ex: the routine "lapack_diagd" (which diagonalises a real hermitian matrix) is located in the file + qp2/src/utils/linear_algebra.irp.f + therefore it "belongs" to the module "utils" + : the routine "ao_to_mo" (which converts a given matrix A from the AO basis to the MO basis) is located in the file + qp2/src/mo_one_e_ints/ao_to_mo.irp.f + therefore it "belongs" to the module "mo_one_e_ints" + : the provider "ao_one_e_integrals" (which is the integrals of one-body part of H on the AO basis) is located in the file + qp2/src/mo_one_e_ints/ao_to_mo.irp.f + therefore it belongs to the module "mo_one_e_ints" + : the provider "one_e_dm_mo_beta_average" (which is the state average beta density matrix on the MO basis) is located in the file + qp2/src/determinants/density_matrix.irp.f + therefore it belongs to the module "determinants" + +To import all the variables that you need, you just need to write the name of the plugins in the file "NEED" +Ex: to import all the variables/routines of the module "utils", "determinants" and "mo_one_e_ints" you will have the following NEED file: +utils +determinants +mo_one_e_ints + +TIPS +---- +There are many many routines/providers in the core modules of QP. Nevertheless, as everything is coded with the IRPF90, you can use the following amazing tools: irpman +irpman can be used in command line in bash to obtain all the info on a routine or variable ! +Ex: execute the following command line : +irpman ao_one_e_integrals +Then it appears all the information you want on ao_one_e_integrals, including where it is created, the type, dimension if it is an array, what providers it needs to be built, and what providers need this provider. + + diff --git a/plugins/tuto_plugins/n2.xyz b/plugins/tuto_plugins/n2.xyz new file mode 100644 index 00000000..016732d8 --- /dev/null +++ b/plugins/tuto_plugins/n2.xyz @@ -0,0 +1,4 @@ +2 +N2 Geo: Experiment Mult: 1 symmetry: 14 +N 0.0 0.0 0.5488 +N 0.0 0.0 -0.5488 diff --git a/plugins/tuto_plugins/tuto_I/print_one_e_h.irp.f b/plugins/tuto_plugins/tuto_I/print_one_e_h.irp.f new file mode 100644 index 00000000..5d8dc1e7 --- /dev/null +++ b/plugins/tuto_plugins/tuto_I/print_one_e_h.irp.f @@ -0,0 +1,20 @@ +program my_program_to_print_stuffs + implicit none + BEGIN_DOC +! TODO : Put the documentation of the program here + END_DOC + integer :: i,j + print*,'AO integrals ' + do i = 1, ao_num + do j = 1, ao_num + print*,j,i,ao_one_e_integrals(j,i) + enddo + enddo + + print*,'MO integrals ' + do i = 1, mo_num + do j = 1, mo_num + print*,j,i,mo_one_e_integrals(j,i) + enddo + enddo +end diff --git a/plugins/tuto_plugins/tuto_I/tuto_I.rst b/plugins/tuto_plugins/tuto_I/tuto_I.rst new file mode 100644 index 00000000..05db8635 --- /dev/null +++ b/plugins/tuto_plugins/tuto_I/tuto_I.rst @@ -0,0 +1,97 @@ +====================================== +Tutorial for plugin I: One-e integrals +====================================== + +!!! Requirements: + a) you know how to create an EZFIO file and run calculations with QP + (check the tuto: ``), + b) you have an EZFIO file in the sto-3g from the file H2.xyz in plugins/tuto_plugins, + and you have run an HF calculation giving an energy of -1.116759 a.u., + c) you made an qp set_file YOUR_EZFIO_FILE_FOR_H2 in order to be, + d) you have READ the ../README.rst file to HAVE THE VOCABULARY. + +Our goals: +---------- +We want to create a plugin to do the following things: + a) print out one- and two-electron integrals on the AO/MO basis, + b) creates two providers which manipulate these objects, + c) print out these providers, + +I) Starting: creating the plugin +-------------------------------- +We will go step-by-step through these plugins. + +The name of the plugin will be "plugin_I", and its location is in "tuto_plugins". +Therefore to create the plugin, we do + +$ qp plugins create -n plugin_I -r tuto_plugins +Then to an "ls" in qp2/plugins/tuto_plugins/ +and you will find a directory called "plugin_I". +In that directory you will find: + i) a "NEED" file that will eventually contain all the other modules/plugins needed by our "plugin_I" + ii) a "README.rst" file that you can AND SHOULD modify in order to document what is doing the plugin. + iii) a "plugin_I.irp.f" file that is a program to be compiled and just printing "Hello world" + +II) Specifying the dependencies +------------------------------- +The next step is to know what are the other modules/plugins that we need to do what we want. +We need here + a) the one-electron integrals on the AO basis, which are computed in qp2/src/ao_one_e_ints/ + b) the one-electron integrals on the MO basis, which are computed in qp2/src/mo_one_e_ints/ + c) the two-electron integrals on the AO basis, which are computed in qp2/src/ao_two_e_ints/ + d) the two-electron integrals on the MO basis, which are computed in qp2/src/mo_two_e_ints/ + +Therefore, we will need the following four modules: +a) ao_one_e_ints +b) mo_one_e_ints +c) ao_two_e_ints +d) mo_two_e_ints + +You can then create the following "NEED" file by executing the following command +$ cat < NEED +ao_one_e_ints +mo_one_e_ints +ao_two_e_ints +mo_two_e_ints +EOF + +II) Installing the plugin +------------------------- +Now that we have specified the various depenencies we need now to INSTALL the plugin, which means to create the equivalent of a Makefile for the compilation. +To do it we simply do +$ qp plugins install plugin_I + +III) Compiling the void plugin +------------------------------ +It is customary to compile first your "void" plugin, void in the sense that it does not contain anything else than the program printing "Hello world". +To do so, just go in the plugin and execute the following command +$ ninja +It does a lot of stuffs, but it must conclude with something like +" +make: Leaving directory 'SOME_PATH_TOWARD_YOUR_QP2_DIRECTORY/qp2/ocaml' +" + +Since that it has compiled, an executable "plugin_I" has been created. +Also, if you make "ls" in the "plugin_I" you will notice that many symbolink links have been created, and among which the four modules that you included in the NEED file. +All the other modules (Ex:"ao_basis", "utils") are here because they are need by some of the four modules that you need. +The variables that we need are +ao_one_e_integrals +mo_one_e_integrals +You can check them with +irpman ao_one_e_integral +irpman mo_one_e_integral +in order to get some information on where they are created, and many more information. +We will modify the executable such that it prints out the integrals. + + +IV) Printing out the one-electron integrals +-------------------------------------------- +We will create a program that will print out the one-electron integrals on the AO and MO basis. +You can then copy the file "print_one_e_h.irp.f" in your plugin. +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. +You can check these variables with irpman ! +If you recompile using "ninja" as before, and another executable has been created "print_one_e_h". +Then, you can run the program on the ezfio file by doing +qp run print_one_e_h +and will print out the data you need :) + From 7bc6b888549cf976ce7bee7b06e85109636552a7 Mon Sep 17 00:00:00 2001 From: eginer Date: Thu, 21 Mar 2024 15:31:23 +0100 Subject: [PATCH 2/8] added H2.xyz in tuto_plugins --- plugins/tuto_plugins/H2.xyz | 6 ++++++ 1 file changed, 6 insertions(+) create mode 100644 plugins/tuto_plugins/H2.xyz diff --git a/plugins/tuto_plugins/H2.xyz b/plugins/tuto_plugins/H2.xyz new file mode 100644 index 00000000..7af12291 --- /dev/null +++ b/plugins/tuto_plugins/H2.xyz @@ -0,0 +1,6 @@ +2 +H2, equilibrium geometry +H 0.0 0.0 0. +H 0.0 0.0 0.74 + + From 9d3743e530f2b7d342778a32bc2ca89e36f97044 Mon Sep 17 00:00:00 2001 From: eginer Date: Fri, 22 Mar 2024 14:56:39 +0100 Subject: [PATCH 3/8] added some providers and the first tutorial for plugins --- plugins/README.rst | 4 +- .../tuto_I/print_traces_on_e.irp.f | 24 ++++ .../tuto_plugins/tuto_I/print_two_e_h.irp.f | 32 +++++ .../tuto_plugins/tuto_I/traces_one_e.irp.f | 111 ++++++++++++++++++ plugins/tuto_plugins/tuto_I/tuto_I.rst | 65 +++++++--- src/ao_one_e_ints/ao_one_e_ints.irp.f | 10 ++ src/scf_utils/fock_matrix.irp.f | 4 + src/utils/linear_algebra.irp.f | 19 +++ 8 files changed, 250 insertions(+), 19 deletions(-) create mode 100644 plugins/tuto_plugins/tuto_I/print_traces_on_e.irp.f create mode 100644 plugins/tuto_plugins/tuto_I/print_two_e_h.irp.f create mode 100644 plugins/tuto_plugins/tuto_I/traces_one_e.irp.f diff --git a/plugins/README.rst b/plugins/README.rst index 7f3f3c75..7fc011a3 100644 --- a/plugins/README.rst +++ b/plugins/README.rst @@ -22,6 +22,8 @@ we will go through a series of examples that allow you to do the following thing IV) print out the one- and two-electron rdms, V) obtain the AOs and MOs on the DFT grid, together with the density, +How the tutorial will be done +----------------------------- This tuto is as follows: i) you READ THIS FILE UNTIL THE END in order to get the big picture and vocabulary, ii) you go to the directory qp2/plugins/tuto_plugins/ and you will find detailed tuto there for each of the 5 examples. @@ -32,7 +34,7 @@ The first thing to do is to be in the QPSH mode: you execute the qp2/bin/qpsh sc the environement variables and allows for the completion of command lines in bash (that is an AMAZING feature :) Then, you need to known where you want to create your plugin, and what is the name of the plugin. -!!!! WARINING: The plugins are NECESSARILY located in qp2/plugins/ !!!! +!!!! WARNING: The plugins are NECESSARILY located in qp2/plugins/ !!!! Ex: If you want to create a plugin named "my_fancy_plugin" in the directory plugins/plugins_test/, this goes with the command qp plugins create -n my_fancy_plugin -r plugins_test/ diff --git a/plugins/tuto_plugins/tuto_I/print_traces_on_e.irp.f b/plugins/tuto_plugins/tuto_I/print_traces_on_e.irp.f new file mode 100644 index 00000000..2bf3b86b --- /dev/null +++ b/plugins/tuto_plugins/tuto_I/print_traces_on_e.irp.f @@ -0,0 +1,24 @@ +program my_program + implicit none + BEGIN_DOC +! This program is there essentially to show how one can use providers in programs + END_DOC + integer :: i,j + double precision :: accu + print*,'Trace on the AO basis ' + print*,trace_ao_one_e_ints + print*,'Trace on the AO basis after projection on the MO basis' + print*,trace_ao_one_e_ints_from_mo + print*,'Trace of MO integrals ' + print*,trace_mo_one_e_ints + print*,'ao_num = ',ao_num + print*,'mo_num = ',mo_num + if(ao_num .ne. mo_num)then + print*,'The AO basis and MO basis are different ...' + print*,'Trace on the AO basis should not be the same as Trace of MO integrals' + print*,'Only the second one must be equal to the trace on the MO integrals' + else + print*,'The AO basis and MO basis are the same !' + print*,'All traces should coincide ' + endif +end diff --git a/plugins/tuto_plugins/tuto_I/print_two_e_h.irp.f b/plugins/tuto_plugins/tuto_I/print_two_e_h.irp.f new file mode 100644 index 00000000..eaeb6c98 --- /dev/null +++ b/plugins/tuto_plugins/tuto_I/print_two_e_h.irp.f @@ -0,0 +1,32 @@ +program my_program_to_print_stuffs + implicit none + BEGIN_DOC +! TODO : Put the documentation of the program here + END_DOC + integer :: i,j,k,l + double precision :: integral + double precision :: get_ao_two_e_integral, get_two_e_integral ! declaration of the functions + print*,'AO integrals, physicist notations : ' + do i = 1, ao_num + do j = 1, ao_num + do k = 1, ao_num + do l = 1, ao_num + integral = get_ao_two_e_integral(i, j, k, l, ao_integrals_map) + print*,i,j,k,l,integral + enddo + enddo + enddo + enddo + + print*,'MO integrals, physicist notations : ' + do i = 1, mo_num + do j = 1, mo_num + do k = 1, mo_num + do l = 1, mo_num + integral = get_two_e_integral(i, j, k, l, mo_integrals_map) + print*,i,j,k,l,integral + enddo + enddo + enddo + enddo +end diff --git a/plugins/tuto_plugins/tuto_I/traces_one_e.irp.f b/plugins/tuto_plugins/tuto_I/traces_one_e.irp.f new file mode 100644 index 00000000..e71d49fc --- /dev/null +++ b/plugins/tuto_plugins/tuto_I/traces_one_e.irp.f @@ -0,0 +1,111 @@ + +! This file is an example of the kind of manipulations that you can do with providers +! + +!!!!!!!!!!!!!!!!!!!!!!!!!! Main providers useful for the program !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + +!!! type name +BEGIN_PROVIDER [ double precision, trace_mo_one_e_ints] + implicit none + BEGIN_DOC +! trace_mo_one_e_ints = Trace of the one-electron integrals on the MO basis +! +! = sum_i mo_one_e_integrals(i,i) + END_DOC + integer :: i + trace_mo_one_e_ints = 0.d0 + do i = 1, mo_num + trace_mo_one_e_ints += mo_one_e_integrals(i,i) + enddo +END_PROVIDER + +BEGIN_PROVIDER [ double precision, trace_ao_one_e_ints] + implicit none + BEGIN_DOC +! trace_ao_one_e_ints = Trace of the one-electron integrals on the AO basis taking into account the non orthogonality +! +! 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) +! +! WARNING: it is equal to the trace on the MO basis if and only if the AO basis and MO basis +! have the same number of functions + END_DOC + integer :: i,j + double precision, allocatable :: inv_overlap_times_integrals(:,:) ! = h S^{-1} + allocate(inv_overlap_times_integrals(ao_num,ao_num)) + ! routine that computes the product of two matrices, you can check it with + ! irpman get_AB_prod + call get_AB_prod(ao_one_e_integrals,ao_num,ao_num,s_inv,ao_num,inv_overlap_times_integrals) + ! Tr(inv_overlap_times_integrals) = Tr(h S^{-1}) + trace_ao_one_e_ints = 0.d0 + do i = 1, ao_num + trace_ao_one_e_ints += inv_overlap_times_integrals(i,i) + enddo + ! + ! testing the formula Tr(A S^{-1}) = \sum_{m,n}(A_mn S^{-1}_mn) + double precision :: test + test = 0.d0 + do i = 1, ao_num + do j = 1, ao_num + test += ao_one_e_integrals(j,i) * s_inv(i,j) + enddo + enddo + if(dabs(accu - trace_ao_one_e_ints).gt.1.d-12)then + print*,'Warning ! ' + print*,'Something is wrong because Tr(AB) \ne sum_{mn}A_mn B_nm' + endif +END_PROVIDER + +BEGIN_PROVIDER [ double precision, trace_ao_one_e_ints_from_mo] + implicit none + BEGIN_DOC +! trace_ao_one_e_ints_from_mo = Trace of the one-electron integrals on the AO basis after projection on the MO basis +! +! = Tr([SC h {SC}^+] S^{-1}) +! +! = Be aware that the trace of an operator in a non orthonormal basis is = Tr(A S^{-1}) where S is the metric +! Must be equal to the trace_mo_one_e_ints + END_DOC + integer :: i + double precision, allocatable :: inv_overlap_times_integrals(:,:) + allocate(inv_overlap_times_integrals(ao_num,ao_num)) + ! Using the provider ao_one_e_integrals_from_mo = [SC h {SC}^+] + call get_AB_prod(ao_one_e_integrals_from_mo,ao_num,ao_num,s_inv,ao_num,inv_overlap_times_integrals) + ! inv_overlap_times_integrals = [SC h {SC}^+] S^{-1} + trace_ao_one_e_ints_from_mo = 0.d0 + ! Computing the trace + do i = 1, ao_num + trace_ao_one_e_ints_from_mo += inv_overlap_times_integrals(i,i) + enddo +END_PROVIDER + +!!!!!!!!!!!!!!!!!!!!!!!!!!! Additional providers to check some stuffs !!!!!!!!!!!!!!!!!!!!!!!!! + +BEGIN_PROVIDER [ double precision, ao_one_e_int_no_ov_from_mo, (ao_num, ao_num) ] + BEGIN_DOC + ! ao_one_e_int_no_ov_from_mo = C mo_one_e_integrals C^T + ! + ! WARNING : NON EQUAL TO ao_one_e_integrals due to the non orthogonality + END_DOC + call mo_to_ao_no_overlap(mo_one_e_integrals,mo_num,ao_one_e_int_no_ov_from_mo,ao_num) +END_PROVIDER + +BEGIN_PROVIDER [ double precision, ao_one_e_int_no_ov_from_mo_ov_ov, (ao_num, ao_num)] + BEGIN_DOC + ! 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 + ! + ! EQUAL TO ao_one_e_integrals ONLY IF ao_num = mo_num + END_DOC + double precision, allocatable :: tmp(:,:) + allocate(tmp(ao_num, ao_num)) + call get_AB_prod(ao_overlap,ao_num,ao_num,ao_one_e_int_no_ov_from_mo,ao_num,tmp) + call get_AB_prod(tmp,ao_num,ao_num,ao_overlap,ao_num,ao_one_e_int_no_ov_from_mo_ov_ov) +END_PROVIDER + +BEGIN_PROVIDER [ double precision, c_t_s_c, (mo_num, mo_num)] + implicit none + BEGIN_DOC +! C^T S C = should be the identity + END_DOC + call get_AB_prod(mo_coef_transp,mo_num,ao_num,S_mo_coef,mo_num,c_t_s_c) +END_PROVIDER + diff --git a/plugins/tuto_plugins/tuto_I/tuto_I.rst b/plugins/tuto_plugins/tuto_I/tuto_I.rst index 05db8635..fea07e3d 100644 --- a/plugins/tuto_plugins/tuto_I/tuto_I.rst +++ b/plugins/tuto_plugins/tuto_I/tuto_I.rst @@ -1,14 +1,15 @@ -====================================== -Tutorial for plugin I: One-e integrals -====================================== +===================================================================== +Tutorial for plugin I: One-e integrals (duration: 20 minutes at most) +===================================================================== -!!! Requirements: - a) you know how to create an EZFIO file and run calculations with QP +Requirements +------------ + a) You know how to create an EZFIO file and run calculations with QP (check the tuto: ``), - b) you have an EZFIO file in the sto-3g from the file H2.xyz in plugins/tuto_plugins, - and you have run an HF calculation giving an energy of -1.116759 a.u., - c) you made an qp set_file YOUR_EZFIO_FILE_FOR_H2 in order to be, - d) you have READ the ../README.rst file to HAVE THE VOCABULARY. + b) You have an EZFIO file with MOs created (with the 'scf' executable for instance). + As we are going to print out some integrals, don't take a too large system/basis (Ex: H2, cc-pVDZ is ok :) + c) You made an qp set_file YOUR_EZFIO_FILE_FOR_H2 in order to work on that ezfio folder, + d) You have READ the ../README.rst file to HAVE THE VOCABULARY. Our goals: ---------- @@ -22,14 +23,14 @@ I) Starting: creating the plugin We will go step-by-step through these plugins. The name of the plugin will be "plugin_I", and its location is in "tuto_plugins". -Therefore to create the plugin, we do +Therefore to create the plugin, we do: -$ qp plugins create -n plugin_I -r tuto_plugins -Then to an "ls" in qp2/plugins/tuto_plugins/ -and you will find a directory called "plugin_I". +qp plugins create -n plugin_I -r tuto_plugins + +Then do an "ls" in qp2/plugins/tuto_plugins/ and you will find a directory called "plugin_I". In that directory you will find: - i) a "NEED" file that will eventually contain all the other modules/plugins needed by our "plugin_I" - ii) a "README.rst" file that you can AND SHOULD modify in order to document what is doing the plugin. + i) a "NEED" file that will eventually contain all the other modules/plugins needed by our "plugin_I" + ii) a "README.rst" file that you can AND SHOULD modify in order to document what is doing the plugin. iii) a "plugin_I.irp.f" file that is a program to be compiled and just printing "Hello world" II) Specifying the dependencies @@ -78,8 +79,8 @@ The variables that we need are ao_one_e_integrals mo_one_e_integrals You can check them with -irpman ao_one_e_integral -irpman mo_one_e_integral +irpman ao_one_e_integrals +irpman mo_one_e_integrals in order to get some information on where they are created, and many more information. We will modify the executable such that it prints out the integrals. @@ -87,7 +88,7 @@ We will modify the executable such that it prints out the integrals. IV) Printing out the one-electron integrals -------------------------------------------- We will create a program that will print out the one-electron integrals on the AO and MO basis. -You can then copy the file "print_one_e_h.irp.f" in your plugin. +You can then copy the file "print_one_e_h.irp.f" located in "plugins/tuto_plugins/tuto_I" in your plugin. 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. You can check these variables with irpman ! If you recompile using "ninja" as before, and another executable has been created "print_one_e_h". @@ -95,3 +96,31 @@ Then, you can run the program on the ezfio file by doing qp run print_one_e_h and will print out the data you need :) +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. +V) Printing out the two-electron integrals +------------------------------------------ +We will now create a file that prints out the two-electron integrals in the AO and MO basis. +These can be accessed with the following subroutines : ++) get_ao_two_e_integral for the AO basis ++) get_two_e_integral for the MO basis +check them with irpman ! +To print the two-electron integrals, you can copy the file "print_two_e_h.irp.f" in your plugin and recompile. +Then just run the program +qp run print_two_e_h +and it will print all the things you want :) + +VI) Creating new providers and a program to print them +------------------------------------------------------ +We will now create new providers that manipulates the objects that we just printed. +As an example, we will compute the trace of the one electron integrals in the AO and MO basis. +In the file "traces_one_e.irp.f" you will find the several new providers among which + a) trace_mo_one_e_ints : simply the sum of the diagonal matrix element of the one-electron integrals + b) trace_ao_one_e_ints : the corresponding trace on the AO basis : Sum(m,n) S^{-1}_{mn} h_{mn} + c) trace_ao_one_e_ints_from_mo : the trace on the AO basis with the integrals obtained first from the MO basis +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. +(You can check with "qp create_ezfio -h" for the option to create an EZFIO with cartesian basis functions) + +In the file "print_traces_on_e.irp.f" you will find an example of executable that prints out the various providers. +Copy these two files in your plugin and recompile to execute it. + +Execute the program print_traces_on_e and check for the results ! diff --git a/src/ao_one_e_ints/ao_one_e_ints.irp.f b/src/ao_one_e_ints/ao_one_e_ints.irp.f index 65981dc9..9b914dee 100644 --- a/src/ao_one_e_ints/ao_one_e_ints.irp.f +++ b/src/ao_one_e_ints/ao_one_e_ints.irp.f @@ -45,3 +45,13 @@ BEGIN_PROVIDER [ double precision, ao_one_e_integrals_imag,(ao_num,ao_num)] END_PROVIDER + +BEGIN_PROVIDER [ double precision, ao_one_e_integrals_from_mo, (ao_num, ao_num)] + implicit none + BEGIN_DOC +! Integrals of the one e hamiltonian obtained from the integrals on the MO basis +! +! WARNING : this is equal to ao_one_e_integrals only if the AO and MO basis have the same number of functions + END_DOC + call mo_to_ao(mo_one_e_integrals,mo_num,ao_one_e_integrals_from_mo,ao_num) +END_PROVIDER diff --git a/src/scf_utils/fock_matrix.irp.f b/src/scf_utils/fock_matrix.irp.f index 1942e542..c8fa8333 100644 --- a/src/scf_utils/fock_matrix.irp.f +++ b/src/scf_utils/fock_matrix.irp.f @@ -166,6 +166,10 @@ if(frozen_orb_scf)then integer :: iorb,jorb + ! active|core|active + !active | | 0 | + !core | 0 | | 0 + !active | | 0 | do i = 1, n_core_orb iorb = list_core(i) do j = 1, n_act_orb diff --git a/src/utils/linear_algebra.irp.f b/src/utils/linear_algebra.irp.f index 26e390b7..20386b30 100644 --- a/src/utils/linear_algebra.irp.f +++ b/src/utils/linear_algebra.irp.f @@ -2041,3 +2041,22 @@ subroutine get_A_squared(A,n,A2) double precision, intent(out):: A2(n,n) call dgemm('N','N',n,n,n,1.d0,A,size(A,1),A,size(A,1),0.d0,A2,size(A2,1)) end + +subroutine get_AB_prod(A,n,m,B,l,AB) + implicit none + BEGIN_DOC +! AB = A B where A is n x m, B is m x l. Use the dgemm routine + END_DOC + double precision, intent(in) :: A(n,m),B(m,l) + integer, intent(in) :: n,m,l + double precision, intent(out):: AB(n,l) + if(size(A,2).ne.m.or.size(B,1).ne.m)then + print*,'error in get_AB_prod ! ' + print*,'matrices do not have the good dimension ' + print*,'size(A,2) = ',size(A,2) + print*,'size(B,1) = ',size(B,1) + print*,'m = ',m + stop + endif + call dgemm('N','N',n,l,m,1.d0,A,size(A,1),B,size(B,1),0.d0,AB,size(AB,1)) +end From dd2f0a2c0770b9d1e26522fa7a80f1ee55865408 Mon Sep 17 00:00:00 2001 From: eginer Date: Fri, 22 Mar 2024 16:30:08 +0100 Subject: [PATCH 4/8] added the introduction to the plugins tutorial --- docs/source/appendix/contributors.rst | 1 + docs/source/index.rst | 3 +- external/irpf90 | 2 +- plugins/README.rst | 148 +++++++++++++++++--------- 4 files changed, 104 insertions(+), 50 deletions(-) diff --git a/docs/source/appendix/contributors.rst b/docs/source/appendix/contributors.rst index e3574e5a..74837282 100644 --- a/docs/source/appendix/contributors.rst +++ b/docs/source/appendix/contributors.rst @@ -46,6 +46,7 @@ The following people have contributed to this project (by alphabetical order): * Nicolas Renon * Lorenzo Tenti * Julien Toulouse +* Diata Traoré * Mikaël Véril diff --git a/docs/source/index.rst b/docs/source/index.rst index 4231b1f8..e7e63260 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -39,9 +39,9 @@ programmers_guide/programming programmers_guide/ezfio programmers_guide/plugins + programmers_guide/plugins_tuto_intro programmers_guide/new_ks programmers_guide/index - programmers_guide/plugins .. toctree:: @@ -52,5 +52,6 @@ appendix/benchmarks appendix/license appendix/contributors + appendix/references diff --git a/external/irpf90 b/external/irpf90 index ba1a2837..4ab1b175 160000 --- a/external/irpf90 +++ b/external/irpf90 @@ -1 +1 @@ -Subproject commit ba1a2837aa61cb8f9892860cec544d7c6659badd +Subproject commit 4ab1b175fc7ed0d96c1912f13dc53579b24157a6 diff --git a/plugins/README.rst b/plugins/README.rst index 7fc011a3..3214a619 100644 --- a/plugins/README.rst +++ b/plugins/README.rst @@ -3,76 +3,128 @@ Tutorial for creating a plugin ============================== Introduction: what is a plugin, and what this tuto will be about ? -============================================================ -The QP is split into two kinds of routines/global variables (i.e. providers): - i) the core modules locatedin qp2/src/, which contains all the bulk of a quantum chemistry software (integrals, matrix elements between Slater determinants, linear algebra routines, DFT stuffs etc..) - ii) the plugins which are external stuffs connected to the qp2/src/ stuffs. +================================================================== + +The |QP| is split into two kinds of routines/global variables (i.e. *providers*): + i) the **core modules** locatedin qp2/src/, which contains all the bulk of a quantum chemistry software (integrals, matrix elements between Slater determinants, linear algebra routines, DFT stuffs etc..) + ii) the **plugins** which are external routines/*providers* connected to the qp2/src/ routines/*providers*. -More precisely, a plugin of the QP is a directory where you can create routines, +More precisely, a **plugin** of the |QP| is a directory where you can create routines, providers and executables that use all the global variables/functions/routines already created -in the modules ofqp2/src or in other plugins. +in the modules of qp2/src or in other plugins. Instead of giving a theoretical lecture on what is a plugin, we will go through a series of examples that allow you to do the following thing: - I) print out one- and two-electron integrals on the AO/MO basis, - creates two providers which manipulate these objects, - print out these providers, - II) browse the Slater determinants stored in the EZFIO wave function and compute their matrix elements, - III) build the Hamiltonian matrix and diagonalize it either with Lapck or Davidson, - IV) print out the one- and two-electron rdms, - V) obtain the AOs and MOs on the DFT grid, together with the density, + +i) print out **one- and two-electron integrals** on the AO/MO basis, creates two providers which manipulate these objects, print out these providers, + +ii) browse the **Slater determinants stored** in the |EZFIO| wave function and compute their matrix elements, + +iii) build the **Hamiltonian matrix** and **diagonalize** it either with **Lapack or Davidson**, + +iv) print out the **one- and two-electron rdms**, + +v) obtain the **AOs** and **MOs** on the **DFT grid**, together with the **density**, How the tutorial will be done ----------------------------- + This tuto is as follows: - i) you READ THIS FILE UNTIL THE END in order to get the big picture and vocabulary, - ii) you go to the directory qp2/plugins/tuto_plugins/ and you will find detailed tuto there for each of the 5 examples. + + i) you **READ THIS FILE UNTIL THE END** in order to get the big picture and vocabulary, + + ii) you go to the directory :file:`qp2/plugins/tuto_plugins/` and you will find detailed tutorials for each of the 5 examples. Creating a plugin: the basic ---------------------------- + The first thing to do is to be in the QPSH mode: you execute the qp2/bin/qpsh script that essentially loads all the environement variables and allows for the completion of command lines in bash (that is an AMAZING feature :) -Then, you need to known where you want to create your plugin, and what is the name of the plugin. -!!!! WARNING: The plugins are NECESSARILY located in qp2/plugins/ !!!! +Then, you need to known **where** you want to create your plugin, and what is the **name** of the plugin. + +.. important:: + + The plugins are **NECESSARILY** located in qp2/plugins/, and from there you can create any structures of directories. + + Ex: If you want to create a plugin named "my_fancy_plugin" in the directory plugins/plugins_test/, this goes with the command -qp plugins create -n my_fancy_plugin -r plugins_test/ -Then, to create plugin of your dreams, the two questions you need to answer are the following: -a) What do I need to compute what I want, which means what are the objects that I need ? +.. code:: bash + + qp plugins create -n my_fancy_plugin -r plugins_test/ + +Then, to create the plugin of your dreams, the two questions you need to answer are the following: + +1) What do I **need** to compute what I want, which means what are the **objects** that I need ? + There are two kind of objects: - + the routines/functions + + + the *routines/functions*: + Ex: Linear algebra routines, integration routines etc ... - + the global variables which are called the PROVIDERS + + + the global variables which are called the *providers*: + Ex: one-electron integrals, Slater determinants, density matrices etc ... -b) Where do I find these objects ? - The objects (routines/functions/providers) are necessarily created in other modules/plugins - Ex: the routine "lapack_diagd" (which diagonalises a real hermitian matrix) is located in the file - qp2/src/utils/linear_algebra.irp.f - therefore it "belongs" to the module "utils" - : the routine "ao_to_mo" (which converts a given matrix A from the AO basis to the MO basis) is located in the file - qp2/src/mo_one_e_ints/ao_to_mo.irp.f - therefore it "belongs" to the module "mo_one_e_ints" - : the provider "ao_one_e_integrals" (which is the integrals of one-body part of H on the AO basis) is located in the file - qp2/src/mo_one_e_ints/ao_to_mo.irp.f - therefore it belongs to the module "mo_one_e_ints" - : the provider "one_e_dm_mo_beta_average" (which is the state average beta density matrix on the MO basis) is located in the file - qp2/src/determinants/density_matrix.irp.f - therefore it belongs to the module "determinants" -To import all the variables that you need, you just need to write the name of the plugins in the file "NEED" -Ex: to import all the variables/routines of the module "utils", "determinants" and "mo_one_e_ints" you will have the following NEED file: -utils -determinants -mo_one_e_ints +2) **Where do I find** these objects ? -TIPS ----- -There are many many routines/providers in the core modules of QP. Nevertheless, as everything is coded with the IRPF90, you can use the following amazing tools: irpman -irpman can be used in command line in bash to obtain all the info on a routine or variable ! -Ex: execute the following command line : -irpman ao_one_e_integrals -Then it appears all the information you want on ao_one_e_integrals, including where it is created, the type, dimension if it is an array, what providers it needs to be built, and what providers need this provider. + The objects (routines/functions/providers) are necessarily created in other *modules/plugins*. + +.. seealso:: + + The routine :c:func:`lapack_diagd` (which diagonalises a real hermitian matrix) is located in the file + :file:`qp2/src/utils/linear_algebra.irp.f` + therefore it "belongs" to the module "utils" + + The routine :c:func:`ao_to_mo` (which converts a given matrix A from the AO basis to the MO basis) is located in the file + :file:`qp2/src/mo_one_e_ints/ao_to_mo.irp.f` + therefore it "belongs" to the module "mo_one_e_ints" + + The provider :c:data:`ao_one_e_integrals` (which is the integrals of one-body part of H on the AO basis) is located in the file + :file:`qp2/src/mo_one_e_ints/ao_to_mo.irp.f` + therefore it belongs to the module "mo_one_e_ints" + + The provider :c:data:`one_e_dm_mo_beta_average` (which is the state average beta density matrix on the MO basis) is located in the file + :file:`qp2/src/determinants/density_matrix.irp.f` + therefore it belongs to the module "determinants" + +To import all the variables that you need, you just need to write the name of the plugins in the :file:`NEED` file . + +To import all the variables/routines of the module "utils", "determinants" and "mo_one_e_ints", the :file:`NEED` file you will need is simply the following: + +.. code:: bash + + cat NEED + + utils + determinants + mo_one_e_ints + + +.. important:: + + There are **many** routines/providers in the core modules of QP. + + Nevertheless, as everything is coded with the |IRPF90|, you can use the following amazing tools: :command:`irpman` + + :command:`irpman` can be used in command line in bash to obtain all the info on a routine or variable ! + + +Example: execute the following command line : + +.. code:: bash + + irpman ao_one_e_integrals + +Then all the information you need on :c:data:`ao_one_e_integrals` will appear on the screen. +This includes + - **where** the provider is created, (*i.e.* the actual file where the provider is designed) + - the **type** of the provider (*i.e.* a logical, integer etc ...) + - the **dimension** if it is an array, + - what other *providers* are **needed** to build this provider, + - what other *providers* **need** this provider. From e0af6d84258ebc3540628d59c62d3d937ca5a9e3 Mon Sep 17 00:00:00 2001 From: eginer Date: Fri, 22 Mar 2024 17:29:32 +0100 Subject: [PATCH 5/8] added properly the first tuto! --- docs/source/index.rst | 1 + plugins/README.rst | 35 ++-- plugins/tuto_plugins/tuto_I/tuto_I.rst | 220 ++++++++++++++++++------- 3 files changed, 175 insertions(+), 81 deletions(-) diff --git a/docs/source/index.rst b/docs/source/index.rst index e7e63260..273582d4 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -40,6 +40,7 @@ programmers_guide/ezfio programmers_guide/plugins programmers_guide/plugins_tuto_intro + programmers_guide/plugins_tuto_I programmers_guide/new_ks programmers_guide/index diff --git a/plugins/README.rst b/plugins/README.rst index 3214a619..3dc50873 100644 --- a/plugins/README.rst +++ b/plugins/README.rst @@ -2,12 +2,12 @@ Tutorial for creating a plugin ============================== -Introduction: what is a plugin, and what this tuto will be about ? -================================================================== +Introduction: what is a plugin, and what tutorial will be about ? +================================================================= The |QP| is split into two kinds of routines/global variables (i.e. *providers*): - i) the **core modules** locatedin qp2/src/, which contains all the bulk of a quantum chemistry software (integrals, matrix elements between Slater determinants, linear algebra routines, DFT stuffs etc..) - ii) the **plugins** which are external routines/*providers* connected to the qp2/src/ routines/*providers*. + 1) the **core modules** locatedin qp2/src/, which contains all the bulk of a quantum chemistry software (integrals, matrix elements between Slater determinants, linear algebra routines, DFT stuffs etc..) + 2) the **plugins** which are external routines/*providers* connected to the qp2/src/ routines/*providers*. More precisely, a **plugin** of the |QP| is a directory where you can create routines, providers and executables that use all the global variables/functions/routines already created @@ -16,24 +16,24 @@ in the modules of qp2/src or in other plugins. Instead of giving a theoretical lecture on what is a plugin, we will go through a series of examples that allow you to do the following thing: -i) print out **one- and two-electron integrals** on the AO/MO basis, creates two providers which manipulate these objects, print out these providers, +1) print out **one- and two-electron integrals** on the AO/MO basis, creates two providers which manipulate these objects, print out these providers, -ii) browse the **Slater determinants stored** in the |EZFIO| wave function and compute their matrix elements, +2) browse the **Slater determinants stored** in the |EZFIO| wave function and compute their matrix elements, -iii) build the **Hamiltonian matrix** and **diagonalize** it either with **Lapack or Davidson**, +3) build the **Hamiltonian matrix** and **diagonalize** it either with **Lapack or Davidson**, -iv) print out the **one- and two-electron rdms**, +4) print out the **one- and two-electron rdms**, -v) obtain the **AOs** and **MOs** on the **DFT grid**, together with the **density**, +5) obtain the **AOs** and **MOs** on the **DFT grid**, together with the **density**, How the tutorial will be done ----------------------------- This tuto is as follows: - i) you **READ THIS FILE UNTIL THE END** in order to get the big picture and vocabulary, + 1) you **READ THIS FILE UNTIL THE END** in order to get the big picture and vocabulary, - ii) you go to the directory :file:`qp2/plugins/tuto_plugins/` and you will find detailed tutorials for each of the 5 examples. + 2) you go to the directory :file:`qp2/plugins/tuto_plugins/` and you will find detailed tutorials for each of the 5 examples. Creating a plugin: the basic ---------------------------- @@ -77,23 +77,23 @@ Then, to create the plugin of your dreams, the two questions you need to answer The routine :c:func:`lapack_diagd` (which diagonalises a real hermitian matrix) is located in the file :file:`qp2/src/utils/linear_algebra.irp.f` - therefore it "belongs" to the module "utils" + therefore it "belongs" to the module :ref:`module_utils` The routine :c:func:`ao_to_mo` (which converts a given matrix A from the AO basis to the MO basis) is located in the file :file:`qp2/src/mo_one_e_ints/ao_to_mo.irp.f` - therefore it "belongs" to the module "mo_one_e_ints" + therefore it "belongs" to the module :ref:`module_mo_one_e_ints` The provider :c:data:`ao_one_e_integrals` (which is the integrals of one-body part of H on the AO basis) is located in the file - :file:`qp2/src/mo_one_e_ints/ao_to_mo.irp.f` - therefore it belongs to the module "mo_one_e_ints" + :file:`qp2/src/ao_one_e_ints/ao_one_e_ints.irp.f` + therefore it belongs to the module :ref:`module_ao_one_e_ints` The provider :c:data:`one_e_dm_mo_beta_average` (which is the state average beta density matrix on the MO basis) is located in the file :file:`qp2/src/determinants/density_matrix.irp.f` - therefore it belongs to the module "determinants" + therefore it belongs to the module :ref:`module_determinants` To import all the variables that you need, you just need to write the name of the plugins in the :file:`NEED` file . -To import all the variables/routines of the module "utils", "determinants" and "mo_one_e_ints", the :file:`NEED` file you will need is simply the following: +To import all the variables/routines of the module :ref:`module_utils`, :ref:`module_determinants` and :ref:`module_mo_one_e_ints`, the :file:`NEED` file you will need is simply the following: .. code:: bash @@ -121,6 +121,7 @@ Example: execute the following command line : Then all the information you need on :c:data:`ao_one_e_integrals` will appear on the screen. This includes + - **where** the provider is created, (*i.e.* the actual file where the provider is designed) - the **type** of the provider (*i.e.* a logical, integer etc ...) - the **dimension** if it is an array, diff --git a/plugins/tuto_plugins/tuto_I/tuto_I.rst b/plugins/tuto_plugins/tuto_I/tuto_I.rst index fea07e3d..43b4af0b 100644 --- a/plugins/tuto_plugins/tuto_I/tuto_I.rst +++ b/plugins/tuto_plugins/tuto_I/tuto_I.rst @@ -1,126 +1,218 @@ -===================================================================== -Tutorial for plugin I: One-e integrals (duration: 20 minutes at most) -===================================================================== +============================================= +Tuto I: One- and two-e integrals (20 minutes) +============================================= Requirements ------------ - a) You know how to create an EZFIO file and run calculations with QP - (check the tuto: ``), - b) You have an EZFIO file with MOs created (with the 'scf' executable for instance). - As we are going to print out some integrals, don't take a too large system/basis (Ex: H2, cc-pVDZ is ok :) - c) You made an qp set_file YOUR_EZFIO_FILE_FOR_H2 in order to work on that ezfio folder, - d) You have READ the ../README.rst file to HAVE THE VOCABULARY. +1) You know how to create an |EZFIO| file and run calculations with |QP| (check the tuto: ``_), + +2) You have an |EZFIO| file with MOs created (with the :ref:`scf` executable for instance). As we are going to print out some integrals, don't take a too large system/basis (Ex: H2, cc-pVDZ is ok :) + +3) You made an qp set_file YOUR_EZFIO_FILE_FOR_H2 in order to work on that ezfio folder. + +4) You have READ the :file:`qp2/plugins/README.rst` file to HAVE THE **VOCABULARY**. Our goals: ---------- We want to create a plugin to do the following things: - a) print out one- and two-electron integrals on the AO/MO basis, - b) creates two providers which manipulate these objects, - c) print out these providers, + 1) print out one- and two-electron integrals on the AO/MO basis, -I) Starting: creating the plugin --------------------------------- + 2) creates two providers which manipulate these objects, + + 3) print out these providers. + +I) Getting started: creating the plugin +--------------------------------------- We will go step-by-step through these plugins. -The name of the plugin will be "plugin_I", and its location is in "tuto_plugins". +We will create a plugin named "plugin_I", and its location will be in "tuto_plugins". Therefore to create the plugin, we do: -qp plugins create -n plugin_I -r tuto_plugins +.. code:: bash + + qp plugins create -n plugin_I -r tuto_plugins Then do an "ls" in qp2/plugins/tuto_plugins/ and you will find a directory called "plugin_I". + In that directory you will find: - i) a "NEED" file that will eventually contain all the other modules/plugins needed by our "plugin_I" - ii) a "README.rst" file that you can AND SHOULD modify in order to document what is doing the plugin. - iii) a "plugin_I.irp.f" file that is a program to be compiled and just printing "Hello world" + +1) a :file:`NEED` file that will eventually contain all the other modules/plugins needed by our "plugin_I", + +2) a :file:`README.rst` file that you can and **SHOULD** modify in order to **DOCUMENT** what is doing the plugin, + +3) a :file:`plugin_I.irp.f` file that is a program to be compiled and just printing "Hello world" II) Specifying the dependencies ------------------------------- The next step is to know what are the other modules/plugins that we need to do what we want. We need here - a) the one-electron integrals on the AO basis, which are computed in qp2/src/ao_one_e_ints/ - b) the one-electron integrals on the MO basis, which are computed in qp2/src/mo_one_e_ints/ - c) the two-electron integrals on the AO basis, which are computed in qp2/src/ao_two_e_ints/ - d) the two-electron integrals on the MO basis, which are computed in qp2/src/mo_two_e_ints/ + +a) the one-electron integrals on the AO basis, which are computed in :file:`qp2/src/ao_one_e_ints/` + +b) the one-electron integrals on the MO basis, which are computed in :file:`qp2/src/mo_one_e_ints/` + +c) the two-electron integrals on the AO basis, which are computed in :file:`qp2/src/ao_two_e_ints/` + +d) the two-electron integrals on the MO basis, which are computed in :file:`qp2/src/mo_two_e_ints/` Therefore, we will need the following four modules: -a) ao_one_e_ints -b) mo_one_e_ints -c) ao_two_e_ints -d) mo_two_e_ints + + a) ao_one_e_ints + b) mo_one_e_ints + c) ao_two_e_ints + d) mo_two_e_ints You can then create the following "NEED" file by executing the following command -$ cat < NEED -ao_one_e_ints -mo_one_e_ints -ao_two_e_ints -mo_two_e_ints -EOF + +.. code:: bash + + cat < NEED + ao_one_e_ints + mo_one_e_ints + ao_two_e_ints + mo_two_e_ints + EOF II) Installing the plugin ------------------------- Now that we have specified the various depenencies we need now to INSTALL the plugin, which means to create the equivalent of a Makefile for the compilation. + To do it we simply do -$ qp plugins install plugin_I + +.. code:: bash + + qp plugins install plugin_I + III) Compiling the void plugin ------------------------------ It is customary to compile first your "void" plugin, void in the sense that it does not contain anything else than the program printing "Hello world". + To do so, just go in the plugin and execute the following command -$ ninja + +.. code:: bash + + ninja + It does a lot of stuffs, but it must conclude with something like -" -make: Leaving directory 'SOME_PATH_TOWARD_YOUR_QP2_DIRECTORY/qp2/ocaml' -" + +.. code:: bash + + make: Leaving directory 'SOME_PATH_TOWARD_YOUR_QP2_DIRECTORY/qp2/ocaml' + Since that it has compiled, an executable "plugin_I" has been created. + Also, if you make "ls" in the "plugin_I" you will notice that many symbolink links have been created, and among which the four modules that you included in the NEED file. -All the other modules (Ex:"ao_basis", "utils") are here because they are need by some of the four modules that you need. + +All the other modules (Ex::ref:`module_ao_basis`, :ref:`module_utils`) are here because they are need by some of the four modules that you need. The variables that we need are -ao_one_e_integrals -mo_one_e_integrals + +:data:`ao_one_e_integrals` + +:data:`mo_one_e_integrals` + You can check them with -irpman ao_one_e_integrals -irpman mo_one_e_integrals + +.. code:: bash + + irpman ao_one_e_integrals + + +.. code:: bash + + irpman mo_one_e_integrals + in order to get some information on where they are created, and many more information. -We will modify the executable such that it prints out the integrals. +We will now create an executable such that it prints out the integrals. IV) Printing out the one-electron integrals -------------------------------------------- -We will create a program that will print out the one-electron integrals on the AO and MO basis. -You can then copy the file "print_one_e_h.irp.f" located in "plugins/tuto_plugins/tuto_I" in your plugin. -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. -You can check these variables with irpman ! -If you recompile using "ninja" as before, and another executable has been created "print_one_e_h". +We will now create a program that will print out the one-electron integrals on the AO and MO basis. + +You can then copy the file :file:`qp2/plugins/tuto_plugins/tuto_I/print_one_e_h.irp.f` in your plugin. + +In this file you will see that we simply browse the two arrays :data:`ao_one_e_integrals` and :data:`mo_one_e_integrals`, which are the providers and we browse them until either :data:`ao_num` or :data:`mo_num` which are also providers representing the number of AOs or MOs. + + +.. seealso:: + + You can check these variables with :command:`irpman` ! + +If you recompile using |ninja| as before, and another executable has been created "print_one_e_h". Then, you can run the program on the ezfio file by doing -qp run print_one_e_h + +.. code:: bash + + qp run print_one_e_h + and will print out the data you need :) -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. +By the way, as the file :file:`plugin_I.irp.f` contains nothing but a "Hello world" print, you can simply remove it if you want. + V) Printing out the two-electron integrals ------------------------------------------ We will now create a file that prints out the two-electron integrals in the AO and MO basis. These can be accessed with the following subroutines : -+) get_ao_two_e_integral for the AO basis -+) get_two_e_integral for the MO basis -check them with irpman ! -To print the two-electron integrals, you can copy the file "print_two_e_h.irp.f" in your plugin and recompile. + +1- :c:func:`get_ao_two_e_integral` for the AO basis + +2- :c:func:`get_two_e_integral` for the MO basis + + +.. seealso:: + + check them with irpman ! + +To print the two-electron integrals, you can copy the file :file:`qp2/plugins/tuto_plugins/tuto_I/print_two_e_h.irp.f` in your plugin and recompile with |ninja|. Then just run the program -qp run print_two_e_h + +.. code:: bash + + qp run print_two_e_h + and it will print all the things you want :) VI) Creating new providers and a program to print them ------------------------------------------------------ We will now create new providers that manipulates the objects that we just printed. As an example, we will compute the trace of the one electron integrals in the AO and MO basis. -In the file "traces_one_e.irp.f" you will find the several new providers among which - a) trace_mo_one_e_ints : simply the sum of the diagonal matrix element of the one-electron integrals - b) trace_ao_one_e_ints : the corresponding trace on the AO basis : Sum(m,n) S^{-1}_{mn} h_{mn} - c) trace_ao_one_e_ints_from_mo : the trace on the AO basis with the integrals obtained first from the MO basis -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. -(You can check with "qp create_ezfio -h" for the option to create an EZFIO with cartesian basis functions) +In the file :file:`qp2/plugins/tuto_plugins/tuto_I/traces_one_e.irp.f` you will find the several new providers among which -In the file "print_traces_on_e.irp.f" you will find an example of executable that prints out the various providers. + 1- :c:data:`trace_mo_one_e_ints` : simply the sum of the diagonal matrix element of the one-electron integrals + + 2- :c:data:`trace_ao_one_e_ints` : the corresponding trace on the AO basis + .. math:: + + \text{Tr}({\bf h}{\bf S}^{-1}) = \sum_{m,n} S^{-1}_{mn} h_{mn} + + + 3- :c:data:`trace_ao_one_e_ints_from_mo` : the trace on the AO basis with the integrals obtained first from the MO basis + .. math:: + + \text{Tr}({\bf \tilde{h}}{\bf S}^{-1}) = \text{Tr}\big({\bf SC h}({\bf SC }^T){\bf S}^{-1}\big) + +Just copy the :file:`qp2/plugins/tuto_plugins/tuto_I/traces_one_e.irp.f` in your plugin and recompile. + +.. seealso:: + + Once it has compiled, check your new providers with :command:`irpman` ! + +As explained in the files :file:`qp2/plugins/tuto_plugins/tuto_I/traces_one_e.irp.f` and :file:`qp2/plugins/tuto_plugins/tuto_I/print_traces_on_e.irp.f`, :c:data:`trace_mo_one_e_ints` is equal to :c:data:`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. + + +.. seealso:: + + You can check with :command:`qp create_ezfio -h` for the option to create an |EZFIO| with cartesian basis functions + +In the file :file:`qp2/plugins/tuto_plugins/tuto_I/print_traces_on_e.irp.f` you will find an example of executable that prints out the various providers. Copy these two files in your plugin and recompile to execute it. -Execute the program print_traces_on_e and check for the results ! +Execute the program print_traces_on_e and check for the results with + +.. code:: bash + + qp run print_traces_on_e + +The code in :file:`qp2/plugins/tuto_plugins/tuto_I/print_traces_on_e.irp.f` should be easy to read, I let the reader interpret it. From 64523de3aecf31a90ed791fbb87be40094f1f930 Mon Sep 17 00:00:00 2001 From: eginer Date: Fri, 22 Mar 2024 18:33:17 +0100 Subject: [PATCH 6/8] minor modifs in cipsi_tc_bi_ortho/selection.irp.f --- plugins/local/cipsi_tc_bi_ortho/selection.irp.f | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/plugins/local/cipsi_tc_bi_ortho/selection.irp.f b/plugins/local/cipsi_tc_bi_ortho/selection.irp.f index e0637fa5..12163e06 100644 --- a/plugins/local/cipsi_tc_bi_ortho/selection.irp.f +++ b/plugins/local/cipsi_tc_bi_ortho/selection.irp.f @@ -960,7 +960,7 @@ subroutine fill_buffer_double(i_generator, sp, h1, h2, bannedOrb, banned, fock_d ! endif e_pert(istate) = 0.25 * val / delta_E ! e_pert(istate) = 0.5d0 * (tmp - delta_E) - if(dsqrt(dabs(tmp)).gt.1.d-4.and.dabs(alpha_h_psi).gt.1.d-4)then + if(dsqrt(tmp).gt.1.d-4.and.dabs(psi_h_alpha).gt.1.d-4)then coef(istate) = e_pert(istate) / psi_h_alpha else coef(istate) = alpha_h_psi / delta_E From 9abc0c996af808e0cd77c4cbe0fb4ffa1c585a47 Mon Sep 17 00:00:00 2001 From: eginer Date: Mon, 25 Mar 2024 17:00:14 +0100 Subject: [PATCH 7/8] mv tuto_plugins in local --- plugins/{ => local}/tuto_plugins/H2.xyz | 0 plugins/{ => local}/tuto_plugins/n2.xyz | 0 plugins/{ => local}/tuto_plugins/tuto_I/print_one_e_h.irp.f | 0 plugins/{ => local}/tuto_plugins/tuto_I/print_traces_on_e.irp.f | 0 plugins/{ => local}/tuto_plugins/tuto_I/print_two_e_h.irp.f | 0 plugins/{ => local}/tuto_plugins/tuto_I/traces_one_e.irp.f | 0 plugins/{ => local}/tuto_plugins/tuto_I/tuto_I.rst | 0 7 files changed, 0 insertions(+), 0 deletions(-) rename plugins/{ => local}/tuto_plugins/H2.xyz (100%) rename plugins/{ => local}/tuto_plugins/n2.xyz (100%) rename plugins/{ => local}/tuto_plugins/tuto_I/print_one_e_h.irp.f (100%) rename plugins/{ => local}/tuto_plugins/tuto_I/print_traces_on_e.irp.f (100%) rename plugins/{ => local}/tuto_plugins/tuto_I/print_two_e_h.irp.f (100%) rename plugins/{ => local}/tuto_plugins/tuto_I/traces_one_e.irp.f (100%) rename plugins/{ => local}/tuto_plugins/tuto_I/tuto_I.rst (100%) diff --git a/plugins/tuto_plugins/H2.xyz b/plugins/local/tuto_plugins/H2.xyz similarity index 100% rename from plugins/tuto_plugins/H2.xyz rename to plugins/local/tuto_plugins/H2.xyz diff --git a/plugins/tuto_plugins/n2.xyz b/plugins/local/tuto_plugins/n2.xyz similarity index 100% rename from plugins/tuto_plugins/n2.xyz rename to plugins/local/tuto_plugins/n2.xyz diff --git a/plugins/tuto_plugins/tuto_I/print_one_e_h.irp.f b/plugins/local/tuto_plugins/tuto_I/print_one_e_h.irp.f similarity index 100% rename from plugins/tuto_plugins/tuto_I/print_one_e_h.irp.f rename to plugins/local/tuto_plugins/tuto_I/print_one_e_h.irp.f diff --git a/plugins/tuto_plugins/tuto_I/print_traces_on_e.irp.f b/plugins/local/tuto_plugins/tuto_I/print_traces_on_e.irp.f similarity index 100% rename from plugins/tuto_plugins/tuto_I/print_traces_on_e.irp.f rename to plugins/local/tuto_plugins/tuto_I/print_traces_on_e.irp.f diff --git a/plugins/tuto_plugins/tuto_I/print_two_e_h.irp.f b/plugins/local/tuto_plugins/tuto_I/print_two_e_h.irp.f similarity index 100% rename from plugins/tuto_plugins/tuto_I/print_two_e_h.irp.f rename to plugins/local/tuto_plugins/tuto_I/print_two_e_h.irp.f diff --git a/plugins/tuto_plugins/tuto_I/traces_one_e.irp.f b/plugins/local/tuto_plugins/tuto_I/traces_one_e.irp.f similarity index 100% rename from plugins/tuto_plugins/tuto_I/traces_one_e.irp.f rename to plugins/local/tuto_plugins/tuto_I/traces_one_e.irp.f diff --git a/plugins/tuto_plugins/tuto_I/tuto_I.rst b/plugins/local/tuto_plugins/tuto_I/tuto_I.rst similarity index 100% rename from plugins/tuto_plugins/tuto_I/tuto_I.rst rename to plugins/local/tuto_plugins/tuto_I/tuto_I.rst From a7a43dafb6cb6f41b41a5b417206c6d090f24186 Mon Sep 17 00:00:00 2001 From: eginer Date: Mon, 25 Mar 2024 17:02:28 +0100 Subject: [PATCH 8/8] modified the doc according to the new path of tuto plugin --- docs/source/programmers_guide/plugins_tuto_I.rst | 1 + docs/source/programmers_guide/plugins_tuto_intro.rst | 1 + 2 files changed, 2 insertions(+) create mode 100644 docs/source/programmers_guide/plugins_tuto_I.rst create mode 100644 docs/source/programmers_guide/plugins_tuto_intro.rst diff --git a/docs/source/programmers_guide/plugins_tuto_I.rst b/docs/source/programmers_guide/plugins_tuto_I.rst new file mode 100644 index 00000000..27864487 --- /dev/null +++ b/docs/source/programmers_guide/plugins_tuto_I.rst @@ -0,0 +1 @@ +.. include:: ../../../plugins/local/tuto_plugins/tuto_I/tuto_I.rst diff --git a/docs/source/programmers_guide/plugins_tuto_intro.rst b/docs/source/programmers_guide/plugins_tuto_intro.rst new file mode 100644 index 00000000..63482462 --- /dev/null +++ b/docs/source/programmers_guide/plugins_tuto_intro.rst @@ -0,0 +1 @@ +.. include:: ../../../plugins/README.rst