From 0c2db61521eb1413e687d0626bf84e95915cb119 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Tue, 1 Apr 2014 17:49:29 +0200 Subject: [PATCH] Added documentation and Makefile --- .gitignore | 3 + Makefile | 27 ++++ README.md | 2 + doc/.gitignore | 1 + doc/Makefile | 154 ++++++++++++++++++ doc/source/Intro.rst | 156 +++++++++++++++++++ doc/source/_static/.empty | 0 doc/source/code_doc_intro.rst | 228 +++++++++++++++++++++++++++ doc/source/conf.py | 285 ++++++++++++++++++++++++++++++++++ doc/source/index.rst | 25 +++ doc/source/install.rst | 40 +++++ doc/source/wavefunction.rst | 169 ++++++++++++++++++++ setup_environment.sh | 19 +++ 13 files changed, 1109 insertions(+) create mode 100644 .gitignore create mode 100644 Makefile create mode 100644 doc/.gitignore create mode 100644 doc/Makefile create mode 100644 doc/source/Intro.rst create mode 100644 doc/source/_static/.empty create mode 100644 doc/source/code_doc_intro.rst create mode 100644 doc/source/conf.py create mode 100644 doc/source/index.rst create mode 100644 doc/source/install.rst create mode 100644 doc/source/wavefunction.rst create mode 100755 setup_environment.sh diff --git a/.gitignore b/.gitignore new file mode 100644 index 00000000..da318243 --- /dev/null +++ b/.gitignore @@ -0,0 +1,3 @@ +sci.rc +EZFIO +irpf90 diff --git a/Makefile b/Makefile new file mode 100644 index 00000000..92cd68e3 --- /dev/null +++ b/Makefile @@ -0,0 +1,27 @@ +WWW_SERVER = http://qmcchem.ups-tlse.fr/files/scemama +IRPF90_TGZ = irpf90-latest-noarch-src.tar.gz +EZFIO_TGZ = EZFIO.latest.tar.gz + +.PHONY: doc src + +default: src + +EZFIO: + $(info ===== Fetching EZFIO from the web =====) + @wget "$(WWW_SERVER)/$(EZFIO_TGZ)" || \ + (echo Unable to download EZFIO : $(WWW_SERVER)/$(EZFIO_TGZ) ; exit 1) + @tar -zxf $(EZFIO_TGZ) && rm $(EZFIO_TGZ) + +irpf90: + $(info ===== Fetching IRPF90 from the web =====) + @wget "$(WWW_SERVER)/$(IRPF90_TGZ)" || \ + (echo Unable to download IRPF90 : $(WWW_SERVER)/$(IRPF90_TGZ) ; exit 1) + @tar -zxf $(IRPF90_TGZ) && rm $(IRPF90_TGZ) + $(MAKE) -C irpf90 + +doc: + $(MAKE) -C doc + +src: irpf90 EZFIO + export SCI_ROOT=$$PWD ; \ + $(MAKE) -C src diff --git a/README.md b/README.md index c41a0404..8de94373 100644 --- a/README.md +++ b/README.md @@ -3,4 +3,6 @@ Quantum package Set of quantum chemistry programs and libraries. +For more information, you can visit the +`wiki of the project `_ diff --git a/doc/.gitignore b/doc/.gitignore new file mode 100644 index 00000000..378eac25 --- /dev/null +++ b/doc/.gitignore @@ -0,0 +1 @@ +build diff --git a/doc/Makefile b/doc/Makefile new file mode 100644 index 00000000..29a05ba5 --- /dev/null +++ b/doc/Makefile @@ -0,0 +1,154 @@ +# Makefile for Sphinx documentation +# + +# You can set these variables from the command line. +SPHINXOPTS = +SPHINXBUILD = sphinx-build +PAPER = +BUILDDIR = build + +# Internal variables. +PAPEROPT_a4 = -D latex_paper_size=a4 +PAPEROPT_letter = -D latex_paper_size=letter +ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source +# the i18n builder cannot share the environment and doctrees with the others +I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source + +.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext default +default: html + +help: + @echo "Please use \`make ' where is one of" + @echo " html to make standalone HTML files" + @echo " dirhtml to make HTML files named index.html in directories" + @echo " singlehtml to make a single large HTML file" + @echo " pickle to make pickle files" + @echo " json to make JSON files" + @echo " htmlhelp to make HTML files and a HTML help project" + @echo " qthelp to make HTML files and a qthelp project" + @echo " devhelp to make HTML files and a Devhelp project" + @echo " epub to make an epub" + @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter" + @echo " latexpdf to make LaTeX files and run them through pdflatex" + @echo " text to make text files" + @echo " man to make manual pages" + @echo " texinfo to make Texinfo files" + @echo " info to make Texinfo files and run them through makeinfo" + @echo " gettext to make PO message catalogs" + @echo " changes to make an overview of all changed/added/deprecated items" + @echo " linkcheck to check all external links for integrity" + @echo " doctest to run all doctests embedded in the documentation (if enabled)" + +clean: + -rm -rf $(BUILDDIR)/* + +html: + $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html + @echo + @echo "Build finished. The HTML pages are in $(BUILDDIR)/html." + +dirhtml: + $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml + @echo + @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml." + +singlehtml: + $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml + @echo + @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml." + +pickle: + $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle + @echo + @echo "Build finished; now you can process the pickle files." + +json: + $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json + @echo + @echo "Build finished; now you can process the JSON files." + +htmlhelp: + $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp + @echo + @echo "Build finished; now you can run HTML Help Workshop with the" \ + ".hhp project file in $(BUILDDIR)/htmlhelp." + +qthelp: + $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp + @echo + @echo "Build finished; now you can run "qcollectiongenerator" with the" \ + ".qhcp project file in $(BUILDDIR)/qthelp, like this:" + @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/SelectedCI.qhcp" + @echo "To view the help file:" + @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/SelectedCI.qhc" + +devhelp: + $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp + @echo + @echo "Build finished." + @echo "To view the help file:" + @echo "# mkdir -p $$HOME/.local/share/devhelp/SelectedCI" + @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/SelectedCI" + @echo "# devhelp" + +epub: + $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub + @echo + @echo "Build finished. The epub file is in $(BUILDDIR)/epub." + +latex: + $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex + @echo + @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex." + @echo "Run \`make' in that directory to run these through (pdf)latex" \ + "(use \`make latexpdf' here to do that automatically)." + +latexpdf: + $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex + @echo "Running LaTeX files through pdflatex..." + $(MAKE) -C $(BUILDDIR)/latex all-pdf + @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." + +text: + $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text + @echo + @echo "Build finished. The text files are in $(BUILDDIR)/text." + +man: + $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man + @echo + @echo "Build finished. The manual pages are in $(BUILDDIR)/man." + +texinfo: + $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo + @echo + @echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo." + @echo "Run \`make' in that directory to run these through makeinfo" \ + "(use \`make info' here to do that automatically)." + +info: + $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo + @echo "Running Texinfo files through makeinfo..." + make -C $(BUILDDIR)/texinfo info + @echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo." + +gettext: + $(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale + @echo + @echo "Build finished. The message catalogs are in $(BUILDDIR)/locale." + +changes: + $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes + @echo + @echo "The overview file is in $(BUILDDIR)/changes." + +linkcheck: + $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck + @echo + @echo "Link check complete; look for any errors in the above output " \ + "or in $(BUILDDIR)/linkcheck/output.txt." + +doctest: + $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest + @echo "Testing of doctests in the sources finished, look at the " \ + "results in $(BUILDDIR)/doctest/output.txt." diff --git a/doc/source/Intro.rst b/doc/source/Intro.rst new file mode 100644 index 00000000..57833a18 --- /dev/null +++ b/doc/source/Intro.rst @@ -0,0 +1,156 @@ +============================================================ +What is a selected CI caculation ? Some theoretical concepts +============================================================ + +Generalities +============ + + The selected CI algorithm can be seen as a way to compute the energies (and various properties) of a given number of eigenstates + of a given :term:`target space` (ex : CISD, CAS-CI, DDCI etc ...), + but by taking the freedom of splitting the wave function of the target space in term + of :term:`internal determinants` treated variationally and :term:`perturbers` treated perturbatively. + Why this freedom ? Because in a given :term:`target space` (except some really special cases) most of the information + is concentrated within a tiny fraction of the :term:`target wave function`, and the remaining part can be reasonabely estimated by perturbtation. + + + This splitting of the wave function is not done in one shot, it is done iteratively. The iterative procedure needs a :term:`stopping criterion` to end the calculation and to control the quality of the calculation. + This :term:`stopping criterion` can be for example the number of determinants in the :term:`intern space`, + or the value of the :term:`energetic perturbative correction` to estimate the importance of the perturbation, or the convergence of the :term:`estimated target energy`, or anything that can + be defined in terms of available informations during the calculation. + + The heart of the selected CI algorithm is based on the CIPSI algorithm (ref Malrieu). + + +Selected CI in a few words +========================== + + First you define a :term:`target space`. Once the target space is defined, you define the :term:`stopping criterion`. + After that, a starting wave function is chosen by the user (HF by default). + This starting wave function is the first :term:`Internal determinants` wave function. + After that, one would like to extend this :term:`Internal determinants` wave function by adding + some :term:`perturbers` determinants. + + How do we select the good :term:`perturbers` ? + + + do while (:term:`stopping criterion` is reached) + + + 1) Generates :term:`perturbers` determinants according to your chosen :term:`target space`. + + :math:`\Rightarrow` generates a set of :term:`perturbers` :math:`\{|D_P\rangle\}` + 2) The :term:`perturbers` importance are estimated by perturbation thanks to the current :term:`internal determinants`. + 3) The most important of the :math:`\{|D_P\rangle\}` are chosen to enter in the :term:`internal determinants`. + 4) You rediagonalize the H matrix with the previous set of :term:`internal determinants` and the chosen :term:`perturbers`. + + :math:`\Rightarrow` create a new wave function and a new set of the :term:`internal determinants` + 5) iterate + +Once the iterative procedure is stopped, the :term:`internal determinants` wave function have a :term:`variational energy`, +and by adding the :term:`energetic perturbative correction` one have the :term:`estimated target energy` +which is an approximation of the :term:`target energy`. One should notice that if one takes +a :term:`stopping criterion` such as the all the determinants of the target space are in the :term:`intern space`, +the :term:`estimated target energy` is the :term:`target energy`. + + +If one is interested of how is built the selected CI wave function into more details, one can read the further section. + +What is a selected CI iteration in practice (and some details) +============================================================== + + From the previous section we have roughly seen how the selected CI works. Now, getting a bit more into details, + we will see what is done in practice during a selected CI iteration. To illustrate this, a simple CISD example wil be given. + +The general picture +^^^^^^^^^^^^^^^^^^^ + +The :term:`target space` defines entirely the method that is going to be approximated, and the stopping criterion will be the only approximation. +This :term:`target space` can always be defined in terms of application of an :term:`H operator` +(with some :term:`excitation restrictions`) on a given set of determinants that we shall call the :term:`generators` determinants. +We call :term:`restricted H operator` this precise H operator. +The target space intirely defines the :term:`restricted H operator`. +The only flexibility is the perturbation theory to be used to estimate the coeficients of the :term:`perturbers`. +If the target space is just defines in term of a CI matrix to diagonalize, the standard :term:`Diagonalization EN EG` perturbation will be used. +If some other constraints are imposed in addition to the CI matrix +(e.g. some physical conditions of size extensivity such as in the :term:`CISD+SC2` method), +then the perturbation must be adapted to properly respect the :term:`target space`. + +CISD : the :term:`target space` is here defined intirely by all the single and double excitations acting on the HF determinant. +So the :term:`generators` subset of determinants here is only the HF determinant and will not change along the iteration. +If some occupied orbitals are chosen to be frozen (no excitations from those orbitals) +or some virtuals are chosen to be deleted (no excitations going to these virtuals orbitals), +this constraint imposes the :term:`excitation restrictions`. So here the :term:`restricted H operator` will be all the single and double excitations except those involving either a frozen core orbital or a deleted virtual orbital. +Different choices of perturbation theory can be made for the CISD, but the standard :term:`Diagonalization EN EG` can be trustly used. + +Once the :term:`target space` have been defined, what does in practice a selected CI iteration. +For the sake of simplicity, here we emphasize on the ground state :math:`| \psi_0 \rangle`. At a given iteration, one have a :term:`selected wave function` :math:`|\psi_0\rangle`, and the selected CI algorithm performs : + + do G = 1, N_Generators + + 1) Apply the :term:`restricted H operator` on the :math:`|D_G \rangle` :term:`generators` determinant belonging to :math:`| \psi_0 \rangle` + + :math:`\Rightarrow` generates a set of :term:`perturbers` :math:`|D_P\rangle` + + 2) Estimate the perturbative importance of each perturbers + + :math:`\Rightarrow` example for the :term:`EN EG` perturbation theory + + .. math:: + + c_{D_P}^0= \frac{ \sum_{S=1,N_{\rm selectors}} c_S^0 \langle D_S|H|D_P\rangle}{ \langle \psi_0 |H|\psi_0 \rangle - \langle D_P |H|D_P\rangle } \\ + e_{D_P}^0= \frac{(\sum_{S=1,N_{\rm selectors}} c_S^0 \langle D_S|H|D_P\rangle) ^2}{\langle \psi_0 |H|\psi_0 \rangle - \langle D_P |H|D_P\rangle} + + 3) Keep the most important :term:`perturbers` :math:`|D_P \rangle` + + :math:`\Rightarrow` they enter in the :term:`intern space` + + 4) Rediagonalize H within this new subset of determinants + + :math:`\Rightarrow` better :term:`selected wave function` + + 5) Iterate + +An important point here is that at a given iteration, the estimation of the perturbative coefficients of the :term:`perturbers` +depends on the quality of the :term:`selected wave function` . +As the iterations go on, the :term:`selected wave function` becomes closer +and closer to the :term:`target wave function`, and so the perturbative estimation of the :term:`perturbers` coefficients or energetic contribution becomes more and more precise. + + +CISD : At the first iteration, starting from the HF determinant : + 1) By applying H on the :term:`generators` (HF) one generates all singles and doubles + 2) For each :term:`perturbers` you estimate by perturbation its coefficient of energetic contribution. + + i) Here the :term:`selectors` is only the HF determinant. + + ii) If the :term:`Brillouin theorem` is respected, all the singles have zero coefficients since the :term:`selectors` here is only the HF determinant. + iii) The most important double excitations entered + iv) The :term:`energetic perturbative correction` is calculated + v) The :term:`estimated target energy` is just the sum of the HF energy and the :term:`energetic perturbative correction` + + 3) H is rediagonlaized in the new set of determinants : HF + the selected doubles + + :math:`\Rightarrow` better :term:`variational energy` and :term:`selected wave function` + + 4) The :term:`generators` subset does not change. + + + At the second iteration : + 1) By applying H on the :term:`generators` (still HF) one generates all singles and doubles + 2) For each :term:`perturbers` you estimate by perturbation its coefficient of energetic contribution. + + i) Here the :term:`selectors` is now HF + the previously selected doubles + + :math:`\Rightarrow` the :term:`perturbers` now interact with all the previously selected doubles + :math:`\Rightarrow` better estimation of the coefficients of the :term:`perturbers` + :math:`\Rightarrow` the singles have non zero coefficients + + ii) The most important :term:`perturbers` enter in the :term:`intern space` + + iv) The :term:`energetic perturbative correction` is re estimated + + v) The :term:`estimated target energy` is now the sum of the variational energy of the :term:`selected wave function` and the :term:`energetic perturbative correction` + + :math:`\Rightarrow` better estimation of the :term:`target energy` + + Iterate untill you reached the desired :term:`stopping criterion` + diff --git a/doc/source/_static/.empty b/doc/source/_static/.empty new file mode 100644 index 00000000..e69de29b diff --git a/doc/source/code_doc_intro.rst b/doc/source/code_doc_intro.rst new file mode 100644 index 00000000..ef113adc --- /dev/null +++ b/doc/source/code_doc_intro.rst @@ -0,0 +1,228 @@ +============================= +The Documentation of the code +============================= + + + +The heart of the problem : how do we compute the perturbation ? +=============================================================== + +In this section we will present the basic ideas of how do we compute any kind of perturbative quantity. + +The main problem +^^^^^^^^^^^^^^^^ + +Consider a simple problem of perturbation theory in which you have a *general* multireference wave function :math:`| \psi \rangle` +(no trivial way to know the kind of relations between those determinants) : + +.. math:: + | \psi \rangle = \sum_{I=1,N_{det}} c_I | D_I \rangle + +and you would like to compute its second order :term:`perturbative energetic correction`, which we can write like this for the sake of simplicity: + +.. math:: + E_{PT2} = \sum_{P \, \rm{that} \, \rm{are} \, \rm{not} \, \rm{in} \, | \psi \rangle } \frac{\langle \psi | H | D_P \rangle^2}{\Delta E_P} + +and the :math:`\Delta E_P` will determine what kind of PT you use. Note that you must not double count a determinant :math:`| D_P \rangle` and that you must not count those which are in :math:`| \psi \rangle`. + +What you have to do is to apply the :math:`H` operator on this :math:`| \psi \rangle` that would generate a lot of determinants :math:`|D \rangle`, +and you must find a way to see if : + + #) the determinant :math:`|D \rangle` is in :math:`| \psi \rangle` + + #) the determinant :math:`|D \rangle` have already been counted + +How do we do in practice ? We apply :math:`H` succesively on each determinant of :math:`| \psi \rangle` and each :math:`H` application generates a lot of determinant :math:`|D \rangle`. For each determinants :math:`|D \rangle` we check with a very optimized subroutine if + + #) :math:`|D\rangle` was a single or a double excitation respect to all the determinant on which we previously applyed :math:`H` + + :math:`\Rightarrow` if it is the case then it have already been computed in the past and so we don't double count it. + + #) :math:`|D\rangle` is already in the rest of the :math:`| \psi \rangle` + + :math:`\Rightarrow` if it is the case you must not count it. + +This subroutine (:samp:`connected_to_ref` ) is called a **HUGE** number of times and so it have been optimized in a proper way. +Its basis is the :samp:`popcnt` hardware instruction that figures in the :samp:`SSE4.2` releases of processors. +It allows to know how many bites are set to one in an integer within a few cycles of CPU. +By manipulation of bits masks you can easily extract the excitation degree between two determinants. + +One interesting feature of this approach is that it is easily and efficiently parallelizable (which of cours have been done), +and you can easily reach an parallel efficiency of about :math:`95\%`. + + +The link between the perturbation and the selection +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +In the selected CI algorithm you have general :math:`| \psi \rangle` multi determinantal wave function and you want to make it better +by proposing some new candidates to enter in this wave function. +Those candidates must of course not be already in :math:`| \psi \rangle` and since their are selected thanks to their perturbative properties (on the energy or on the coefficient), their are generated through some application of the :math:`H` operator. So we see that we have exactly the same kind of feature than in the perturbation. + +How do we select the determinant in practice ? Exactly like we do the perturbation ! + +do G = 1, :term:`N_{Generators}` + + #) We apply :math:`H` on one :term:`generators` + + :math:`\Rightarrow` :math:`H|D_G \rangle = \sum_D \langle D | H |D_G \rangle |D \rangle` + + #) For each determinant :math:`|D \rangle` we check if it could have been generated from previous :term:`generators` :math:`| D_{G'} \rangle` + + :math:`\Rightarrow` If it is not the case we check if it belongs to :math:`| \psi \rangle` + + #) We compute its perturbative property + + #) If it is important we put it in a buffer of the potential candidates to the new set of :term:`internal determinants` + + #) go to 1 + +enddo + + +So once you have applyed :math:`H` on all the :term:`generators`, you sort all the buffer of the candidates by their importance, +and after you pick up the most important ones, which will enter in the wave function and be diagonalized. + + +Just to be more precise, what we drescribe here is the standard CIPSI algorithm (which :term:`target space` is always the FCI). In practice, if you replace the :math:`H` operator by the :term:`restricted H operator` defined by the :term:`target` space you have exactly what is emplemented. + +The typical feature of an iteration +=================================== + +An iteration of the selected CI program is always built in the same way. This can be resumed in the following simple tasks. + +Iteration : + + #) :term:`restricted H operator` applyed on the :term:`generators` + + :math:`\Rightarrow` :term:`perturbativ action` (*e.g* Selection of some :term:`perturbers`, calculation of the :math:`E_{PT2}^m`, etc ...) + + #) Some update induced by the :term:`perturbative action` (*e.g* diagonalization of the new :math:`H` matrix, etc ...) + #) Check the :term:`stopping criterion` + #) Update the :term:`generators` subset + #) Save restart data if needed + #) Iterate + +To go into details we list the various available options for each task. + +The :samp:`restricted_H_apply` like subroutines +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + + Here we enter into details on the part of the subroutines that is responsible for the :term:`restricted H operator` part of the tasks. + +The general ideas +^^^^^^^^^^^^^^^^^ + + This subroutine takes in input a determinant (in term of an integer key) and some bits masks + that are used to restrict the excitations (see the :term:`excitations bits masks` and :term:`excitations restrictions`). + It generates the singles and doubles excitations from the input determinant and these :term:`excitations bits masks`. + This subroutine will be applyed on the :term:`generators` determinants to generate the :term:`perturbers`. + + This subroutine in itself does not exist, it is just a skeleton that generates all possible singles and doubles. + As seen in the previsous section, once you apply :math:`H` on a given determinant, you will use the generated determinants + to do a certain number of things that deal with in general a perturbative quantity, this is the :term:`perturbative action`. + + A way to resume what is done in the subroutine and to make a mental representation can be explained like this : + + +.. code-block:: fortran + + subroutine restricted_H_apply(key_in) + + do i = 1, available_holes(1) + do j = 1, available_holes(2) + do k = 1, available_particles(1) + do l = 1, available_particles(2) + ! you generate some excitations on key_in that will generate some key_out + call excitation(i,j,k,l,key_in,key_out) + ! you exploit key_out to do some perturbative work + call perturbative_action(key_out) + enddo + enddo + enddo + enddo + + end + + +So we see that here once we have made an excitation on :samp:`key_in` that generates :samp:`key_out`, +we can do some work related to the :term:`perturbative action` on this :samp:`key_out`. + +In this simple representation of the subroutine, there are some :samp:`available_holes` and :samp:`available_particle`. +This is due to the :term:`excitation restrictions` that are implicitly defined by the :term:`target space`, +and to the :term:`restricted orbitals` that are defined by the user. +In practice those :term:`excitation restrictions` are just the excitations that are going to be allowed to a given :term:`generator determinant`. +We do this by using some :term:`excitations bits masks`. +The :term:`excitation restrictions` and the :term:`restricted orbitals` are built thanks to the use of :term:`excitations bits masks`. + +Available :term:`excitation restrictions` +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +The :term:`excitation restrictions` prohibits some kind of excitations because it is in the definition +of the :term:`target space` to avoid a certain class of excitation. +For instance, in the :term:`CAS+DDCI` method, you will apply all the single and double excitations on the top of the :term:`CAS wave function`. +After those :term:`excitation restrictions` defined by the :term:`target space`, there can be some kind of excitations that the user wishes to avoid. +For instance, within a :term:`CISD` or a :term:`CAS+DDCI` you can wish that all the excitations of the core electrons can be neglected, +or that there are some virtuals that are not relevant for a certain kind of correlation effects. + +This restrictions are done in the program by defining some classes of orbitals that depend both on the method you would like to use, +and by the specific restrictions you would like to do on the top of that. So we see that there are classes of orbitals that depend on the method, +and other classes that can be defined for any class of method. + +This classes are the the :term:`frozen occupied orbitals` and the :term:`deleted virtual orbitals` . + +Available :term:`perturbative action` +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +From what we saw previously, when an excitation is performed on a given :term:`generator`, +depending on the method defined by the user, different actions can be performed at that point of the calculation. + +Nevertheless, all this actions here deal with the perturbation, that is why we called this step the :term:`perturbative action`. + +The :term:`perturbative action` is very flexible. It consists in doing (or not) a certain kind of things. + +When a given determinant :samp:`key_out` is generated, you can : + + #) check if this determinants have to be taken into account (see :samp:`connected_to_ref` and :samp:`is_in_ref`) + #) compute its :term:`perturbative energetic contribution` and its :term:`perturbative coefficient` (see :term:`perturbation theory`) + #) use those perturbative quantities to do something that deals with it (see :term:`perturbative possibility` ) + +In principle, for each of those actions one would put a :samp:`if` statement and decline all the possible actions to do. +However, because there can exist a *lot* of possible action and because this loop is really intern, putting a lot of :samp:`if` statement +is not a good idea and will slow the code. + +To avoid that we generate with a python script all possible subroutines corresponding to some actions, and the program will use the one +that will be defined by the method desired by the user. In this way there is no unnecessary tests in the intern loop, it done in the input. + +The :term:`perturbative possibility` +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +Once you have compute the :term:`perturbative energetic contribution` and the :term:`perturbative coefficient` of a given :term:`perturber`, +you must use those quantities. Here is listed what is available : + + #) accumulate it :term:`perturbative energetic contribution` to compute the :term:`Energetic perturbative correction` + #) accumulate it :term:`perturbative coefficient` to compute the :term:`first order perturbative norm` + #) put or not the :samp:`key_out` determinant in a buffer to select some new :term:`intenal determinants` see :term:`selection` + #) update the arrays of the :term:`correlation energy by holes and particles` (see :term:`CISD+SC2`) + #) dress all the diagonal matrix elements of the :term:`internal determiants` (see :term:`Dressed MRCI`) + + + + +Connected to ref / is in ref +^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + This subroutine takes in input a determinant (in term of an integer key), an array of determinants :samp:`keys` (containing :samp:`N_det` determinants) + and an integer :samp:`i_past` which is smaller or equal to :samp:`N_det`. + + It checks if the input determinant is connected by the :math:`H` matrix to all the determinants in :samp:`keys` that are before :samp:`i_past`. + It also check if the input determinant is in the whole list of determinants :samp:`keys`. + + In output you have an integer :samp:`c_ref` that have the following values : + + #) 0 : the input determinant is not in :samp:`keys` and is not connected to any determinant + in :samp:`keys` that is before :samp:`i_past`. + + #) +m : the input determinant is connected by the :math:`H` matrix to the *m* th determinant :samp:`keys`. + + #) -m : the input determinant is already in :samp:`keys` and it is the *m* th determinant in :samp:`keys` + + diff --git a/doc/source/conf.py b/doc/source/conf.py new file mode 100644 index 00000000..c77267ea --- /dev/null +++ b/doc/source/conf.py @@ -0,0 +1,285 @@ +# -*- coding: utf-8 -*- +# +# Selected CI documentation build configuration file, created by +# sphinx-quickstart on Mon Feb 10 15:53:11 2014. +# +# This file is execfile()d with the current directory set to its containing dir. +# +# Note that not all possible configuration values are present in this +# autogenerated file. +# +# All configuration values have a default; values that are commented out +# serve to show the default. + +import sys, os + +# If extensions (or modules to document with autodoc) are in another directory, +# add these directories to sys.path here. If the directory is relative to the +# documentation root, use os.path.abspath to make it absolute, like shown here. +#sys.path.insert(0, os.path.abspath('.')) + +# -- General configuration ----------------------------------------------------- + +# If your documentation needs a minimal Sphinx version, state it here. +#needs_sphinx = '1.0' + +# Add any Sphinx extension module names here, as strings. They can be extensions +# coming with Sphinx (named 'sphinx.ext.*') or your custom ones. +extensions = ['sphinx.ext.autodoc', 'sphinx.ext.doctest', 'sphinx.ext.todo', 'sphinx.ext.pngmath', 'sphinx.ext.mathjax', 'sphinx.ext.viewcode'] + +# Add any paths that contain templates here, relative to this directory. +templates_path = ['_templates'] + +# The suffix of source filenames. +source_suffix = '.rst' + +# The encoding of source files. +#source_encoding = 'utf-8-sig' + +# The master toctree document. +master_doc = 'index' + +# General information about the project. +project = u'Selected CI' +copyright = u'2014, Giner Emmanuel , Scemama Anthony' + +# The version info for the project you're documenting, acts as replacement for +# |version| and |release|, also used in various other places throughout the +# built documents. +# +# The short X.Y version. +version = '1.0' +# The full version, including alpha/beta/rc tags. +release = version+'.1' + +# The language for content autogenerated by Sphinx. Refer to documentation +# for a list of supported languages. +#language = None + +# There are two options for replacing |today|: either, you set today to some +# non-false value, then it is used: +#today = '' +# Else, today_fmt is used as the format for a strftime call. +#today_fmt = '%B %d, %Y' + +# List of patterns, relative to source directory, that match files and +# directories to ignore when looking for source files. +exclude_patterns = [] + +# The reST default role (used for this markup: `text`) to use for all documents. +#default_role = None + +# If true, '()' will be appended to :func: etc. cross-reference text. +#add_function_parentheses = True + +# If true, the current module name will be prepended to all description +# unit titles (such as .. function::). +#add_module_names = True + +# If true, sectionauthor and moduleauthor directives will be shown in the +# output. They are ignored by default. +#show_authors = False + +# The name of the Pygments (syntax highlighting) style to use. +pygments_style = 'sphinx' + +# A list of ignored prefixes for module index sorting. +#modindex_common_prefix = [] + + +# -- Options for HTML output --------------------------------------------------- + +# The theme to use for HTML and HTML Help pages. See the documentation for +# a list of builtin themes. +html_theme = 'default' + +# Theme options are theme-specific and customize the look and feel of a theme +# further. For a list of options available for each theme, see the +# documentation. +#html_theme_options = {} + +# Add any paths that contain custom themes here, relative to this directory. +#html_theme_path = [] + +# The name for this set of Sphinx documents. If None, it defaults to +# " v documentation". +#html_title = None + +# A shorter title for the navigation bar. Default is the same as html_title. +#html_short_title = None + +# The name of an image file (relative to this directory) to place at the top +# of the sidebar. +#html_logo = None + +# The name of an image file (within the static path) to use as favicon of the +# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 +# pixels large. +#html_favicon = None + +# Add any paths that contain custom static files (such as style sheets) here, +# relative to this directory. They are copied after the builtin static files, +# so a file named "default.css" will overwrite the builtin "default.css". +html_static_path = ['_static'] + +# If not '', a 'Last updated on:' timestamp is inserted at every page bottom, +# using the given strftime format. +#html_last_updated_fmt = '%b %d, %Y' + +# If true, SmartyPants will be used to convert quotes and dashes to +# typographically correct entities. +#html_use_smartypants = True + +# Custom sidebar templates, maps document names to template names. +#html_sidebars = {} + +# Additional templates that should be rendered to pages, maps page names to +# template names. +#html_additional_pages = {} + +# If false, no module index is generated. +#html_domain_indices = True + +# If false, no index is generated. +#html_use_index = True + +# If true, the index is split into individual pages for each letter. +#html_split_index = False + +# If true, links to the reST sources are added to the pages. +#html_show_sourcelink = True + +# If true, "Created using Sphinx" is shown in the HTML footer. Default is True. +#html_show_sphinx = True + +# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. +#html_show_copyright = True + +# If true, an OpenSearch description file will be output, and all pages will +# contain a tag referring to it. The value of this option must be the +# base URL from which the finished HTML is served. +#html_use_opensearch = '' + +# This is the file name suffix for HTML files (e.g. ".xhtml"). +#html_file_suffix = None + +# Output file base name for HTML help builder. +htmlhelp_basename = 'SelectedCIdoc' + + +# -- Options for LaTeX output -------------------------------------------------- + +latex_elements = { +# The paper size ('letterpaper' or 'a4paper'). +#'papersize': 'letterpaper', + +# The font size ('10pt', '11pt' or '12pt'). +#'pointsize': '10pt', + +# Additional stuff for the LaTeX preamble. +#'preamble': '', +} + +# Grouping the document tree into LaTeX files. List of tuples +# (source start file, target name, title, author, documentclass [howto/manual]). +latex_documents = [ + ('index', 'SelectedCI.tex', u'Selected CI Documentation', + u'Giner Emmanuel ', 'manual'), +] + +# The name of an image file (relative to this directory) to place at the top of +# the title page. +#latex_logo = None + +# For "manual" documents, if this is true, then toplevel headings are parts, +# not chapters. +#latex_use_parts = False + +# If true, show page references after internal links. +#latex_show_pagerefs = False + +# If true, show URL addresses after external links. +#latex_show_urls = False + +# Documents to append as an appendix to all manuals. +#latex_appendices = [] + +# If false, no module index is generated. +#latex_domain_indices = True + + +# -- Options for manual page output -------------------------------------------- + +# One entry per manual page. List of tuples +# (source start file, name, description, authors, manual section). +man_pages = [ + ('index', 'selectedci', u'Selected CI Documentation', + [u'Giner Emmanuel '], 1) +] + +# If true, show URL addresses after external links. +#man_show_urls = False + + +# -- Options for Texinfo output ------------------------------------------------ + +# Grouping the document tree into Texinfo files. List of tuples +# (source start file, target name, title, author, +# dir menu entry, description, category) +texinfo_documents = [ + ('index', 'SelectedCI', u'Selected CI Documentation', + u'Giner Emmanuel ', 'SelectedCI', 'One line description of project.', + 'Miscellaneous'), +] + +# Documents to append as an appendix to all manuals. +#texinfo_appendices = [] + +# If false, no module index is generated. +#texinfo_domain_indices = True + +# How to display URL addresses: 'footnote', 'no', or 'inline'. +#texinfo_show_urls = 'footnote' + + +# -- Options for Epub output --------------------------------------------------- + +# Bibliographic Dublin Core info. +epub_title = u'Selected CI' +epub_author = u'Giner Emmanuel ' +epub_publisher = u'Giner Emmanuel ' +epub_copyright = u'2014, Giner Emmanuel ' + +# The language of the text. It defaults to the language option +# or en if the language is not set. +#epub_language = '' + +# The scheme of the identifier. Typical schemes are ISBN or URL. +#epub_scheme = '' + +# The unique identifier of the text. This can be a ISBN number +# or the project homepage. +#epub_identifier = '' + +# A unique identification for the text. +#epub_uid = '' + +# A tuple containing the cover image and cover page html template filenames. +#epub_cover = () + +# HTML files that should be inserted before the pages created by sphinx. +# The format is a list of tuples containing the path and title. +#epub_pre_files = [] + +# HTML files shat should be inserted after the pages created by sphinx. +# The format is a list of tuples containing the path and title. +#epub_post_files = [] + +# A list of files that should not be packed into the epub file. +#epub_exclude_files = [] + +# The depth of the table of contents in toc.ncx. +#epub_tocdepth = 3 + +# Allow duplicate toc entries. +#epub_tocdup = True diff --git a/doc/source/index.rst b/doc/source/index.rst new file mode 100644 index 00000000..6e1ace01 --- /dev/null +++ b/doc/source/index.rst @@ -0,0 +1,25 @@ +.. Selected CI documentation master file, created by + sphinx-quickstart on Mon Feb 10 15:53:11 2014. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +Welcome to Selected CI's documentation! +======================================= + +Contents: + +.. toctree:: + :maxdepth: 1 + + install + Intro + code_doc_intro + wavefunction + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` + diff --git a/doc/source/install.rst b/doc/source/install.rst new file mode 100644 index 00000000..44b86b8a --- /dev/null +++ b/doc/source/install.rst @@ -0,0 +1,40 @@ +============ +Installation +============ + +Requirements +------------ + +* `GNU make `_ +* `The Intel Fortran Compiler with MKL `_ +* `IRPF90 `_ +* `EZFIO `_ + +Optional Requirements +--------------------- + +* `Sphinx `_ is used to build the documentation + +Setup +----- + +#) Run the :file:`setup_environment.sh` script. This will create the :file:`sci.rc` file + that contains all the environment variables :: + + $ ./setup_environment.sh + +#) Source this file into your shell :: + + $ source sci.rc + +#) Go into the :file:`src` directory and create the :file:`Makefile.config` file using the + :file:`Makefile.config.example` file as a template + +#) Build the program :: + + $ make + +#) Build the documentation :: + + $ make doc + diff --git a/doc/source/wavefunction.rst b/doc/source/wavefunction.rst new file mode 100644 index 00000000..a3215e6d --- /dev/null +++ b/doc/source/wavefunction.rst @@ -0,0 +1,169 @@ +===================================== +Selection, perturbation ... keywords +===================================== + +.. |CISD| replace:: :abbr:`CISD (Configuration Interaction with Single and Double excitations)` +.. |HF| replace:: :abbr:`HF (Hartree Fock)` +.. |CAS-CI| replace:: :abbr:`CAS-CI (Complete Active Space Configuration Interaction)` +.. |DDCI| replace:: :abbr:`DDCI (Difference Dedicated Configuration Interaction)` + +.. glossary:: + :sorted: + + Energetic perturbative correction + Corresponds to the correction to the energy at the second order of a given perturbtation theory + to a given state m. + By convention it noted :math:`E_{PT2}^m` + + Variational energy + Corresponds to the variational energy of the :term:`selected wave function` for a given state . + By convention it noted :math:`E_{Var}^m` for the mth eigenvector. + + .. math:: + E_{Var}^m = \langle \psi_m |H|\psi_m \rangle + + Estimated target energy + Corresponds to the estimation of the target energy for a given :term:`selected wave function` and a given state. + By convention it noted :math:`E_{Target}^m`. + Its mathematical expression is : + + .. math:: + E_{Target}^m = E_{Var}^m + E_{PT2}^m + + Selected wave function + Corresponds to the wave function that have been previously selected for a given state m at a current iteration. + This wave function is defined by the set of the :term:`internal determinants` and by their coefficients + on the state m. + By convention it is noted :math:`|\psi_m\rangle` + + .. math:: + | \psi_m \rangle = \sum_{I=1,N_{selected}} c_I^m | D_I \rangle + + + + + EN EG + Stands for Eipstein Nesbet with EigenValues zeroth order energy perturbation theory. + It is a state specific 2nd order perturbation theory. Here m is the index of the eigenstate. + The :math:`H_0` of this PT is defined as the diagonal part of the Hamiltonian such as + the :math:`E_m` is equal to the average value of the Hamiltonian on the :term:`selected wave function` + and the :math:`E_P` is equal to the average value of the Hamiltonian on the :term:`perturbers` + + This perturbation have bad formal properties but some nice numerical features of convergence. + + + From the definition, one get the first order coefficient and its related second order energetic contribution of a a perturber : + + .. math:: + c_{D_P}^m= \sum_{S=1,N_{\rm selectors}} \frac{c_S^m \langle D_S|H|D_P\rangle}{ \langle \psi_m |H|\psi_m \rangle - \langle D_P|H| D_P \rangle } \\ + e_{D_P}^m= \frac{(\sum_{S=1,N_{\rm selectors}} c_S^m \langle D_S|H|D_P\rangle)^2}{\langle \psi_m |H|\psi_m \rangle - \langle D_P|H| D_P \rangle } + + + Stopping criterion + Condition decided by the user to stop the calculation. + This criterion might be on the :term:`Energetic perturbative correction`, on the number of :term:`internal determinants` N_selected_max + or on the stability of the :term:`estimated target energy` + The user can also send a Ctrl+C to stop the calculation, and it will kill itself properly, saving the datas that need to be saved. + + + Target wave function + Wave function of the :term:`target space` + + + + Target space + Target of the CI calculation. Defining a method (CISD, CAS-CI and so on) is equivalent to define the :term:`target space`. + + The target space defines the rules to define the :term:`Generators` , + the rules of the :term:`excitation restrictions`, + and the perturbation theory to be used. + + There are two type of methods/:term:`target space` proposed in the code : + + #) the CAS-CI type methods where you do not restrict any kind of excitation degree within a given list of orbitals. + #) the singles and doubles excitations on the top of a given reference wave function (:term:`CISD`, :term:`CISD+SC2`, :term:`CAS+SD`, :term:`CAS+DDCI`, :term:`CAS+MRPT2`) + + Their is a great difference between those two types of method in the way it is implemented. + + In the CAS-CI method, when you have chosen an :term:`active space` (so a list of orbitals and electrons to make a FCI within this active space), + all the :term:`Internal determinants` that have been selected and that form the :term:`selected wave function` + can potentially be part of the :term:`generators`, by mean that the :term:`restricted H operator` + could be potentially applyed on all the :term:`internal determinants` to generate some other :term:`perturbers`. + + In the singles and doubles excitation on the top of a given reference wave function, the subset of :term:`generators` + and so the rules to recognize them, is fixed at the begining of the method. Those :term:`generators` are precisely + all the determinants forming the :term:`reference wave function`. + + + There are the different :term:`target space` that are available : + + #) :term:`CISD` + #) :term:`CISD+SC2` + #) :term:`CASCI` + #) :term:`CASCI+S` + #) :term:`CASCI+SD` + #) :term:`CASCI+DDCI` + #) :term:`CASCI+DDCI+(2h-2p)PT2` + #) :term:`CAS-CI+MRPT2` + + + Target energy + Energy of the target space. + + H operator + Hamiltonian operator defined in terms of creation and anihilation operators in the spin orbital space. + + Excitation restrictions + Restriction in the :term:`H operator` that the user imposes to define the target sapce. + For example : + + 1) If one freeze some core orbitals or delete some virtuals, it is an :term:`excitation restrictions` + 2) If one prohibits the pure inactive double excitations in a CAS+SD one get a DDCI + 3) any kind of restriction in the full application of the :term:`H operator` + + + Restricted H operator + :term:`H operator` taking into account the :term:`Excitation restrictions` + + + CISD+SC2 + Method developped by JP. Malrieu that can be seen as a cheap approximation of the CCSD. + It makes a CISD size consistant and separable for closed shell systems. + It is based on a CISD calculation + where the diagonal part of the H matrix is dressed by the repeatable correlation energy previsously obtained. + So it is a CISD dressed by the disconnected triples and quadruples. + + Generators + Set of generator determinants. + By convention a generator is written as :math:`|D_G\rangle` . + A generator determinant is a determinant on which + the :term:`restricted H operator` is being applied for the selection and/or the perturbation. + + Internal determinants + Selected determinants in terms of integers keys. + By convention an Internal determinant is written as :math:`|D_I\rangle` . + By convention, the :term:`Generators` are at the begining of the array. + + Intern space + Set of all the :term:`internal determinants`. + + Perturbers + Determinants within the :term:`target space` but taht are not already included in the :term:`intern space`. + They are created from the :term:`Generators` that belongs :term:`Intern space` for a given :term:`selected wave function`. + By convention a perturber is written as :math:`|D_P\rangle`. + + Selectors + Determinants that are used to compute the perturbative properties of the :term:`perturbers`. + By convention a selector is written as :math:`|D_S\rangle` . + The selectors are a subset of determinant of the total wave function (that is the :term:`Internal determinants`). + This subset contains at least the :term:`Generators` determinants. + The perturbative properties (energy, coefficient or else) of the :term:`perturbers` are calculated on all the :term:`selectors` :math:`|D_S\rangle` + + .. math:: + + c_{D_S}= \sum_{S=1,N_{\rm selectors}} \frac{c_S\langle D_S|H|D_P\rangle}{\Delta E_{P,S}} \\ + e_{D_S}= \frac{(\sum_{S=1,N_{\rm selectors}} c_S \langle D_S|H|D_P\rangle) ^2}{\Delta E_{P,S}} + + + + diff --git a/setup_environment.sh b/setup_environment.sh new file mode 100755 index 00000000..caa6ef3d --- /dev/null +++ b/setup_environment.sh @@ -0,0 +1,19 @@ +#!/bin/bash + +SCI_ROOT=${PWD} + +IRPF90=$(which irpf90) + +if [[ -z ${IRPF90} ]] ; +then + make irpf90 + IRPF90=${SCI_ROOT}/irpf90/bin/irpf90 +fi +make EZFIO + +cat << EOF > sci.rc +export IRPF90=${IRPF90} +export SCI_ROOT=${SCI_ROOT} +export PATH+=:${SCI_ROOT}/scripts +export PATH+=:${SCI_ROOT}/bin +EOF