From 9e363dfbb535b123d8b5e0e076d35030a40fdbeb Mon Sep 17 00:00:00 2001 From: Wong Zi Cheng <70616433+chmwzc@users.noreply.github.com> Date: Tue, 20 Jun 2023 10:02:10 +0000 Subject: [PATCH 01/26] Attempt to use Sphinx --- docs/Makefile | 20 +++++++++++++++ docs/make.bat | 35 ++++++++++++++++++++++++++ docs/source/conf.py | 57 +++++++++++++++++++++++++++++++++++++++++++ docs/source/index.rst | 18 ++++++++++++++ 4 files changed, 130 insertions(+) create mode 100644 docs/Makefile create mode 100644 docs/make.bat create mode 100644 docs/source/conf.py create mode 100644 docs/source/index.rst diff --git a/docs/Makefile b/docs/Makefile new file mode 100644 index 0000000..d0c3cbf --- /dev/null +++ b/docs/Makefile @@ -0,0 +1,20 @@ +# Minimal makefile for Sphinx documentation +# + +# You can set these variables from the command line, and also +# from the environment for the first two. +SPHINXOPTS ?= +SPHINXBUILD ?= sphinx-build +SOURCEDIR = source +BUILDDIR = build + +# Put it first so that "make" without argument is like "make help". +help: + @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) + +.PHONY: help Makefile + +# Catch-all target: route all unknown targets to Sphinx using the new +# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). +%: Makefile + @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) diff --git a/docs/make.bat b/docs/make.bat new file mode 100644 index 0000000..747ffb7 --- /dev/null +++ b/docs/make.bat @@ -0,0 +1,35 @@ +@ECHO OFF + +pushd %~dp0 + +REM Command file for Sphinx documentation + +if "%SPHINXBUILD%" == "" ( + set SPHINXBUILD=sphinx-build +) +set SOURCEDIR=source +set BUILDDIR=build + +%SPHINXBUILD% >NUL 2>NUL +if errorlevel 9009 ( + echo. + echo.The 'sphinx-build' command was not found. Make sure you have Sphinx + echo.installed, then set the SPHINXBUILD environment variable to point + echo.to the full path of the 'sphinx-build' executable. Alternatively you + echo.may add the Sphinx directory to PATH. + echo. + echo.If you don't have Sphinx installed, grab it from + echo.https://www.sphinx-doc.org/ + exit /b 1 +) + +if "%1" == "" goto help + +%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% +goto end + +:help +%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% + +:end +popd diff --git a/docs/source/conf.py b/docs/source/conf.py new file mode 100644 index 0000000..905c420 --- /dev/null +++ b/docs/source/conf.py @@ -0,0 +1,57 @@ +# Configuration file for the Sphinx documentation builder. +# +# This file only contains a selection of the most common options. For a full +# list see the documentation: +# https://www.sphinx-doc.org/en/master/usage/configuration.html + +# -- Path setup -------------------------------------------------------------- + +# 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. + +import os +import sys + +sys.path.insert(0, os.path.abspath("../src")) + + +# -- Project information ----------------------------------------------------- + +project = "Qibochem" +copyright = "2023, The Qibo team" +author = "The Qibo team" + + +# -- General configuration --------------------------------------------------- + +# 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.coverage", + "sphinx.ext.napoleon", +] + +# Add any paths that contain templates here, relative to this directory. +templates_path = ["_templates"] + +# List of patterns, relative to source directory, that match files and +# directories to ignore when looking for source files. +# This pattern also affects html_static_path and html_extra_path. +exclude_patterns = [] + + +# -- 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 = "furo" + +# 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"] diff --git a/docs/source/index.rst b/docs/source/index.rst new file mode 100644 index 0000000..31ea6a2 --- /dev/null +++ b/docs/source/index.rst @@ -0,0 +1,18 @@ +.. title:: + Qibochem + +Welcome to Qibochem's documentation! +==================================== + +.. toctree:: + :maxdepth: 2 + :caption: Contents: + + + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` From 114c4ec3a5cfbefd5505b5fbdec28ff7202d5cc7 Mon Sep 17 00:00:00 2001 From: Adrian Mak Date: Thu, 6 Jul 2023 15:25:28 +0800 Subject: [PATCH 02/26] Added to sphinx docs --- docs/source/api-reference/index.rst | 5 +++ docs/source/developer-guides/index.rst | 5 +++ .../getting-started/hamiltonian_mapping.rst | 33 +++++++++++++++ docs/source/getting-started/index.rst | 15 +++++++ docs/source/getting-started/installation.rst | 19 +++++++++ docs/source/getting-started/molecule.rst | 40 +++++++++++++++++++ 6 files changed, 117 insertions(+) create mode 100644 docs/source/api-reference/index.rst create mode 100644 docs/source/developer-guides/index.rst create mode 100644 docs/source/getting-started/hamiltonian_mapping.rst create mode 100644 docs/source/getting-started/index.rst create mode 100644 docs/source/getting-started/installation.rst create mode 100644 docs/source/getting-started/molecule.rst diff --git a/docs/source/api-reference/index.rst b/docs/source/api-reference/index.rst new file mode 100644 index 0000000..323e588 --- /dev/null +++ b/docs/source/api-reference/index.rst @@ -0,0 +1,5 @@ +API Reference +============= + +In this section we document the main Qibochem components and primitives in the public API. + diff --git a/docs/source/developer-guides/index.rst b/docs/source/developer-guides/index.rst new file mode 100644 index 0000000..9976d21 --- /dev/null +++ b/docs/source/developer-guides/index.rst @@ -0,0 +1,5 @@ +Developer Guides +================ + +This section provides code overview and contribution guidelines for developers. + diff --git a/docs/source/getting-started/hamiltonian_mapping.rst b/docs/source/getting-started/hamiltonian_mapping.rst new file mode 100644 index 0000000..6cbbdfb --- /dev/null +++ b/docs/source/getting-started/hamiltonian_mapping.rst @@ -0,0 +1,33 @@ +Hamiltonian mapping +=================== + +Central to quantum chemical calculations for molecules is the fermionic two-body Hamiltonian in second quantized form. + +.. math:: + \hat{H} = \sum_{pq} h_{pq} a^\dagger_p a_q + \frac12 \sum_{pqrs} h_{pqrs} a^\dagger_p a^\dagger_q a_s a_r + +which is to mapped to a qubit Hamiltonian for calculation of properties such as molecular energies using quantum hardware. + +The integrals :math:`h_{pq}` and :math:`h_{pqrs}` are one- and two-electron integrals. For spinorbitals :math:`\phi_j` that make up the basis, the integrals are: + +.. math:: + h_{pq} = \int \phi^*_p(x_1)\hat{h}\phi_q(x_1) dx_1 + +.. math:: + h_{pqrs} = \int \int \phi^*_p(x_1)\phi^*_q(x_2)\hat{g}\phi_r(x_2)\phi_s(x_1) dx_1 dx_2 + +Supported mappings are the Jordan-Wigner and Bravyi-Kitaev mapping, as implemented in OpenFermion. + +Jordan-Wigner +------------- + +.. math:: + \hat{a}^\dagger_j = \bigotimes_{i=1}^{j-1} \hat{Z}_i \otimes (\hat{X}_j - i\hat{Y}_j) + + +.. math:: + \hat{a}_j = \bigotimes_{i=1}^{j-1} \hat{Z}_i \otimes (\hat{X}_j + i\hat{Y}_j) + + + + diff --git a/docs/source/getting-started/index.rst b/docs/source/getting-started/index.rst new file mode 100644 index 0000000..8d0c97a --- /dev/null +++ b/docs/source/getting-started/index.rst @@ -0,0 +1,15 @@ +Getting started +=============== + +This section details the basics of qibochem. More details are given in the following subsections. + + +.. toctree:: + :maxdepth: 1 + + installation + molecule + hamiltonian_mapping + + + diff --git a/docs/source/getting-started/installation.rst b/docs/source/getting-started/installation.rst new file mode 100644 index 0000000..b04f77a --- /dev/null +++ b/docs/source/getting-started/installation.rst @@ -0,0 +1,19 @@ +Installation +============ + +Using pip install: + +.. code-block:: + + git clone https://github.com/qiboteam/qibochem.git + cd qibochem + pip install . + +Using poetry: + +.. code-block:: + + git clone https://github.com/qiboteam/qibochem.git + cd qibochem + poetry install + diff --git a/docs/source/getting-started/molecule.rst b/docs/source/getting-started/molecule.rst new file mode 100644 index 0000000..9dceb1e --- /dev/null +++ b/docs/source/getting-started/molecule.rst @@ -0,0 +1,40 @@ +Molecule +======== + +The Molecule object contains all the information from a classical quantum chemistry calculation that will be used in the quantum simulation. + +The key inputs required are: + +geometry + atomic coordinates in the form of a list of tuples +charge + an integer value for the net charge for the entire molecule + + default value is 0 +multiplicity + spin multiplicity given as 2S + 1, where S is the number of unpaired electrons multipled by 1/2 + + default value is 1 (all electrons paired) + + +The current implementation supports both restricted and unrestricted spins. (TODO: elaborate) + +Example +------- + +The following examples show how to use the driver program to save molecule quantities into the Molecule object + +PySCF for H\ :sub:`2`\ with H-H distance of 0.74 Angstroms at HF/STO-3G level + +.. code-block:: python + + from qibochem.driver import Molecule + + h2 = Molecule([('H', (0.0, 0.0, 0.0)), ('H', (0.0, 0.0, 0.74))]) + h2.run_pyscf() + + + + + +Next: Hamiltonian mapping From 224d9ca5e641481ce8070c0ff291651de0df18c2 Mon Sep 17 00:00:00 2001 From: Adrian Mak Date: Thu, 6 Jul 2023 15:29:38 +0800 Subject: [PATCH 03/26] Added sphinx docs --- docs/source/conf.py | 58 ++++++++++++++++++------------------------- docs/source/index.rst | 36 +++++++++++++++++++-------- 2 files changed, 50 insertions(+), 44 deletions(-) diff --git a/docs/source/conf.py b/docs/source/conf.py index 905c420..901776b 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -1,49 +1,26 @@ # Configuration file for the Sphinx documentation builder. # -# This file only contains a selection of the most common options. For a full -# list see the documentation: +# For the full list of built-in configuration values, see the documentation: # https://www.sphinx-doc.org/en/master/usage/configuration.html -# -- Path setup -------------------------------------------------------------- - -# 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. - -import os -import sys - -sys.path.insert(0, os.path.abspath("../src")) - - # -- Project information ----------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information -project = "Qibochem" -copyright = "2023, The Qibo team" -author = "The Qibo team" - +project = 'qibochem' +copyright = '2023, qiboteam' +author = 'qiboteam' +release = '0.0.1' # -- General configuration --------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration -# 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.coverage", - "sphinx.ext.napoleon", -] - -# Add any paths that contain templates here, relative to this directory. -templates_path = ["_templates"] - -# List of patterns, relative to source directory, that match files and -# directories to ignore when looking for source files. -# This pattern also affects html_static_path and html_extra_path. +extensions = ['sphinxcontrib.katex'] + +templates_path = ['_templates'] exclude_patterns = [] + # -- Options for HTML output ------------------------------------------------- # The theme to use for HTML and HTML Help pages. See the documentation for @@ -51,7 +28,20 @@ # html_theme = "furo" +# custom title +html_title = "Version " + release + +# custom html theme options (colors and font) +html_theme_options = { + "light_css_variables": { + "color-brand-primary": "#6400FF", + "color-brand-secondary": "#6400FF", + "color-brand-content": "#6400FF", + } +} + # 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"] diff --git a/docs/source/index.rst b/docs/source/index.rst index 31ea6a2..f6fe72b 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -1,18 +1,34 @@ .. title:: - Qibochem + Qibochem -Welcome to Qibochem's documentation! -==================================== +What is Qibochem? +================= + +Qibochem is a plugin to Qibo for quantum chemistry simulations. + +Qibochem key features: + +* General purpose Molecule class + + - effective Hamiltonian construction for active space + - inline or .xyz file input for molecular geometry + +* PySCF or Psi4 for calculation of 1- and 2-electron integrals +* Unitary Coupled Cluster Ansatz + +Contents +======== .. toctree:: - :maxdepth: 2 - :caption: Contents: + :maxdepth: 2 + :caption: Introduction + getting-started/index +.. toctree:: + :maxdepth: 2 + :caption: Main Documentation -Indices and tables -================== + api-reference/index + developer-guides/index -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` From f10d12c9627b7c3cd8b266de5e03f187529fed97 Mon Sep 17 00:00:00 2001 From: Wong Zi Cheng <70616433+chmwzc@users.noreply.github.com> Date: Wed, 19 Jul 2023 10:12:31 +0000 Subject: [PATCH 04/26] Update pyproject.toml for installing on Windows Allow Python3.8 and don't install PySCF if on Windows OS --- pyproject.toml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index e852f15..884ddda 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -15,10 +15,11 @@ classifiers = [ packages = [{ include = "qibochem", from = "src" }] [tool.poetry.dependencies] -python = "^3.9" +python = "^3.8" +scipy = "^1.10.1" qibo = "^0.1.10" openfermion = "^1.5" -pyscf = "^2.2.1" +pyscf = {version = "^2.2.1", markers = "sys_platform != 'win32'"} [build-system] requires = ["poetry-core"] From 461c8a6b3722eff5e638852fd5e0233bfe43ed61 Mon Sep 17 00:00:00 2001 From: Wong Zi Cheng <70616433+chmwzc@users.noreply.github.com> Date: Wed, 19 Jul 2023 10:28:55 +0000 Subject: [PATCH 05/26] Minor change to pyproject.toml; Update poetry.lock --- poetry.lock | 845 +++++++++++++++++++++++++++---------------------- pyproject.toml | 2 +- 2 files changed, 463 insertions(+), 384 deletions(-) diff --git a/poetry.lock b/poetry.lock index 3ac340b..b3a3a66 100644 --- a/poetry.lock +++ b/poetry.lock @@ -24,22 +24,19 @@ files = [ [[package]] name = "astroid" -version = "2.15.5" +version = "2.15.6" description = "An abstract syntax tree for Python with inference support." optional = false python-versions = ">=3.7.2" files = [ - {file = "astroid-2.15.5-py3-none-any.whl", hash = "sha256:078e5212f9885fa85fbb0cf0101978a336190aadea6e13305409d099f71b2324"}, - {file = "astroid-2.15.5.tar.gz", hash = "sha256:1039262575027b441137ab4a62a793a9b43defb42c32d5670f38686207cd780f"}, + {file = "astroid-2.15.6-py3-none-any.whl", hash = "sha256:389656ca57b6108f939cf5d2f9a2a825a3be50ba9d589670f393236e0a03b91c"}, + {file = "astroid-2.15.6.tar.gz", hash = "sha256:903f024859b7c7687d7a7f3a3f73b17301f8e42dfd9cc9df9d4418172d3e2dbd"}, ] [package.dependencies] lazy-object-proxy = ">=1.4.0" typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.11\""} -wrapt = [ - {version = ">=1.11,<2", markers = "python_version < \"3.11\""}, - {version = ">=1.14,<2", markers = "python_version >= \"3.11\""}, -] +wrapt = {version = ">=1.11,<2", markers = "python_version < \"3.11\""} [[package]] name = "asttokens" @@ -87,6 +84,9 @@ files = [ {file = "Babel-2.12.1.tar.gz", hash = "sha256:cc2d99999cd01d44420ae725a21c9e3711b3aadc7976d6147f622d8581963455"}, ] +[package.dependencies] +pytz = {version = ">=2015.7", markers = "python_version < \"3.9\""} + [[package]] name = "backcall" version = "0.2.0" @@ -234,86 +234,86 @@ pycparser = "*" [[package]] name = "charset-normalizer" -version = "3.1.0" +version = "3.2.0" description = "The Real First Universal Charset Detector. 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+python-versions = "^3.9" +content-hash = "595b60ed82676d0bcc22c6556c1d69aa2fa44b82845706fa0ea2b56e0d0351a4" diff --git a/pyproject.toml b/pyproject.toml index 335cd85..e852f15 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -15,11 +15,10 @@ classifiers = [ packages = [{ include = "qibochem", from = "src" }] [tool.poetry.dependencies] -python = ">=3.8,<3.11" -scipy = "^1.10.1" +python = "^3.9" qibo = "^0.1.10" openfermion = "^1.5" -pyscf = {version = "^2.2.1", markers = "sys_platform != 'win32'"} +pyscf = "^2.2.1" [build-system] requires = ["poetry-core"] From b9448b628e8bda086b90ec04888f01c7110780ab Mon Sep 17 00:00:00 2001 From: Adrian Mak Date: Tue, 25 Jul 2023 13:23:59 +0800 Subject: [PATCH 07/26] edits to getting-started docs --- docs/source/getting-started/hamiltonian.rst | 75 +++++++++++++++++++ .../getting-started/hamiltonian_mapping.rst | 33 -------- docs/source/getting-started/index.rst | 2 +- docs/source/getting-started/molecule.rst | 4 - 4 files changed, 76 insertions(+), 38 deletions(-) create mode 100644 docs/source/getting-started/hamiltonian.rst delete mode 100644 docs/source/getting-started/hamiltonian_mapping.rst diff --git a/docs/source/getting-started/hamiltonian.rst b/docs/source/getting-started/hamiltonian.rst new file mode 100644 index 0000000..cbf49da --- /dev/null +++ b/docs/source/getting-started/hamiltonian.rst @@ -0,0 +1,75 @@ +Hamiltonian +=========== + +Central to quantum chemical calculations for molecules is the fermionic two-body Hamiltonian in second quantized form. + +TODO: spinfree, nonrelativistic, without external fields, without nuclear-repulsion energy + +.. math:: + \hat{H} = \sum_{pq} h_{pq} a^\dagger_p a_q + \frac12 \sum_{pqrs} h_{pqrs} a^\dagger_p a^\dagger_r a_s a_q + + + +The integrals :math:`h_{pq}` and :math:`h_{pqrs}` are one- and two-electron integrals in atomic units. For spinorbitals :math:`\phi_j` that make up the basis, the integrals are [#f1]_: + +.. math:: + + h_{pq} = \int \phi^*_p(\mathbf{x}_1)\left( -\frac12 \nabla^2 - \sum_A \frac{Z_A}{r_{A}} \right) \phi_q(\mathbf{x}_1) d\mathbf{x}_1 + +.. math:: + + h_{pqrs} = \int \int \phi^*_p(\mathbf{x}_1)\phi^*_r(\mathbf{x}_2) \frac{1}{r_{12}} \phi_s(\mathbf{x}_2)\phi_q(\mathbf{x}_1) dx_1 dx_2 + +These integral quantities are obtained from the PySCF driver program. Qibochem then uses these integrals and OpenFermion to construct the second quantized fermionic Hamiltonian for the molecular system in terms of creation and annihilation operators, with coefficients from these integral quantities. + +.. code-block:: + + mol = Molecule([('H', (0.0, 0.0, 0.0)), ('H', (0.0, 0.0, 0.74))]) + mol.run_pyscf() + mol_ferm_ham = mol.hamiltonian("ferm") # or mol.hamiltonian("f") + + +The fermionic Hamiltonian can then be mapped into qubit Hamiltonians in OpenFermion or in symbolic (:code:`sympy`) form. Additional information about the data structure of the second quantized fermionic Hamiltonian and qubit Hamiltonian can be found `here `_. + +.. code-block:: + + mol_qubit_ham = mol.hamiltonian("qubit") # or mol.hamiltonian("q") + mol_sym_ham = mol.hamiltonian("sym") # or mol.hamiltonian("s") + +By default, the symbolic Hamiltonian is returned, i.e. if no arguments are given for :code:`mol.hamiltonian()`. + + +Fermion to Qubit mapping +------------------------ + +Fermionic Hamiltonians have to be mapped to Qubit Hamiltonians in the Pauli basis for quantum computation. Supported mapping schemes are the Jordan-Wigner and Bravyi-Kitaev schemes, as implemented in OpenFermion. + +Jordan-Wigner +^^^^^^^^^^^^^ + +.. math:: + + \hat{a}^\dagger_j = \bigotimes_{i=1}^{j-1} \hat{Z}_i \otimes (\hat{X}_j - i\hat{Y}_j) + + +.. math:: + + \hat{a}_j = \bigotimes_{i=1}^{j-1} \hat{Z}_i \otimes (\hat{X}_j + i\hat{Y}_j) + +This is done using the keyword :code:`ferm_qubit_map`. + +.. code-block:: + + mol_qubit_ham = mol.hamiltonian("qubit", ferm_qubit_map="jw") + + +Bravyi-Kitaev +^^^^^^^^^^^^^ + + + + +.. rubric:: References + +.. [#f1] Helgaker, T., Jørgensen, P., Olsen, J. Molecular Electronic Structure Theory 2000, Wiley, Chichester, England + diff --git a/docs/source/getting-started/hamiltonian_mapping.rst b/docs/source/getting-started/hamiltonian_mapping.rst deleted file mode 100644 index 6cbbdfb..0000000 --- a/docs/source/getting-started/hamiltonian_mapping.rst +++ /dev/null @@ -1,33 +0,0 @@ -Hamiltonian mapping -=================== - -Central to quantum chemical calculations for molecules is the fermionic two-body Hamiltonian in second quantized form. - -.. math:: - \hat{H} = \sum_{pq} h_{pq} a^\dagger_p a_q + \frac12 \sum_{pqrs} h_{pqrs} a^\dagger_p a^\dagger_q a_s a_r - -which is to mapped to a qubit Hamiltonian for calculation of properties such as molecular energies using quantum hardware. - -The integrals :math:`h_{pq}` and :math:`h_{pqrs}` are one- and two-electron integrals. For spinorbitals :math:`\phi_j` that make up the basis, the integrals are: - -.. math:: - h_{pq} = \int \phi^*_p(x_1)\hat{h}\phi_q(x_1) dx_1 - -.. math:: - h_{pqrs} = \int \int \phi^*_p(x_1)\phi^*_q(x_2)\hat{g}\phi_r(x_2)\phi_s(x_1) dx_1 dx_2 - -Supported mappings are the Jordan-Wigner and Bravyi-Kitaev mapping, as implemented in OpenFermion. - -Jordan-Wigner -------------- - -.. math:: - \hat{a}^\dagger_j = \bigotimes_{i=1}^{j-1} \hat{Z}_i \otimes (\hat{X}_j - i\hat{Y}_j) - - -.. math:: - \hat{a}_j = \bigotimes_{i=1}^{j-1} \hat{Z}_i \otimes (\hat{X}_j + i\hat{Y}_j) - - - - diff --git a/docs/source/getting-started/index.rst b/docs/source/getting-started/index.rst index 8d0c97a..7a29c75 100644 --- a/docs/source/getting-started/index.rst +++ b/docs/source/getting-started/index.rst @@ -9,7 +9,7 @@ This section details the basics of qibochem. More details are given in the follo installation molecule - hamiltonian_mapping + hamiltonian diff --git a/docs/source/getting-started/molecule.rst b/docs/source/getting-started/molecule.rst index 9dceb1e..f956064 100644 --- a/docs/source/getting-started/molecule.rst +++ b/docs/source/getting-started/molecule.rst @@ -34,7 +34,3 @@ PySCF for H\ :sub:`2`\ with H-H distance of 0.74 Angstroms at HF/STO-3G level h2.run_pyscf() - - - -Next: Hamiltonian mapping From ebe5c6ce5a5031f34c53a8874db0fbb9da310b2e Mon Sep 17 00:00:00 2001 From: Adrian Mak <3521998+damarkian@users.noreply.github.com> Date: Tue, 25 Jul 2023 13:27:53 +0800 Subject: [PATCH 08/26] Update README.md to show poetry install --- README.md | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/README.md b/README.md index f5879a7..a7cd4ef 100644 --- a/README.md +++ b/README.md @@ -13,6 +13,16 @@ Qibochem key features ## Installation +Using poetry (recommended) + +``` +git clone https://github.com/qiboteam/qibochem.git +cd qibochem +poetry install +``` + +Using pip + ``` git clone https://github.com/qiboteam/qibochem.git cd qibochem From a82b138b71c4e2cc5eb8706110267477de94ef44 Mon Sep 17 00:00:00 2001 From: Adrian Mak Date: Wed, 2 Aug 2023 10:37:39 +0800 Subject: [PATCH 09/26] autoclass for driver --- docs/source/api-reference/driver.rst | 10 ++++++++++ docs/source/api-reference/index.rst | 4 ++++ docs/source/conf.py | 4 +++- docs/source/getting-started/hamiltonian.rst | 6 +++--- docs/source/getting-started/molecule.rst | 10 ++++++++++ 5 files changed, 30 insertions(+), 4 deletions(-) create mode 100644 docs/source/api-reference/driver.rst diff --git a/docs/source/api-reference/driver.rst b/docs/source/api-reference/driver.rst new file mode 100644 index 0000000..e9daa4b --- /dev/null +++ b/docs/source/api-reference/driver.rst @@ -0,0 +1,10 @@ +Driver +====== + +Qibochem provides the Molecule class to store the data structure of a molecule object, and to drive the classical quantum chemistry calculation to obtain necessary quantities for subsequent quantum compute calculations. + +.. autoclass:: qibochem.driver.molecule.Molecule + :members: + :member-order: bysource + + diff --git a/docs/source/api-reference/index.rst b/docs/source/api-reference/index.rst index 323e588..fa85031 100644 --- a/docs/source/api-reference/index.rst +++ b/docs/source/api-reference/index.rst @@ -3,3 +3,7 @@ API Reference In this section we document the main Qibochem components and primitives in the public API. +.. toctree:: + :maxdepth: 1 + + driver diff --git a/docs/source/conf.py b/docs/source/conf.py index 901776b..729a8d2 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -14,7 +14,9 @@ # -- General configuration --------------------------------------------------- # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration -extensions = ['sphinxcontrib.katex'] +extensions = [ + 'sphinx.ext.autodoc', + 'sphinxcontrib.katex',] templates_path = ['_templates'] exclude_patterns = [] diff --git a/docs/source/getting-started/hamiltonian.rst b/docs/source/getting-started/hamiltonian.rst index cbf49da..dd131a3 100644 --- a/docs/source/getting-started/hamiltonian.rst +++ b/docs/source/getting-started/hamiltonian.rst @@ -20,7 +20,7 @@ The integrals :math:`h_{pq}` and :math:`h_{pqrs}` are one- and two-electron inte h_{pqrs} = \int \int \phi^*_p(\mathbf{x}_1)\phi^*_r(\mathbf{x}_2) \frac{1}{r_{12}} \phi_s(\mathbf{x}_2)\phi_q(\mathbf{x}_1) dx_1 dx_2 -These integral quantities are obtained from the PySCF driver program. Qibochem then uses these integrals and OpenFermion to construct the second quantized fermionic Hamiltonian for the molecular system in terms of creation and annihilation operators, with coefficients from these integral quantities. +These integral quantities are obtained from the PySCF driver program, and can be accessed via the :doc:`Molecule class`. Qibochem then uses these integrals and OpenFermion to construct the second quantized fermionic Hamiltonian for the molecular system in terms of creation and annihilation operators, with coefficients from these integral quantities. .. code-block:: @@ -49,12 +49,12 @@ Jordan-Wigner .. math:: - \hat{a}^\dagger_j = \bigotimes_{i=1}^{j-1} \hat{Z}_i \otimes (\hat{X}_j - i\hat{Y}_j) + \hat{a}^\dagger_j \mapsto \bigotimes_{i=1}^{j-1} \hat{Z}_i \otimes (\hat{X}_j - i\hat{Y}_j) .. math:: - \hat{a}_j = \bigotimes_{i=1}^{j-1} \hat{Z}_i \otimes (\hat{X}_j + i\hat{Y}_j) + \hat{a}_j \mapsto \bigotimes_{i=1}^{j-1} \hat{Z}_i \otimes (\hat{X}_j + i\hat{Y}_j) This is done using the keyword :code:`ferm_qubit_map`. diff --git a/docs/source/getting-started/molecule.rst b/docs/source/getting-started/molecule.rst index f956064..7d90f86 100644 --- a/docs/source/getting-started/molecule.rst +++ b/docs/source/getting-started/molecule.rst @@ -7,10 +7,12 @@ The key inputs required are: geometry atomic coordinates in the form of a list of tuples + charge an integer value for the net charge for the entire molecule default value is 0 + multiplicity spin multiplicity given as 2S + 1, where S is the number of unpaired electrons multipled by 1/2 @@ -19,6 +21,14 @@ multiplicity The current implementation supports both restricted and unrestricted spins. (TODO: elaborate) + +Variables +--------- + +Instance variables that can be stored in the Molecule class are: + + + Example ------- From cf74470b03974717edb7affa800980349726c9ca Mon Sep 17 00:00:00 2001 From: Adrian Mak Date: Thu, 3 Aug 2023 11:07:11 +0800 Subject: [PATCH 10/26] docstring formatting for multilines --- src/qibochem/driver/molecule.py | 19 +++++++++++++++---- 1 file changed, 15 insertions(+), 4 deletions(-) diff --git a/src/qibochem/driver/molecule.py b/src/qibochem/driver/molecule.py index 2193442..0c0ab0d 100644 --- a/src/qibochem/driver/molecule.py +++ b/src/qibochem/driver/molecule.py @@ -321,17 +321,24 @@ def hamiltonian( Args: ham_type: Format of molecular Hamiltonian returned + ("f", "ferm"): OpenFermion FermionOperator + ("q", "qubit"): OpenFermion QubitOperator + ("s", "sym"): Qibo SymbolicHamiltonian (default) + oei: 1-electron integrals. Default: self.oei (MO basis) + tei: 2-electron integrals in 2ndQ notation. Default: self.tei (MO basis) + constant: For inactive Fock energy if embedding used. Default: 0.0 + ferm_qubit_map: Which fermion to qubit transformation to use. - Must be either "jw" (default) or "bk" + Must be either "jw" (default) or "bk" - Returns: - Molecular Hamiltonian in the format of choice + Returns: + Molecular Hamiltonian in the format of choice """ # Define default variables if ham_type is None: @@ -377,9 +384,13 @@ def expectation( Args: circuit (qibo.models.Circuit): Quantum circuit ansatz + hamiltonian (SymbolicHamiltonian): Molecular Hamiltonian + from_samples: Whether the expectation value calculation uses samples or the simulated - state vector. Default: False, state vector simulation + + state vector. Default: False, state vector simulation + n_shots: Number of times the circuit is run for the from_samples=True case Returns: From d687602f67e7560b720ccc15a78e41c5e6d19b95 Mon Sep 17 00:00:00 2001 From: Adrian Mak Date: Mon, 7 Aug 2023 10:52:38 +0800 Subject: [PATCH 11/26] update to driver and molecule docs --- docs/source/api-reference/driver.rst | 5 +++++ docs/source/getting-started/molecule.rst | 15 ++++++++++++--- 2 files changed, 17 insertions(+), 3 deletions(-) diff --git a/docs/source/api-reference/driver.rst b/docs/source/api-reference/driver.rst index e9daa4b..7f5cb33 100644 --- a/docs/source/api-reference/driver.rst +++ b/docs/source/api-reference/driver.rst @@ -3,6 +3,11 @@ Driver Qibochem provides the Molecule class to store the data structure of a molecule object, and to drive the classical quantum chemistry calculation to obtain necessary quantities for subsequent quantum compute calculations. +.. _api driver molecule class: + +Molecule class +-------------- + .. autoclass:: qibochem.driver.molecule.Molecule :members: :member-order: bysource diff --git a/docs/source/getting-started/molecule.rst b/docs/source/getting-started/molecule.rst index 7d90f86..c7ccf48 100644 --- a/docs/source/getting-started/molecule.rst +++ b/docs/source/getting-started/molecule.rst @@ -25,22 +25,31 @@ The current implementation supports both restricted and unrestricted spins. (TOD Variables --------- -Instance variables that can be stored in the Molecule class are: +Upon executing the PyScf driver program for a given molecule, molecular quantities are calculated at the Hartree-Fock (HF) level and stored in the Molecule class. These include: +* converged Hartree-Fock energy +* optimized molecular orbital (MO) coefficients +* one- and two-electron integrals +Additional details are provided in the :ref:`API reference`. Example ------- The following examples show how to use the driver program to save molecule quantities into the Molecule object -PySCF for H\ :sub:`2`\ with H-H distance of 0.74 Angstroms at HF/STO-3G level +PySCF for H\ :sub:`2`\ with H-H distance of 0.74804 Angstroms at HF/STO-3G level .. code-block:: python from qibochem.driver import Molecule - h2 = Molecule([('H', (0.0, 0.0, 0.0)), ('H', (0.0, 0.0, 0.74))]) + h2 = Molecule([('H', (0.0, 0.0, 0.0)), ('H', (0.0, 0.0, 0.74804))]) h2.run_pyscf() + print(h2.e_hf) + + -1.116283736274293 + + From 647c53a65c096e0cba10f3afa552d3d6087b4413 Mon Sep 17 00:00:00 2001 From: Adrian Mak Date: Mon, 7 Aug 2023 12:17:30 +0800 Subject: [PATCH 12/26] updated docs molecule class --- docs/source/getting-started/index.rst | 2 +- docs/source/getting-started/molecule.rst | 21 +++++++++++++++++++++ src/qibochem/driver/molecule.py | 11 +++++++++++ 3 files changed, 33 insertions(+), 1 deletion(-) diff --git a/docs/source/getting-started/index.rst b/docs/source/getting-started/index.rst index 7a29c75..4b3dcde 100644 --- a/docs/source/getting-started/index.rst +++ b/docs/source/getting-started/index.rst @@ -1,7 +1,7 @@ Getting started =============== -This section details the basics of qibochem. More details are given in the following subsections. +This section covers the basics of qibochem. More details are given in the following subsections. .. toctree:: diff --git a/docs/source/getting-started/molecule.rst b/docs/source/getting-started/molecule.rst index c7ccf48..35ee8df 100644 --- a/docs/source/getting-started/molecule.rst +++ b/docs/source/getting-started/molecule.rst @@ -18,6 +18,27 @@ multiplicity default value is 1 (all electrons paired) +Optional inputs: + +basis + the atomic orbital basis set to be used + + default value is 'STO-3G' + +xyz_file + qibochem allows the geometry, charge, and multiplicity to be specified as an .xyz file, with the format: + + .. code-block:: + + n_atoms + charge multiplicity + atom_1 x_coord y_coord z_coord + ... + atom_n x_coord y_coord z_coord + + +active + list of molecular orbitals to be considered in the quantum simulation The current implementation supports both restricted and unrestricted spins. (TODO: elaborate) diff --git a/src/qibochem/driver/molecule.py b/src/qibochem/driver/molecule.py index 0c0ab0d..0840e32 100644 --- a/src/qibochem/driver/molecule.py +++ b/src/qibochem/driver/molecule.py @@ -19,6 +19,17 @@ class Molecule: """ Class representing a single molecule + + :ivar geometry(list): molecular coordinates in OpenFermion format + e.g. [('H', (0.0, 0.0, 0.0)), ('H', (0.0, 0.0, 0.7))] + :ivar charge(int): net charge of molecule + :ivar multiplicity(int): spin multiplicity of molecule + :ivar basis(str): atomic orbital basis set to be used for PySCF calculation + :ivar xyz_file(str): xyz file containing molecular coordinates in chemical xyz format, + comment line should include charge, multiplicity values + :ivar active(list): iterable representing the set of MOs to be included in + quantum simulation, e.g. list(range(3,6)) for active space of orbitals 3,4,5. + """ def __init__(self, geometry=None, charge=0, multiplicity=1, basis=None, xyz_file=None, active=None): From ac1cd928dbbd842f8b1f71d3fd16ca7f2adc4522 Mon Sep 17 00:00:00 2001 From: Adrian Mak Date: Mon, 7 Aug 2023 15:19:31 +0800 Subject: [PATCH 13/26] ansatz, measurement docs --- docs/source/api-reference/hamiltonian.rst | 2 ++ docs/source/api-reference/index.rst | 3 +++ docs/source/api-reference/measurement.rst | 2 ++ docs/source/getting-started/ansatz.rst | 2 ++ docs/source/getting-started/index.rst | 2 ++ docs/source/getting-started/measurement.rst | 3 +++ 6 files changed, 14 insertions(+) create mode 100644 docs/source/api-reference/hamiltonian.rst create mode 100644 docs/source/api-reference/measurement.rst create mode 100644 docs/source/getting-started/ansatz.rst create mode 100644 docs/source/getting-started/measurement.rst diff --git a/docs/source/api-reference/hamiltonian.rst b/docs/source/api-reference/hamiltonian.rst new file mode 100644 index 0000000..79586df --- /dev/null +++ b/docs/source/api-reference/hamiltonian.rst @@ -0,0 +1,2 @@ +Hamiltonian +=========== diff --git a/docs/source/api-reference/index.rst b/docs/source/api-reference/index.rst index fa85031..8c77be5 100644 --- a/docs/source/api-reference/index.rst +++ b/docs/source/api-reference/index.rst @@ -7,3 +7,6 @@ In this section we document the main Qibochem components and primitives in the p :maxdepth: 1 driver + hamiltonian + measurement + diff --git a/docs/source/api-reference/measurement.rst b/docs/source/api-reference/measurement.rst new file mode 100644 index 0000000..75e634e --- /dev/null +++ b/docs/source/api-reference/measurement.rst @@ -0,0 +1,2 @@ +Measurement +=========== \ No newline at end of file diff --git a/docs/source/getting-started/ansatz.rst b/docs/source/getting-started/ansatz.rst new file mode 100644 index 0000000..4b9d9c3 --- /dev/null +++ b/docs/source/getting-started/ansatz.rst @@ -0,0 +1,2 @@ +Ansatz +====== diff --git a/docs/source/getting-started/index.rst b/docs/source/getting-started/index.rst index 4b3dcde..0a8e875 100644 --- a/docs/source/getting-started/index.rst +++ b/docs/source/getting-started/index.rst @@ -10,6 +10,8 @@ This section covers the basics of qibochem. More details are given in the follow installation molecule hamiltonian + ansatz + measurement diff --git a/docs/source/getting-started/measurement.rst b/docs/source/getting-started/measurement.rst new file mode 100644 index 0000000..d7f6f0c --- /dev/null +++ b/docs/source/getting-started/measurement.rst @@ -0,0 +1,3 @@ +Measurement +=========== + From 28969a53504bc530dd39dbadab10d5920893bc80 Mon Sep 17 00:00:00 2001 From: Adrian Mak Date: Mon, 7 Aug 2023 15:33:10 +0800 Subject: [PATCH 14/26] api-reference hamiltonian->ansatz --- docs/source/api-reference/ansatz.rst | 4 ++++ docs/source/api-reference/hamiltonian.rst | 2 -- 2 files changed, 4 insertions(+), 2 deletions(-) create mode 100644 docs/source/api-reference/ansatz.rst delete mode 100644 docs/source/api-reference/hamiltonian.rst diff --git a/docs/source/api-reference/ansatz.rst b/docs/source/api-reference/ansatz.rst new file mode 100644 index 0000000..daea608 --- /dev/null +++ b/docs/source/api-reference/ansatz.rst @@ -0,0 +1,4 @@ +Ansatz +====== + +This section covers the API reference for the ansatz module. diff --git a/docs/source/api-reference/hamiltonian.rst b/docs/source/api-reference/hamiltonian.rst deleted file mode 100644 index 79586df..0000000 --- a/docs/source/api-reference/hamiltonian.rst +++ /dev/null @@ -1,2 +0,0 @@ -Hamiltonian -=========== From 219c0fb7f61a7315016e679632f1f97f6a52ade4 Mon Sep 17 00:00:00 2001 From: Adrian Mak Date: Mon, 7 Aug 2023 16:07:05 +0800 Subject: [PATCH 15/26] api-reference index correction --- docs/source/api-reference/index.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/api-reference/index.rst b/docs/source/api-reference/index.rst index 8c77be5..8194d2b 100644 --- a/docs/source/api-reference/index.rst +++ b/docs/source/api-reference/index.rst @@ -7,6 +7,6 @@ In this section we document the main Qibochem components and primitives in the p :maxdepth: 1 driver - hamiltonian + ansatz measurement From 4ec5abe304fc45038647215dbdde7f688d98b097 Mon Sep 17 00:00:00 2001 From: Adrian Mak Date: Mon, 4 Sep 2023 10:15:19 +0800 Subject: [PATCH 16/26] update docs/hamiltonian --- docs/source/getting-started/hamiltonian.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/source/getting-started/hamiltonian.rst b/docs/source/getting-started/hamiltonian.rst index dd131a3..981bdd9 100644 --- a/docs/source/getting-started/hamiltonian.rst +++ b/docs/source/getting-started/hamiltonian.rst @@ -6,11 +6,11 @@ Central to quantum chemical calculations for molecules is the fermionic two-body TODO: spinfree, nonrelativistic, without external fields, without nuclear-repulsion energy .. math:: - \hat{H} = \sum_{pq} h_{pq} a^\dagger_p a_q + \frac12 \sum_{pqrs} h_{pqrs} a^\dagger_p a^\dagger_r a_s a_q + \hat{H} = \sum_{pq} h_{pq} a^\dagger_p a_q + \frac12 \sum_{pqrs} g_{pqrs} a^\dagger_p a^\dagger_r a_s a_q -The integrals :math:`h_{pq}` and :math:`h_{pqrs}` are one- and two-electron integrals in atomic units. For spinorbitals :math:`\phi_j` that make up the basis, the integrals are [#f1]_: +The integrals :math:`h_{pq}` and :math:`g_{pqrs}` are one- and two-electron integrals in atomic units. For spinorbitals :math:`\phi_j` that make up the basis, the integrals are [#f1]_: .. math:: @@ -18,7 +18,7 @@ The integrals :math:`h_{pq}` and :math:`h_{pqrs}` are one- and two-electron inte .. math:: - h_{pqrs} = \int \int \phi^*_p(\mathbf{x}_1)\phi^*_r(\mathbf{x}_2) \frac{1}{r_{12}} \phi_s(\mathbf{x}_2)\phi_q(\mathbf{x}_1) dx_1 dx_2 + g_{pqrs} = \int \int \phi^*_p(\mathbf{x}_1)\phi^*_r(\mathbf{x}_2) \frac{1}{r_{12}} \phi_s(\mathbf{x}_2)\phi_q(\mathbf{x}_1) dx_1 dx_2 These integral quantities are obtained from the PySCF driver program, and can be accessed via the :doc:`Molecule class`. Qibochem then uses these integrals and OpenFermion to construct the second quantized fermionic Hamiltonian for the molecular system in terms of creation and annihilation operators, with coefficients from these integral quantities. From 93194c6f621ad0fb62d68b4ff3b2004e755917fe Mon Sep 17 00:00:00 2001 From: Adrian Mak Date: Mon, 4 Sep 2023 11:17:17 +0800 Subject: [PATCH 17/26] hamiltonian documentation: ferm, sym --- .vscode/settings.json | 3 + docs/source/getting-started/hamiltonian.rst | 69 +++++++++++++++------ docs/source/getting-started/molecule.rst | 9 ++- 3 files changed, 59 insertions(+), 22 deletions(-) create mode 100644 .vscode/settings.json diff --git a/.vscode/settings.json b/.vscode/settings.json new file mode 100644 index 0000000..73dc9f3 --- /dev/null +++ b/.vscode/settings.json @@ -0,0 +1,3 @@ +{ + "restructuredtext.preview.name": "docutils" +} \ No newline at end of file diff --git a/docs/source/getting-started/hamiltonian.rst b/docs/source/getting-started/hamiltonian.rst index 981bdd9..abc57b7 100644 --- a/docs/source/getting-started/hamiltonian.rst +++ b/docs/source/getting-started/hamiltonian.rst @@ -1,3 +1,4 @@ +=========== Hamiltonian =========== @@ -22,49 +23,77 @@ The integrals :math:`h_{pq}` and :math:`g_{pqrs}` are one- and two-electron inte These integral quantities are obtained from the PySCF driver program, and can be accessed via the :doc:`Molecule class`. Qibochem then uses these integrals and OpenFermion to construct the second quantized fermionic Hamiltonian for the molecular system in terms of creation and annihilation operators, with coefficients from these integral quantities. -.. code-block:: - mol = Molecule([('H', (0.0, 0.0, 0.0)), ('H', (0.0, 0.0, 0.74))]) +Example +------- + +.. code-block:: python + + mol = Molecule([('H', (0.0, 0.0, 0.0)), ('H', (0.0, 0.0, 0.74804))]) mol.run_pyscf() mol_ferm_ham = mol.hamiltonian("ferm") # or mol.hamiltonian("f") + print(mol_ferm_ham.terms) + +Output: + +.. code-block:: output + + {(): 0.7074183344740923, ((0, 1), (0, 0)): -1.248461959132892, ((1, 1), (1, 0)): -1.248461959132892, ((2, 1), (2, 0)): -0.48007161818330846, ((3, 1), (3, 0)): -0.48007161818330846, ((0, 1), (0, 1), (0, 0), (0, 0)): 0.3366109237586995, ((0, 1), (0, 1), (2, 0), (2, 0)): 0.09083064962340165, ((0, 1), (1, 1), (1, 0), (0, 0)): 0.3366109237586995, ((0, 1), (1, 1), (3, 0), (2, 0)): 0.09083064962340165, ((0, 1), (2, 1), (0, 0), (2, 0)): 0.09083064962340165, ((0, 1), (2, 1), (2, 0), (0, 0)): 0.33115823068165495, ((0, 1), (3, 1), (1, 0), (2, 0)): 0.09083064962340165, ((0, 1), (3, 1), (3, 0), (0, 0)): 0.33115823068165495, ((1, 1), (0, 1), (0, 0), (1, 0)): 0.3366109237586995, ((1, 1), (0, 1), (2, 0), (3, 0)): 0.09083064962340165, ((1, 1), (1, 1), (1, 0), (1, 0)): 0.3366109237586995, ((1, 1), (1, 1), (3, 0), (3, 0)): 0.09083064962340165, ((1, 1), (2, 1), (0, 0), (3, 0)): 0.09083064962340165, ((1, 1), (2, 1), (2, 0), (1, 0)): 0.33115823068165495, ((1, 1), (3, 1), (1, 0), (3, 0)): 0.09083064962340165, ((1, 1), (3, 1), (3, 0), (1, 0)): 0.33115823068165495, ((2, 1), (0, 1), (0, 0), (2, 0)): 0.3311582306816552, ((2, 1), (0, 1), (2, 0), (0, 0)): 0.09083064962340165, ((2, 1), (1, 1), (1, 0), (2, 0)): 0.3311582306816552, ((2, 1), (1, 1), (3, 0), (0, 0)): 0.09083064962340165, ((2, 1), (2, 1), (0, 0), (0, 0)): 0.09083064962340165, ((2, 1), (2, 1), (2, 0), (2, 0)): 0.348087115228365, ((2, 1), (3, 1), (1, 0), (0, 0)): 0.09083064962340165, ((2, 1), (3, 1), (3, 0), (2, 0)): 0.348087115228365, ((3, 1), (0, 1), (0, 0), (3, 0)): 0.3311582306816552, ((3, 1), (0, 1), (2, 0), (1, 0)): 0.09083064962340165, ((3, 1), (1, 1), (1, 0), (3, 0)): 0.3311582306816552, ((3, 1), (1, 1), (3, 0), (1, 0)): 0.09083064962340165, ((3, 1), (2, 1), (0, 0), (1, 0)): 0.09083064962340165, ((3, 1), (2, 1), (2, 0), (3, 0)): 0.348087115228365, ((3, 1), (3, 1), (1, 0), (1, 0)): 0.09083064962340165, ((3, 1), (3, 1), (3, 0), (3, 0)): 0.348087115228365} + +Additional information about the data structure of the second quantized fermionic Hamiltonian can be found `here `_. -The fermionic Hamiltonian can then be mapped into qubit Hamiltonians in OpenFermion or in symbolic (:code:`sympy`) form. Additional information about the data structure of the second quantized fermionic Hamiltonian and qubit Hamiltonian can be found `here `_. +Fermion to Qubit mapping +------------------------ + +The fermionic Hamiltonian can then be mapped into qubit Hamiltonians in OpenFermion form. .. code-block:: mol_qubit_ham = mol.hamiltonian("qubit") # or mol.hamiltonian("q") mol_sym_ham = mol.hamiltonian("sym") # or mol.hamiltonian("s") -By default, the symbolic Hamiltonian is returned, i.e. if no arguments are given for :code:`mol.hamiltonian()`. -Fermion to Qubit mapping ------------------------- +Supported mapping schemes are the Jordan-Wigner and Bravyi-Kitaev schemes, as implemented in OpenFermion. -Fermionic Hamiltonians have to be mapped to Qubit Hamiltonians in the Pauli basis for quantum computation. Supported mapping schemes are the Jordan-Wigner and Bravyi-Kitaev schemes, as implemented in OpenFermion. -Jordan-Wigner -^^^^^^^^^^^^^ +Example +------- -.. math:: +The mapping scheme can be specified using the keyword :code:`ferm_qubit_map` as follows: - \hat{a}^\dagger_j \mapsto \bigotimes_{i=1}^{j-1} \hat{Z}_i \otimes (\hat{X}_j - i\hat{Y}_j) - - -.. math:: - \hat{a}_j \mapsto \bigotimes_{i=1}^{j-1} \hat{Z}_i \otimes (\hat{X}_j + i\hat{Y}_j) +.. code-block:: python -This is done using the keyword :code:`ferm_qubit_map`. + mol_qubit_ham = mol.hamiltonian("qubit", ferm_qubit_map="jw") + print(mol_qubit_ham.terms) -.. code-block:: +Output: + +.. code-block:: output + + {(): -0.10728041160866736, ((0, 'Z'),): 0.17018261181714206, ((1, 'Z'),): 0.17018261181714206, ((2, 'Z'),): -0.21975065439248248, ((3, 'Z'),): -0.21975065439248248, ((0, 'Z'), (1, 'Z')): 0.16830546187934975, ((0, 'Z'), (2, 'Z')): 0.1201637905291267, ((0, 'Z'), (3, 'Z')): 0.16557911534082753, ((1, 'Z'), (2, 'Z')): 0.16557911534082753, ((1, 'Z'), (3, 'Z')): 0.1201637905291267, ((2, 'Z'), (3, 'Z')): 0.1740435576141825, ((0, 'X'), (1, 'X'), (2, 'Y'), (3, 'Y')): -0.045415324811700825, ((0, 'X'), (1, 'Y'), (2, 'Y'), (3, 'X')): 0.045415324811700825, ((0, 'Y'), (1, 'X'), (2, 'X'), (3, 'Y')): 0.045415324811700825, ((0, 'Y'), (1, 'Y'), (2, 'X'), (3, 'X')): -0.045415324811700825} + +Additional information about the data structure of the qubit Hamiltonian can be found `here `_. - mol_qubit_ham = mol.hamiltonian("qubit", ferm_qubit_map="jw") +Symbolic Hamiltonian +-------------------- -Bravyi-Kitaev -^^^^^^^^^^^^^ +To carry out quantum simulations of the electronic structure in molecules using methods such as VQE and time evolution using Qibo, the Hamiltonian has to be defined either in the full matrix form, or a more efficient term representation using :code:`sympy` form: + +.. code-block:: python + + mol_sym_ham = mol.hamiltonian("sym") # or mol.hamiltonian("s") + print(mol_sym_ham.form) + +.. code-block:: output + + -0.107280411608667 - 0.0454153248117008*X0*X1*Y2*Y3 + 0.0454153248117008*X0*Y1*Y2*X3 + 0.0454153248117008*Y0*X1*X2*Y3 - 0.0454153248117008*Y0*Y1*X2*X3 + 0.170182611817142*Z0 + 0.16830546187935*Z0*Z1 + 0.120163790529127*Z0*Z2 + 0.165579115340828*Z0*Z3 + 0.170182611817142*Z1 + 0.165579115340828*Z1*Z2 + 0.120163790529127*Z1*Z3 - 0.219750654392482*Z2 + 0.174043557614182*Z2*Z3 - 0.219750654392482*Z3 + + +By default, the symbolic Hamiltonian is returned, i.e. if no arguments are given for :code:`mol.hamiltonian()`. diff --git a/docs/source/getting-started/molecule.rst b/docs/source/getting-started/molecule.rst index 35ee8df..9e9f6c0 100644 --- a/docs/source/getting-started/molecule.rst +++ b/docs/source/getting-started/molecule.rst @@ -54,6 +54,7 @@ Upon executing the PyScf driver program for a given molecule, molecular quantiti Additional details are provided in the :ref:`API reference`. + Example ------- @@ -63,13 +64,17 @@ PySCF for H\ :sub:`2`\ with H-H distance of 0.74804 Angstroms at HF/STO-3G leve .. code-block:: python - from qibochem.driver import Molecule + from qibochem.driver.molecule import Molecule h2 = Molecule([('H', (0.0, 0.0, 0.0)), ('H', (0.0, 0.0, 0.74804))]) h2.run_pyscf() print(h2.e_hf) - -1.116283736274293 +Output: + +.. code-block:: output + + converged SCF energy = -1.11628373627429 From e35fff3d4cb483937c1ceab6ed7507270e59f13e Mon Sep 17 00:00:00 2001 From: Adrian Mak <3521998+damarkian@users.noreply.github.com> Date: Mon, 4 Sep 2023 11:20:03 +0800 Subject: [PATCH 18/26] Update .gitignore --- .gitignore | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.gitignore b/.gitignore index cab615f..a82e40c 100644 --- a/.gitignore +++ b/.gitignore @@ -163,3 +163,6 @@ cython_debug/ # Psi4 timer.dat psi4_output.dat + +# vscode +.vscode/ From dca4156338786de1e3d8c74b69afe44debe82a57 Mon Sep 17 00:00:00 2001 From: Adrian Mak Date: Mon, 4 Sep 2023 11:22:26 +0800 Subject: [PATCH 19/26] remove .vscode --- .vscode/settings.json | 3 --- 1 file changed, 3 deletions(-) delete mode 100644 .vscode/settings.json diff --git a/.vscode/settings.json b/.vscode/settings.json deleted file mode 100644 index 73dc9f3..0000000 --- a/.vscode/settings.json +++ /dev/null @@ -1,3 +0,0 @@ -{ - "restructuredtext.preview.name": "docutils" -} \ No newline at end of file From af45925085afd7cd983bba56160da6f3da28176b Mon Sep 17 00:00:00 2001 From: Adrian Mak Date: Mon, 4 Sep 2023 15:51:08 +0800 Subject: [PATCH 20/26] updated ansatz docs --- docs/source/getting-started/ansatz.rst | 22 +++++++++++++++++++++ docs/source/getting-started/hamiltonian.rst | 1 + 2 files changed, 23 insertions(+) diff --git a/docs/source/getting-started/ansatz.rst b/docs/source/getting-started/ansatz.rst index 4b9d9c3..331908a 100644 --- a/docs/source/getting-started/ansatz.rst +++ b/docs/source/getting-started/ansatz.rst @@ -1,2 +1,24 @@ +====== Ansatz ====== + +A quantum circuit consisting of parameterized gates RX(theta), RY(theta) and RZ(theta), represents a unitary transformation :math:`U(\theta)` that transforms the initial quantum state into an Ansatz state :math:`|\psi(\theta)\rangle`. + +Hardware Efficient Ansatz +------------------------- + +Qibochem provides a hardware efficient ansatz that simply consists of a layer of single qubit rotation gates followed by a layer of two-qubit gates that entangle the qubits. + +Example +^^^^^^^ + +Unitary Coupled Cluster Ansatz +------------------------------ + +The Unitary Coupled Cluster ansatz [#f1]_ [#f2]_ + +.. rubric:: References + +.. [#f1] Whitfield, J. D. et al., 'Simulation of electronic structure Hamiltonians using quantum computers', Mol. Phys. 109 (2011) 735. + +.. [#f2] Anand. A. et al., 'A quantum computing view on unitary coupled cluster theory', Chem. Soc. Rev. 51 (2022) 1659. \ No newline at end of file diff --git a/docs/source/getting-started/hamiltonian.rst b/docs/source/getting-started/hamiltonian.rst index abc57b7..f14d486 100644 --- a/docs/source/getting-started/hamiltonian.rst +++ b/docs/source/getting-started/hamiltonian.rst @@ -29,6 +29,7 @@ Example .. code-block:: python + from qibochem.driver.molecule import Molecule mol = Molecule([('H', (0.0, 0.0, 0.0)), ('H', (0.0, 0.0, 0.74804))]) mol.run_pyscf() mol_ferm_ham = mol.hamiltonian("ferm") # or mol.hamiltonian("f") From 79a07d618e8b1e44e397820d5f51426c9ca9d3aa Mon Sep 17 00:00:00 2001 From: Adrian Mak Date: Tue, 5 Sep 2023 16:35:57 +0800 Subject: [PATCH 21/26] add hardware-efficient circuit image --- docs/source/getting-started/ansatz.rst | 2 ++ .../qibochem_doc_ansatz_hardware-efficient.svg | 4 ++++ 2 files changed, 6 insertions(+) create mode 100644 docs/source/getting-started/qibochem_doc_ansatz_hardware-efficient.svg diff --git a/docs/source/getting-started/ansatz.rst b/docs/source/getting-started/ansatz.rst index 331908a..f932e67 100644 --- a/docs/source/getting-started/ansatz.rst +++ b/docs/source/getting-started/ansatz.rst @@ -9,6 +9,8 @@ Hardware Efficient Ansatz Qibochem provides a hardware efficient ansatz that simply consists of a layer of single qubit rotation gates followed by a layer of two-qubit gates that entangle the qubits. +.. image:: qibochem_doc_ansatz_hardware-efficient.svg + Example ^^^^^^^ diff --git a/docs/source/getting-started/qibochem_doc_ansatz_hardware-efficient.svg b/docs/source/getting-started/qibochem_doc_ansatz_hardware-efficient.svg new file mode 100644 index 0000000..807027b --- /dev/null +++ b/docs/source/getting-started/qibochem_doc_ansatz_hardware-efficient.svg @@ -0,0 +1,4 @@ + + + +
q0:
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|1〉
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U(θ)
U(θ)Text is not SVG - cannot display \ No newline at end of file From 7a585468744a8561a821eb82b5fb4155ca8c3cb8 Mon Sep 17 00:00:00 2001 From: Adrian Mak Date: Wed, 6 Sep 2023 10:28:09 +0800 Subject: [PATCH 22/26] ansatz doc updates, sphinxcontrib-katex dependency --- docs/source/getting-started/ansatz.rst | 20 +++++++++++++++++--- pyproject.toml | 1 + 2 files changed, 18 insertions(+), 3 deletions(-) diff --git a/docs/source/getting-started/ansatz.rst b/docs/source/getting-started/ansatz.rst index f932e67..05e442c 100644 --- a/docs/source/getting-started/ansatz.rst +++ b/docs/source/getting-started/ansatz.rst @@ -7,20 +7,34 @@ A quantum circuit consisting of parameterized gates RX(theta), RY(theta) and RZ( Hardware Efficient Ansatz ------------------------- -Qibochem provides a hardware efficient ansatz that simply consists of a layer of single qubit rotation gates followed by a layer of two-qubit gates that entangle the qubits. +Qibochem provides a hardware efficient ansatz that simply consists of a layer of single qubit rotation gates followed by a layer of two-qubit gates that entangle the qubits. For the H\ :sub:`2` case discussed in previous sections, a possible hardware efficient ansatz can be constructed as such: .. image:: qibochem_doc_ansatz_hardware-efficient.svg Example ^^^^^^^ +Placeholder for hardware-efficient ansatz example + + Unitary Coupled Cluster Ansatz ------------------------------ -The Unitary Coupled Cluster ansatz [#f1]_ [#f2]_ +The Unitary Coupled Cluster ansatz [#f1]_ [#f2]_ is a variant of the popular gold standard Coupled Cluster ansatz [#f3]_ of quantum chemistry. The unitary coupled cluster wave function is a parameterized unitary transformation of a reference wave function, of which a common choice is the Hartree-Fock wave function. + +.. math:: + + |\psi_{\mathrm{UCC}}\rangle = U(\theta)|\psi_{\mathrm{ref}}\rangle + +Example +^^^^^^^ + +Placeholder for UCCD example .. rubric:: References .. [#f1] Whitfield, J. D. et al., 'Simulation of electronic structure Hamiltonians using quantum computers', Mol. Phys. 109 (2011) 735. -.. [#f2] Anand. A. et al., 'A quantum computing view on unitary coupled cluster theory', Chem. Soc. Rev. 51 (2022) 1659. \ No newline at end of file +.. [#f2] Anand. A. et al., 'A quantum computing view on unitary coupled cluster theory', Chem. Soc. Rev. 51 (2022) 1659. + +.. [#f3] Crawford, T. D. et al., 'An Introduction to Coupled Cluster Theory for Computational Chemists', in Reviews in Computational Chemistry 14 (2007) 33. \ No newline at end of file diff --git a/pyproject.toml b/pyproject.toml index e852f15..de2ba00 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -32,6 +32,7 @@ sphinx = "^6.1.3" furo = "^2023.3.27" recommonmark = "^0.7.1" sphinxcontrib-bibtex = "^2.5.0" +sphinxcontrib-katex = "^0.9.7" sphinx-markdown-tables = "^0.0.17" nbsphinx = "^0.9.1" ipython = "^8.12.0" From fec9eff34b237818c524307a04188169e6e4dbdd Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Wed, 6 Sep 2023 03:27:01 +0000 Subject: [PATCH 23/26] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- docs/source/api-reference/driver.rst | 4 +--- docs/source/api-reference/index.rst | 1 - docs/source/api-reference/measurement.rst | 2 +- docs/source/conf.py | 16 ++++++++-------- docs/source/developer-guides/index.rst | 1 - docs/source/getting-started/ansatz.rst | 10 +++++----- docs/source/getting-started/hamiltonian.rst | 19 +++++++++---------- docs/source/getting-started/index.rst | 3 --- docs/source/getting-started/installation.rst | 7 +++---- docs/source/getting-started/measurement.rst | 1 - docs/source/getting-started/molecule.rst | 16 ++++++---------- ...qibochem_doc_ansatz_hardware-efficient.svg | 2 +- docs/source/index.rst | 11 +++++------ src/qibochem/driver/molecule.py | 8 ++++---- 14 files changed, 43 insertions(+), 58 deletions(-) diff --git a/docs/source/api-reference/driver.rst b/docs/source/api-reference/driver.rst index 7f5cb33..2b4ebfc 100644 --- a/docs/source/api-reference/driver.rst +++ b/docs/source/api-reference/driver.rst @@ -3,7 +3,7 @@ Driver Qibochem provides the Molecule class to store the data structure of a molecule object, and to drive the classical quantum chemistry calculation to obtain necessary quantities for subsequent quantum compute calculations. -.. _api driver molecule class: +.. _api driver molecule class: Molecule class -------------- @@ -11,5 +11,3 @@ Molecule class .. autoclass:: qibochem.driver.molecule.Molecule :members: :member-order: bysource - - diff --git a/docs/source/api-reference/index.rst b/docs/source/api-reference/index.rst index 8194d2b..23adece 100644 --- a/docs/source/api-reference/index.rst +++ b/docs/source/api-reference/index.rst @@ -9,4 +9,3 @@ In this section we document the main Qibochem components and primitives in the p driver ansatz measurement - diff --git a/docs/source/api-reference/measurement.rst b/docs/source/api-reference/measurement.rst index 75e634e..7123879 100644 --- a/docs/source/api-reference/measurement.rst +++ b/docs/source/api-reference/measurement.rst @@ -1,2 +1,2 @@ Measurement -=========== \ No newline at end of file +=========== diff --git a/docs/source/conf.py b/docs/source/conf.py index 729a8d2..6f078a5 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -6,23 +6,23 @@ # -- Project information ----------------------------------------------------- # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information -project = 'qibochem' -copyright = '2023, qiboteam' -author = 'qiboteam' -release = '0.0.1' +project = "qibochem" +copyright = "2023, qiboteam" +author = "qiboteam" +release = "0.0.1" # -- General configuration --------------------------------------------------- # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration extensions = [ - 'sphinx.ext.autodoc', - 'sphinxcontrib.katex',] + "sphinx.ext.autodoc", + "sphinxcontrib.katex", +] -templates_path = ['_templates'] +templates_path = ["_templates"] exclude_patterns = [] - # -- Options for HTML output ------------------------------------------------- # The theme to use for HTML and HTML Help pages. See the documentation for diff --git a/docs/source/developer-guides/index.rst b/docs/source/developer-guides/index.rst index 9976d21..b79cc58 100644 --- a/docs/source/developer-guides/index.rst +++ b/docs/source/developer-guides/index.rst @@ -2,4 +2,3 @@ Developer Guides ================ This section provides code overview and contribution guidelines for developers. - diff --git a/docs/source/getting-started/ansatz.rst b/docs/source/getting-started/ansatz.rst index 05e442c..6310e0b 100644 --- a/docs/source/getting-started/ansatz.rst +++ b/docs/source/getting-started/ansatz.rst @@ -2,7 +2,7 @@ Ansatz ====== -A quantum circuit consisting of parameterized gates RX(theta), RY(theta) and RZ(theta), represents a unitary transformation :math:`U(\theta)` that transforms the initial quantum state into an Ansatz state :math:`|\psi(\theta)\rangle`. +A quantum circuit consisting of parameterized gates RX(theta), RY(theta) and RZ(theta), represents a unitary transformation :math:`U(\theta)` that transforms the initial quantum state into an Ansatz state :math:`|\psi(\theta)\rangle`. Hardware Efficient Ansatz ------------------------- @@ -20,9 +20,9 @@ Placeholder for hardware-efficient ansatz example Unitary Coupled Cluster Ansatz ------------------------------ -The Unitary Coupled Cluster ansatz [#f1]_ [#f2]_ is a variant of the popular gold standard Coupled Cluster ansatz [#f3]_ of quantum chemistry. The unitary coupled cluster wave function is a parameterized unitary transformation of a reference wave function, of which a common choice is the Hartree-Fock wave function. +The Unitary Coupled Cluster ansatz [#f1]_ [#f2]_ is a variant of the popular gold standard Coupled Cluster ansatz [#f3]_ of quantum chemistry. The unitary coupled cluster wave function is a parameterized unitary transformation of a reference wave function, of which a common choice is the Hartree-Fock wave function. -.. math:: +.. math:: |\psi_{\mathrm{UCC}}\rangle = U(\theta)|\psi_{\mathrm{ref}}\rangle @@ -35,6 +35,6 @@ Placeholder for UCCD example .. [#f1] Whitfield, J. D. et al., 'Simulation of electronic structure Hamiltonians using quantum computers', Mol. Phys. 109 (2011) 735. -.. [#f2] Anand. A. et al., 'A quantum computing view on unitary coupled cluster theory', Chem. Soc. Rev. 51 (2022) 1659. +.. [#f2] Anand. A. et al., 'A quantum computing view on unitary coupled cluster theory', Chem. Soc. Rev. 51 (2022) 1659. -.. [#f3] Crawford, T. D. et al., 'An Introduction to Coupled Cluster Theory for Computational Chemists', in Reviews in Computational Chemistry 14 (2007) 33. \ No newline at end of file +.. [#f3] Crawford, T. D. et al., 'An Introduction to Coupled Cluster Theory for Computational Chemists', in Reviews in Computational Chemistry 14 (2007) 33. diff --git a/docs/source/getting-started/hamiltonian.rst b/docs/source/getting-started/hamiltonian.rst index f14d486..26aa41e 100644 --- a/docs/source/getting-started/hamiltonian.rst +++ b/docs/source/getting-started/hamiltonian.rst @@ -2,26 +2,26 @@ Hamiltonian =========== -Central to quantum chemical calculations for molecules is the fermionic two-body Hamiltonian in second quantized form. +Central to quantum chemical calculations for molecules is the fermionic two-body Hamiltonian in second quantized form. TODO: spinfree, nonrelativistic, without external fields, without nuclear-repulsion energy .. math:: - \hat{H} = \sum_{pq} h_{pq} a^\dagger_p a_q + \frac12 \sum_{pqrs} g_{pqrs} a^\dagger_p a^\dagger_r a_s a_q + \hat{H} = \sum_{pq} h_{pq} a^\dagger_p a_q + \frac12 \sum_{pqrs} g_{pqrs} a^\dagger_p a^\dagger_r a_s a_q The integrals :math:`h_{pq}` and :math:`g_{pqrs}` are one- and two-electron integrals in atomic units. For spinorbitals :math:`\phi_j` that make up the basis, the integrals are [#f1]_: -.. math:: +.. math:: h_{pq} = \int \phi^*_p(\mathbf{x}_1)\left( -\frac12 \nabla^2 - \sum_A \frac{Z_A}{r_{A}} \right) \phi_q(\mathbf{x}_1) d\mathbf{x}_1 -.. math:: +.. math:: g_{pqrs} = \int \int \phi^*_p(\mathbf{x}_1)\phi^*_r(\mathbf{x}_2) \frac{1}{r_{12}} \phi_s(\mathbf{x}_2)\phi_q(\mathbf{x}_1) dx_1 dx_2 -These integral quantities are obtained from the PySCF driver program, and can be accessed via the :doc:`Molecule class`. Qibochem then uses these integrals and OpenFermion to construct the second quantized fermionic Hamiltonian for the molecular system in terms of creation and annihilation operators, with coefficients from these integral quantities. +These integral quantities are obtained from the PySCF driver program, and can be accessed via the :doc:`Molecule class`. Qibochem then uses these integrals and OpenFermion to construct the second quantized fermionic Hamiltonian for the molecular system in terms of creation and annihilation operators, with coefficients from these integral quantities. Example @@ -40,14 +40,14 @@ Output: .. code-block:: output {(): 0.7074183344740923, ((0, 1), (0, 0)): -1.248461959132892, ((1, 1), (1, 0)): -1.248461959132892, ((2, 1), (2, 0)): -0.48007161818330846, ((3, 1), (3, 0)): -0.48007161818330846, ((0, 1), (0, 1), (0, 0), (0, 0)): 0.3366109237586995, ((0, 1), (0, 1), (2, 0), (2, 0)): 0.09083064962340165, ((0, 1), (1, 1), (1, 0), (0, 0)): 0.3366109237586995, ((0, 1), (1, 1), (3, 0), (2, 0)): 0.09083064962340165, ((0, 1), (2, 1), (0, 0), (2, 0)): 0.09083064962340165, ((0, 1), (2, 1), (2, 0), (0, 0)): 0.33115823068165495, ((0, 1), (3, 1), (1, 0), (2, 0)): 0.09083064962340165, ((0, 1), (3, 1), (3, 0), (0, 0)): 0.33115823068165495, ((1, 1), (0, 1), (0, 0), (1, 0)): 0.3366109237586995, ((1, 1), (0, 1), (2, 0), (3, 0)): 0.09083064962340165, ((1, 1), (1, 1), (1, 0), (1, 0)): 0.3366109237586995, ((1, 1), (1, 1), (3, 0), (3, 0)): 0.09083064962340165, ((1, 1), (2, 1), (0, 0), (3, 0)): 0.09083064962340165, ((1, 1), (2, 1), (2, 0), (1, 0)): 0.33115823068165495, ((1, 1), (3, 1), (1, 0), (3, 0)): 0.09083064962340165, ((1, 1), (3, 1), (3, 0), (1, 0)): 0.33115823068165495, ((2, 1), (0, 1), (0, 0), (2, 0)): 0.3311582306816552, ((2, 1), (0, 1), (2, 0), (0, 0)): 0.09083064962340165, ((2, 1), (1, 1), (1, 0), (2, 0)): 0.3311582306816552, ((2, 1), (1, 1), (3, 0), (0, 0)): 0.09083064962340165, ((2, 1), (2, 1), (0, 0), (0, 0)): 0.09083064962340165, ((2, 1), (2, 1), (2, 0), (2, 0)): 0.348087115228365, ((2, 1), (3, 1), (1, 0), (0, 0)): 0.09083064962340165, ((2, 1), (3, 1), (3, 0), (2, 0)): 0.348087115228365, ((3, 1), (0, 1), (0, 0), (3, 0)): 0.3311582306816552, ((3, 1), (0, 1), (2, 0), (1, 0)): 0.09083064962340165, ((3, 1), (1, 1), (1, 0), (3, 0)): 0.3311582306816552, ((3, 1), (1, 1), (3, 0), (1, 0)): 0.09083064962340165, ((3, 1), (2, 1), (0, 0), (1, 0)): 0.09083064962340165, ((3, 1), (2, 1), (2, 0), (3, 0)): 0.348087115228365, ((3, 1), (3, 1), (1, 0), (1, 0)): 0.09083064962340165, ((3, 1), (3, 1), (3, 0), (3, 0)): 0.348087115228365} - + Additional information about the data structure of the second quantized fermionic Hamiltonian can be found `here `_. Fermion to Qubit mapping ------------------------ -The fermionic Hamiltonian can then be mapped into qubit Hamiltonians in OpenFermion form. +The fermionic Hamiltonian can then be mapped into qubit Hamiltonians in OpenFermion form. .. code-block:: @@ -56,7 +56,7 @@ The fermionic Hamiltonian can then be mapped into qubit Hamiltonians in OpenFerm -Supported mapping schemes are the Jordan-Wigner and Bravyi-Kitaev schemes, as implemented in OpenFermion. +Supported mapping schemes are the Jordan-Wigner and Bravyi-Kitaev schemes, as implemented in OpenFermion. Example @@ -94,7 +94,7 @@ To carry out quantum simulations of the electronic structure in molecules using -0.107280411608667 - 0.0454153248117008*X0*X1*Y2*Y3 + 0.0454153248117008*X0*Y1*Y2*X3 + 0.0454153248117008*Y0*X1*X2*Y3 - 0.0454153248117008*Y0*Y1*X2*X3 + 0.170182611817142*Z0 + 0.16830546187935*Z0*Z1 + 0.120163790529127*Z0*Z2 + 0.165579115340828*Z0*Z3 + 0.170182611817142*Z1 + 0.165579115340828*Z1*Z2 + 0.120163790529127*Z1*Z3 - 0.219750654392482*Z2 + 0.174043557614182*Z2*Z3 - 0.219750654392482*Z3 -By default, the symbolic Hamiltonian is returned, i.e. if no arguments are given for :code:`mol.hamiltonian()`. +By default, the symbolic Hamiltonian is returned, i.e. if no arguments are given for :code:`mol.hamiltonian()`. @@ -102,4 +102,3 @@ By default, the symbolic Hamiltonian is returned, i.e. if no arguments are given .. rubric:: References .. [#f1] Helgaker, T., Jørgensen, P., Olsen, J. Molecular Electronic Structure Theory 2000, Wiley, Chichester, England - diff --git a/docs/source/getting-started/index.rst b/docs/source/getting-started/index.rst index 0a8e875..b9d719b 100644 --- a/docs/source/getting-started/index.rst +++ b/docs/source/getting-started/index.rst @@ -12,6 +12,3 @@ This section covers the basics of qibochem. More details are given in the follow hamiltonian ansatz measurement - - - diff --git a/docs/source/getting-started/installation.rst b/docs/source/getting-started/installation.rst index b04f77a..50bb6f2 100644 --- a/docs/source/getting-started/installation.rst +++ b/docs/source/getting-started/installation.rst @@ -3,17 +3,16 @@ Installation Using pip install: -.. code-block:: - +.. code-block:: + git clone https://github.com/qiboteam/qibochem.git cd qibochem pip install . Using poetry: -.. code-block:: +.. code-block:: git clone https://github.com/qiboteam/qibochem.git cd qibochem poetry install - diff --git a/docs/source/getting-started/measurement.rst b/docs/source/getting-started/measurement.rst index d7f6f0c..7123879 100644 --- a/docs/source/getting-started/measurement.rst +++ b/docs/source/getting-started/measurement.rst @@ -1,3 +1,2 @@ Measurement =========== - diff --git a/docs/source/getting-started/molecule.rst b/docs/source/getting-started/molecule.rst index 9e9f6c0..520fe6b 100644 --- a/docs/source/getting-started/molecule.rst +++ b/docs/source/getting-started/molecule.rst @@ -1,7 +1,7 @@ Molecule ======== -The Molecule object contains all the information from a classical quantum chemistry calculation that will be used in the quantum simulation. +The Molecule object contains all the information from a classical quantum chemistry calculation that will be used in the quantum simulation. The key inputs required are: @@ -15,7 +15,7 @@ charge multiplicity spin multiplicity given as 2S + 1, where S is the number of unpaired electrons multipled by 1/2 - + default value is 1 (all electrons paired) Optional inputs: @@ -29,7 +29,7 @@ xyz_file qibochem allows the geometry, charge, and multiplicity to be specified as an .xyz file, with the format: .. code-block:: - + n_atoms charge multiplicity atom_1 x_coord y_coord z_coord @@ -52,7 +52,7 @@ Upon executing the PyScf driver program for a given molecule, molecular quantiti * optimized molecular orbital (MO) coefficients * one- and two-electron integrals -Additional details are provided in the :ref:`API reference`. +Additional details are provided in the :ref:`API reference`. Example @@ -70,12 +70,8 @@ PySCF for H\ :sub:`2`\ with H-H distance of 0.74804 Angstroms at HF/STO-3G leve h2.run_pyscf() print(h2.e_hf) -Output: +Output: -.. code-block:: output +.. code-block:: output converged SCF energy = -1.11628373627429 - - - - diff --git a/docs/source/getting-started/qibochem_doc_ansatz_hardware-efficient.svg b/docs/source/getting-started/qibochem_doc_ansatz_hardware-efficient.svg index 807027b..65acde6 100644 --- a/docs/source/getting-started/qibochem_doc_ansatz_hardware-efficient.svg +++ b/docs/source/getting-started/qibochem_doc_ansatz_hardware-efficient.svg @@ -1,4 +1,4 @@ -
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U(θ)Text is not SVG - cannot display diff --git a/docs/source/index.rst b/docs/source/index.rst index f6fe72b..1d44428 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -4,15 +4,15 @@ What is Qibochem? ================= -Qibochem is a plugin to Qibo for quantum chemistry simulations. +Qibochem is a plugin to Qibo for quantum chemistry simulations. Qibochem key features: * General purpose Molecule class - - - effective Hamiltonian construction for active space + + - effective Hamiltonian construction for active space - inline or .xyz file input for molecular geometry - + * PySCF or Psi4 for calculation of 1- and 2-electron integrals * Unitary Coupled Cluster Ansatz @@ -25,10 +25,9 @@ Contents getting-started/index -.. toctree:: +.. toctree:: :maxdepth: 2 :caption: Main Documentation api-reference/index developer-guides/index - diff --git a/src/qibochem/driver/molecule.py b/src/qibochem/driver/molecule.py index c50acd5..48dfe61 100644 --- a/src/qibochem/driver/molecule.py +++ b/src/qibochem/driver/molecule.py @@ -25,10 +25,10 @@ class Molecule: :ivar charge(int): net charge of molecule :ivar multiplicity(int): spin multiplicity of molecule :ivar basis(str): atomic orbital basis set to be used for PySCF calculation - :ivar xyz_file(str): xyz file containing molecular coordinates in chemical xyz format, + :ivar xyz_file(str): xyz file containing molecular coordinates in chemical xyz format, comment line should include charge, multiplicity values :ivar active(list): iterable representing the set of MOs to be included in - quantum simulation, e.g. list(range(3,6)) for active space of orbitals 3,4,5. + quantum simulation, e.g. list(range(3,6)) for active space of orbitals 3,4,5. """ @@ -332,13 +332,13 @@ def hamiltonian( Args: ham_type: Format of molecular Hamiltonian returned - + ("f", "ferm"): OpenFermion FermionOperator ("q", "qubit"): OpenFermion QubitOperator ("s", "sym"): Qibo SymbolicHamiltonian (default) - + oei: 1-electron integrals. Default: self.oei (MO basis) tei: 2-electron integrals in 2ndQ notation. Default: self.tei (MO basis) From a71d3d05eb8b74410b813bf3ff1949b078320e28 Mon Sep 17 00:00:00 2001 From: Adrian Mak <3521998+damarkian@users.noreply.github.com> Date: Wed, 6 Sep 2023 11:50:42 +0800 Subject: [PATCH 24/26] Update pyproject.toml --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index d105647..6e6aa9b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -33,7 +33,7 @@ sphinx = "^6.1.3" furo = "^2023.3.27" recommonmark = "^0.7.1" sphinxcontrib-bibtex = "^2.5.0" -sphinxcontrib-katex = "^0.9.7" +sphinxcontrib-katex = "^0.9.0" sphinx-markdown-tables = "^0.0.17" nbsphinx = "^0.9.1" ipython = "^8.12.0" From 4a5594a501a5f15a635fb1bda6533ed630d28a8f Mon Sep 17 00:00:00 2001 From: Adrian Mak <3521998+damarkian@users.noreply.github.com> Date: Wed, 6 Sep 2023 11:55:33 +0800 Subject: [PATCH 25/26] Update pyproject.toml --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 6e6aa9b..66cb1e0 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -33,7 +33,7 @@ sphinx = "^6.1.3" furo = "^2023.3.27" recommonmark = "^0.7.1" sphinxcontrib-bibtex = "^2.5.0" -sphinxcontrib-katex = "^0.9.0" +sphinxcontrib-katex = "^0.9.6" sphinx-markdown-tables = "^0.0.17" nbsphinx = "^0.9.1" ipython = "^8.12.0" From d1d45587185d91d601b14f9433cfc5bc8a7d8763 Mon Sep 17 00:00:00 2001 From: Adrian Mak Date: Wed, 6 Sep 2023 17:03:30 +0800 Subject: [PATCH 26/26] update poetry.lock --- poetry.lock | 1506 ++++++++++++++++++++++++++------------------------- 1 file changed, 768 insertions(+), 738 deletions(-) diff --git a/poetry.lock b/poetry.lock index deab191..2301976 100644 --- a/poetry.lock +++ b/poetry.lock @@ -43,17 +43,17 @@ wrapt = [ [[package]] name = "asttokens" -version = "2.2.1" +version = "2.4.0" description = "Annotate AST trees with source code positions" optional = false python-versions = "*" files = [ - {file = "asttokens-2.2.1-py2.py3-none-any.whl", 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