Merge branch 'main' of https://github.com/flowerthrower/qutip-qoc

.github/workflows/build_documentation.yml

@@ -36,9 +36,8 @@ jobs:
       - name: Build documentation
         working-directory: doc
         run: |
-          make html SPHINXOPTS="-W --keep-going -T"
+          make html SPHINXOPTS="--keep-going -T"
           # Above flags are:
-          #   -W : turn warnings into errors
           #   --keep-going : do not stop after the first error
           #   -T : display a full traceback if a Python exception occurs
 

.github/workflows/test.yml

@@ -21,6 +21,30 @@ jobs:
             os: windows-latest
             qutip-version: "@master"
             python-version: "3.10"
+          - case-name: ubuntu-python3.11
+            os: ubuntu-latest
+            qutip-version: "@master"
+            python-version: "3.11"
+          - case-name: macOs-python3.11
+            os: macOS-latest
+            qutip-version: "@master"
+            python-version: "3.11"
+          - case-name: windows-python3.11
+            os: windows-latest
+            qutip-version: "@master"
+            python-version: "3.11"
+          - case-name: ubuntu-python3.12
+            os: ubuntu-latest
+            qutip-version: "@master"
+            python-version: "3.12"
+          - case-name: macOs-python3.12
+            os: macOS-latest
+            qutip-version: "@master"
+            python-version: "3.12"
+          - case-name: windows-python3.12
+            os: windows-latest
+            qutip-version: "@master"
+            python-version: "3.12"
 
     steps:
       - uses: actions/checkout@v3
@@ -39,19 +63,25 @@ jobs:
         run: |
           python -m pip install 'git+https://github.com/qutip/qutip-qtrl.git'
 
-      - name: Install qutip-jax from GitHub
+      - name: Install jax
+        run: |
+          python -m pip install jax jaxlib
+
+      - name: Install qutip-jax
         if: ${{ matrix.qutip-version == '@master'}}
         run: |
-          python -m pip install 'git+https://github.com/qutip/qutip-jax.git'
+          python -m pip install qutip-jax
 
       - name: Install qutip-qoc
         # Installing in-place so that coveralls can locate the source code.
         run: |
           pip install -e .[full]
+
       - name: Test with pytest and generate coverage report
         run: |
           pip install pytest-cov coveralls
           pytest tests --strict-markers --cov=qutip_qoc --cov-report= --color=yes
+
       - name: Upload to Coveralls
         env:
           GITHUB_TOKEN: ${{ secrets.github_token }}

.pre-commit-config.yaml

@@ -63,10 +63,10 @@ repos:
       - id: ruff
         args: ["--fix", "--show-fixes"]
         types_or: [python, pyi, jupyter]
-        exclude: "^src/qutip_qoc/[^/]*\\.ipynb$|^src/qutip_qoc/paper\\.py$"
+        exclude: "^src/qutip_qoc/[^/]*\\.ipynb"
       - id: ruff-format
         types_or: [python, pyi, jupyter]
-        exclude: "^src/qutip_qoc/[^/]*\\.ipynb$|^src/qutip_qoc/paper\\.py$"
+        exclude: "^src/qutip_qoc/[^/]*\\.ipynb"
 
   # Also run Black on examples in the documentation
   - repo: https://github.com/adamchainz/blacken-docs
@@ -80,14 +80,15 @@ repos:
     hooks:
       - id: mypy
         files: ^(src|tests)
-        exclude: "^src/qutip_qoc/[^/]*\\.ipynb$|^src/qutip_qoc/paper\\.py$"
+        exclude: "^src/qutip_qoc/[^/]*\\.ipynb"
         args: []
         additional_dependencies:
           - qutip
           - qutip-qip
           - qutip-qtrl
           - numpy
           - scipy
+          - jax
           - jaxlib
           - diffrax
           - pytest

README.md

@@ -16,7 +16,7 @@ As with qutip-qtrl, the qutip-qoc package aims at providing advanced tools for t
 Compared to other libraries for quantum optimal control, qutip-qoc puts additional emphasis on the physics layer and the interaction with the QuTiP package.
 Along with the extended GOAT and JOPT algorithms the package offers support for both the CRAB and GRAPE methods defined in `qutip-qtrl`.
 
-If you would like to know the future development plan and ideas, have a look at the [qutip documentation for ideas](https://qutip.org/docs/latest/development/ideas.html).
+If you would like to know the future development plan and ideas, have a look at the [qutip roadmap and ideas](https://qutip.readthedocs.io/en/latest/development/roadmap.html).
 
 ## Quick start
 

VERSION

@@ -1 +1 @@
-0.0.0.dev1
+0.0.1

doc/Makefile

@@ -18,3 +18,9 @@ help:
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
 	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+html:
+	sphinx-apidoc -f -e -P -o ./apidoc/ ../src/qutip_qoc/
+	@$(SPHINXBUILD) -M html "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."

doc/apidoc.rst

@@ -37,10 +37,8 @@ Internal interfaces to the optimal control features.
    :toctree: apidoc/
    :template: autosummary/module.rst
 
-   qutip_qtrl.pulseoptim
-
-   qutip_qoc.optimizer
-   qutip_qoc.goat
-   qutip_qoc.jopt
-   qutip_qoc.grape
-   qutip_qoc.crab
+   qutip_qoc._optimizer
+   qutip_qoc._goat
+   qutip_qoc._jopt
+   qutip_qoc._grape
+   qutip_qoc._crab

doc/changelog.rst

@@ -3,6 +3,12 @@ Changelog
 *********
 
 
+Version 0.1.0 (April xx, 2024)
++++++++++++++++++++++++++++++++++
+
+TODO: Add release notes
+
+
 Version 0.0.0 (December 26, 2023)
 +++++++++++++++++++++++++++++++++
 

doc/conf.py

@@ -75,7 +75,7 @@ def qutip_qoc_version():
 # apidoc folder. This is particularly useful for modules with lots of
 # functions/classes. However, pay attention that some api docs files are
 # adjusted manually for better illustration and should not be overwritten.
-autosummary_generate = True
+autosummary_generate = ["apidoc/*.rst"]
 autosummary_imported_members = True
 
 # -- Options for biblatex ---------------------------------------
@@ -86,5 +86,5 @@ def qutip_qoc_version():
 # -- Options for intersphinx ---------------------------------------
 
 intersphinx_mapping = {
-    "qutip": ("https://qutip.org/docs/latest/", None),
+    "qutip": ("https://qutip.readthedocs.io/en/latest/", None),
 }

doc/guide/guide-control.rst

@@ -58,8 +58,10 @@ We can use optimal control algorithms to determine a set of :math:`u_j` that wil
 
 The GOAT Algorithm
 ===================
-To be described in detail.
-
+The GOAT method, like CRAB, operates with analytical control functions :cite:`GOAT`.
+It constructs a system of coupled equations of motion, enabling the calculation of the derivative of the evolution operator (time-ordered) with respect to the control parameters, following numerical forward integration.
+This implementation supports arbitrary control functions along with their corresponding derivatives.
+To further accelerate convergence, our implementation enhances the original algorithm by providing the option to optimize controls with respect to the overall pulse duration.
 
 The GRAPE algorithm
 ===================
@@ -86,7 +88,7 @@ If the objective is state-to-state transfer then :math:`X_0=\ket{\psi_0}` and th
 A *figure of merit* or *fidelity* is some measure of how close the evolution is to the target, based on the  control amplitudes in the timeslots. The typical figure of merit for unitary systems is the normalised overlap of the evolution and the target.
 
 .. math::
-
+    \DeclareMathOperator{\tr}{tr}
     f_{PSU} = \tfrac{1}{d} \big| \tr \{X_{targ}^{\dagger} X(T)\} \big|
 
 where :math:`d` is the system dimension. In this figure of merit the absolute value is taken to ignore any differences in global phase, and :math:`0 \le f \le 1`. Typically the fidelity error (or *infidelity*) is more useful, in this case defined as :math:`\varepsilon = 1 - f_{PSU}`.  There are many other possible objectives, and hence figures of merit.
@@ -252,9 +254,6 @@ It requires some extra arguments to prepare the optimization.
   # boundaries for the parameters
   p_bounds = q_bounds = [(-1, 1), (-1, 1)]
 
-  # time interval for the evolution
-  t_interval = qoc.TimeInterval(evo_time=1.)
-
 
 Eventually, the optimization for a desired `fid_err_targ` can be started by calling the ``optimize`` function.
 
@@ -266,7 +265,7 @@ Eventually, the optimization for a desired `fid_err_targ` can be started by call
         "p": {"guess": p_guess, "bounds": p_bounds},
         "q": {"guess": q_guess, "bounds": q_bounds}
     },
-    time_interval=t_interval,
+    tlist=np.linspace(0, 1, 100),
     algorithm_kwargs={
         "alg": "GOAT",
         "fid_err_targ": 0.1,

doc/installation.rst

@@ -23,7 +23,7 @@ In particular, following packages are necessary for running qutip-qoc:
 
 .. code-block:: bash
 
-    numpy scipy cython qutip qutip-jax qutip-qtrl
+    numpy scipy jax jaxlib cython qutip qutip-jax qutip-qtrl
 
 The following to packages are used for plotting and testing:
 

doc/requirements.txt

@@ -1,5 +1,7 @@
 numpy>=1.16.6
 scipy>=1.10.1
+jax>=0.4.23
+jaxlib>=0.4.23
 qutip==4.7.0
 cython==0.29.33
 sphinx==6.1.3

doc/rtd-environment.yml

@@ -4,6 +4,8 @@ channels:
 dependencies:
   - numpy>=1.16.6
   - scipy>=1.10.1
+  - jax>=0.4.23
+  - jaxlib>=0.4.23
   - cython==0.29.33
   - sphinx==6.1.3
   - sphinx_rtd_theme==1.2.0
@@ -15,5 +17,5 @@ dependencies:
   - wheel==0.38.4
   - pip
   - pip:
-      - qutip==5.0.0a1
+      - qutip==5.0.1
       - ..[full]

requirements.txt

@@ -1,7 +1,9 @@
 cython>=1.0
 numpy>=1.16.6
 scipy>=1.10.1
-qutip @ git+https://github.com/qutip/qutip.git@master
+jax>=0.4.23
+jaxlib>=0.4.23
+qutip>=5.0.1
 qutip-qtrl @ git+https://github.com/flowerthrower/qutip-qtrl@patrick/parameterize_crab
-qutip-jax @ git+https://github.com/qutip/qutip-jax.git@master
+qutip-jax
 pre-commit

setup.cfg

@@ -18,7 +18,7 @@ classifiers =
     Operating System :: POSIX
     Operating System :: Unix
     Operating System :: Microsoft :: Windows
-author = Alexander Pitchford, Paul D. Nation, Robert J. Johansson, Chris Granade, Arne Grimsmo, Nathan Shammah, Shahnawaz Ahmed, Neill Lambert, Eric Giguere, Boxi Li, Jake Lishman
+author = Patrick Hopf, Paul Menczel, Alexander Pitchford, Neil Lambert
 author_email = [email protected]
 platforms = Linux, Mac OSX, Unix, Windows
 
@@ -28,10 +28,12 @@ package_dir=
 packages = find:
 include_package_data = True
 install_requires =
-    qutip @ git+https://github.com/qutip/qutip.git@master
-    qutip-qtrl @ git+https://github.com/qutip/qutip-qtrl.git@master
-    qutip-jax @ git+https://github.com/qutip/qutip-jax.git@master
+    jax
+    jaxlib
     packaging
+    qutip
+    qutip-qtrl @ git+https://github.com/flowerthrower/qutip-qtrl@patrick/parameterize_crab
+    qutip-jax
 setup_requires =
     cython>=1.0
     packaging

src/qutip_qoc/_crab.py

@@ -0,0 +1,65 @@
+"""
+This module provides an interface to the CRAB optimization algorithm in qutip-qtrl.
+It defines the _CRAB class, which uses a qutip_qtrl.optimizer.Optimizer object
+to store the control problem and calculate the fidelity error function and its gradient
+with respect to the control parameters, according to the CRAB algorithm.
+"""
+
+import qutip_qtrl.logging_utils as logging
+import copy
+
+logger = logging.get_logger()
+
+
+class _CRAB:
+    """
+    Class to interface with the CRAB optimization algorithm in qutip-qtrl.
+    It has an attribute `qtrl` that is a `qutip_qtrl.optimizer.Optimizer` object
+    for storing the control problem and calculating the fidelity error function
+    and its gradient wrt the control parameters, according to the CRAB algorithm.
+    The class does only provide the infidelity method, as the CRAB algorithm is
+    not a gradient-based optimization.
+    """
+
+    def __init__(self, qtrl_optimizer):
+        self._qtrl = copy.deepcopy(qtrl_optimizer)
+        self.gradient = None
+
+    def infidelity(self, *args):
+        """
+        This method is adapted from the original
+        `qutip_qtrl.optimizer.Optimizer.fid_err_func_wrapper`
+
+        Get the fidelity error achieved using the ctrl amplitudes passed
+        in as the first argument.
+
+        This is called by generic optimisation algorithm as the
+        func to the minimised. The argument is the current
+        variable values, i.e. control amplitudes, passed as
+        a flat array. Hence these are reshaped as [nTimeslots, n_ctrls]
+        and then used to update the stored ctrl values (if they have changed)
+        """
+        self._qtrl.num_fid_func_calls += 1
+        # *** update stats ***
+        if self._qtrl.stats is not None:
+            self._qtrl.stats.num_fidelity_func_calls = self._qtrl.num_fid_func_calls
+            if self._qtrl.log_level <= logging.DEBUG:
+                logger.debug(
+                    "fidelity error call {}".format(
+                        self._qtrl.stats.num_fidelity_func_calls
+                    )
+                )
+
+        amps = self._qtrl._get_ctrl_amps(args[0].copy())
+        self._qtrl.dynamics.update_ctrl_amps(amps)
+
+        err = self._qtrl.dynamics.fid_computer.get_fid_err()
+
+        if self._qtrl.iter_summary:
+            self._qtrl.iter_summary.fid_func_call_num = self._qtrl.num_fid_func_calls
+            self._qtrl.iter_summary.fid_err = err
+
+        if self._qtrl.dump and self._qtrl.dump.dump_fid_err:
+            self._qtrl.dump.update_fid_err_log(err)
+
+        return err