Merge branch 'qutip:main' into fitting-heom

Author: gsuarezr

.github/workflows/nightly_ci.yaml

@@ -65,6 +65,7 @@ jobs:
         cd ..
         python -m pip install git+https://github.com/qutip/qutip-qip
         python -m pip install --no-deps git+https://github.com/qutip/qutip-jax
+        python -m pip install --no-deps git+https://github.com/qutip/qutip-qoc
 
         git clone -b master https://github.com/qutip/qutip-qtrl.git
         cd qutip-qtrl
@@ -95,7 +96,7 @@ jobs:
       run: |
         jupyter kernel &
         cd notebooks
-        find . -name '*.ipynb' -exec pytest --nbmake --overwrite --nbmake-timeout=600 {} +
+        find . -name '*.ipynb' -exec pytest --nbmake --overwrite --nbmake-timeout=900 {} +
         rm template.ipynb
 
     - name: Create Notebook Artifact

.github/workflows/notebook_ci.yaml

@@ -29,7 +29,7 @@ jobs:
         folder-path: tutorials-v${{ matrix.qutip-version }}
         #use config file to define 403 and 405 errors as valid links
         #(APS blocks this link check)
-        config-file: mlc_config.json
+        config-file: mlc_external_config.json
 
     - name: Setup Conda
       uses: conda-incubator/setup-miniconda@v3
@@ -59,14 +59,15 @@ jobs:
     - name: Install QuTiP
       run: |
         pip install --upgrade pip
-        python -m pip install jax jax[cpu] equinox diffrax
+        python -m pip install "jax<0.7.0" "jax[cpu]<0.7.0" equinox diffrax
         git clone -b ${{ matrix.qutip-branch }} https://github.com/qutip/qutip.git
         cd qutip
         pip install -r requirements.txt
         pip install .
         cd ..
         python -m pip install git+https://github.com/qutip/qutip-qip
         python -m pip install --no-deps git+https://github.com/qutip/qutip-jax
+        python -m pip install --no-deps git+https://github.com/qutip/qutip-qoc
 
         git clone -b master https://github.com/qutip/qutip-qtrl.git
         cd qutip-qtrl
@@ -97,7 +98,7 @@ jobs:
       run: |
         jupyter kernel &
         cd notebooks
-        find . -name '*.ipynb' -exec pytest --nbmake --overwrite --nbmake-timeout=600 {} +
+        find . -name '*.ipynb' -exec pytest --nbmake --overwrite --nbmake-timeout=900 {} +
         rm template.ipynb
 
     - name: Create Notebook Artifact
@@ -107,6 +108,15 @@ jobs:
         path: |
           notebooks/*.ipynb
           notebooks/**/*.ipynb
+   
+    - uses: gaurav-nelson/github-action-markdown-link-check@v1
+      with:
+        use-quiet-mode: 'yes'
+        folder-path: tutorials-v${{ matrix.qutip-version }}
+        #use config file to define 403 and 405 errors as valid links
+        #(APS blocks this link check)
+        config-file: mlc_config.json
+
   publish:
     needs: pytests
     runs-on: ubuntu-latest
@@ -133,20 +143,21 @@ jobs:
           # Download resources from qutip.github.io repository
           mkdir css
           cd css
-          wget https://raw.githubusercontent.com/qutip/qutip.github.io/master/css/bootstrap.css
           wget https://raw.githubusercontent.com/qutip/qutip.github.io/master/css/site.css
           cd ..
 
           mkdir _includes
           cd _includes
-          wget https://raw.githubusercontent.com/qutip/qutip.github.io/master/_includes/footer.html
-          wget https://raw.githubusercontent.com/qutip/qutip.github.io/master/_includes/header.html
+          wget https://raw.githubusercontent.com/qutip/qutip.github.io/master/_includes/head.html
           wget https://raw.githubusercontent.com/qutip/qutip.github.io/master/_includes/navbar.html
+          wget https://raw.githubusercontent.com/qutip/qutip.github.io/master/_includes/footer.html
+          wget https://raw.githubusercontent.com/qutip/qutip.github.io/master/_includes/scripts.html
           cd ..
 
           mkdir images
           cd images
           wget https://raw.githubusercontent.com/qutip/qutip.github.io/master/images/favicon.ico
+          wget https://raw.githubusercontent.com/langhaarzombie/langhaarzombie.github.io/develop/images/logo_small.png
           cd ..
 
           # build the website

mlc_external_config.json

@@ -0,0 +1,14 @@
+{
+    "projectBaseUrl":"${workspaceFolder}",
+    "timeout": "20s",
+    "retryOn429": true,
+    "retryCount": 5,
+    "fallbackRetryDelay": "30s",
+    "aliveStatusCodes": [200, 206, 403, 405],
+    "ignorePatterns": [
+    {
+      "pattern": "^(/|\\.\\/|\\.\\./)"  
+    }
+    ]
+}
+  

tutorials-v5/heom/heom-2-fmo-example.md

@@ -66,9 +66,6 @@ def timer(label):
 options = {
     "nsteps": 15000,
     "store_states": True,
-    "rtol": 1e-12,
-    "atol": 1e-12,
-    "min_step": 1e-18,
     "method": "vern9",
     "progress_bar": "enhanced",
 }
@@ -83,9 +80,9 @@ And let us set up the system Hamiltonian and bath parameters:
 #
 # We use the Hamiltonian employed in
 # https://www.pnas.org/content/106/41/17255 and operate
-# in units of Hz:
+# in units of GHz:
 
-Hsys = 3e10 * 2 * np.pi * Qobj([
+Hsys = 30 * 2 * np.pi * Qobj([
     [200, -87.7, 5.5, -5.9, 6.7, -13.7, -9.9],
     [-87.7, 320, 30.8, 8.2, 0.7, 11.8, 4.3],
     [5.5, 30.8, 0, -53.5, -2.2, -9.6, 6.0],
@@ -99,9 +96,9 @@ Hsys = 3e10 * 2 * np.pi * Qobj([
 ```{code-cell} ipython3
 # Bath parameters
 
-lam = 35 * 3e10 * 2 * np.pi
-gamma = 1 / 166e-15
-T = 300 * 0.6949 * 3e10 * 2 * np.pi
+lam = 35 * 30 * 2 * np.pi
+gamma = 1 / 166e-6
+T = 300 * 0.6949 * 30 * 2 * np.pi
 beta = 1 / T
 ```
 
@@ -114,18 +111,18 @@ env = DrudeLorentzEnvironment(T=T, lam=lam, gamma=gamma)
 ```
 
 ```{code-cell} ipython3
-wlist = np.linspace(0, 200 * 3e10 * 2 * np.pi, 100)
-tlist = np.linspace(0, 1e-12, 1000)
+wlist = np.linspace(0, 200 * 30 * 2 * np.pi, 100)
+tlist = np.linspace(0, 1e-3, 1000)
 
-J = env.spectral_density(wlist) / (3e10 * 2 * np.pi)
+J = env.spectral_density(wlist) / (30 * 2 * np.pi)
 
 fig, axes = plt.subplots(1, 2, sharex=False, figsize=(10, 3))
 
 fig.subplots_adjust(hspace=0.1)  # reduce space between plots
 
 # Spectral density plot:
 
-axes[0].plot(wlist / (3e10 * 2 * np.pi), J, color='r', ls='--', label="J(w)")
+axes[0].plot(wlist / (30 * 2 * np.pi), J, color='r', ls='--', label="J(w)")
 axes[0].set_xlabel(r'$\omega$ (cm$^{-1}$)', fontsize=20)
 axes[0].set_ylabel(r"$J(\omega)$ (cm$^{-1}$)", fontsize=16)
 axes[0].legend()
@@ -193,7 +190,7 @@ linestyles = [
 for m in range(7):
     Q = basis(7, m) * basis(7, m).dag()
     axes.plot(
-        np.array(tlist) * 1e15,
+        np.array(tlist) * 1e6,
         np.real(expect(outputFMO_HEOM.states, Q)),
         label=m + 1,
         color=colors[m % len(colors)],
@@ -232,7 +229,7 @@ And now let's plot the Bloch-Redfield solver results:
 fig, axes = plt.subplots(1, 1, figsize=(12, 8))
 
 for m, Q in enumerate(Q_list):
-    axes.plot(tlist * 1e15, expect(outputFMO_BR.states, Q), label=m + 1)
+    axes.plot(tlist * 1e6, expect(outputFMO_BR.states, Q), label=m + 1)
 
 axes.set_xlabel(r'$t$ (fs)', fontsize=30)
 axes.set_ylabel(r"Population", fontsize=30)
@@ -334,7 +331,7 @@ with timer("ME ODE solver"):
 fig, axes = plt.subplots(1, 1, figsize=(12, 8))
 
 for m, Q in enumerate(Q_list):
-    axes.plot(tlist * 1e15, expect(outputFMO_ME.states, Q), label=m + 1)
+    axes.plot(tlist * 1e6, expect(outputFMO_ME.states, Q), label=m + 1)
 
 axes.set_xlabel(r'$t$', fontsize=20)
 axes.set_ylabel(r"Population", fontsize=16)
@@ -363,7 +360,7 @@ with timer("ME ODE solver"):
 fig, axes = plt.subplots(1, 1, figsize=(12, 8))
 for m, Q in enumerate(Q_list):
     axes.plot(
-        tlist * 1e15,
+        tlist * 1e6,
         expect(outputFMO_ME_nodephase.states, Q),
         label=m + 1,
     )