Deploying to gh-pages from @ 4fe528c 🚀

Author: albertomercurio

HierarchicalEOM.jl/SIAM.html

@@ -502,7 +502,7 @@ <h2 class="anchored" data-anchor-id="construct-heomls-matrix">Construct HEOMLS m
 <span id="cb6-3"><a href="#cb6-3"></a>M_odd <span class="op">=</span> <span class="fu">M_Fermion</span>(Hsys, tier, bath_list, ODD)</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
 <div class="cell-output cell-output-stdout">
 <pre><code>Preparing block matrices for HEOM Liouvillian superoperator (using 4 threads)...
-Progress: [                              ]   0.0% --- Elapsed Time: 0h 00m 01s (ETA: 0h 38m 44s)Progress: [==============================] 100.0% --- Elapsed Time: 0h 00m 01s (ETA: 0h 00m 00s)
+Progress: [==============================] 100.0% --- Elapsed Time: 0h 00m 00s (ETA: 0h 00m 00s)
 Constructing matrix...[DONE]
 Preparing block matrices for HEOM Liouvillian superoperator (using 4 threads)...
 Progress: [==============================] 100.0% --- Elapsed Time: 0h 00m 00s (ETA: 0h 00m 00s)
@@ -538,7 +538,7 @@ <h2 class="anchored" data-anchor-id="calculate-density-of-states-dos">Calculate
 <span id="cb12-2"><a href="#cb12-2"></a>dos <span class="op">=</span> <span class="fu">DensityOfStates</span>(M_odd, ados_s, d_up, ωlist)</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
 <div class="cell-output cell-output-stdout">
 <pre><code>Calculating density of states in frequency domain...
-Progress: [====                          ]  14.3% --- Elapsed Time: 0h 00m 01s (ETA: 0h 00m 06s)Progress: [=======                       ]  23.8% --- Elapsed Time: 0h 00m 02s (ETA: 0h 00m 06s)Progress: [==========                    ]  33.3% --- Elapsed Time: 0h 00m 03s (ETA: 0h 00m 06s)Progress: [============                  ]  42.9% --- Elapsed Time: 0h 00m 05s (ETA: 0h 00m 06s)Progress: [===============               ]  52.4% --- Elapsed Time: 0h 00m 06s (ETA: 0h 00m 05s)Progress: [==================            ]  61.9% --- Elapsed Time: 0h 00m 07s (ETA: 0h 00m 04s)Progress: [=====================         ]  71.4% --- Elapsed Time: 0h 00m 09s (ETA: 0h 00m 03s)Progress: [========================      ]  81.0% --- Elapsed Time: 0h 00m 10s (ETA: 0h 00m 02s)Progress: [===========================   ]  90.5% --- Elapsed Time: 0h 00m 11s (ETA: 0h 00m 01s)Progress: [==============================] 100.0% --- Elapsed Time: 0h 00m 12s (ETA: 0h 00m 00s)
+Progress: [====                          ]  14.3% --- Elapsed Time: 0h 00m 01s (ETA: 0h 00m 06s)Progress: [=======                       ]  23.8% --- Elapsed Time: 0h 00m 02s (ETA: 0h 00m 06s)Progress: [==========                    ]  33.3% --- Elapsed Time: 0h 00m 03s (ETA: 0h 00m 06s)Progress: [============                  ]  42.9% --- Elapsed Time: 0h 00m 04s (ETA: 0h 00m 05s)Progress: [===============               ]  52.4% --- Elapsed Time: 0h 00m 06s (ETA: 0h 00m 05s)Progress: [==================            ]  61.9% --- Elapsed Time: 0h 00m 07s (ETA: 0h 00m 04s)Progress: [=====================         ]  71.4% --- Elapsed Time: 0h 00m 08s (ETA: 0h 00m 03s)Progress: [=========================     ]  85.7% --- Elapsed Time: 0h 00m 10s (ETA: 0h 00m 01s)Progress: [==============================] 100.0% --- Elapsed Time: 0h 00m 11s (ETA: 0h 00m 00s)
 [DONE]</code></pre>
 </div>
 <div class="cell-output cell-output-display" data-execution_count="1">
@@ -607,12 +607,12 @@ <h2 class="anchored" data-anchor-id="version-information">Version Information</h
 
 Package information:
 ====================================
-Julia              Ver. 1.11.7
+Julia              Ver. 1.12.0
 HierarchicalEOM    Ver. 2.7.0
 QuantumToolbox     Ver. 0.36.0
-SciMLOperators     Ver. 1.7.2
+SciMLOperators     Ver. 1.9.0
 LinearSolve        Ver. 3.28.0
-OrdinaryDiffEqCore Ver. 1.34.0
+OrdinaryDiffEqCore Ver. 1.36.0
 
 System information:
 ====================================
@@ -621,7 +621,7 @@ <h2 class="anchored" data-anchor-id="version-information">Version Information</h
 Memory   : 15.621 GB
 WORD_SIZE: 64
 LIBM     : libopenlibm
-LLVM     : libLLVM-16.0.6 (ORCJIT, znver3)
+LLVM     : libLLVM-18.1.7 (ORCJIT, znver3)
 BLAS     : libopenblas64_.so (ilp64)
 Threads  : 4 (on 4 virtual cores)
 

HierarchicalEOM.jl/SIAM.ipynb

@@ -47,7 +47,7 @@
         "[`QuantumToolbox.jl`](https://github.com/qutip/QuantumToolbox.jl) to\n",
         "construct the operators."
       ],
-      "id": "1e991c7c-f062-4021-955a-38d67ceb9736"
+      "id": "0f6e8b03-8fed-47ce-87ce-e909f46054fe"
     },
     {
       "cell_type": "code",
@@ -116,7 +116,7 @@
         "-   the chemical potential $\\mu$\n",
         "-   the total number of exponentials for the reservoir $2(N + 1)$"
       ],
-      "id": "2d91d9f6-98d7-496d-97f0-33770e3a9413"
+      "id": "bde4fa37-f32c-4d06-9028-2c16d4aae908"
     },
     {
       "cell_type": "code",
@@ -154,7 +154,7 @@
       "source": [
         "## Construct HEOMLS matrix"
       ],
-      "id": "18c552c8-6a2e-4dd7-96df-acc1c303fb59"
+      "id": "121df3f3-50d4-49ea-bf49-658d120854f5"
     },
     {
       "cell_type": "code",
@@ -166,7 +166,7 @@
           "name": "stdout",
           "text": [
             "Preparing block matrices for HEOM Liouvillian superoperator (using 4 threads)...\n",
-            "Progress: [                              ]   0.0% --- Elapsed Time: 0h 00m 01s (ETA: 0h 38m 44s)Progress: [==============================] 100.0% --- Elapsed Time: 0h 00m 01s (ETA: 0h 00m 00s)\n",
+            "Progress: [==============================] 100.0% --- Elapsed Time: 0h 00m 00s (ETA: 0h 00m 00s)\n",
             "Constructing matrix...[DONE]\n",
             "Preparing block matrices for HEOM Liouvillian superoperator (using 4 threads)...\n",
             "Progress: [==============================] 100.0% --- Elapsed Time: 0h 00m 00s (ETA: 0h 00m 00s)\n",
@@ -200,7 +200,7 @@
       "source": [
         "## Solve stationary state of ADOs"
       ],
-      "id": "c8ca3830-3f28-4f84-8f7d-b3a8f71244a3"
+      "id": "22c6c211-b447-48d8-a719-6fda383e714a"
     },
     {
       "cell_type": "code",
@@ -237,7 +237,7 @@
       "source": [
         "## Calculate density of states (DOS)"
       ],
-      "id": "fbf27d76-6e10-4e34-80eb-6d8eeec39a8f"
+      "id": "14cc4211-01b1-46aa-8a8c-0647a2a0a3bd"
     },
     {
       "cell_type": "code",
@@ -249,7 +249,7 @@
           "name": "stdout",
           "text": [
             "Calculating density of states in frequency domain...\n",
-            "Progress: [====                          ]  14.3% --- Elapsed Time: 0h 00m 01s (ETA: 0h 00m 06s)Progress: [=======                       ]  23.8% --- Elapsed Time: 0h 00m 02s (ETA: 0h 00m 06s)Progress: [==========                    ]  33.3% --- Elapsed Time: 0h 00m 03s (ETA: 0h 00m 06s)Progress: [============                  ]  42.9% --- Elapsed Time: 0h 00m 05s (ETA: 0h 00m 06s)Progress: [===============               ]  52.4% --- Elapsed Time: 0h 00m 06s (ETA: 0h 00m 05s)Progress: [==================            ]  61.9% --- Elapsed Time: 0h 00m 07s (ETA: 0h 00m 04s)Progress: [=====================         ]  71.4% --- Elapsed Time: 0h 00m 09s (ETA: 0h 00m 03s)Progress: [========================      ]  81.0% --- Elapsed Time: 0h 00m 10s (ETA: 0h 00m 02s)Progress: [===========================   ]  90.5% --- Elapsed Time: 0h 00m 11s (ETA: 0h 00m 01s)Progress: [==============================] 100.0% --- Elapsed Time: 0h 00m 12s (ETA: 0h 00m 00s)\n",
+            "Progress: [====                          ]  14.3% --- Elapsed Time: 0h 00m 01s (ETA: 0h 00m 06s)Progress: [=======                       ]  23.8% --- Elapsed Time: 0h 00m 02s (ETA: 0h 00m 06s)Progress: [==========                    ]  33.3% --- Elapsed Time: 0h 00m 03s (ETA: 0h 00m 06s)Progress: [============                  ]  42.9% --- Elapsed Time: 0h 00m 04s (ETA: 0h 00m 05s)Progress: [===============               ]  52.4% --- Elapsed Time: 0h 00m 06s (ETA: 0h 00m 05s)Progress: [==================            ]  61.9% --- Elapsed Time: 0h 00m 07s (ETA: 0h 00m 04s)Progress: [=====================         ]  71.4% --- Elapsed Time: 0h 00m 08s (ETA: 0h 00m 03s)Progress: [=========================     ]  85.7% --- Elapsed Time: 0h 00m 10s (ETA: 0h 00m 01s)Progress: [==============================] 100.0% --- Elapsed Time: 0h 00m 11s (ETA: 0h 00m 00s)\n",
             "[DONE]"
           ]
         },
@@ -295,7 +295,7 @@
       "source": [
         "plot the results"
       ],
-      "id": "60bd3a00-c6bc-47d2-93ed-b57c5e148274"
+      "id": "5dcb5588-d636-4f5a-bc45-c0d6fc6615cc"
     },
     {
       "cell_type": "code",
@@ -325,7 +325,7 @@
       "source": [
         "## Version Information"
       ],
-      "id": "0fd52e5c-6ad3-4e9b-9d14-45555b206eef"
+      "id": "65638f0a-cb7b-4602-9b5e-cd58b7c5d070"
     },
     {
       "cell_type": "code",
@@ -347,7 +347,7 @@
         "Systems.” *Communications Physics* 6 (1): 313.\n",
         "<https://doi.org/10.1038/s42005-023-01427-2>."
       ],
-      "id": "4afe4645-58e7-4bd6-9995-9a6e364b0511"
+      "id": "6fcddff6-4815-413e-8ce0-0f132222e49d"
     }
   ],
   "nbformat": 4,
@@ -364,7 +364,7 @@
     "language_info": {
       "name": "julia",
       "codemirror_mode": "julia",
-      "version": "1.11.7"
+      "version": "1.12.0"
     }
   }
 }

HierarchicalEOM.jl/cavityQED.html

@@ -524,7 +524,7 @@ <h2 class="anchored" data-anchor-id="construct-heomls-matrix">Construct HEOMLS m
 <div class="cell-output cell-output-stdout">
 <pre><code>Checking the importance value for each ADOs...[DONE]
 Preparing block matrices for HEOM Liouvillian superoperator (using 4 threads)...
-Progress: [                              ]   1.0% --- Elapsed Time: 0h 00m 01s (ETA: 0h 01m 36s)Progress: [==============================] 100.0% --- Elapsed Time: 0h 00m 01s (ETA: 0h 00m 00s)
+Progress: [==============================] 100.0% --- Elapsed Time: 0h 00m 00s (ETA: 0h 00m 00s)
 Constructing matrix...[DONE]</code></pre>
 </div>
 <div class="cell-output cell-output-display" data-execution_count="1">
@@ -543,7 +543,7 @@ <h2 class="anchored" data-anchor-id="solve-time-evolution-of-ados">Solve time ev
 <span id="cb9-2"><a href="#cb9-2"></a>sol_H <span class="op">=</span> <span class="fu">HEOMsolve</span>(M_Heom, ψ<span class="fl">0</span>, t_list; e_ops <span class="op">=</span> [σz, a<span class="op">'</span> <span class="op">*</span> a])</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
 <div class="cell-output cell-output-stdout">
 <pre><code>Solving time evolution for ADOs by Ordinary Differential Equations method...
-Progress: [                              ]   0.2% --- Elapsed Time: 0h 00m 02s (ETA: 0h 16m 40s)Progress: [=======================       ]  78.8% --- Elapsed Time: 0h 00m 03s (ETA: 0h 00m 00s)Progress: [==============================] 100.0% --- Elapsed Time: 0h 00m 03s (ETA: 0h 00m 00s)</code></pre>
+Progress: [                              ]   0.2% --- Elapsed Time: 0h 00m 02s (ETA: 0h 16m 40s)Progress: [=====================         ]  70.7% --- Elapsed Time: 0h 00m 03s (ETA: 0h 00m 01s)Progress: [==============================] 100.0% --- Elapsed Time: 0h 00m 03s (ETA: 0h 00m 00s)</code></pre>
 </div>
 <div class="cell-output cell-output-display" data-execution_count="1">
 <pre><code>Solution of hierarchical EOM
@@ -626,7 +626,7 @@ <h2 class="anchored" data-anchor-id="power-spectrum">Power spectrum</h2>
 <span id="cb19-9"><a href="#cb19-9"></a>fig</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
 <div class="cell-output cell-output-stdout">
 <pre><code>Calculating power spectrum in frequency domain...
-Progress: [=                             ]   4.5% --- Elapsed Time: 0h 00m 01s (ETA: 0h 00m 21s)Progress: [==                            ]   9.0% --- Elapsed Time: 0h 00m 02s (ETA: 0h 00m 20s)Progress: [====                          ]  13.4% --- Elapsed Time: 0h 00m 03s (ETA: 0h 00m 19s)Progress: [=====                         ]  17.9% --- Elapsed Time: 0h 00m 04s (ETA: 0h 00m 18s)Progress: [======                        ]  22.4% --- Elapsed Time: 0h 00m 05s (ETA: 0h 00m 17s)Progress: [=======                       ]  26.4% --- Elapsed Time: 0h 00m 06s (ETA: 0h 00m 16s)Progress: [=========                     ]  30.3% --- Elapsed Time: 0h 00m 07s (ETA: 0h 00m 16s)Progress: [==========                    ]  33.8% --- Elapsed Time: 0h 00m 08s (ETA: 0h 00m 15s)Progress: [===========                   ]  36.8% --- Elapsed Time: 0h 00m 09s (ETA: 0h 00m 15s)Progress: [===========                   ]  39.3% --- Elapsed Time: 0h 00m 10s (ETA: 0h 00m 15s)Progress: [============                  ]  41.3% --- Elapsed Time: 0h 00m 11s (ETA: 0h 00m 15s)Progress: [=============                 ]  43.8% --- Elapsed Time: 0h 00m 13s (ETA: 0h 00m 16s)Progress: [=============                 ]  45.8% --- Elapsed Time: 0h 00m 14s (ETA: 0h 00m 16s)Progress: [==============                ]  47.8% --- Elapsed Time: 0h 00m 15s (ETA: 0h 00m 16s)Progress: [==============                ]  49.8% --- Elapsed Time: 0h 00m 16s (ETA: 0h 00m 16s)Progress: [===============               ]  52.2% --- Elapsed Time: 0h 00m 17s (ETA: 0h 00m 15s)Progress: [================              ]  54.7% --- Elapsed Time: 0h 00m 18s (ETA: 0h 00m 14s)Progress: [=================             ]  57.2% --- Elapsed Time: 0h 00m 19s (ETA: 0h 00m 14s)Progress: [=================             ]  59.7% --- Elapsed Time: 0h 00m 20s (ETA: 0h 00m 13s)Progress: [==================            ]  62.7% --- Elapsed Time: 0h 00m 21s (ETA: 0h 00m 12s)Progress: [===================           ]  65.7% --- Elapsed Time: 0h 00m 22s (ETA: 0h 00m 11s)Progress: [====================          ]  69.7% --- Elapsed Time: 0h 00m 24s (ETA: 0h 00m 10s)Progress: [======================        ]  74.1% --- Elapsed Time: 0h 00m 25s (ETA: 0h 00m 08s)Progress: [=======================       ]  79.6% --- Elapsed Time: 0h 00m 26s (ETA: 0h 00m 06s)Progress: [=========================     ]  85.6% --- Elapsed Time: 0h 00m 27s (ETA: 0h 00m 04s)Progress: [===========================   ]  92.0% --- Elapsed Time: 0h 00m 28s (ETA: 0h 00m 02s)Progress: [============================= ]  99.0% --- Elapsed Time: 0h 00m 29s (ETA: 0h 00m 00s)Progress: [==============================] 100.0% --- Elapsed Time: 0h 00m 29s (ETA: 0h 00m 00s)
+Progress: [=                             ]   3.5% --- Elapsed Time: 0h 00m 01s (ETA: 0h 00m 27s)Progress: [==                            ]   8.0% --- Elapsed Time: 0h 00m 02s (ETA: 0h 00m 23s)Progress: [===                           ]  12.4% --- Elapsed Time: 0h 00m 03s (ETA: 0h 00m 21s)Progress: [=====                         ]  16.9% --- Elapsed Time: 0h 00m 04s (ETA: 0h 00m 19s)Progress: [======                        ]  21.4% --- Elapsed Time: 0h 00m 05s (ETA: 0h 00m 18s)Progress: [=======                       ]  25.4% --- Elapsed Time: 0h 00m 06s (ETA: 0h 00m 17s)Progress: [========                      ]  29.4% --- Elapsed Time: 0h 00m 07s (ETA: 0h 00m 16s)Progress: [=========                     ]  32.8% --- Elapsed Time: 0h 00m 08s (ETA: 0h 00m 16s)Progress: [==========                    ]  35.8% --- Elapsed Time: 0h 00m 09s (ETA: 0h 00m 16s)Progress: [===========                   ]  38.3% --- Elapsed Time: 0h 00m 10s (ETA: 0h 00m 16s)Progress: [============                  ]  40.8% --- Elapsed Time: 0h 00m 11s (ETA: 0h 00m 15s)Progress: [============                  ]  43.3% --- Elapsed Time: 0h 00m 12s (ETA: 0h 00m 15s)Progress: [=============                 ]  45.3% --- Elapsed Time: 0h 00m 13s (ETA: 0h 00m 15s)Progress: [==============                ]  47.3% --- Elapsed Time: 0h 00m 15s (ETA: 0h 00m 16s)Progress: [==============                ]  49.3% --- Elapsed Time: 0h 00m 16s (ETA: 0h 00m 16s)Progress: [===============               ]  51.2% --- Elapsed Time: 0h 00m 17s (ETA: 0h 00m 16s)Progress: [===============               ]  53.2% --- Elapsed Time: 0h 00m 18s (ETA: 0h 00m 15s)Progress: [================              ]  55.2% --- Elapsed Time: 0h 00m 19s (ETA: 0h 00m 15s)Progress: [=================             ]  57.7% --- Elapsed Time: 0h 00m 20s (ETA: 0h 00m 14s)Progress: [==================            ]  60.2% --- Elapsed Time: 0h 00m 21s (ETA: 0h 00m 13s)Progress: [==================            ]  63.2% --- Elapsed Time: 0h 00m 22s (ETA: 0h 00m 12s)Progress: [====================          ]  66.7% --- Elapsed Time: 0h 00m 23s (ETA: 0h 00m 11s)Progress: [=====================         ]  70.6% --- Elapsed Time: 0h 00m 24s (ETA: 0h 00m 09s)Progress: [======================        ]  75.1% --- Elapsed Time: 0h 00m 25s (ETA: 0h 00m 08s)Progress: [========================      ]  80.6% --- Elapsed Time: 0h 00m 26s (ETA: 0h 00m 06s)Progress: [=========================     ]  86.6% --- Elapsed Time: 0h 00m 27s (ETA: 0h 00m 04s)Progress: [===========================   ]  93.0% --- Elapsed Time: 0h 00m 28s (ETA: 0h 00m 02s)Progress: [==============================] 100.0% --- Elapsed Time: 0h 00m 30s (ETA: 0h 00m 00s)
 [DONE]</code></pre>
 </div>
 <div class="cell-output cell-output-display" data-execution_count="1">
@@ -757,12 +757,12 @@ <h2 class="anchored" data-anchor-id="version-information">Version Information</h
 
 Package information:
 ====================================
-Julia              Ver. 1.11.7
+Julia              Ver. 1.12.0
 HierarchicalEOM    Ver. 2.7.0
 QuantumToolbox     Ver. 0.36.0
-SciMLOperators     Ver. 1.7.2
+SciMLOperators     Ver. 1.9.0
 LinearSolve        Ver. 3.28.0
-OrdinaryDiffEqCore Ver. 1.34.0
+OrdinaryDiffEqCore Ver. 1.36.0
 
 System information:
 ====================================
@@ -771,7 +771,7 @@ <h2 class="anchored" data-anchor-id="version-information">Version Information</h
 Memory   : 15.621 GB
 WORD_SIZE: 64
 LIBM     : libopenlibm
-LLVM     : libLLVM-16.0.6 (ORCJIT, znver3)
+LLVM     : libLLVM-18.1.7 (ORCJIT, znver3)
 BLAS     : libopenblas64_.so (ilp64)
 Threads  : 4 (on 4 virtual cores)