You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
" SpinEvolution is fast, powerful software for NMR dynamics simulations. It is also behind a significant paywall, where dynamics simulations require a $1650 annual subscription. We think SLEEPY has a wider range of dynamics capabilities, but we weren't interested in paying the annual fee to make sure.....\n",
" Gamma is a very flexible C++ based package that allows a broad range of dynamics simulations. While not widely used, it is still applied by a few of the expert groups in dynamics. Not for the faint of heart, but if you like coding in C++, go for it.\n",
78
83
" \n",
79
84
"\n",
80
85
"There's a lot else out there: these are three of the most well-known. For getting familiar with dynamic effects, however, we think SLEEPY is a great place to start."
Copy file name to clipboardExpand all lines: JupyterBook/Ampere2026/SLEEPY_colab.ipynb
+4Lines changed: 4 additions & 0 deletions
Original file line number
Diff line number
Diff line change
@@ -62,7 +62,11 @@
62
62
"\n",
63
63
" SpinEvolution is fast, powerful software for NMR dynamics simulations. It is also behind a significant paywall, where dynamics simulations require a $1650 annual subscription. We think SLEEPY has a wider range of dynamics capabilities, but we weren't interested in paying the annual fee to make sure.....\n",
" Gamma is a very flexible C++ based package that allows a broad range of dynamics simulations. While not widely used, it is still applied by a few of the expert groups in dynamics. Not for the faint of heart, but if you like coding in C++, go for it.\n",
68
+
"\n",
69
+
"\n",
66
70
"There's a lot else out there: these are three of the most well-known. For getting familiar with dynamic effects, however, we think SLEEPY is a great place to start."
<p>SpinEvolution is fast, powerful software for NMR dynamics simulations. It is also behind a significant paywall, where dynamics simulations require a $1650 annual subscription. We think SLEEPY has a wider range of dynamics capabilities, but we weren’t interested in paying the annual fee to make sure…..</p>
<p>Gamma is a very flexible C++ based package that allows a broad range of dynamics simulations. While not widely used, it is still applied by a few of the expert groups in dynamics. Not for the faint of heart, but if you like coding in C++, go for it.</p>
489
+
</li>
487
490
</ul>
488
491
<p>There’s a lot else out there: these are three of the most well-known. For getting familiar with dynamic effects, however, we think SLEEPY is a great place to start.</p>
<p>SpinEvolution is fast, powerful software for NMR dynamics simulations. It is also behind a significant paywall, where dynamics simulations require a $1650 annual subscription. We think SLEEPY has a wider range of dynamics capabilities, but we weren’t interested in paying the annual fee to make sure…..</p>
<p>Gamma is a very flexible C++ based package that allows a broad range of dynamics simulations. While not widely used, it is still applied by a few of the expert groups in dynamics. Not for the faint of heart, but if you like coding in C++, go for it.</p>
488
+
</li>
486
489
</ul>
487
490
<p>There’s a lot else out there: these are three of the most well-known. For getting familiar with dynamic effects, however, we think SLEEPY is a great place to start.</p>
488
491
</section>
@@ -563,15 +566,15 @@ <h3>Define the experimental conditions<a class="headerlink" href="#define-the-ex
563
566
<divclass="cell docutils container">
564
567
<divclass="cell_input docutils container">
565
568
<divclass="highlight-ipython3 notranslate"><divclass="highlight"><pre><span></span><spanclass="c1"># Define an experimental system at 500 MHz field, with just a single proton</span>
566
-
<spanclass="n">ex</span><spanclass="o">=</span><spanclass="c1">#Use a 500 MHz magnetic field, include a single 1H, Nucs=['1H']</span>
567
-
<spanclass="c1"># Add a chemical shift with ex.set_inter, set to 500 Hz</span>
569
+
<spanclass="n">ex</span><spanclass="o">=</span><spanclass="c1">#Use a 500 MHz magnetic field, v0H=500, include a single 1H, Nucs=['1H']</span>
568
570
</pre></div>
569
571
</div>
570
572
</div>
571
573
</div>
572
574
<divclass="cell docutils container">
573
575
<divclass="cell_input docutils container">
574
-
<divclass="highlight-ipython3 notranslate"><divclass="highlight"><pre><span></span><spanclass="n">ex</span><spanclass="o">.</span><spanclass="n">set</span><spanclass="c1">#Interaction type, spin index (use i for spin-field interaction, i0,i1 for spin-spin coupling)</span>
576
+
<divclass="highlight-ipython3 notranslate"><divclass="highlight"><pre><span></span><spanclass="c1"># Add a chemical shift with ex.set_inter, set to 500 Hz</span>
577
+
<spanclass="n">ex</span><spanclass="o">.</span><spanclass="n">set</span><spanclass="c1">#Interaction type, spin index (use i for spin-field interaction, i0,i1 for spin-spin coupling)</span>
575
578
<spanclass="c1">#Use Hz= to define in Hz, ppm= to define in ppm</span>
576
579
</pre></div>
577
580
</div>
@@ -599,15 +602,16 @@ <h3>Define the experimental conditions<a class="headerlink" href="#define-the-ex
599
602
<divclass="cell docutils container">
600
603
<divclass="cell_input docutils container">
601
604
<divclass="highlight-ipython3 notranslate"><divclass="highlight"><pre><span></span><spanclass="n">H</span><spanclass="o">=</span><spanclass="c1">#Create the Hamiltonian</span>
602
-
<spanclass="c1">#Plot the Hamiltonian, real part (most SLEEPY objects have some kind of plotting)</span>
605
+
<spanclass="c1">#Plot the Hamiltonian, real part (mode='re')</span>
606
+
<spanclass="c1">#Note, most SLEEPY objects have some kind of plotting, usually found in .plot()</span>
603
607
</pre></div>
604
608
</div>
605
609
</div>
606
610
</div>
607
611
<divclass="cell docutils container">
608
612
<divclass="cell_input docutils container">
609
613
<divclass="highlight-ipython3 notranslate"><divclass="highlight"><pre><span></span><spanclass="n">L</span><spanclass="o">=</span><spanclass="c1">#Create the Liouvillian</span>
610
-
<spanclass="c1">#Plot the Liouvillian, imaginary part</span>
614
+
<spanclass="c1">#Plot the Liouvillian, imaginary part (mode='im')</span>
611
615
</pre></div>
612
616
</div>
613
617
</div>
@@ -619,8 +623,7 @@ <h3>Add dynamics<a class="headerlink" href="#add-dynamics" title="Link to this h
619
623
<divclass="cell docutils container">
620
624
<divclass="cell_input docutils container">
621
625
<divclass="highlight-ipython3 notranslate"><divclass="highlight"><pre><span></span><spanclass="n">ex1</span><spanclass="o">=</span><spanclass="n">ex</span><spanclass="o">.</span><spanclass="n">copy</span><spanclass="p">()</span><spanclass="c1">#Copy the experimental system</span>
622
-
<spanclass="n">_</span><spanclass="o">=</span><spanclass="n">ex1</span><spanclass="c1">#Change the chemical shift to 100 Hz</span>
623
-
<spanclass="c1">#Suppress text output by setting equal to _</span>
626
+
<spanclass="n">ex1</span><spanclass="c1">#Change the chemical shift to 100 Hz</span>
624
627
</pre></div>
625
628
</div>
626
629
</div>
@@ -630,6 +633,7 @@ <h3>Add dynamics<a class="headerlink" href="#add-dynamics" title="Link to this h
630
633
<divclass="cell_input docutils container">
631
634
<divclass="highlight-ipython3 notranslate"><divclass="highlight"><pre><span></span><spanclass="n">L</span><spanclass="o">=</span><spanclass="c1">#Create the Liouvillian</span>
632
635
<spanclass="n">_</span><spanclass="o">=</span><spanclass="n">L</span><spanclass="o">.</span><spanclass="n">plot</span><spanclass="p">(</span><spanclass="s1">'Lcoh'</span><spanclass="p">,</span><spanclass="n">mode</span><spanclass="o">=</span><spanclass="s1">'im'</span><spanclass="p">)</span><spanclass="c1">#Plot the coherent Liouvillian</span>
636
+
<spanclass="c1">#Suppress text output by setting equal to _</span>
" SpinEvolution is fast, powerful software for NMR dynamics simulations. It is also behind a significant paywall, where dynamics simulations require a $1650 annual subscription. We think SLEEPY has a wider range of dynamics capabilities, but we weren't interested in paying the annual fee to make sure.....\n",
" Gamma is a very flexible C++ based package that allows a broad range of dynamics simulations. While not widely used, it is still applied by a few of the expert groups in dynamics. Not for the faint of heart, but if you like coding in C++, go for it.\n",
78
83
" \n",
79
84
"\n",
80
85
"There's a lot else out there: these are three of the most well-known. For getting familiar with dynamic effects, however, we think SLEEPY is a great place to start."
Copy file name to clipboardExpand all lines: JupyterBook/_build/html/_sources/Ampere2026/SLEEPY_colab.ipynb
+16-11Lines changed: 16 additions & 11 deletions
Original file line number
Diff line number
Diff line change
@@ -62,7 +62,11 @@
62
62
"\n",
63
63
" SpinEvolution is fast, powerful software for NMR dynamics simulations. It is also behind a significant paywall, where dynamics simulations require a $1650 annual subscription. We think SLEEPY has a wider range of dynamics capabilities, but we weren't interested in paying the annual fee to make sure.....\n",
" Gamma is a very flexible C++ based package that allows a broad range of dynamics simulations. While not widely used, it is still applied by a few of the expert groups in dynamics. Not for the faint of heart, but if you like coding in C++, go for it.\n",
68
+
"\n",
69
+
"\n",
66
70
"There's a lot else out there: these are three of the most well-known. For getting familiar with dynamic effects, however, we think SLEEPY is a great place to start."
67
71
]
68
72
},
@@ -259,8 +263,7 @@
259
263
"outputs": [],
260
264
"source": [
261
265
"# Define an experimental system at 500 MHz field, with just a single proton\n",
262
-
"ex= #Use a 500 MHz magnetic field, include a single 1H, Nucs=['1H']\n",
263
-
"# Add a chemical shift with ex.set_inter, set to 500 Hz"
266
+
"ex= #Use a 500 MHz magnetic field, v0H=500, include a single 1H, Nucs=['1H']"
264
267
]
265
268
},
266
269
{
@@ -276,6 +279,7 @@
276
279
},
277
280
"outputs": [],
278
281
"source": [
282
+
"# Add a chemical shift with ex.set_inter, set to 500 Hz\n",
279
283
"ex.set #Interaction type, spin index (use i for spin-field interaction, i0,i1 for spin-spin coupling)\n",
280
284
" #Use Hz= to define in Hz, ppm= to define in ppm"
281
285
]
@@ -360,7 +364,8 @@
360
364
"outputs": [],
361
365
"source": [
362
366
"H= #Create the Hamiltonian\n",
363
-
" #Plot the Hamiltonian, real part (most SLEEPY objects have some kind of plotting)"
367
+
" #Plot the Hamiltonian, real part (mode='re')\n",
368
+
"#Note, most SLEEPY objects have some kind of plotting, usually found in .plot()"
364
369
]
365
370
},
366
371
{
@@ -377,7 +382,7 @@
377
382
"outputs": [],
378
383
"source": [
379
384
"L= #Create the Liouvillian\n",
380
-
" #Plot the Liouvillian, imaginary part"
385
+
" #Plot the Liouvillian, imaginary part (mode='im')"
381
386
]
382
387
},
383
388
{
@@ -391,7 +396,7 @@
391
396
},
392
397
{
393
398
"cell_type": "code",
394
-
"execution_count": 9,
399
+
"execution_count": null,
395
400
"id": "3afd314d",
396
401
"metadata": {
397
402
"editable": true,
@@ -403,8 +408,7 @@
403
408
"outputs": [],
404
409
"source": [
405
410
"ex1=ex.copy() #Copy the experimental system\n",
406
-
"_=ex1 #Change the chemical shift to 100 Hz\n",
407
-
"#Suppress text output by setting equal to _"
411
+
"ex1 #Change the chemical shift to 100 Hz"
408
412
]
409
413
},
410
414
{
@@ -429,7 +433,8 @@
429
433
"outputs": [],
430
434
"source": [
431
435
"L= #Create the Liouvillian\n",
432
-
"_=L.plot('Lcoh',mode='im') #Plot the coherent Liouvillian"
436
+
"_=L.plot('Lcoh',mode='im') #Plot the coherent Liouvillian\n",
437
+
"#Suppress text output by setting equal to _"
433
438
]
434
439
},
435
440
{
@@ -769,11 +774,11 @@
769
774
"# Calculate size of the one-bond dipole coupling for H–N\n",
0 commit comments