MinimizationReporter example #34
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| "\n", | ||
| "You can report the status of [`simulation.minimizeEnergy()`](http://docs.openmm.org/development/api-python/generated/openmm.app.simulation.Simulation.html?#openmm.app.simulation.Simulation.minimizeEnergy) using a [`MinimizerReporter`](http://docs.openmm.org/development/api-python/generated/openmm.openmm.MinimizationReporter.html).\n", | ||
| "\n", | ||
| "The syntax for doing this is somewhat different to typical OpenMM functionality. Read the [API documentation](http://docs.openmm.org/development/api-python/generated/openmm.openmm.MinimizationReporter.html) for more explanation.\n", |
| "# Create an instance of our reporter\n", | ||
| "reporter = Reporter()\n", | ||
| "\n", | ||
| "# Perform local energy minimization \n", | ||
| "simulation.minimizeEnergy(reporter=reporter)\n", | ||
| "\n", | ||
| "# plot the minimization progress\n", |
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Just a personal preference, but I'd remove the comments. We don't need a separate comment for every line of code, especially when all they do is repeat what you just said immediately above: "We now create an instance of the reporter and minimize the system with the reporter attached." I'd show the two lines that do that without additional comments, then break to a text cell that says, "Now let's plot the energies that were recorded by the reporter," and then put the plotting code in its own cell.
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| "We then create a `MinimizationReporter` class that will print the current energy to the screen every 100 steps and save the energies to an array which we can plot later" |
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That should be, "every 100 iterations," not, "every 100 steps." Does it even take 100 iterations to minimize? You probably want to print more often.
It would be good to give a little more explanation of what we're doing. Something like this: "A MinimizationReporter is called after every iteration of minimization. It is an abstract class. To use it, you define your own subclass that reports results in whatever way you want. The reporter shown here prints the current energy to the screen..."
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| "## Reporting Minimization\n", | ||
| "\n", | ||
| "You can report the status of [`simulation.minimizeEnergy()`](http://docs.openmm.org/development/api-python/generated/openmm.app.simulation.Simulation.html?#openmm.app.simulation.Simulation.minimizeEnergy) using a [`MinimizerReporter`](http://docs.openmm.org/development/api-python/generated/openmm.openmm.MinimizationReporter.html).\n", |
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Maybe add another sentence saying why you would want to do that?
| "source": [ | ||
| "## Reporting Minimization\n", | ||
| "\n", | ||
| "You can report the status of [simulation.minimizeEnergy()](http://docs.openmm.org/latest/api-python/generated/openmm.app.simulation.Simulation.html?#openmm.app.simulation.Simulation.minimizeEnergy) using a [MinimizationReporter](http://docs.openmm.org/development/api-python/latest/openmm.openmm.MinimizationReporter.html). Note that `MinimizationReporter` was introduced in OpenMM 8.1.\n", |
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The URL for MinimizationReporter is broken. It should be http://docs.openmm.org/latest/api-python/generated/openmm.openmm.MinimizationReporter.html.
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Thanks for spotting that!
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Looks good. Is it ready to merge? I notice that none of the cells have been run so no output is shown. |
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The cookbook notebooks all get run by the website building workflow, they are then rendered on the webpage with the output generated during the github worlfow. |
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Thanks! |
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It still isn't showing up on the website... |
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Its on the /dev page: https://openmm.github.io/openmm-cookbook/dev/notebooks/cookbook/report_minimization.html |
This adds an example for using the new MinimizationReporter in OpenMM 8.1: openmm/openmm#4207