diff --git a/4_mstis_sampling_tutorial.ipynb b/4_mstis_sampling_tutorial.ipynb index 116bbed..81290e0 100644 --- a/4_mstis_sampling_tutorial.ipynb +++ b/4_mstis_sampling_tutorial.ipynb @@ -219,9 +219,9 @@ "source": [ "# some aspects of storage depend on Python version\n", "if sys.version_info > (3,):\n", - " filename = \"mstis_bootstrap_py3.nc\"\n", + " filename = \"./inputs/mstis_bootstrap_py3.nc\"\n", "else:\n", - " filename = \"mstis_bootstrap_py2.nc\"" + " filename = \"./inputs/mstis_bootstrap_py2.nc\"" ] }, { diff --git a/5_advanced_customize_shooting.ipynb b/5_advanced_customize_shooting.ipynb index 8cf72b0..5e2819a 100644 --- a/5_advanced_customize_shooting.ipynb +++ b/5_advanced_customize_shooting.ipynb @@ -49,7 +49,7 @@ "metadata": {}, "outputs": [], "source": [ - "storage = paths.Storage(\"2_state_toy.nc\", mode='r')\n", + "storage = paths.Storage(\"./inputs/2_state_toy.nc\", mode='r')\n", "state_A = storage.volumes['A']\n", "state_B = storage.volumes['B']\n", "cv = storage.cvs['x']\n", diff --git a/README.md b/README.md index aa45b00..d1f9b06 100644 --- a/README.md +++ b/README.md @@ -1,3 +1,7 @@ +[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/openpathsampling/ops_tutorial/HEAD?urlpath=lab) +![Tests](https://github.com/openpathsampling/ops_tutorial/workflows/Tests/badge.svg) +![GitHub last commit](https://img.shields.io/github/last-commit/openpathsampling/ops_tutorial) + # OpenPathSampling Alanine Dipeptide Tutorial This is an introductory tutorial for OpenPathSampling, and is generally the @@ -23,6 +27,12 @@ and ## Requirements +If you'd prefer not to install things locally, you can try out the tutorial +using [this Binder +link](https://mybinder.org/v2/gh/openpathsampling/ops_tutorial/HEAD?urlpath=lab). +Performance is likely to be better on your own computer than on Binder, but +Binder is useful if you can't/don't want to install the software. + ### Software Note that OpenPathSampling does not support Windows; if you're using a Windows @@ -90,12 +100,17 @@ Notebook 4 is optional, and has no exercises in it. It provides setup for a very different kind of system (a 2D toy model), and illustrates that the overall setup process is the same, regardless of the underlying engine. +Notebook 5 contains some more advanced exercises related to TIS, and also shows +how to use the OPS command line interface. In addition to the requirements +listed above, it requires installation of `openpathsampling-cli`. + ## History This tutorial has been used in multiple classes and workshops, including several E-CAM Extended Software Development Workshops (Leiden, The Netherlands, -2017; Lyon, France, 2019), and Master's-level courses in Biomolecular -Simulation at the University of Amsterdam (2017--2019). +2017; Lyon, France, 2019), Master's-level courses in Biomolecular Simulation at +the University of Amsterdam (since 2017), and the CECAM flagship school MolSim +(2021). This tutorial was developed with financial support from the European Union's Horizon 2020 research and innovation program, under grant agreement No. 676531 diff --git a/2_state_toy.nc b/inputs/2_state_toy.nc similarity index 100% rename from 2_state_toy.nc rename to inputs/2_state_toy.nc diff --git a/mstis_bootstrap_py2.nc b/inputs/mstis_bootstrap_py2.nc similarity index 100% rename from mstis_bootstrap_py2.nc rename to inputs/mstis_bootstrap_py2.nc diff --git a/mstis_bootstrap_py3.nc b/inputs/mstis_bootstrap_py3.nc similarity index 100% rename from mstis_bootstrap_py3.nc rename to inputs/mstis_bootstrap_py3.nc