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improve the text a little bit
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DomFijan committed Jul 4, 2024
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"cell_type": "markdown",
"metadata": {},
"source": [
"# Writing high frequency trajectories when event is detected\n",
"In this tutorial we will showcase how dupin's on-line capabilites can be used to triger\n",
"HOOMD's burst writer to dump very high resolution trajectory dump but only of the event\n",
"that dupin detects. This approach carries some important consequnces for performance and\n",
"storage. The purpose of such approach is to only write to disk parts of trajctories of\n",
"interest at extremenly tight frequency, but instead of dumping the whole trajctory we\n",
"only dump part of the trajectory around the event detected by dupin.\n",
"\n",
"To enable this we make a temporary buffer that stores trajectory frames in memory and\n",
"when dupin triggers this buffer is dumpeed onto the disk. On line detection requires\n",
"some CPU cycles to run every so often, which can impact performance based on order\n",
"parameters used for detection. In practice, it is often enough to track very simple\n",
"properties that are computed by the MDdriver (this case HOOMD) anyways, such as pressure\n",
"or total system energy or volume (depending if we run NVT/NVE or NPT).\n",
"\n",
"Here we give one such example:\n"
"# Writing High-Frequency Trajectories When an Event is Detected\n",
"\n",
"In this tutorial, we will showcase how Dupin's online capabilities can be used to\n",
"trigger HOOMD's burst writer to dump high-resolution trajectory data only during\n",
"specific events detected by Dupin. This approach has significant implications for\n",
"performance and storage. The main advantage is that it allows us to write to disk only\n",
"the segments of the trajectory that are of interest, at an extremely high frequency,\n",
"without dumping the entire trajectory.\n",
"\n",
"To achieve this, we create a temporary buffer that stores trajectory frames in memory.\n",
"When Dupin triggers, this buffer is dumped onto the disk. Online detection requires some\n",
"CPU cycles to run periodically, which can impact performance of the MD program depending\n",
"on the order parameters used for detection. In practice, it is often sufficient to track\n",
"very simple properties that are computed by the MD driver (in this case, HOOMD) anyway,\n",
"such as pressure, total system energy, or volume (depending on whether we are running\n",
"NVT/NVE or NPT ensembles).\n",
"\n",
"Here, we provide an example:"
]
},
{
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