in progress activity

.devcontainer/devcontainer.json

@@ -2,8 +2,12 @@
   "build": { "dockerfile": "Dockerfile" },
   "customizations": {
     "vscode": {
-      "extensions": ["ms-python.python", "ms-toolsai.jupyter"]
+      "extensions": ["ms-python.python", "ms-toolsai.jupyter"],
+      "settings": {
+        "python.defaultInterpreterPath": "/opt/conda/envs/workshop/bin/python",
+        "jupyter.defaultKernel": "workshop"
+      }
     }
   },
-  "postStartCommand": ". /opt/conda/etc/profile.d/conda.sh && conda activate workshop"
+  "postStartCommand": ". /opt/conda/etc/profile.d/conda.sh && conda activate workshop && python -m ipykernel install --user --name workshop --display-name 'workshop'"
 }

activity/graph_utils.py

@@ -0,0 +1,48 @@
+import matplotlib.pyplot as plt
+from IPython.display import display, clear_output
+import numpy as np
+
+
+class LiveTimeseriesGraph:
+    def __init__(self, time_window, dt, title="", y_label="", legend_label=""):
+        plt.ion()
+        self.time_window = time_window
+        self.n_times = (int)(time_window / dt)
+        self.time = np.zeros(self.n_times, dtype=np.float32)
+        self.vals = np.zeros(self.n_times, dtype=np.float32)
+        self.dt = dt
+
+        self.fig, self.ax = plt.subplots(figsize=(10, 6))
+        (self.p1,) = self.ax.plot([], [], label=legend_label)
+        self.ax.set_xlabel("Time (ps)")
+        self.ax.set_ylabel(y_label)
+        self.ax.set_xlim(0, time_window)
+
+        self.ax.set_title(title)
+        self.ax.legend()
+        self.ax.grid(True)
+
+        self.i = 0
+
+    def update(self, time, val):
+        self.idx = self.i % self.n_times
+        self.time[self.idx] = time
+        self.vals[self.idx] = val
+
+        if self.idx == 0:
+            self.ax.set_xlim(
+                self.time[self.idx],
+                self.time[self.idx] + self.n_times * self.dt,
+            )
+
+        valid_indices = range(0, self.idx + 1)
+
+        self.ax.set_ylim(
+            np.min(self.vals[valid_indices]) - 1, np.max(self.vals) + 1
+        )
+
+        self.p1.set_data(self.time[valid_indices], self.vals[valid_indices])
+        clear_output(wait=True)
+        display(self.fig)
+
+        self.i += 1

activity/run.sh

@@ -1,13 +1,30 @@
 #!/bin/bash
 
+## TMP
+source /usr/local/gromacs/bin/GMXRC
+
+## WAIT UNTIL PORT IS OPEN
+SECONDS=0
+while lsof -n -i :8889; do
+    echo "Waiting for port 8889 to open"
+    sleep 1
+
+    if [ $SECONDS -ge 30 ]; then
+        echo "Timeout reached. Port 8889 did not open."
+        exit 1
+    fi
+done
+
 mkdir -p sample_simulation
 cd sample_simulation
+
+## RUN GROMPP
 if [ ! -f sample_simulation/topol.tpr ]; then
 echo "Running grompp"
 gmx grompp -f imd.mdp -c start.gro -p topol.top -o >& grompp.out
 fi
 echo "Starting mdrun"
-# modify gromacs execution string according to available resources
-# here we use 2 parallel threads
-gmx mdrun -v -nt 2 -imdwait -imdport 8889
+
+## START MDRUN
+gmx mdrun -v -nt 1 -imdwait -imdport 8889
 cd ..

activity/sample_simulation/imd.mdp

@@ -45,7 +45,7 @@ pbc                     = xyz       ; 3-D PBC
 ; Velocity generation
 gen_vel                 = no
 ; IMD group
-IMD-group               = Protein
+IMD-group               = System
 IMD-version             = 3
 IMD-nst                 = 10
 IMD-time                = yes

streaming-101/imd-mda/imd-mda.ipynb

@@ -0,0 +1,259 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## IMDClient package architecture\n",
+    "\n",
+    "## TODO:\n",
+    "\n",
+    "a context manager?\n",
+    "better error messages\n",
+    "remove unprofessional log messages\n",
+    "add docs for some of the messages (timeout at least)\n",
+    "make a nice diagram"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# ./run.sh \n",
+    "\n",
+    "import imdclient\n",
+    "\n",
+    "client = imdclient.IMDClient(\"localhost\", 8889, n_atoms=100)\n",
+    "\n",
+    "info = client.get_imdsessioninfo()\n",
+    "## TODO: show what's in dict\n",
+    "## design principle: reduce redundancy in data entry\n",
+    "\n",
+    "client.stop()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "client = imdclient.IMDClient(\"localhost\", 8889, n_atoms=100)\n",
+    "\n",
+    "## Design principle: simplest possible API so anyone can use it\n",
+    "## Even if you hate mdanalysis, you can use this\n",
+    "\n",
+    "while True:\n",
+    "    try:\n",
+    "        frame = client.get_imdframe()\n",
+    "    except EOFError:\n",
+    "        break\n",
+    "\n",
+    "client.stop()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Options"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "client = imdclient.IMDClient(\"localhost\", 8889, n_atoms=100, timeout=10)\n",
+    "\n",
+    "while True:\n",
+    "    try:\n",
+    "        ## Add a little wait time widget\n",
+    "        frame = client.get_imdframe()\n",
+    "    except EOFError:\n",
+    "        break\n",
+    "\n",
+    "client.stop()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## The buffer size is optional, pausing is automatic"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# ./run.sh\n",
+    "\n",
+    "import time\n",
+    "import logging\n",
+    "\n",
+    "logger = logging.getLogger(\"imdclient.IMDClient\")\n",
+    "# Modify to use \n",
+    "# file_handler = logging.FileHandler(\"gromacs_test.log\")\n",
+    "formatter = logging.Formatter(\n",
+    "    \"%(asctime)s - %(name)s - %(levelname)s - %(message)s\"\n",
+    ")\n",
+    "# file_handler.setFormatter(formatter)\n",
+    "# logger.addHandler(file_handler)\n",
+    "# logger.setLevel(logging.DEBUG)\n",
+    "\n",
+    "## Show the logs of the client stopping automatically\n",
+    "\n",
+    "client = imdclient.IMDClient(\"localhost\", 8889, n_atoms=100, buffer_size=100)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Reader wraps client, handles its limitations"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from imdclient.IMDREADER import IMDReader\n",
+    "import MDAnalysis as mda\n",
+    "\n",
+    "u = mda.Universe(top, \"imd://localhost:8889\")\n",
+    "\n",
+    "for ts in u.trajectory[:]:\n",
+    "    pass\n",
+    "\n",
+    "try:\n",
+    "    for ts in u.trajectory[:]:\n",
+    "        pass\n",
+    "except RuntimeError:\n",
+    "    print(\"A stream is not a file!\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Stepping is allowed, but specifying an end frame isn't"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [
+    {
+     "ename": "NameError",
+     "evalue": "name 'top' is not defined",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mNameError\u001b[0m                                 Traceback (most recent call last)",
+      "Cell \u001b[0;32mIn[1], line 4\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mimdclient\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mIMDREADER\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m IMDReader\n\u001b[1;32m      2\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01mMDAnalysis\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m \u001b[38;5;21;01mmda\u001b[39;00m\n\u001b[0;32m----> 4\u001b[0m u \u001b[38;5;241m=\u001b[39m mda\u001b[38;5;241m.\u001b[39mUniverse(top, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mimd://localhost:8889\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m      6\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m ts \u001b[38;5;129;01min\u001b[39;00m u\u001b[38;5;241m.\u001b[39mtrajectory[:]:\n\u001b[1;32m      7\u001b[0m     \u001b[38;5;28;01mpass\u001b[39;00m\n",
+      "\u001b[0;31mNameError\u001b[0m: name 'top' is not defined"
+     ]
+    }
+   ],
+   "source": [
+    "from imdclient.IMDREADER import IMDReader\n",
+    "import MDAnalysis as mda\n",
+    "\n",
+    "u = mda.Universe(top, \"imd://localhost:8889\")\n",
+    "\n",
+    "for ts in u.trajectory[::10]:\n",
+    "    pass"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## The client works out of the box with MDAnalysis analysis classes"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from imdclient.IMDREADER import IMDReader\n",
+    "import MDAnalysis as mda\n",
+    "from MDAnalysis.analysis.rms import RMSF\n",
+    "\n",
+    "u = mda.Universe(top, \"imd://localhost:8889\")\n",
+    "\n",
+    "imd_rmsf = RMSF(u.atoms).run()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Running multiple analysis classes on the same stream\n",
+    "\n",
+    "We showed you examples earlier that look like this:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## But you can also do this:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from imdclient.IMDREADER import IMDReader\n",
+    "import MDAnalysis as mda\n",
+    "from MDAnalysis.analysis.rms import RMSF\n",
+    "\n",
+    "r1 = RMSF(u.atoms)\n",
+    "r2 = RMSF(u.atoms)\n",
+    "imdclient.StackableAnalysis(u.trajectory, [r1, r2]).run()"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "imdclient-test",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.0"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}