HDF5 documentation

conf.py

@@ -72,9 +72,9 @@
 # -- project information -----------------------------------------------------
 #
 project = 'EXP'
-copyright = '2023-2025, EXP-code collaboration'
+copyright = '2023-2026, EXP-code collaboration'
 author = 'EXP-code collaboration'
-release = '0.172'
+release = '0.174'
 version = '7.x'
 
 # -- General configuration ---------------------------------------------------
@@ -99,7 +99,14 @@
 
 
 templates_path = ['_templates']
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', 'README.rst']
+
+exclude_patterns = [
+    '_build',
+    'Thumbs.db',
+    '.DS_Store',
+    'README.rst',
+    'exp_repo/**',
+]
 
 breathe_projects = {"EXP": "exp_repo/doc/xml/"}
 breathe_default_project = "EXP"

index.rst

@@ -94,6 +94,8 @@ EXP concepts
    topics/centering
    topics/yamlconfig
    topics/howtosim
+   topics/exp-phase-space
+   topics/output-hdf5
 
 These topics provide some background detail on the software and
 mathematics used in EXP.
@@ -122,6 +124,12 @@ mathematics used in EXP.
 :doc:`topics/howtosim`
     A guide for running EXP simulations
 
+:doc:`topics/exp-phase-space`
+    How to use and manipulate the EXP native phase-space format
+
+:doc:`topics/output-hdf5`
+    The EXP HDF5 phase-space format
+
 .. toctree::
    :caption: Frequently Asked Questions (FAQ)
 
@@ -145,7 +153,6 @@ How to solve specific problems
    topics/using-mssa
    topics/orbits
    topics/replay
-   topics/exp-phase-space
    topics/EXP-output
    topics/flatdisk
    topics/debug
@@ -175,9 +182,6 @@ How to solve specific problems
     Compute orbits in the gravitational potential fields implied by
     your coefficients, and why you might want to do this
 
-:doc:`topics/exp-phase-space`
-    How to use and manipulate the EXP native phase-space format
-
 :doc:`topics/EXP-output`
     A description of the EXP N-body output generator
 

intro/Tutorials/Part1-Coefficients.ipynb

@@ -17,11 +17,30 @@
    "execution_count": 1,
    "id": "1ed1fc36",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\n",
+      "%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\n",
+      "%%%%% This is EXP 7.9.3 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\n",
+      "%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\n",
+      "%%%%% Repository URL | https://github.com/EXP-code/EXP                         %\n",
+      "%%%%% Current branch | main                                                    %\n",
+      "%%%%% Current commit | 6cbd08fe546ff42ec833ecca423f46f3ba1f0aa9                %\n",
+      "%%%%% Compile time   | 2026-04-08 10:25:43 BST                                 %\n",
+      "%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\n",
+      "\n"
+     ]
+    }
+   ],
    "source": [
     "import os\n",
     "import yaml\n",
+    "\n",
     "import pyEXP\n",
+    "pyEXP.util.getVersionInfo()\n",
     "\n",
     "# As described in the README, we assume that you have started Jupyter in the `Tutorials` directory and have provided all of the\n",
     "# necessary data in the `Data` subdirectory.  We move to that directory as a first step:\n",
@@ -254,7 +273,7 @@
       "file group is ['OUT.run0.00010']\n",
       "The component names are: ['dark halo', 'star disk']\n",
       "Selected dark halo\n",
-      " for 100000 particles at Time 0.09999999999998707\n",
+      "Call createFromReader at Time 0.09999999999998707 for 100000 particles\n",
       "Created coef\n",
       "Added coef\n",
       "------------------------------------------------------------\n",
@@ -371,6 +390,10 @@
     "    #                                             |\n",
     "    if coefs is None:           #                 v\n",
     "        coefs = pyEXP.coefs.Coefs.makecoefs(coef, compname)\n",
+    "\n",
+    "        # Set the units of the coefficients\n",
+    "        coefs.setUnits([(\"length\", \"none\", 1.0),(\"mass\", \"none\", 1.0),(\"time\", \"none\", 1.0), (\"G\", \"none\", 1.0)])\n",
+    "\n",
     "    else:\n",
     "        coefs.add(coef)\n",
     "\n",
@@ -451,19 +474,19 @@
       "----------------------------------------\n",
       "---- azi force\n",
       "----------------------------------------\n",
-      "[[-0.00087384 -0.00098027 -0.00113208 ...  0.00053854  0.00058888\n",
-      "   0.00065692]\n",
-      " [-0.00104563 -0.00117976 -0.00136719 ...  0.00044353  0.00050006\n",
-      "   0.00057894]\n",
-      " [-0.00120132 -0.0013625  -0.00158698 ...  0.00027801  0.00034734\n",
-      "   0.00044279]\n",
+      "[[-0.0006179  -0.00071115 -0.00084254 ...  0.0004008   0.00042721\n",
+      "   0.00046451]\n",
+      " [-0.00075857 -0.00087931 -0.00104691 ...  0.00033963  0.00037271\n",
+      "   0.00042   ]\n",
+      " [-0.00089408 -0.00104332 -0.00125041 ...  0.00021905  0.00026597\n",
+      "   0.00032954]\n",
       " ...\n",
-      " [-0.00086897 -0.00120733 -0.00153372 ...  0.00364213  0.00354581\n",
-      "   0.00338669]\n",
-      " [-0.00081985 -0.00113707 -0.00144417 ...  0.00372749  0.00363169\n",
-      "   0.00347801]\n",
-      " [-0.00079396 -0.00109152 -0.00138081 ...  0.00380656  0.00370932\n",
-      "   0.00355781]]\n",
+      " [-0.00064673 -0.00092449 -0.00120845 ...  0.0028697   0.00271516\n",
+      "   0.00252051]\n",
+      " [-0.00059477 -0.00084749 -0.00110585 ...  0.00285428  0.0027068\n",
+      "   0.00252317]\n",
+      " [-0.00056141 -0.00079186 -0.00102766 ...  0.002833    0.00269098\n",
+      "   0.00251575]]\n",
       "----------------------------------------\n",
       "---- dens\n",
       "----------------------------------------\n",
@@ -503,19 +526,19 @@
       "----------------------------------------\n",
       "---- mer force\n",
       "----------------------------------------\n",
-      "[[ 0.00116107  0.0012984   0.00143422 ...  0.00141841  0.00133688\n",
-      "   0.00125844]\n",
-      " [ 0.0010585   0.00120293  0.00134758 ...  0.00156861  0.00148209\n",
-      "   0.00139784]\n",
-      " [ 0.00094972  0.00110494  0.00126318 ...  0.00172921  0.00163881\n",
-      "   0.00154933]\n",
+      "[[ 0.000821    0.00094195  0.00106741 ...  0.00105564  0.00096986\n",
+      "   0.00088985]\n",
+      " [ 0.0007679   0.00089658  0.00103189 ...  0.00120115  0.00110464\n",
+      "   0.00101408]\n",
+      " [ 0.00070682  0.0008461   0.00099529 ...  0.00136248  0.0012549\n",
+      "   0.00115308]\n",
       " ...\n",
-      " [-0.00298936 -0.003173   -0.00336324 ...  0.00119402  0.00105672\n",
-      "   0.00093735]\n",
-      " [-0.00276366 -0.00292988 -0.0031003  ...  0.00081658  0.00071328\n",
-      "   0.00062615]\n",
-      " [-0.00254213 -0.00269264 -0.00284517 ...  0.0004661   0.0003963\n",
-      "   0.00034138]]\n",
+      " [-0.0022248  -0.00242968 -0.00264996 ...  0.00094079  0.00080917\n",
+      "   0.00069761]\n",
+      " [-0.00200493 -0.00218372 -0.00237401 ...  0.00062529  0.00053163\n",
+      "   0.00045425]\n",
+      " [-0.00179756 -0.00195341 -0.00211749 ...  0.00034689  0.0002875\n",
+      "   0.00024139]]\n",
       "----------------------------------------\n",
       "---- potl\n",
       "----------------------------------------\n",
@@ -629,6 +652,16 @@
      "output_type": "stream",
      "text": [
       "Nothing to delete\n",
+      "Coefs::WriteH5Units: wrote units to HDF5 file:\n",
+      "------------------------------------------------\n",
+      "Name            Unit            Value           \n",
+      "----------      ----------      ----------      \n",
+      "G               none            1               \n",
+      "length          none            1               \n",
+      "mass            none            1               \n",
+      "time            none            1               \n",
+      "------------------------------------------------\n",
+      "\n",
       "Coefficient file saved\n"
      ]
     }
@@ -639,6 +672,8 @@
     "    os.remove('test_coefs')\n",
     "except:\n",
     "    print('Nothing to delete')\n",
+    "\n",
+    "\n",
     "coefs.WriteH5Coefs('test_coefs')\n",
     "print('Coefficient file saved')"
    ]
@@ -667,9 +702,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Type is sphere\n",
-      "Times are the same, now checking parameters at each time\n",
-      "Parameters are the same, now checking coefficients\n"
+      "Type is sphere\n"
      ]
     },
     {
@@ -681,6 +714,14 @@
      "execution_count": 7,
      "metadata": {},
      "output_type": "execute_result"
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Times are the same, now checking parameters at each time\n",
+      "Parameters are the same, now checking coefficients\n"
+     ]
     }
    ],
    "source": [
@@ -714,11 +755,17 @@
     "- [Return to Table of Contents](../README.ipynb)\n",
     "- [Go to next notebook](./Part2-Analysis.ipynb)\n"
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "0af68cfa",
+   "metadata": {},
+   "source": []
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "Python 3",
    "language": "python",
    "name": "python3"
   },
@@ -732,7 +779,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.3"
+   "version": "3.11.6"
   }
  },
  "nbformat": 4,