example.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "0b0acc08-6ce4-4c7a-abec-966e5abdf370",
   "metadata": {},
   "source": [
    "# NEMO examples\n",
    "\n",
    "In a clean directory we will install NEMO, with a non-graphics device driver. We will create and integrate a Plummer sphere, and manually compile a NEMO program.\n",
    "\n",
    "This first cell will re-install a clean version of the source code, from github. Since the code is open source, you will not need an account on github, but the **git** command needs to be present.\n",
    "\n",
    "# Installing NEMO"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "1321a220-12cc-4bf1-99d4-deb454c2c239",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Cloning into 'nemo_demo'...\n",
      "remote: Enumerating objects: 82683, done.\u001b[K\n",
      "remote: Counting objects: 100% (7587/7587), done.\u001b[K\n",
      "remote: Compressing objects: 100% (2605/2605), done.\u001b[K\n",
      "remote: Total 82683 (delta 5155), reused 7369 (delta 4945), pack-reused 75096\u001b[K\n",
      "Receiving objects: 100% (82683/82683), 43.86 MiB | 30.29 MiB/s, done.\n",
      "Resolving deltas: 100% (59369/59369), done.\n"
     ]
    }
   ],
   "source": [
    "cd $HOME\n",
    "mkdir -p NEMO\n",
    "cd NEMO\n",
    "mkdir -p demo\n",
    "cd demo\n",
    "rm -rf nemo_demo\n",
    "git clone https://github.com/teuben/nemo nemo_demo"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "62e2bfbd-82ca-446c-82e9-3d4801206327",
   "metadata": {},
   "source": [
    "The next cell can always be revisited to redo a configure and build. But we show the version of NEMO just to make sure we are in the right directory"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "0adaa63d-4a52-4984-86c3-e0319f59cd11",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "4.4.3\n"
     ]
    }
   ],
   "source": [
    "cd $HOME/NEMO/demo/nemo_demo\n",
    "cat VERSION"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "8eeb144a-fc34-4769-9b32-c5640fa6d956",
   "metadata": {},
   "source": [
    "Now we can configure the package.  We configure with a simple non-graphics YAPP graphics driver.  YAPP stands for *Yet Another Plotting Package*.  We pick the \"ps\" (postscript) driver.   There is also an \"svg\" (in development) which might be more fun to display actual results, though in practice the pgplot driver is used."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "aee511ff-a61e-4497-8111-e5ab2ea18bcd",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "checking NEMO config... checking build system type... x86_64-unknown-linux-gnu\n",
      "checking host system type... x86_64-unknown-linux-gnu\n",
      "Found CANONICAL_HOST = linux-gnu or x86_64-unknown-linux-gnu or x86_64\n",
      "Found CANONICAL_BUILD = x86_64-unknown-linux-gnu\n",
      "checking target system type... x86_64-unknown-linux-gnu\n",
      "Found CANONICAL_TARGET = x86_64-unknown-linux-gnu\n",
      "checking for gcc... gcc\n",
      "checking whether the C compiler works... yes\n",
      "checking for C compiler default output file name... a.out\n",
      "checking for suffix of executables... \n",
      "checking whether we are cross compiling... no\n",
      "checking for suffix of object files... o\n",
      "checking whether the compiler supports GNU C... yes\n",
      "checking whether gcc accepts -g... yes\n",
      "checking for gcc option to enable C11 features... none needed\n",
      "checking for stdio.h... yes\n",
      "checking for stdlib.h... yes\n",
      "checking for string.h... yes\n",
      "checking for inttypes.h... yes\n",
      "checking for stdint.h... yes\n",
      "checking for strings.h... yes\n",
      "checking for sys/stat.h... yes\n",
      "checking for sys/types.h... yes\n",
      "checking for unistd.h... yes\n",
      "checking for sys/time.h... yes\n",
      "checking for sys/param.h... yes\n",
      "checking for vfork.h... no\n",
      "checking size of float... 4\n",
      "checking size of double... 8\n",
      "checking size of long double... 16\n",
      "checking size of char... 1\n",
      "checking size of short... 2\n",
      "checking size of int... 4\n",
      "checking size of long... 8\n",
      "checking size of long long... 8\n",
      "checking for grep that handles long lines and -e... /usr/bin/grep\n",
      "checking for egrep... /usr/bin/grep -E\n",
      "checking for strchr... yes\n",
      "checking for memcpy... yes\n",
      "checking for vendor's cc to be used instead of gcc... checking for cc... gcc\n",
      "checking whether the compiler supports GNU C... (cached) yes\n",
      "checking whether gcc accepts -g... (cached) yes\n",
      "checking for gcc option to enable C11 features... (cached) none needed\n",
      "checking for g++... g++\n",
      "checking whether the compiler supports GNU C++... yes\n",
      "checking whether g++ accepts -g... yes\n",
      "checking for g++ option to enable C++11 features... none needed\n",
      "checking for gawk... gawk\n",
      "checking for a BSD-compatible install... /usr/bin/install -c\n",
      "checking whether ln -s works... yes\n",
      "checking whether make sets $(MAKE)... yes\n",
      "checking for ranlib... ranlib\n",
      "checking for the (t)csh shell yes... yes\n",
      "checking for gmake... gmake\n",
      "checking whether gmake is GNU Make... yes\n",
      "checking which precision NEMO is going to use... \n",
      "checking if the gnu coverage tool is to be used... no\n",
      "LFS selected, note that some filesystems may not support Large File anyways\n",
      "Test this with the NEMO command:\n",
      "     mkspiral s000 1000000 nmodel=40\n",
      "checking how to run the C preprocessor... gcc -E\n",
      "checking for X... libraries , headers \n",
      "checking for gethostbyname... yes\n",
      "checking for connect... yes\n",
      "checking for remove... yes\n",
      "checking for shmat... yes\n",
      "checking for IceConnectionNumber in -lICE... yes\n",
      "checking for glBegin in -lGL... yes\n",
      "checking for gluProject in -lGLU... yes\n",
      "checking for XMesaGetBackBuffer... no\n",
      "checking whether we have a FORTRAN 77 compiler... checking for gfortran... gfortran\n",
      "checking whether the compiler supports GNU Fortran 77... yes\n",
      "checking whether gfortran accepts -g... yes\n",
      "checking how to get verbose linking output from gfortran... -v\n",
      "checking for Fortran 77 libraries of gfortran...  -L/usr/lib/gcc/x86_64-linux-gnu/11 -L/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/11/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/11/../../.. -lgfortran -lm -lquadmath\n",
      "checking how f77 mangles function names... lowercase-underscore\n",
      "checking if f77 functions with an underscore get an extra underscore... no\n",
      "checking for f77 flags to use C main function... none\n",
      "configure: WARNING: f77 cmain ok\n",
      "checking size of unformatted fortran I/O header/footer... 4\n",
      "checking what flags we need to created shared libs... -fpic\n",
      "checking whether we have PGPLOT... yes, found $PGPLOT_DIR=/home/teuben/NEMO/nemo/lib\n",
      "yes, /home/teuben/NEMO/nemo/lib\n",
      "no\n",
      "checking for PLPlot pkg-config info... no\n",
      "checking for plplot.h... no\n",
      "checking for plplot/plplot.h... yes\n",
      "checking for c_plinit in -lplplotd... no\n",
      "configure: WARNING: PLPlot library not found/incomplete! Plotting deactivated.\n",
      "Trying to find LOADOBJ options for linux-gnu ; host=x86_64-unknown-linux-gnu\n",
      "checking for sqrt in -lm... yes\n",
      "checking whether we have HDF4... no\n",
      "configure: WARNING: could not find HDF library\n",
      "configure: WARNING: CFITSIO disabled\n",
      "checking whether we have MIRIAD... no\n",
      "configure: WARNING: could not find MIRIAD library...\n",
      "configure: WARNING: TCL disabled\n",
      "checking for tputs in -lncurses... yes\n",
      "checking for readline/history.h... no\n",
      "checking for readline/readline.h... no\n",
      "checking for DFSDndataset in -ldf... no\n",
      "checking for foreground in -lvogl... no\n",
      "checking for inflate in -lz... yes\n",
      "checking for strtoll in -lc... yes\n",
      "checking for strtoull in -lc... yes\n",
      "checking for dlopen in -ldl... yes\n",
      "checking for shl_load in -ldld... no\n",
      "checking for library containing dlopen... none required\n",
      "checking for library containing sin... -lm\n",
      "checking for library containing cblas_daxpy... -lgslcblas\n",
      "checking for library containing gsl_version... -lgsl\n",
      "checking for dirent.h that defines DIR... yes\n",
      "checking for library containing opendir... none required\n",
      "checking for egrep... (cached) /usr/bin/grep -E\n",
      "checking for sys/wait.h that is POSIX.1 compatible... yes\n",
      "checking for fcntl.h... yes\n",
      "checking for limits.h... yes\n",
      "checking for malloc.h... yes\n",
      "checking for sgtty.h... yes\n",
      "checking for strings.h... (cached) yes\n",
      "checking for sys/file.h... yes\n",
      "checking for sys/ioctl.h... yes\n",
      "checking for sys/time.h... (cached) yes\n",
      "checking for unistd.h... (cached) yes\n",
      "checking for an ANSI C-conforming const... yes\n",
      "checking for inline... inline\n",
      "checking for off_t... yes\n",
      "checking for size_t... yes\n",
      "checking whether struct tm is in sys/time.h or time.h... time.h\n",
      "checking for long file names... yes\n",
      "checking for special C compiler options needed for large files... no\n",
      "checking for _FILE_OFFSET_BITS value needed for large files... no\n",
      "checking for uid_t in sys/types.h... yes\n",
      "checking type of array argument to getgroups... gid_t\n",
      "checking whether gcc needs -traditional... no\n",
      "checking for working memcmp... yes\n",
      "checking for getpagesize... yes\n",
      "checking for fork... yes\n",
      "checking for vfork... yes\n",
      "checking for vprintf... yes\n",
      "checking for working mmap... yes\n",
      "checking return type of signal handlers... void\n",
      "checking for pid_t... yes\n",
      "checking for working fork... yes\n",
      "checking for working vfork... (cached) yes\n",
      "checking for ftime... yes\n",
      "checking for gethostname... yes\n",
      "checking for gettimeofday... yes\n",
      "checking for getwd... yes\n",
      "checking for mkdir... yes\n",
      "checking for select... yes\n",
      "checking for strdup... yes\n",
      "checking for strtod... yes\n",
      "checking for strtol... yes\n",
      "checking for strtoul... yes\n",
      "checking for dprintf... yes\n",
      "checking for log2... yes\n",
      "checking whether byte ordering is bigendian... no\n",
      "Using NEMOTARS=/home/teuben/NEMO/demo/tar\n",
      "checking looking for a reasonable YAPP... ps\n",
      "configure: WARNING: not using opt\n",
      "*** Warning: NEMO=/home/teuben/NEMO/demo/nemo_demo, maybe you are running NEMO already\n",
      "configure: creating ./config.status\n",
      "config.status: creating Makefile\n",
      "config.status: creating makedefs\n",
      "config.status: creating nemo-config\n",
      "config.status: creating nemo_start.csh\n",
      "config.status: creating nemo_start.sh\n",
      "config.status: creating nemo_start.py\n",
      "config.status: creating usr/dehnen/utils/make.sh\n",
      "config.status: creating config.h\n",
      "\n",
      "-------------------------------------------------------------------------\n",
      "All done configuring, continue with your installation with\n",
      "\n",
      "     make build check bench5\n",
      "\n",
      "Users need to source the nemo_start.(c)sh file in their shell to\n",
      "enable NEMO commands and set up their NEMO environment.\n",
      "If there any compile or linkings problems, check out $NEMOLIB/makedefs\n",
      "-------------------------------------------------------------------------\n",
      "\n"
     ]
    }
   ],
   "source": [
    "date0=$(date)\n",
    "\n",
    "./configure --with-yapp=ps\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "9c9c1adf-434c-4a93-a924-a124668c8d5a",
   "metadata": {},
   "source": [
    "The next step is building the software (libraries and binaries) in place. NEMO does normally not install itself in some /usr/local/bin type directory, the build is done in-place. This has some impact how users can use NEMO. More about that later.\n",
    "\n",
    "The **make build** will do a basic install:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "073e0ba5-a522-4544-95d3-d20fbd455d38",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(source nemo_start.sh ; make postconfig mknemos)\n",
      "make[1]: Entering directory '/home/teuben/NEMO/demo/nemo_demo'\n",
      "Checking directory structure on Wed Jan 31 08:33:36 PM EST 2024\n",
      "By teuben on k2\n",
      "No tar symlink\n",
      "Updating /home/teuben/NEMO/demo/nemo_demo/adm/TIMESTAMP file on Wed Jan 31 08:33:36 PM EST 2024\n",
      "Creating /home/teuben/NEMO/demo/nemo_demo/etc/motd file on Wed Jan 31 08:33:36 PM EST 2024\n",
      "Creating /home/teuben/NEMO/demo/nemo_demo/nemo_local.csh file on Wed Jan 31 08:33:36 PM EST 2024\n",
      "Creating /home/teuben/NEMO/demo/nemo_demo/nemo_local.sh file on Wed Jan 31 08:33:36 PM EST 2024\n",
      "Done with dirs at Wed Jan 31 08:33:36 PM EST 2024\n",
      "cp config.h makedefs /home/teuben/NEMO/demo/nemo_demo/lib\n",
      "Installing scripts on Wed Jan 31 08:33:36 PM EST 2024\n",
      "By teuben on k2\n",
      "(cd /home/teuben/NEMO/demo/nemo_demo/src/scripts; make install)\n",
      "make[2]: Entering directory '/home/teuben/NEMO/demo/nemo_demo/src/scripts'\n",
      "cp Makefile.lib /home/teuben/NEMO/demo/nemo_demo/lib\n",
      "cp mknemo mkpdoc manlaser nemoman nemobench ldso nemo.version fitsedit fitsmerge nds9 shtool nemo.coverage showvar mir2nemo getline pedit wgetc yapp_query nemoplot nemopars sbatch_nemo.sh nemo_functions.sh progress_bar.sh python/tabplot.py python/fitsplot.py /home/teuben/NEMO/demo/nemo_demo/bin\n",
      "utilities installed\n",
      "make[2]: Leaving directory '/home/teuben/NEMO/demo/nemo_demo/src/scripts'\n",
      "MKNEMOS=\n",
      "make[1]: Leaving directory '/home/teuben/NEMO/demo/nemo_demo'\n",
      "Continue with \"make build2 (or build2a build2b)\"\n",
      "(source nemo_start.sh ; make scripts libs)\n",
      "make[1]: Entering directory '/home/teuben/NEMO/demo/nemo_demo'\n",
      "Installing scripts on Wed Jan 31 08:33:36 PM EST 2024\n",
      "By teuben on k2\n",
      "(cd /home/teuben/NEMO/demo/nemo_demo/src/scripts; make install)\n",
      "make[2]: Entering directory '/home/teuben/NEMO/demo/nemo_demo/src/scripts'\n",
      "cp Makefile.lib /home/teuben/NEMO/demo/nemo_demo/lib\n",
      "cp mknemo mkpdoc manlaser nemoman nemobench ldso nemo.version fitsedit fitsmerge nds9 shtool nemo.coverage showvar mir2nemo getline pedit wgetc yapp_query nemoplot nemopars sbatch_nemo.sh nemo_functions.sh progress_bar.sh python/tabplot.py python/fitsplot.py /home/teuben/NEMO/demo/nemo_demo/bin\n",
      "utilities installed\n",
      "make[2]: Leaving directory '/home/teuben/NEMO/demo/nemo_demo/src/scripts'\n",
      "Starting at Wed Jan 31 08:33:36 PM EST 2024, tail -f /home/teuben/NEMO/demo/nemo_demo/install.log\n",
      "(cd src/tutor/main; rm -f maine.o; make -f /home/teuben/NEMO/demo/nemo_demo/lib/makedefs  maine.o CFLAGS=\"-v -c\")  >> install.log 2>&1 \n",
      "(cd src;make -i -j  clean install) >> install.log 2>&1\n",
      "(cd usr/dehnen; make -i clean all) >> install.log 2>&1 \n",
      "Done at Wed Jan 31 08:34:50 PM EST 2024\n",
      "make[1]: Leaving directory '/home/teuben/NEMO/demo/nemo_demo'\n",
      "Continue with \"make build3\"\n",
      "(source nemo_start.sh ; make -j  bins)\n",
      "make[1]: Entering directory '/home/teuben/NEMO/demo/nemo_demo'\n",
      "Starting at Wed Jan 31 08:34:50 PM EST 2024, tail -f /home/teuben/NEMO/demo/nemo_demo/install.log\n",
      "cd src;make -i -j  bins >> ../install.log 2>&1 \n",
      "cd usr;make -i -j  bins >> ../install.log 2>&1 \n",
      "Done at Wed Jan 31 08:35:08 PM EST 2024\n",
      "make[1]: Leaving directory '/home/teuben/NEMO/demo/nemo_demo'\n",
      "Continue with \"make build4 for advanced runs\"\n",
      " and/or \"make check bench5\" for a final check\n"
     ]
    }
   ],
   "source": [
    "make build"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "e92c25b4-4cb5-45da-bde8-4da5ff537a7a",
   "metadata": {},
   "source": [
    "Check if the build was ok. A number of tests produce a data file which is regressed against a known answer. If these fail, you would see lines starting with **BSF** on the screen. \n",
    "\n",
    "The **make check** will do this:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "6aaa76a2-df8d-4993-86be-7f34d252cba3",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(source nemo_start.sh; src/scripts/testsuite | tee -a install.log )\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/nemo_demo/src/image/fits\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/nemo_demo/src/image/io\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/nemo_demo/src/image/misc\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/nemo_demo/src/image/rotcur\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/nemo_demo/src/image/trans\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/nemo_demo/src/image/wcs\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/nemo_demo/src/kernel/fortran\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/nemo_demo/src/kernel/io\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/nemo_demo/src/kernel/misc\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/nemo_demo/src/kernel/tab\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/nemo_demo/src/nbody/cores\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/nemo_demo/src/nbody/evolve/aarseth/nbody0\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/nemo_demo/src/nbody/evolve/aarseth/tools\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/nemo_demo/src/nbody/evolve/dehnen\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/nemo_demo/src/nbody/evolve/directcode\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/nemo_demo/src/nbody/evolve/flowcode\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/nemo_demo/src/nbody/evolve/hackcode/hackcode1\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/nemo_demo/src/nbody/evolve/hackcode/treecode1\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/nemo_demo/src/nbody/evolve/scfm\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/nemo_demo/src/nbody/evolve/sellwood/tools\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/nemo_demo/src/nbody/image\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/nemo_demo/src/nbody/init\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/nemo_demo/src/nbody/io_nemo\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/nemo_demo/src/nbody/io/starlab\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/nemo_demo/src/nbody/io\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/nemo_demo/src/nbody/reduc\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/nemo_demo/src/nbody/trans\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/nemo_demo/src/nbody/xyz\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/nemo_demo/src/orbit/misc\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/nemo_demo/src/orbit/potential\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/nemo_demo/usr/wolfire\n",
      "Results in /home/teuben/NEMO/demo/nemo_demo/tmp/test360751/testsuite.log\n",
      "A copy in /home/teuben/NEMO/demo/nemo_demo/testsuite.log is kept as well as the latest.\n",
      "BSF regressions that are OK: 63\n",
      "There are 298 binaries in NEMO\n",
      "TESTSUITE started Wed Jan 31 08:35:09 PM EST 2024\n",
      "TESTSUITE   ended Wed Jan 31 08:35:15 PM EST 2024\n"
     ]
    }
   ],
   "source": [
    "make check\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "5fabc543-1178-46b5-8e34-0c7fca002e0b",
   "metadata": {},
   "source": [
    "And finally a benchmark to check how the speed compares with an otherwise random 2020-type laptop. Currently 6 nbody codes are run, each of them typically taking 5 seconds to compute.\n",
    "\n",
    "The **make bench5** will do this:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "0f432f58-e93a-4469-8754-83474b0d0e2d",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(source nemo_start.sh; /usr/bin/time src/scripts/nemo.bench mode=5 | tee -a install.log )\n",
      "NEMOBENCH: (2022-09-14) bench362389 : nbody0=3072 nbody1=10240 nbody3=1000000 size=256 ften=1 clean=1 bsf=0 tmp=bench362389\n",
      "k2\n",
      "Linux k2 6.2.0-35-generic #35~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Fri Oct 6 10:23:26 UTC 2 x86_64 x86_64 x86_64 GNU/Linux\n",
      "Wed Jan 31 08:35:15 PM EST 2024\n",
      "Equal 5sec CPU time per code, no output files to check\n",
      "Codes:  directcode [mkplummer] gyrfalcON hackcode1 [mkorbit] orbint potcode treecode1\n",
      "Tstop: 4.28*1 5.64*1 7.89*1 787400.0*1 6.66*1 3.00*1 [5sec CPU for each on a 11th Gen Intel(R) Core(TM) i5-1135G7 up to 4.2GHz using gcc-11]\n",
      ".1.23.456.\n",
      "CPU_USAGE  directcode  :  4.66  4.65  0.00  0.00  0.00  1730299965\n",
      "CPU_USAGE  gyrfalcON   :  4.60  4.59  0.00  0.00  0.00  1730300432\n",
      "CPU_USAGE  hackcode1   :  4.90  4.90  0.00  0.00  0.00  1730300892\n",
      "CPU_USAGE  orbint      :  4.58  4.56  0.00  0.00  0.00  1730301382\n",
      "CPU_USAGE  potcode     :  4.98  4.97  0.00  0.00  0.00  1730301840\n",
      "CPU_USAGE  treecode1   :  5.11  5.11  0.00  0.00  0.00  1730302339\n",
      "NEMOBENCH5 score:   1040.58\n",
      "Cleaning bench362389 (use clean=0 to prevent this)\n",
      "28.84user 0.03system 0:28.87elapsed 100%CPU (0avgtext+0avgdata 8312maxresident)k\n",
      "0inputs+4080outputs (2major+10150minor)pagefaults 0swaps\n"
     ]
    }
   ],
   "source": [
    "make bench5\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "f404780a-63ef-49bb-ba4a-4a4285cf9a1b",
   "metadata": {},
   "source": [
    "# Using NEMO\n",
    "Now the package is ready for anybody to use. For this a user needs to source the **nemo_start.sh** file in their shell before NEMO commands are available. \n",
    "\n",
    "In our case here:\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "927ef176-acf8-4fba-b32d-838436d75ebc",
   "metadata": {},
   "outputs": [],
   "source": [
    "source $HOME/NEMO/demo/nemo_demo/nemo_start.sh"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "c15a7fbf-ad3c-4b5e-ab40-34dc2abacf63",
   "metadata": {},
   "source": [
    "and now the **nemo** command is available to check your active version of NEMO:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "8ab13683-e91b-44be-a516-99a1e8183069",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "NEMO:        /home/teuben/NEMO/demo/nemo_demo  - Version:4.4.3\n",
      "git:         Branch:master     Counter:11692      Date: 2024/01/30_15:11:00\n",
      "python:      /home/teuben/anaconda3/bin/python  - Python 3.10.9\n",
      "OS_release:  Linux Description:\tUbuntu 22.04.3 LTS\n"
     ]
    }
   ],
   "source": [
    "nemo"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "dc2b4aeb-4352-41bb-a353-9f66e3de5808",
   "metadata": {},
   "source": [
    "## A Plummer sphere\n",
    "\n",
    "To create a Plummer (1911) sphere with 128 particles the **mkplummer** program is available.   \n",
    "\n",
    "First a few ways to get help on this program\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "02a07713-7ecc-421e-a6ee-514d6125c100",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "out              : Output file name [???]\n",
      "nbody            : Number of particles [???]\n",
      "mlow             : Low mass fraction cutoff of Plummer dist [0]\n",
      "mfrac            : Mass fraction used of Plummer distribution [0.999]\n",
      "rfrac            : Radius fraction used of Plummer distribution\n",
      "                              NOTE: the above two values are chosen so\n",
      "                                    that m( rfrac ) = mfrac                 [22.8042468]\n",
      "seed             : Seed for the random number generator [0]\n",
      "time             : Time at which snapshot is taken [0.0]\n",
      "zerocm           : Centrate snapshot (t/f)? [t]\n",
      "scale            : Model scale factor (-1=virial 1=natural) [-1]\n",
      "quiet            : 0=noisy 1=somewhat quiet 2=more quiet [0]\n",
      "massname         : If used Mass-function name (e.g. n(m)) []\n",
      "massexpr         : Mass function expression (e.g. pow(m,p)) [pow(m,p)]\n",
      "masspars         : Mass function parameters (e.g. p,0.0) [p,0.0]\n",
      "massrange        : Range for mass-spectrum (e.g. 1,2) [1,1]\n",
      "headline         : Verbiage for output []\n",
      "nmodel           : number of models to produce [1]\n",
      "mode             : 0=no data,  1=data, no analysis 2=data, analysis [1]\n",
      "VERSION          : 2-sep-2021 PJT [3.0b]\n"
     ]
    }
   ],
   "source": [
    "mkplummer help=h"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "7f205416-6dda-4f05-b63a-0a0cbb12bffb",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "MKPLUMMER(1NEMO)                                              MKPLUMMER(1NEMO)\n",
      "\n",
      "NAME\n",
      "       mkplummer - construct a Plummer model\n",
      "\n",
      "SYNOPSIS\n",
      "       mkplummer [parameters=values...]\n",
      "\n",
      "DESCRIPTION\n",
      "       mkplummer  constructs  an N-body realization of a Plummer model, with a\n",
      "       spatial or mass based cut-off, after which it (optionally)  performs  a\n",
      "       coordinate  transformation to the center-of-mass coordinate system. The\n",
      "       data are then written into a file snap-file, in a standard N-body snap‐\n",
      "       shot(5NEMO)   format.    The  model  is  constructed  in  VIRIAL  units\n",
      "       (M=G=-4E=1, with E the total energy), and finite spatial  extent  which\n",
      "       can  be  regulated  by specifying mfrac or rfrac or using their default\n",
      "       values.  The distribution function of a Plummer  model  is  spherically\n",
      "       symmetric  and  isotropic, and is a polytrope of index n = 5.  See also\n",
      "       Aarseth et al. (1974) and Plummer (1911).\n",
      "\n",
      "       There is also an implementation in Dehnen's falcON suite: mkplum(1NEMO)\n",
      "\n",
      "       For more advanced Plummer models, see mcluster(1NEMO).\n",
      "\n",
      "PARAMETERS\n",
      "       The following parameters are recognized in order; they may be given  in\n",
      "       any  order if the keyword is also given. Use --help to confirm this man\n",
      "       page is up to date.\n",
      "\n",
      "       out=snapfile             Output data is written into snapfile, in stan‐\n",
      "                                dard snapshot(5NEMO) format.\n",
      "\n",
      "       nbody=integer            Number  of  particles  nobj in N-body snapshot\n",
      "                                realization of the Plummer model.\n",
      "\n",
      "       mlow=real                inner core mass fraction within which no stars\n",
      "                                will be populated.  (Default: 0)\n",
      "\n",
      "       mfrac=real               mass fraction of the (otherwise infinitely ex‐\n",
      "                                tended) Plummer model; see  rfrac  immediately\n",
      "                                below  Note  that the total mass is still nor‐\n",
      "                                malized to 1.  (Default: rfrac=22.8042468).\n",
      "\n",
      "       rfrac=real               radius fraction of the  (otherwise  infinitely\n",
      "                                extended)  Plummer  model. If mfrac = 1.0 then\n",
      "                                particles will be sprinkled in all over space.\n",
      "                                If mfrac < 1.0 or rfrac > 0.0 then each parti‐\n",
      "                                cle is constrained to lie within both the  ra‐\n",
      "                                dial  and  (cumulative) mass bound.  For exam‐\n",
      "                                ple, if rfrac( mfrac ) > rfrac then  rfrac  is\n",
      "                                the  limiting  factor, but if rfrac( mfrac ) <\n",
      "                                rfrac then mfrac  limits  the  extent  of  the\n",
      "                                Plummer  realization.  Note: specifying either\n",
      "                                value may have no effect if the default  value\n",
      "                                of  the  other parameter is still the limiting\n",
      "                                factor;   Beware!    (Default:    mfrac=0.999;\n",
      "                                rfrac=22.8042468  , chosen so that the cumula‐\n",
      "                                tive mass at rfrac is mfrac).\n",
      "\n",
      "       seed=integer             seed for the random number generator (default:\n",
      "                                0,  which  will be converted into a unique new\n",
      "                                value using  UNIX's  clock  time,  in  seconds\n",
      "                                since 1970.0). See also xrandom(1NEMO).\n",
      "\n",
      "       time=time                Time  at  which the snapshot applies (default:\n",
      "                                time=0.0).\n",
      "\n",
      "       zerocm=t|f               Reset center of mass to zero? [default: t].\n",
      "\n",
      "       scale=scale_factor       A  scale  factor  or  scale  to  virial  units\n",
      "                                (M=G=-4E=1). Use -1 for virial units (see also\n",
      "                                VIRIAL UNITS below), and 1 to get a  model  in\n",
      "                                structural (natural) units.  Note: large scale\n",
      "                                factors means small systems with large  veloc‐\n",
      "                                ity disperson.  [Default: -1].\n",
      "\n",
      "       quiet=level              Level  of  quit  start. 0 is noisy, 1=somewhat\n",
      "                                quiet, 2=more quiet. See \"QUIET  START\"  below\n",
      "                                [default: 0].\n",
      "\n",
      "       massname=name            Identification  of  the  mass  spectrum. It is\n",
      "                                normally only a function of mass, so n(m) will\n",
      "                                suffice.  If nothing specified, all stars will\n",
      "                                have the same mass (total mass M=1). [default:\n",
      "                                not used].\n",
      "\n",
      "       massexpr=expr            Expression  for the mass-spectrum. In addition\n",
      "                                to the mass m from the massname it may contain\n",
      "                                any  variables contained in the masspars to be\n",
      "                                specified next. [default: pow(m,p)].\n",
      "\n",
      "       masspars=pars            List of parameters and their values. They  can\n",
      "                                be  used by name in the massexpr specified be‐\n",
      "                                fore. [default: p,0.0].\n",
      "\n",
      "       massrange=mlow,mhigh     Valid massrange. A  lower  and  higher  cutoff\n",
      "                                must  be supplied. The massrange has arbitrary\n",
      "                                units, since all masses will  be  rescaled  to\n",
      "                                set the total mass M=1. [default: 1,1].\n",
      "\n",
      "       headline=string          Optional  headline,  which  is  written as the\n",
      "                                first item in the snapshot file, the next item\n",
      "                                being   the  snapshot  itself.  [default:  not\n",
      "                                used].\n",
      "\n",
      "       nmodel=integer           Number of models to generate. Although  mostly\n",
      "                                meant  for  benchmarks, generating more then 1\n",
      "                                model can be  useful  to  process  very  large\n",
      "                                snapshots  (that normally won't fit in memory)\n",
      "                                in a serialized fashion. See  also  snapsplit.\n",
      "                                Most NEMO programs will Default: 1.\n",
      "\n",
      "       mode=0|1|2               The  processing  mode,  purely  for  debugging\n",
      "                                benchmarks.  0=no data written.  1=data  writ‐\n",
      "                                ten,  but  no extra analysis.  2=data written,\n",
      "                                and extra analysis done.  [Default: 1].\n",
      "\n",
      "VIRIAL UNITS\n",
      "       The scale length of a Plummer sphere  in  virial  units  is  3.pi/16  ~\n",
      "       0.589.   As  an example the following two commands should plot the same\n",
      "       \"rotation\" curve:\n",
      "\n",
      "        mkplummer - 10000 | radprof - tab=t | tabplot - 1 3 0 2 0 1 yapp=1/xs\n",
      "        rotcurves plummer '0,1,3*pi/16' xrange=0:2 yrange=0:1       yapp=2/xs\n",
      "\n",
      "QUIET START\n",
      "       For small N-body systems it can easily happen that small random fluctu‐\n",
      "       ations  cause  a  unacceptabel  large  deviation  from an ideal Plummer\n",
      "       sphere. One way to achieve more \"quiet\" initial conditions is by  posi‐\n",
      "       tioning  the particles more uniformly in their 1/N mass shells, instead\n",
      "       of uniformly filling the space between 0 and 1. This is  controlled  by\n",
      "       the  quiet=1  setting.    An  even  more quiet start can be achieved by\n",
      "       placing the particles on exactly the radius compatible  with  its  mass\n",
      "       fraction, this is achieved with the the quiet=2 setting.\n",
      "\n",
      "       In  this  example  you can clearly see the difference between the radii\n",
      "       selected:\n",
      "\n",
      "        mkplummer - 10 quiet=0 zerocm=f | snapsort - - r | snapprint - r | tabplot - 0 1 line=1,1 point=2,0.1\n",
      "        mkplummer - 10 quiet=1 zerocm=f | snapsort - - r | snapprint - r | tabplot - 0 1 line=1,1 point=2,0.1\n",
      "        mkplummer - 10 quiet=2 zerocm=f | snapsort - - r | snapprint - r | tabplot - 0 1 line=1,1 point=2,0.1\n",
      "\n",
      "       Important to note that with zerocm=f the center  of  mass  will  drift,\n",
      "       while  the  \"mathematical  center\"  was placed at the origin. This will\n",
      "       counter the quietness, if you will.\n",
      "\n",
      "BUGS\n",
      "       A non-delta function mass-spectrum will not create a  properly  virial‐\n",
      "       ized system yet. See snapvirial(1NEMO)\n",
      "\n",
      "       For  very  large (>1000) ratio in the mass ranges the spline interpola‐\n",
      "       tion, used in frandom(3NEMO), can fail using a valid [0,1] range.\n",
      "\n",
      "EXAMPLES\n",
      "       mkplummer can also be used to create a plummer sphere with a mass spec‐\n",
      "       trum, e.g.  a Salpeter mass spectrum with\n",
      "\n",
      "        mkplummer salpeter.dat 10000 massname='n(m)' massexpr='pow(m,p)' masspars=p,-2.35 massrange=0.1,10\n",
      "\n",
      "       Another  method to create a Plummer sphere is by using the Osipkov-Mer‐\n",
      "       ritt tables in NEMO, e.g.\n",
      "\n",
      "        plummer plum.dat ntab=1024\n",
      "        mkommod plum.dat plum.snap nbody=10000\n",
      "\n",
      "       or in ZENO the new General Spherical Profile:\n",
      "\n",
      "       plumsnap plum1.snap\n",
      "\n",
      "       plumgsp plum.gsp\n",
      "       gsprealize plum.gsp plum.snap zerocm=true\n",
      "       snapcopy plum.snap plum2.snap\n",
      "\n",
      "       with a note that ZENO files may need an  extra  snapcopy(1NEMO)  to  be\n",
      "       compatible with NEMO snapshot(5NEMO) files.\n",
      "\n",
      "BENCHMARKS\n",
      "       The  default benchmark (see Benchfile) creates a 10,000,000 snapshot in\n",
      "       double precision, with and without writing to a local file:\n",
      "\n",
      "       cd $NEMO/nemo/src/nbody/init/\n",
      "       make -f Benchfile bench0 bench1\n",
      "\n",
      "           or\n",
      "\n",
      "       /usr/bin/time mkplummer . 10000000\n",
      "       /usr/bin/time mkplummer bench1.snap 10000000\n",
      "\n",
      "       with some sample CPU for bench0:\n",
      "          xps13       3.1s  or 171 MB/s\n",
      "          t480        4.9s  or  72 MB/s\n",
      "       the time difference betweeen bench0 and bench1 can  be  interpreted  as\n",
      "       the time needed to write 535MB (for 10M particles)\n",
      "\n",
      "FILES\n",
      "       NEMO/src/nbody/init/mkplummer.c\n",
      "\n",
      "SEE ALSO\n",
      "       mkpolytrope(1NEMO),    snapvirial(1NEMO),    mkplummer(3NEMO),    snap‐\n",
      "       mass(1NEMO), snapsplit(1NEM0),  mkplum(1NEMO),  mcluster(1NEMO),  xran‐\n",
      "       dom(3NEMO)\n",
      "\n",
      "       H.C.Plummer (1911), MNRAS, 71, 460.\n",
      "\n",
      "       S.J.  Aarseth,  M.  Henon and R.  Wielen (1974), Astron. and Astrophys.\n",
      "       37, p. 183.\n",
      "\n",
      "       A.H.W. Kuepper, Th. Maschberger, P. Kroupa and H. Baumgardt, 2011,  MN‐\n",
      "       RAS, 417, 2300 (McLuster)\n",
      "\n",
      "       Arnold    et    al.   (2022)   -   https://arxiv.org/abs/2207.10681   -\n",
      "       https://github.com/r-j-arnold/gen_fractal_star_clusters\n",
      "\n",
      "ADS\n",
      "       @ads 1974A&A....37..183A\n",
      "\n",
      "AUTHOR\n",
      "       Piet Hut (Peter Teuben)\n",
      "\n",
      "FILES\n",
      "       ~/src/nbody/init              mkplummer.c\n",
      "\n",
      "HISTORY\n",
      "       23-Apr-87      Version 1.0: created                                   PIET\n",
      "       10-Jun-88      Version 1.1: created                                   PIET\n",
      "       xx-xxx-88      V1.2: zerocm keyword added                             PJT\n",
      "       xx-Mar-89      V2.0: full new snapshot version                        + doc PJT\n",
      "       15-nov-90      V2.3: mass-spectrum and cleanup                        for NEMO 2.xPJT\n",
      "       6-jun-96       V2.5d: report total mass before scaling                PJT\n",
      "       21-mar-04      V2.7: added mlow=                                      PJT+NCM\n",
      "       11-apr-05      V2.8: added nmodel=                                    PJT\n",
      "       15-sep-10      V2.9: clarified rfrac and allow rfrac<0                PJT\n",
      "       2-dec-2017     documented mcluster                                    PJT\n",
      "       29-mar-2021    benchmark                                              PJT\n",
      "       25-sep-2023    describe quiet starts                                  PJT\n",
      "\n",
      "                               20 November 2023               MKPLUMMER(1NEMO)\n"
     ]
    }
   ],
   "source": [
    "mkplummer --man"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "e3618d9c-39cf-44f4-b226-9ca07537a8f1",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "mkplummer out=??? nbody=??? mlow=0 mfrac=0.999 rfrac=22.8042468 seed=0 time=0.0 zerocm=t scale=-1 quiet=0 massname= massexpr=pow(m,p) masspars=p,0.0 massrange=1,1 headline= nmodel=1 mode=1 VERSION=3.0b\n"
     ]
    }
   ],
   "source": [
    "mkplummer --help\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "4eb58e94-4649-4693-bb26-0444c010780d",
   "metadata": {},
   "source": [
    "## Initial conditions\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "9caccf67-7ea6-4319-bb0a-71cebd7a7b0e",
   "metadata": {},
   "outputs": [],
   "source": [
    "mkplummer p128 128"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "0d05dabb-f4f2-42ec-a08c-b00becc4fb00",
   "metadata": {},
   "source": [
    "The contents is binary.  So viewing contents needs a program **tsf** (*type structured file*)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "3ef8397c-1275-44db-a8b0-b7df102cd755",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "char Headline[35] \"init_xrandom: seed used 1706751345\"\n",
      "char History[32] \"mkplummer p128 128 VERSION=3.0b\"\n",
      "set SnapShot\n",
      "  set Parameters\n",
      "    int Nobj 128 \n",
      "    double Time 0.00000 \n",
      "  tes\n",
      "  set Particles\n",
      "    int CoordSystem 66306 \n",
      "    double Mass[128] 0.00781250 0.00781250 0.00781250 0.00781250 \n",
      "      0.00781250 0.00781250 0.00781250 0.00781250 0.00781250 \n",
      "      0.00781250 0.00781250 0.00781250 0.00781250 0.00781250 \n",
      "      0.00781250 0.00781250 0.00781250 0.00781250 0.00781250 \n",
      "      . . .\n",
      "    double PhaseSpace[128][2][3] 0.398609 0.128806 -0.381117 -0.379700 \n",
      "      -0.153210 -0.545662 0.0461589 -0.00924254 -0.342256 0.125321 \n",
      "      -0.184185 0.607058 -0.471192 0.170905 -0.118584 -0.321103 \n",
      "      -0.110769 -0.391427 1.03572 0.906998 -0.0721780 0.0139824 \n",
      "      . . .\n",
      "  tes\n",
      "tes\n"
     ]
    }
   ],
   "source": [
    "tsf p128"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "60d90da4-95b3-4220-95a0-f3d4d944332a",
   "metadata": {},
   "source": [
    "## Integrate it:\n",
    "\n",
    "The **hackcode1** program is the original Barnes and Hut (1985) tree code N-logN algorithm to integrate an N-body system."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "eeef980c-e486-43f5-a181-8d50136e7e33",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "init_xrandom: seed used 1706751345\n",
      "\n",
      "       nbody        freq         eps         tol\n",
      "         128       32.00      0.0500      1.0000\n",
      "\n",
      "\toptions: mass,phase\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.000   -0.2588   -0.4961      6501        30        20      0.00\n",
      "\n",
      "\t        cm pos   -0.0000    0.0000   -0.0000\n",
      "\t        cm vel    0.0000   -0.0000    0.0000\n",
      "\n",
      "\tparticle data written\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.031   -0.2590   -0.4957      6448        31        19      0.00\n",
      "\n",
      "\t        cm pos   -0.0000    0.0000   -0.0000\n",
      "\t        cm vel   -0.0001    0.0001   -0.0001\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.062   -0.2592   -0.4952      6685        33        18      0.00\n",
      "\n",
      "\t        cm pos   -0.0000    0.0000   -0.0000\n",
      "\t        cm vel   -0.0003    0.0001   -0.0002\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.094   -0.2597   -0.4942      6685        32        19      0.00\n",
      "\n",
      "\t        cm pos   -0.0000    0.0000   -0.0000\n",
      "\t        cm vel   -0.0005    0.0002   -0.0002\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.125   -0.2595   -0.4942      6738        34        18      0.00\n",
      "\n",
      "\t        cm pos   -0.0000    0.0000   -0.0000\n",
      "\t        cm vel   -0.0006    0.0002   -0.0002\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.156   -0.2595   -0.4944      6625        33        18      0.00\n",
      "\n",
      "\t        cm pos   -0.0001    0.0000   -0.0000\n",
      "\t        cm vel   -0.0008    0.0003   -0.0003\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.188   -0.2598   -0.4944      6655        33        18      0.00\n",
      "\n",
      "\t        cm pos   -0.0001    0.0000   -0.0000\n",
      "\t        cm vel   -0.0009    0.0003   -0.0003\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.219   -0.2595   -0.4946      6833        34        18      0.00\n",
      "\n",
      "\t        cm pos   -0.0001    0.0000   -0.0000\n",
      "\t        cm vel   -0.0011    0.0003   -0.0004\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.250   -0.2595   -0.4947      6930        36        17      0.00\n",
      "\n",
      "\t        cm pos   -0.0002    0.0000   -0.0001\n",
      "\t        cm vel   -0.0012    0.0003   -0.0005\n",
      "\n",
      "\tparticle data written\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.281   -0.2595   -0.4945      6675        33        18      0.00\n",
      "\n",
      "\t        cm pos   -0.0002    0.0001   -0.0001\n",
      "\t        cm vel   -0.0012    0.0004   -0.0006\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.312   -0.2592   -0.4944      6445        30        20      0.00\n",
      "\n",
      "\t        cm pos   -0.0002    0.0001   -0.0001\n",
      "\t        cm vel   -0.0013    0.0005   -0.0007\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.344   -0.2594   -0.4937      6436        30        20      0.00\n",
      "\n",
      "\t        cm pos   -0.0003    0.0001   -0.0001\n",
      "\t        cm vel   -0.0013    0.0006   -0.0008\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.375   -0.2589   -0.4930      6535        30        20      0.00\n",
      "\n",
      "\t        cm pos   -0.0003    0.0001   -0.0002\n",
      "\t        cm vel   -0.0014    0.0006   -0.0008\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.406   -0.2589   -0.4914      6572        31        20      0.00\n",
      "\n",
      "\t        cm pos   -0.0004    0.0001   -0.0002\n",
      "\t        cm vel   -0.0015    0.0006   -0.0008\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.438   -0.2591   -0.4902      6447        29        20      0.00\n",
      "\n",
      "\t        cm pos   -0.0004    0.0001   -0.0002\n",
      "\t        cm vel   -0.0016    0.0006   -0.0009\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.469   -0.2594   -0.4895      6455        30        19      0.00\n",
      "\n",
      "\t        cm pos   -0.0005    0.0002   -0.0002\n",
      "\t        cm vel   -0.0017    0.0006   -0.0009\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.500   -0.2587   -0.4903      6550        33        18      0.00\n",
      "\n",
      "\t        cm pos   -0.0005    0.0002   -0.0003\n",
      "\t        cm vel   -0.0019    0.0006   -0.0010\n",
      "\n",
      "\tparticle data written\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.531   -0.2588   -0.4905      6445        31        18      0.00\n",
      "\n",
      "\t        cm pos   -0.0006    0.0002   -0.0003\n",
      "\t        cm vel   -0.0020    0.0006   -0.0010\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.562   -0.2585   -0.4908      6405        30        19      0.00\n",
      "\n",
      "\t        cm pos   -0.0006    0.0002   -0.0003\n",
      "\t        cm vel   -0.0021    0.0007   -0.0010\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.594   -0.2585   -0.4904      6491        31        18      0.00\n",
      "\n",
      "\t        cm pos   -0.0007    0.0002   -0.0004\n",
      "\t        cm vel   -0.0021    0.0006   -0.0010\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.625   -0.2591   -0.4896      6482        33        17      0.00\n",
      "\n",
      "\t        cm pos   -0.0008    0.0003   -0.0004\n",
      "\t        cm vel   -0.0022    0.0006   -0.0011\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.656   -0.2591   -0.4895      6658        35        16      0.00\n",
      "\n",
      "\t        cm pos   -0.0008    0.0003   -0.0004\n",
      "\t        cm vel   -0.0023    0.0007   -0.0011\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.688   -0.2596   -0.4884      6675        35        16      0.00\n",
      "\n",
      "\t        cm pos   -0.0009    0.0003   -0.0005\n",
      "\t        cm vel   -0.0023    0.0008   -0.0012\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.719   -0.2594   -0.4876      6443        33        16      0.00\n",
      "\n",
      "\t        cm pos   -0.0010    0.0003   -0.0005\n",
      "\t        cm vel   -0.0024    0.0008   -0.0013\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.750   -0.2594   -0.4868      6503        34        16      0.00\n",
      "\n",
      "\t        cm pos   -0.0011    0.0004   -0.0005\n",
      "\t        cm vel   -0.0024    0.0008   -0.0014\n",
      "\n",
      "\tparticle data written\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.781   -0.2594   -0.4865      6487        34        16      0.00\n",
      "\n",
      "\t        cm pos   -0.0011    0.0004   -0.0006\n",
      "\t        cm vel   -0.0023    0.0007   -0.0014\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.812   -0.2598   -0.4860      6376        33        16      0.00\n",
      "\n",
      "\t        cm pos   -0.0012    0.0004   -0.0006\n",
      "\t        cm vel   -0.0023    0.0007   -0.0015\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.844   -0.2596   -0.4865      6414        32        17      0.00\n",
      "\n",
      "\t        cm pos   -0.0013    0.0004   -0.0007\n",
      "\t        cm vel   -0.0022    0.0006   -0.0015\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.875   -0.2596   -0.4867      6395        31        18      0.00\n",
      "\n",
      "\t        cm pos   -0.0014    0.0004   -0.0007\n",
      "\t        cm vel   -0.0022    0.0005   -0.0015\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.906   -0.2595   -0.4863      6403        32        17      0.00\n",
      "\n",
      "\t        cm pos   -0.0014    0.0005   -0.0008\n",
      "\t        cm vel   -0.0021    0.0004   -0.0014\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.938   -0.2593   -0.4854      6138        29        18      0.00\n",
      "\n",
      "\t        cm pos   -0.0015    0.0005   -0.0008\n",
      "\t        cm vel   -0.0021    0.0004   -0.0014\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.969   -0.2589   -0.4843      6092        29        17      0.00\n",
      "\n",
      "\t        cm pos   -0.0015    0.0005   -0.0009\n",
      "\t        cm vel   -0.0021    0.0004   -0.0014\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.000   -0.2588   -0.4829      6070        29        17      0.00\n",
      "\n",
      "\t        cm pos   -0.0016    0.0005   -0.0009\n",
      "\t        cm vel   -0.0022    0.0004   -0.0014\n",
      "\n",
      "\tparticle data written\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.031   -0.2589   -0.4814      6048        29        17      0.00\n",
      "\n",
      "\t        cm pos   -0.0017    0.0005   -0.0009\n",
      "\t        cm vel   -0.0023    0.0004   -0.0014\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.062   -0.2589   -0.4795      6255        30        18      0.00\n",
      "\n",
      "\t        cm pos   -0.0018    0.0005   -0.0010\n",
      "\t        cm vel   -0.0023    0.0003   -0.0014\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.094   -0.2588   -0.4779      6241        30        18      0.00\n",
      "\n",
      "\t        cm pos   -0.0018    0.0005   -0.0010\n",
      "\t        cm vel   -0.0024    0.0003   -0.0013\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.125   -0.2589   -0.4764      6196        30        17      0.00\n",
      "\n",
      "\t        cm pos   -0.0019    0.0005   -0.0011\n",
      "\t        cm vel   -0.0024    0.0002   -0.0012\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.156   -0.2588   -0.4753      6014        29        17      0.00\n",
      "\n",
      "\t        cm pos   -0.0020    0.0005   -0.0011\n",
      "\t        cm vel   -0.0025    0.0002   -0.0011\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.188   -0.2588   -0.4741      6044        29        17      0.00\n",
      "\n",
      "\t        cm pos   -0.0021    0.0005   -0.0011\n",
      "\t        cm vel   -0.0025    0.0002   -0.0011\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.219   -0.2585   -0.4732      6107        29        18      0.00\n",
      "\n",
      "\t        cm pos   -0.0021    0.0005   -0.0012\n",
      "\t        cm vel   -0.0025    0.0001   -0.0011\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.250   -0.2586   -0.4722      6262        30        18      0.00\n",
      "\n",
      "\t        cm pos   -0.0022    0.0006   -0.0012\n",
      "\t        cm vel   -0.0025    0.0000   -0.0011\n",
      "\n",
      "\tparticle data written\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.281   -0.2586   -0.4712      6272        30        18      0.00\n",
      "\n",
      "\t        cm pos   -0.0023    0.0005   -0.0013\n",
      "\t        cm vel   -0.0025   -0.0001   -0.0011\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.312   -0.2585   -0.4699      6206        30        17      0.00\n",
      "\n",
      "\t        cm pos   -0.0024    0.0005   -0.0013\n",
      "\t        cm vel   -0.0025   -0.0001   -0.0011\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.344   -0.2581   -0.4691      6248        30        18      0.00\n",
      "\n",
      "\t        cm pos   -0.0025    0.0005   -0.0013\n",
      "\t        cm vel   -0.0024   -0.0002   -0.0011\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.375   -0.2581   -0.4683      6236        30        18      0.00\n",
      "\n",
      "\t        cm pos   -0.0025    0.0005   -0.0014\n",
      "\t        cm vel   -0.0024   -0.0003   -0.0011\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.406   -0.2582   -0.4680      6309        31        17      0.00\n",
      "\n",
      "\t        cm pos   -0.0026    0.0005   -0.0014\n",
      "\t        cm vel   -0.0024   -0.0004   -0.0011\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.438   -0.2582   -0.4678      6334        32        17      0.00\n",
      "\n",
      "\t        cm pos   -0.0027    0.0005   -0.0014\n",
      "\t        cm vel   -0.0024   -0.0004   -0.0012\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.469   -0.2583   -0.4675      6430        33        16      0.00\n",
      "\n",
      "\t        cm pos   -0.0028    0.0005   -0.0015\n",
      "\t        cm vel   -0.0024   -0.0004   -0.0012\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.500   -0.2583   -0.4670      6413        33        16      0.00\n",
      "\n",
      "\t        cm pos   -0.0028    0.0005   -0.0015\n",
      "\t        cm vel   -0.0024   -0.0003   -0.0012\n",
      "\n",
      "\tparticle data written\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.531   -0.2578   -0.4672      6277        30        18      0.00\n",
      "\n",
      "\t        cm pos   -0.0029    0.0005   -0.0015\n",
      "\t        cm vel   -0.0024   -0.0001   -0.0013\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.562   -0.2579   -0.4676      6220        30        18      0.00\n",
      "\n",
      "\t        cm pos   -0.0030    0.0005   -0.0016\n",
      "\t        cm vel   -0.0023   -0.0000   -0.0013\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.594   -0.2580   -0.4686      6254        29        19      0.00\n",
      "\n",
      "\t        cm pos   -0.0030    0.0005   -0.0016\n",
      "\t        cm vel   -0.0023    0.0001   -0.0013\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.625   -0.2575   -0.4702      6351        31        18      0.00\n",
      "\n",
      "\t        cm pos   -0.0031    0.0005   -0.0017\n",
      "\t        cm vel   -0.0022    0.0002   -0.0014\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.656   -0.2574   -0.4708      6298        30        18      0.00\n",
      "\n",
      "\t        cm pos   -0.0032    0.0005   -0.0017\n",
      "\t        cm vel   -0.0021    0.0002   -0.0014\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.688   -0.2578   -0.4709      6213        29        18      0.00\n",
      "\n",
      "\t        cm pos   -0.0033    0.0005   -0.0018\n",
      "\t        cm vel   -0.0021    0.0002   -0.0014\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.719   -0.2581   -0.4716      6471        30        19      0.00\n",
      "\n",
      "\t        cm pos   -0.0033    0.0005   -0.0018\n",
      "\t        cm vel   -0.0021    0.0002   -0.0014\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.750   -0.2583   -0.4726      6655        33        18      0.00\n",
      "\n",
      "\t        cm pos   -0.0034    0.0005   -0.0018\n",
      "\t        cm vel   -0.0022    0.0001   -0.0014\n",
      "\n",
      "\tparticle data written\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.781   -0.2581   -0.4737      6766        35        17      0.00\n",
      "\n",
      "\t        cm pos   -0.0035    0.0005   -0.0019\n",
      "\t        cm vel   -0.0022    0.0001   -0.0014\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.812   -0.2575   -0.4748      6774        36        16      0.00\n",
      "\n",
      "\t        cm pos   -0.0035    0.0005   -0.0019\n",
      "\t        cm vel   -0.0022    0.0002   -0.0014\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.844   -0.2577   -0.4750      6776        36        16      0.00\n",
      "\n",
      "\t        cm pos   -0.0036    0.0005   -0.0020\n",
      "\t        cm vel   -0.0022    0.0002   -0.0014\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.875   -0.2578   -0.4754      6791        36        16      0.00\n",
      "\n",
      "\t        cm pos   -0.0037    0.0005   -0.0020\n",
      "\t        cm vel   -0.0023    0.0002   -0.0015\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.906   -0.2583   -0.4759      6746        35        16      0.00\n",
      "\n",
      "\t        cm pos   -0.0037    0.0005   -0.0021\n",
      "\t        cm vel   -0.0022    0.0002   -0.0016\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.938   -0.2578   -0.4774      6605        34        17      0.00\n",
      "\n",
      "\t        cm pos   -0.0038    0.0005   -0.0021\n",
      "\t        cm vel   -0.0021    0.0002   -0.0017\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.969   -0.2581   -0.4782      6598        34        17      0.00\n",
      "\n",
      "\t        cm pos   -0.0039    0.0005   -0.0022\n",
      "\t        cm vel   -0.0021    0.0002   -0.0017\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       2.000   -0.2579   -0.4794      6568        34        16      0.00\n",
      "\n",
      "\t        cm pos   -0.0039    0.0006   -0.0022\n",
      "\t        cm vel   -0.0020    0.0002   -0.0018\n",
      "\n",
      "\tparticle data written\n"
     ]
    }
   ],
   "source": [
    "hackcode1 p128 p128.out tstop=2 "
   ]
  },
  {
   "cell_type": "markdown",
   "id": "ccecb826-155e-4c1b-9455-e09ac1a40fcc",
   "metadata": {},
   "source": [
    "Display some diagnostics, such as energy and center of mass motion"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "id": "6c0ebe67-32c8-40c6-8da1-465175882716",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "### nemo Debug Info: 65 diagnostic frames read\n",
      "Worst fractional energy loss dE/E = (E_t-E_0)/E_0 = -0.00556972 at T = 1.65625\n"
     ]
    }
   ],
   "source": [
    "snapdiagplot p128.out yapp=fig1.ps\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "f89cf800-6c29-4cb9-b788-090f8012ce6b",
   "metadata": {},
   "source": [
    "This gives around 1% energy conservation, whichis not too bad, at least for galactic type simulations. For star clusters probably not too great at all.\n",
    "\n",
    "Now plot in a two by two panel the X-Y projections of the integration at times 0, 1 and 2."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "ef31bc23-25db-48f5-ab4b-5d0e90fffa86",
   "metadata": {},
   "outputs": [],
   "source": [
    "snapplot p128.out nxy=2,2 times=0,1,2 yapp=fig2.ps"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "620bd7c0-3842-4bec-8101-083c6be82436",
   "metadata": {},
   "source": [
    "## Compiling code\n",
    "\n",
    "Although the build has done this, the **mknemo** command will recompile a program. This can be useful if the code needs to be edited for a bug fix and new feature. The **mknemo** command can be issued anywhere, and will show where the file in question lives. It can then easily be edited and recompiled, and added to $NEMOBIN. Except for editing, the **mknemo** command does all of this."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "id": "ff99c466-eb36-4008-a9e3-f4dae78bff41",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "MKNEMO> Searching tsf.c: \n",
      "found one: /home/teuben/NEMO/demo/nemo_demo/src/kernel/io/tsf.c\n",
      "gcc -g -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE  -fpic -rdynamic  -Dlinux -DSYSV  -I/home/teuben/NEMO/demo/nemo_demo/inc -I/home/teuben/NEMO/demo/nemo_demo/lib -I/home/teuben/NEMO/demo/nemo_demo/opt/include    -Wall -Wimplicit-function-declaration  -D_GNU_SOURCE -std=c99  -o tsf tsf.c -L/home/teuben/NEMO/demo/nemo_demo/lib -L/home/teuben/NEMO/demo/nemo_demo/opt/lib          -lnemo -ldl    -lm   -L/usr/lib/gcc/x86_64-linux-gnu/11 -L/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/11/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/11/../../.. -lgfortran -lm -lquadmath \n",
      "\n"
     ]
    }
   ],
   "source": [
    "mknemo tsf"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "322147e8-4bd9-4eee-b0e3-df2356c56b9b",
   "metadata": {},
   "source": [
    "The output also reminds you wehre the **tsf.c** source code lives, so it can be easily put in the editor.\n",
    "\n",
    "\n",
    "Here a program that uses graphics. These can be notoriously hard to link correctly."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "id": "ade3834a-4887-4678-8955-96799126d652",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "MKNEMO> Searching tabplot.c: \n",
      "found one: /home/teuben/NEMO/demo/nemo_demo/src/kernel/tab/tabplot.c\n",
      "gcc -g -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE  -fpic -rdynamic  -Dlinux -DSYSV  -I/home/teuben/NEMO/demo/nemo_demo/inc -I/home/teuben/NEMO/demo/nemo_demo/lib -I/home/teuben/NEMO/demo/nemo_demo/opt/include    -Wall -Wimplicit-function-declaration  -D_GNU_SOURCE -std=c99 -o tabplot tabplot.c \\\n",
      "\t-L/home/teuben/NEMO/demo/nemo_demo/lib -L/home/teuben/NEMO/demo/nemo_demo/opt/lib          -lnemo -ldl    -lm  /home/teuben/NEMO/demo/nemo_demo/lib/yapp_ps.o   -lm\n",
      "\n"
     ]
    }
   ],
   "source": [
    "mknemo tabplot"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "4d5ff810-1c91-4323-b344-eba52c12f84f",
   "metadata": {},
   "source": [
    "and a simple benchmark if graphics works in the **tabgen + tabplot** pipe:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "id": "5b1df81b-00b4-4855-8261-7031e82ffbe0",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "### nemo Debug Info: read 10 points\n",
      "### nemo Debug Info: min and max value in xcolumns 1: [0.011987 : 0.766750]\n",
      "### nemo Debug Info: min and max value in ycolumns 2: [0.004308 : 0.988963]\n",
      "### nemo Debug Info: X:min and max value reset to : [-0.025751 : 0.804488]\n",
      "### nemo Debug Info: Y:min and max value reset to : [-0.044925 : 1.038196]\n"
     ]
    }
   ],
   "source": [
    "tabgen - | tabplot - point=2,0.1 yapp=fig3.ps"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "id": "0d94ba30-5ac9-4838-a642-75cbbe0646c8",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Started at:   Wed Jan 31 08:33:33 PM EST 2024\n",
      "Done at:      Wed Jan 31 08:35:46 PM EST 2024\n"
     ]
    }
   ],
   "source": [
    "date1=$(date)\n",
    "echo \"Started at:   $date0\"\n",
    "echo \"Done at:      $date1\""
   ]
  },
  {
   "cell_type": "markdown",
   "id": "b475becd-f814-4dd0-9d20-59970896b1c4",
   "metadata": {},
   "source": [
    "How did you do?  Did you get 298 executables in $NEMOBIN, did you install take about 2 minutes?"
   ]
  }
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