Improving halo fits (#76)

* Add periodic distances

* Little corrections

* Fix little bug

* Modernise the script

* Small updates

* Remove clump

* Add new halo routines

* Fix weights

* Modernise the script

* Add check ups on convergence

* More convergence check ups

* Edit bounds

* Add default argument

* Update fit heuristic and NaNs

* Change maxiter

* Switch NFW minimization to log-sapce

* Remove print statement

* Turn convert_from_box abstract property required for all boxes.

* Move files

* Simplify script

* Improve the argument parser

* Remove optinal argument

* Improve argument parser

* Add a minimum concentration limit

scripts/old/pre_mmain.py

@@ -0,0 +1,64 @@
+# Copyright (C) 2022 Richard Stiskalek
+# This program is free software; you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by the
+# Free Software Foundation; either version 3 of the License, or (at your
+# option) any later version.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General
+# Public License for more details.
+#
+# You should have received a copy of the GNU General Public License along
+# with this program; if not, write to the Free Software Foundation, Inc.,
+# 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
+"""
+Script to generate the mmain files, i.e. sums up the substructe of children.
+"""
+from datetime import datetime
+
+import numpy
+from mpi4py import MPI
+from taskmaster import master_process, worker_process
+
+try:
+    import csiborgtools
+except ModuleNotFoundError:
+    import sys
+    sys.path.append("../")
+    import csiborgtools
+
+# Get MPI things
+comm = MPI.COMM_WORLD
+rank = comm.Get_rank()
+nproc = comm.Get_size()
+
+paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
+mmain_reader = csiborgtools.read.MmainReader(paths)
+
+
+def do_mmain(nsim):
+    nsnap = max(paths.get_snapshots(nsim))
+    # NOTE: currently works for highest snapshot anyway
+    mmain, ultimate_parent = mmain_reader.make_mmain(nsim, verbose=False)
+    numpy.savez(paths.mmain(nsnap, nsim),
+                mmain=mmain, ultimate_parent=ultimate_parent)
+
+###############################################################################
+#                             MPI task delegation                             #
+###############################################################################
+
+
+if nproc > 1:
+    if rank == 0:
+        tasks = list(paths.get_ics("csiborg"))
+        master_process(tasks, comm, verbose=True)
+    else:
+        worker_process(do_mmain, comm, verbose=False)
+else:
+    tasks = paths.get_ics("csiborg")
+    for task in tasks:
+        print(f"{datetime.now()}: completing task `{task}`.", flush=True)
+        do_mmain(task)
+
+comm.Barrier()

scripts/old/pre_mmain.sh

@@ -0,0 +1,14 @@
+nthreads=102
+memory=5
+queue="cmb"
+env="/mnt/zfsusers/rstiskalek/csiborgtools/venv_csiborg/bin/python"
+file="pre_mmain.py"
+
+# pythoncm="$env $file"
+# $pythoncm
+
+
+cm="addqueue -q $queue -n $nthreads -m $memory $env $file"
+echo "Submitting:"
+echo $cm
+$cm