From 8aec5532e8ae6e1ca9c3fd043d29bb81d4b8cc32 Mon Sep 17 00:00:00 2001
From: Noe Brucy <noe.brucy@cea.fr>
Date: Tue, 5 Jan 2021 16:09:00 +0100
Subject: [PATCH] [comparator] [log extractor] extract cons even without emag
 output

---
 .flake8       |  2 ++
 comparator.py | 16 ++++++++++------
 pp_params.yml |  2 ++
 3 files changed, 14 insertions(+), 6 deletions(-)

diff --git a/.flake8 b/.flake8
index f5fac5c..3551fe6 100644
--- a/.flake8
+++ b/.flake8
@@ -5,3 +5,5 @@ ignore =
        E203
        # Line break before binary operator
        W503
+       # Invalid escape sequence '\['
+       W605
diff --git a/comparator.py b/comparator.py
index e8d5bb9..405a61f 100644
--- a/comparator.py
+++ b/comparator.py
@@ -253,11 +253,13 @@ class Comparator(Aggregator, HDF5Container):
         return series
 
     def _extract_cons_from_log(self, series, log_filename, run):
-        cmd_grep = "grep 'Main step' {} -A 2".format(log_filename)
+        mhd = self.pp_params.input.mhd
+        nlines = 2 + int(mhd)  # Number of useful lines
+        cmd_grep = "grep 'Main step' {} -A {}".format(log_filename, nlines - 1)
         content = os.popen(cmd_grep).readlines()
-        for i in range(0, len(content), 4):
+        for i in range(0, len(content), nlines + 1):
             series["time"][run].append(
-                np.float(content[i + 2].split("=")[2].split()[0])
+                np.float(content[i + nlines - 1].split("=")[2].split()[0])
             )
             series["step"][run].append(np.int(content[i].split("=")[1].split()[0]))
             series["mcons"][run].append(np.float(content[i].split("=")[2].split()[0]))
@@ -265,9 +267,11 @@ class Comparator(Aggregator, HDF5Container):
             series["epot"][run].append(np.float(content[i].split("=")[4].split()[0]))
             series["ekin"][run].append(np.float(content[i].split("=")[5].split()[0]))
             series["eint"][run].append(np.float(content[i].split("=")[6].split()[0]))
-            series["emag"][run].append(
-                np.float(content[i + 1].split("=")[1].split()[0])
-            )
+            if mhd:
+                emag = np.float(content[i + 1].split("=")[1].split()[0])
+                series["emag"][run].append(emag)
+            else:
+                series["emag"][run].append(0.0)
         return series
 
     def _extract_rms_from_log(self, series, log_filename, run):
diff --git a/pp_params.yml b/pp_params.yml
index 55876e3..3e6c2fb 100644
--- a/pp_params.yml
+++ b/pp_params.yml
@@ -45,6 +45,7 @@ pymses: # Parameters for Pymses reader
     variables :  ["rho","vel","Br","Bl","P", "g", "phi"]  # Read these variables
     order     : '<'                                       # Bit order
 
+
     # Processing options
     levelmax : 20                      # Maximal AMR level visited when looking levels
     fft      : False                   # Quick and dirty rendering using FFT
@@ -66,6 +67,7 @@ input: # Parameters on how to look for input files (= output from Ramses)
     log_prefix     : "run.log"         # Prefix of the log file
     label_filename : "label.txt"       # Name of the label file
     nml_filename   : "run.nml"         # name of the namelist file
+    mhd            : True              # Is MHD activated
 
 out: # Parameters for post processing
     tag         : ""                   # Tag for the image