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Hello,

I am trying to compile PeleAnalysis/Src/ModelSpecificAnalysis/plotTransportCoeff.cpp and I had to make the following changes to the GNUMakefile in the above directory to point to the right submodules:

PELE_ANALYSIS_HOME ?= /home/suryanarayan/PeleAnalysis
PELE_PHYSICS_HOME ?= /home/suryanarayan/PeleC/Submodules/PelePhysics
AMREX_HOME ?= /home/suryanarayan/PeleC/Submodules/AMReX

Basically, I used my local PeleC submodules to point to the AMReX and PelePhysics folders instead of installing them again.

I get the following errors while trying to compile plotTransportCoeff.cpp:

plotTransportCoeff.cpp:13:10: fatal error: mechanism.h: No such file or directory
   13 | #include <mechanism.h>
      |          ^~~~~~~~~~~~~
compilation terminated.

When I changed it to mechanism.H instead of mechanism.h I get:

plotTransportCoeff.cpp:14:10: fatal error: chemistry_file.H: No such file or directory
   14 | #include <chemistry_file.H>
      |          ^~~~~~~~~~~~~~~~~~
compilation terminated.

I comment that line and end-up with:

plotTransportCoeff.cpp:17:10: fatal error: Transport_F.H: No such file or directory
   17 | #include <Transport_F.H>
      |          ^~~~~~~~~~~~~~~

Is it possibly an environment issue?

Also, I fixed a few minor errors that popped up during compile time for conditionalMeans. Just a few changes in the header files, adding a few std:: namespaces:

1. PeleAnalysis/Src/conditionalMean.cpp

   Line 10 in 0f30b85

   #include <WritePlotFile.H>

   changed to #include <AMReX_PlotFileUtil.H>
2. Removed

   PeleAnalysis/Src/conditionalMean.cpp

   Line 11 in 0f30b85

   #include <AppendToPlotFile.H>

3. PeleAnalysis/Src/conditionalMean.cpp

   Line 122 in 0f30b85

   Vector<string> compNames;

   becomes Vector<std::string> compNames;

4. PeleAnalysis/Src/conditionalMean.cpp

   Line 130 in 0f30b85

   vector<Real> bbll,bbur;

   becomes std::vector

5. PeleAnalysis/Src/conditionalMean.cpp

   Line 327 in 0f30b85

   string variables = "VARIABLES = " + compNames[0];

   becomes std::string variables...

Originally posted by @RSuryaNarayan in #6 (comment)

I am trying to append data to a plot file using the script grad.cpp. I use the following inputs inp.2d after I have an executable:

infile = pltfile
gradVar = Temp
finestLevel = 2
is_per = 0 0 0
appendPlotFile= 1

The output I get after I do mpirun -np 4 ./grad2d.gnu.MPI.ex inp.2d reads as follows:

MPI initialized with 4 MPI processes
MPI initialized with thread support level 0
AMReX (21.02-18-g7742e1c99f5e-dirty) initialized
Doing FillVar at lev: 0
Doing FillVar at lev: 1
Doing FillVar at lev: 2
Segfault
See Backtrace.1 file for details

I tried to trace it back to the exact line at which it breaks away and it looks like it might be L#163

Anything wrong I might be doing?

I want to calculate flame displacement speed, but I find that it is difficult for me to implement this function by modifying existing code (curvature.cpp). Has anyone encountered this problem before? Thanks in advance.