added lots of if allocated statements

[joanibal]

Purpose

If ADflow has an issue in its init it will often try to deallocate variables that haven't been allocated yet. This will usually obscure the original error. This was particularly annoying for me since I was working on pyAeroProblem, which is used before the preprocessing has been complete.

To solve this I added lots of if (allocated(blah)) statements to prevent it from deallocating variables that don't exist yet.

Before

python test_basics.py
#
# ADflow, multiblock structured flow solver
#
# This code solves the 3D RANS, laminar NS or Euler equations
# on multiblock structured hexahedral grids.
# This is a parallel executable running on 1 processors.
# It has been compiled with the following options:
# - Optimized mode.
# - Size of standard integers: 4 bytes.
# - Size of standard floating point types: 8 bytes.
# - With cgns support
# - With support for signals.
#
-> Alpha... 0.000000 
E[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
[0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
[0]PETSC ERROR: likely location of problem given in stack below
[0]PETSC ERROR: ---------------------  Stack Frames ------------------------------------
[0]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
[0]PETSC ERROR:       INSTEAD the line number of the start of the function
[0]PETSC ERROR:       is given.
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 59.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------

or

> python test_basics.py
#
# ADflow, multiblock structured flow solver
#
# This code solves the 3D RANS, laminar NS or Euler equations
# on multiblock structured hexahedral grids.
# This is a parallel executable running on 1 processors.
# It has been compiled with the following options:
# - Optimized mode.
# - Size of standard integers: 4 bytes.
# - Size of standard floating point types: 8 bytes.
# - With cgns support
# - With support for signals.
#
-> Alpha... 0.000000 
E ---------------------------------------------------------------------------
PETSc or MPI Error. Error Code 64. Detected on Proc  0
Error at line:  4794 in file: ../utils/utils.F90
 ---------------------------------------------------------------------------
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 64.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------

After

> python test_basics.py
#
# ADflow, multiblock structured flow solver
#
# This code solves the 3D RANS, laminar NS or Euler equations
# on multiblock structured hexahedral grids.
# This is a parallel executable running on 1 processors.
# It has been compiled with the following options:
# - Optimized mode.
# - Size of standard integers: 4 bytes.
# - Size of standard floating point types: 8 bytes.
# - With cgns support
# - With support for signals.
#
+----------------------------------------+
|          All ADFLOW Options:           |
+----------------------------------------+
{....}
-> Alpha... 0.000000 
E
======================================================================
ERROR: test_import (__main__.BasicTests)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_basics.py", line 15, in test_import
    ADFLOW(options=options, debug=False)
  File "/home/josh/repos/adflow/adflow/pyADflow.py", line 224, in __init__
    self._setAeroProblemData(dummyAP, firstCall=True)
  File "/home/josh/repos/adflow/adflow/pyADflow.py", line 3006, in _setAeroProblemData
    nameArray, dataArray, groupArray, groupNames, empty = self._getBCDataFromAeroProblem(AP)
  File "/home/josh/repos/adflow/adflow/pyADflow.py", line 3023, in _getBCDataFromAeroProblem
    for tmp in AP.bcVarData:
AttributeError: 'AeroProblem' object has no attribute 'bcVarData'

----------------------------------------------------------------------
Ran 1 test in 0.013s

FAILED (errors=1)

Type of change

• Bugfix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (non-backwards-compatible fix or feature)
• Code style update (formatting, renaming)
• Refactoring (no functional changes, no API changes)
• Documentation update
• Maintenance update
• Other (please describe)

Testing

Checklist

• I have run flake8 and black to make sure the code adheres to PEP-8 and is consistently formatted
• I have run unit and regression tests which pass locally with my changes
• I have added new tests that prove my fix is effective or that my feature works
• I have added necessary documentation

[joanibal]

Why do we use flake8 and pylint? @marcomangano @nwu63
pylint seems upset about files that were not modified by this PR.

[ewu63]

Why do we use flake8 and pylint? @marcomangano @nwu63 pylint seems upset about files that were not modified by this PR.

See mdolab/.github#22 for the discussion on pylint. It catches many problems that flake8 doesn't catch. Since nobody went through and fixed these problems, it's going to fail the check for pretty much all the repos, which is why it's not a required status check.

[codecov]

Codecov Report

Merging #178 (960389f) into master (d17ca9f) will not change coverage.
The diff coverage is 100.00%.

❗ Current head 960389f differs from pull request most recent head 37f573a. Consider uploading reports for the commit 37f573a to get more accurate results

@@           Coverage Diff           @@
##           master     #178   +/-   ##
=======================================
  Coverage   43.10%   43.10%           
=======================================
  Files          15       15           
  Lines        3517     3517           
=======================================
  Hits         1516     1516           
  Misses       2001     2001           

Impacted Files	Coverage Δ
adflow/pyADflow.py	67.46% <100.00%> (ø)

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[sseraj]

Excellent! I tested this locally and it works.

[awccopp]

Everything here looks good to me.