Initiated the regression test setup

tools/regression-tests/run_tests.py

@@ -0,0 +1,172 @@
+'''
+UPDATE: Oct 25, 2023:
+  Launching the LAMMPS binary under testing using a configuration defined in a yaml file (e.g. config.yaml)
+  this way we can launch LAMMPS with mpirun with more flexibility. Also it simplifies the build configuration.
+
+  python3 run_tests.py /path/to/lmp_binary
+
+Original plan: using the LAMMPS Python module
+  The following steps are for setting up regression tests with the LAMMPS Python module
+
+  0) Create a virtual environment, and activate it
+
+    python -m venv lmp-venv
+    source lmp-venv/bin/activate
+    PYTHON_EXECUTABLE=`which python`
+    INSTALL_PREFIX=$(${PYTHON_EXECUTABLE} -c "import sys; print(sys.prefix)")
+
+  1) Build LAMMPS as a shared lib and install the LAMMPS python module into the virtual environment
+
+    git clone https://github.com/lammps/lammps.git lammps
+    cd lammps
+    mkdir build && cd build
+    cmake ../cmake/presets/basic.cmake -DBUILD_SHARED_LIBS=on -DCMAKE_INSTALL_PREFIX=$INSTALL_PREFIX
+    make -j4
+    make install-python
+
+  2) Run this script, after activating the virtual environment and having the input scripts with markers ready:
+
+    source lmp-venv/bin/activate
+    python3 run_tests.py
+
+'''
+
+#from lammps import lammps
+import sys
+import re, yaml
+import subprocess
+
+try:
+    from yaml import CSafeLoader as Loader
+except ImportError:
+    from yaml import SafeLoader as Loader
+
+'''
+  inputFileName:  input file with comments #REG:ADD and #REG:SUB as markers
+  outputFileName: modified input file ready for testing
+'''
+def processing_markers(inputFileName, outputFileName):
+  # read in the script
+  with open(inputFileName, 'r') as file:
+    data = file.read()
+
+    # replace #REG:ADD with empty string (i.e. adding the text at the end of the line)
+    data = data.replace("#REG:ADD", "")
+
+    # replace the line contaning #REG:SUB with a line with the text that follows this marker 
+    data = data.splitlines()
+    separator="#REG:SUB"
+    out = []
+    for line in data:
+      s = line.split(separator)
+      if len(s) < 2:
+        out.append(line)
+      else:
+        out.append(s[1])
+
+  # write data to the new script
+  with open(outputFileName, 'w') as file:
+    for line in out:
+      file.write(line + "\n")
+
+'''
+  yamlFileName: input YAML file with thermo structured as described in https://docs.lammps.org/Howto_structured_data.html
+  return: thermo, which is a list containing a dictionary for each run where the tag "keywords" maps to the list
+    of thermo header strings and the tag “data” has a list of lists where the outer list represents the lines
+    of output and the inner list the values of the columns matching the header keywords for that step.
+'''
+def extract_thermo(yamlFileName):
+  docs = ""
+  with open(yamlFileName) as f:
+      for line in f:
+          m = re.search(r"^(keywords:.*$|data:$|---$|\.\.\.$|  - \[.*\]$)", line)
+          if m: docs += m.group(0) + '\n'
+
+  thermo = list(yaml.load_all(docs, Loader=Loader))
+  return thermo
+
+'''
+  launch LAMMPS using the configuration defined in the dictionary config with an input file
+  TODO:
+    - generate new reference values if needed
+    - wrap subprocess with try/catch to handle exceptions
+'''
+def execute(lmp_binary, config, input_file_name, generate_ref_yaml=False):
+  cmd_str = config['mpiexec'] + " " + config['mpiexec_numproc_flag'] + " " + config['nprocs'] + " "
+  cmd_str += lmp_binary + " -in " + input_file_name + " " + config['args']
+  print(f"Execute: {cmd_str}")
+  p = subprocess.run(cmd_str, shell=True, text=True, capture_output=True)
+  output = p.stdout.split('\n')
+
+'''
+  TODO:
+    - process "lmp -h" to get the list of installed packages
+    - automate tagging the example input scripts of the installed packages
+'''
+if __name__ == "__main__":
+
+  lmp_binary = ""
+  # if lmp binary is specified in the command line
+  if len(sys.argv) >= 2:
+    lmp_binary = sys.argv[1]
+
+  # list of input scripts with markers #REG:SUB and #REG:ADD
+  input_list=['in.lj', 'in.rhodo']
+
+  # read in the configuration of the tests
+  with open("config.yaml", 'r') as f:
+    config = yaml.load(f, Loader=Loader)
+    print(config)
+ 
+  # check if lmp_binary is specified in the config yaml
+  if lmp_binary == "":
+    if config['lmp_binary'] == "":
+       print("Needs a valid LAMMPS binary")
+       exit
+    else:
+       lmp_binary = config['lmp_binary']
+  
+  # iterative over the input scripts
+  for input in input_list:
+    input_test=input + '.test'
+    processing_markers(input, input_test)
+    
+    str_t = "Running " + input_test
+    print(str_t)
+    print(f"-"*len(str_t))
+
+    # using the LAMMPS python module (for single-proc runs)
+    #  lmp = lammps()
+    #  lmp.file(input_test)
+    
+    # or more customizable with config.yaml
+    execute(lmp_binary, config, input_test)
+
+    # process thermo output
+    thermo = extract_thermo("log.lammps")
+
+    num_runs = len(thermo)
+    if num_runs == 0:
+       print(f"Failed with {input_test}\n")
+       continue 
+
+    print(f"Number of runs: {num_runs}")
+
+    # read in the thermo yaml output  
+    thermo_ref_file = 'thermo.' + input + '.yaml'
+    thermo_ref = extract_thermo(thermo_ref_file)
+
+    # comparing output vs reference values
+    width = 20
+    print("Quantities".ljust(width) + "Output".center(width) + "Reference".center(width) + "Diff.".center(width))
+    irun = 0
+    num_fields = len(thermo[irun]['keywords'])
+    for i in range(num_fields):
+       val = thermo[irun]['data'][2][i]
+       ref = thermo[0]['data'][2][i]
+       diff = float(val) - float(ref)
+       print(f"{thermo[0]['keywords'][i].ljust(width)} {str(val).rjust(20)} {str(ref).rjust(20)} {str(diff).rjust(20)}")
+    print("-"*(4*width+3))
+
+
+