Changed indentation
This commit is contained in:
Trung Nguyen
@ -13,6 +13,9 @@ UPDATE: July 5, 2024:
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+ simplify the build configuration (no need to build the Python module)
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+ specify tolerances for individual quantities for any input script to override the global values
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TODO:
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+ distribute the input list across multiple processes via multiprocessing
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Example usage:
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1) Simple use (using the provided tools/regression-tests/config.yaml and the examples/ folder at the top level)
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python3 run_tests.py --lmp-bin=/path/to/lmp_binary
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@ -103,48 +106,48 @@ def extract_thermo(yamlFileName):
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return a YAML data structure as if loaded from a thermo yaml file
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'''
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def extract_data_to_yaml(inputFileName):
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with open(inputFileName, 'r') as file:
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data = file.read()
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lines = data.splitlines()
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reading = False
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data = []
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docs = ""
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for line in lines:
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if "Step" in line:
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line.strip()
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keywords = line.split()
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reading = True
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docs += "---\n"
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docs += str("keywords: [")
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for word in enumerate(keywords):
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docs += "'" + word[1] + "', "
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docs += "]\n"
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docs += "data:\n"
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if "Loop" in line:
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with open(inputFileName, 'r') as file:
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data = file.read()
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lines = data.splitlines()
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reading = False
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docs += "...\n"
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data = []
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docs = ""
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for line in lines:
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if "Step" in line:
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line.strip()
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keywords = line.split()
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reading = True
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docs += "---\n"
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docs += str("keywords: [")
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for word in enumerate(keywords):
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docs += "'" + word[1] + "', "
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docs += "]\n"
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docs += "data:\n"
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if "Loop" in line:
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reading = False
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docs += "...\n"
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if reading == True and "Step" not in line:
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if "WARNING" in line:
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continue
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data = line.split()
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docs += " - ["
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for field in enumerate(data):
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docs += field[1] + ", "
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docs += "]\n"
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if reading == True and "Step" not in line:
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if "WARNING" in line:
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continue
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data = line.split()
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docs += " - ["
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for field in enumerate(data):
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docs += field[1] + ", "
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docs += "]\n"
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# load the docs into a YAML data struture
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#print(docs)
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try:
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yaml_struct = yaml.load_all(docs, Loader=Loader)
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thermo = list(yaml_struct)
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yaml_struct = yaml.load_all(docs, Loader=Loader)
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thermo = list(yaml_struct)
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except yaml.YAMLError as exc:
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if hasattr(exc, 'problem_mark'):
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mark = exc.problem_mark
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print(f"Error parsing {inputFileName} at line {mark.line}, column {mark.column+1}.")
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else:
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print (f"Something went wrong while parsing {inputFileName}.")
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print(docs)
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if hasattr(exc, 'problem_mark'):
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mark = exc.problem_mark
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print(f"Error parsing {inputFileName} at line {mark.line}, column {mark.column+1}.")
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else:
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print (f"Something went wrong while parsing {inputFileName}.")
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print(docs)
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return thermo
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'''
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@ -157,33 +160,33 @@ def get_lammps_build_configuration(lmp_binary):
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packages = ""
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reading = False
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row = 0
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for l in output:
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if l != "":
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if l == "Installed packages:":
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reading = True
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n = row
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if "List of individual style options" in l:
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reading = False
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if reading == True and row > n:
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packages += l.strip() + " "
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for line in output:
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if line != "":
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if line == "Installed packages:":
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reading = True
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n = row
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if "List of individual style options" in line:
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reading = False
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if reading == True and row > n:
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packages += line.strip() + " "
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if "OS:" in l:
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operating_system = l
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if "Git info" in l:
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GitInfo = l
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if "OS:" in line:
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operating_system = line
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if "Git info" in line:
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GitInfo = line
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row += 1
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row += 1
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packages = packages.strip()
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row = 0
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compile_flags = ""
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for l in output:
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if l != "":
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if "-DLAMMPS" in l:
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compile_flags += " " + l.strip()
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for line in output:
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if line != "":
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if "-DLAMMPS" in line:
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compile_flags += " " + line.strip()
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row += 1
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row += 1
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return packages.split(" "), operating_system, GitInfo, compile_flags
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@ -253,34 +256,34 @@ def iterate(lmp_binary, input_list, config, results, removeAnnotatedInput=False)
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# skip the input file if listed
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if 'skip' in config:
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if input in config['skip']:
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continue
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if input in config['skip']:
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continue
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str_t = "\nRunning " + input + f" ({test_id+1}/{num_tests})"
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result = TestResult(name=input, output="", time="", status="passed")
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if using_markers == True:
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input_test = 'test.' + input
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if os.path.isfile(input) == True:
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if has_markers(input):
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process_markers(input, input_test)
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else:
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print(f"WARNING: {input} does not have REG markers")
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input_markers = input + '.markers'
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# if the input file with the REG markers does not exist
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# attempt to plug in the REG markers before each run command
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if os.path.isfile(input_markers) == False:
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input_test = 'test.' + input
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if os.path.isfile(input) == True:
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if has_markers(input):
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process_markers(input, input_test)
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else:
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print(f"WARNING: {input} does not have REG markers")
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input_markers = input + '.markers'
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# if the input file with the REG markers does not exist
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# attempt to plug in the REG markers before each run command
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if os.path.isfile(input_markers) == False:
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cmd_str = "cp " + input + " " + input_markers
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os.system(cmd_str)
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generate_markers(input, input_markers)
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process_markers(input_markers, input_test)
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cmd_str = "cp " + input + " " + input_markers
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os.system(cmd_str)
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generate_markers(input, input_markers)
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process_markers(input_markers, input_test)
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str_t = "\nRunning " + input_test + f" ({test_id+1}/{num_tests})"
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str_t = "\nRunning " + input_test + f" ({test_id+1}/{num_tests})"
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else:
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input_test = input
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input_test = input
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print(str_t)
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print(f"-"*len(str_t))
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@ -293,12 +296,12 @@ def iterate(lmp_binary, input_list, config, results, removeAnnotatedInput=False)
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pattern = f'log.*.{basename}.*'
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max_np = 1
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for file in os.listdir('.'):
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if fnmatch.fnmatch(file, pattern):
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p = file.rsplit('.', 1)
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if max_np < int(p[1]):
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max_np = int(p[1])
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logfile_exist = True
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thermo_ref_file = file
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if fnmatch.fnmatch(file, pattern):
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p = file.rsplit('.', 1)
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if max_np < int(p[1]):
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max_np = int(p[1])
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logfile_exist = True
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thermo_ref_file = file
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# if the maximum number of procs is different from the value in the configuration file
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# then override the setting for this input script
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@ -333,25 +336,25 @@ def iterate(lmp_binary, input_list, config, results, removeAnnotatedInput=False)
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# restore the nprocs value in the configuration
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config['nprocs'] = saved_nprocs
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# process thermo output
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# process error code from the run
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if returncode != 0:
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print(f"ERROR: Failed with {input_test}. Check the log file for the run output.\n")
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logger.info(f"\n{error}")
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continue
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# process thermo output
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thermo = extract_data_to_yaml("log.lammps")
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num_runs = len(thermo)
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if num_runs == 0:
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print(f"ERROR: Failed with {input_test}. Check the log file for the run output.\n")
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#print(f"{output}")
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logger.info(f"The run terminated with the following output:\n")
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logger.info(f"\n{output}")
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result.status = "error"
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results.append(result)
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continue
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print(f"Comparing thermo output from log.lammps with the reference log file {thermo_ref_file}")
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print(f"Comparing thermo output from log.lammps against the reference log file {thermo_ref_file}")
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if num_runs != num_runs_ref:
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print(f"ERROR: Number of runs in log.lammps ({num_runs}) is not the same as that in the reference log ({num_runs_ref})")
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result.status = "error"
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@ -606,43 +609,44 @@ if __name__ == "__main__":
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example_subfolders.append('../../examples/srd')
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all_results = []
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# default setting
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if inplace_input == True:
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# save current working dir
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p = subprocess.run("pwd", shell=True, text=True, capture_output=True)
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pwd = p.stdout.split('\n')[0]
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pwd = os.path.abspath(pwd)
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print("Working directory: " + pwd)
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# save current working dir
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p = subprocess.run("pwd", shell=True, text=True, capture_output=True)
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pwd = p.stdout.split('\n')[0]
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pwd = os.path.abspath(pwd)
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print("Working directory: " + pwd)
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# change dir to a folder under examples/, need to use os.chdir()
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# TODO: loop through the subfolders under examples/, depending on the installed packages
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# change dir to a folder under examples/, need to use os.chdir()
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# TODO: loop through the subfolders under examples/, depending on the installed packages
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total_tests = 0
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passed_tests = 0
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total_tests = 0
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passed_tests = 0
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for directory in example_subfolders:
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for directory in example_subfolders:
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p = subprocess.run("pwd", shell=True, text=True, capture_output=True)
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print("\nEntering " + directory)
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os.chdir(directory)
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p = subprocess.run("pwd", shell=True, text=True, capture_output=True)
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print("\nEntering " + directory)
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os.chdir(directory)
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cmd_str = "ls in.*"
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p = subprocess.run(cmd_str, shell=True, text=True, capture_output=True)
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input_list = p.stdout.split('\n')
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input_list.remove('')
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cmd_str = "ls in.*"
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p = subprocess.run(cmd_str, shell=True, text=True, capture_output=True)
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input_list = p.stdout.split('\n')
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input_list.remove('')
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print(f"List of input scripts: {input_list}")
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total_tests += len(input_list)
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print(f"List of input scripts: {input_list}")
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total_tests += len(input_list)
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# iterate through the input scripts
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results = []
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num_passed = iterate(lmp_binary, input_list, config, results)
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passed_tests += num_passed
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# iterate through the input scripts
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results = []
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num_passed = iterate(lmp_binary, input_list, config, results)
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passed_tests += num_passed
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all_results.extend(results)
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all_results.extend(results)
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# get back to the working dir
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os.chdir(pwd)
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# get back to the working dir
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os.chdir(pwd)
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else:
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# or using the input scripts in the working directory -- for debugging purposes
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