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Tested with more example subfolders

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This commit is contained in:
Trung Nguyen
2024-01-30 17:08:24 -06:00
parent 293e930cb0
commit 91d292fb7c
1 changed files with 91 additions and 46 deletions
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137
tools/regression-tests/run_tests.py
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@ -227,17 +227,19 @@ def has_markers(input):
'''
Iterate over a list of input files using the testing configuration
return total number of tests, and the number of tests with failures
'''
def iterate(input_list, config, removeAnnotatedInput=False):
EPSILON = np.float64(config['epsilon'])
nugget = float(config['nugget'])
nprocs = int(config['nprocs'])
num_tests = len(input_list)
num_passed = 0
test_id = 0
# using REG-commented input scripts
using_markers = False
# iterate over the input scripts
for input in input_list:
@ -268,6 +270,41 @@ def iterate(input_list, config, removeAnnotatedInput=False):
print(str_t)
print(f"-"*len(str_t))
# check if a log file exists in the current folder: log.[date].basename.[nprocs]
basename = input_test.replace('in.','')
logfile_exist = False
# if there are multiple log files for different number of procs, pick the maximum number
pattern = f'log.*.{basename}.*'
max_np = 1
for file in os.listdir('.'):
if fnmatch.fnmatch(file, pattern):
p = file.rsplit('.', 1)
if max_np < int(p[1]):
max_np = int(p[1])
logfile_exist = True
thermo_ref_file = file
# if the maximum number of procs is different from the value in the configuration file
# then override the setting for this input script
saved_nprocs = config['nprocs']
if max_np != int(config['nprocs']):
config['nprocs'] = str(max_np)
if logfile_exist:
thermo_ref = extract_data_to_yaml(thermo_ref_file)
num_runs_ref = len(thermo_ref)
else:
print(f"Cannot find reference log file with {pattern}.")
# try to read in the thermo yaml output from the working directory
thermo_ref_file = 'thermo.' + input + '.yaml'
file_exist = os.path.isfile(thermo_ref_file)
if file_exist == True:
thermo_ref = extract_thermo(thermo_ref_file)
else:
print(f"SKIPPED: {thermo_ref_file} does not exist in the working directory.")
continue
# using the LAMMPS python module (for single-proc runs)
# lmp = lammps()
# lmp.file(input_test)
@ -275,49 +312,28 @@ def iterate(input_list, config, removeAnnotatedInput=False):
# or more customizable with config.yaml
execute(lmp_binary, config, input_test)
# restore the nprocs value in the configuration
config['nprocs'] = saved_nprocs
# process thermo output
#thermo = extract_thermo("log.lammps")
thermo = extract_data_to_yaml("log.lammps")
num_runs = len(thermo)
if num_runs == 0:
print(f"Failed with {input_test}. Check if the run with this input script completed normally.\n")
print(f"Failed with the unning with {input_test}. Check if the run with this input script completed normally.\n")
continue
# check if a log file exists in the current folder: log.[date].basename.[nprocs]
basename = input_test.replace('in.','')
logfile_exist = False
pattern = f'log.*.{basename}.*.{nprocs}'
for file in os.listdir('.'):
if fnmatch.fnmatch(file, pattern):
logfile_exist = True
break
if logfile_exist:
thermo_ref = extract_data_to_yaml(file)
num_runs_ref = len(thermo_ref)
else:
print(f"Cannot find reference log file with {pattern}")
# read in the thermo yaml output from the working directory
thermo_ref_file = 'thermo.' + input + '.yaml'
file_exist = os.path.isfile(thermo_ref_file)
if file_exist == True:
thermo_ref = extract_thermo(thermo_ref_file)
else:
print(f"SKIPPED: {thermo_ref_file} does not exist")
continue
print(f"Comparing thermo output from log.lammps with the reference log {file}")
print(f"Comparing thermo output from log.lammps with the reference log {thermo_ref_file}")
if num_runs != num_runs_ref:
print(f"ERROR: Number of runs in log.lammps ({num_runs}) is not the same as that in the reference log ({num_runs_ref})")
continue
# comparing output vs reference values
width = 20
print("Quantities".ljust(width) + "Output".center(width) + "Reference".center(width) + "Abs Diff Check".center(width) + "Rel Diff Check".center(width))
irun = 0
num_fields = len(thermo[irun]['keywords'])
# get the total number of the thermo output lines
nthermo_steps = len(thermo[irun]['data'])
# get the output at the last timestep
@ -331,12 +347,11 @@ def iterate(input_list, config, removeAnnotatedInput=False):
val = thermo[irun]['data'][thermo_step][i]
ref = thermo_ref[irun]['data'][thermo_step][i]
abs_diff = abs(float(val) - float(ref))
if abs(float(ref)) > EPSILON:
rel_diff = abs(float(val) - float(ref))/abs(float(ref))
else:
rel_diff = abs(float(val) - float(ref))/abs(float(ref)+nugget)
abs_diff_check = "PASSED"
rel_diff_check = "PASSED"
@ -348,18 +363,20 @@ def iterate(input_list, config, removeAnnotatedInput=False):
if rel_diff > float(config['tolerance'][quantity]['rel']):
rel_diff_check = "FAILED"
num_rel_failed = num_rel_failed + 1
else:
abs_diff_check = "N/A"
rel_diff_check = "N/A"
print(f"{thermo[irun]['keywords'][i].ljust(width)} {str(val).rjust(20)} {str(ref).rjust(20)} {abs_diff_check.rjust(20)} {rel_diff_check.rjust(20)}")
if num_abs_failed > 0:
print(f"{num_abs_failed} abs checks failed")
print(f"{num_abs_failed} absolute diff checks failed with the specified tolerances.")
elif num_rel_failed > 0:
print(f"{num_rel_failed} rel checks failed")
print(f"{num_rel_failed} relative diff checks failed with the specified tolerances.")
else:
print("All checks passed. (N/A means tolerance not defined in the config file.)")
num_passed = num_passed + 1
print("-"*(5*width+4))
test_id = test_id + 1
@ -369,10 +386,11 @@ def iterate(input_list, config, removeAnnotatedInput=False):
cmd_str = "rm " + input_test
os.system(cmd_str)
return num_passed
'''
TODO:
- automate annotating the example input scripts of the installed packages
- automate annotating the example input scripts if thermo style is multi (e.g. examples/peptide)
'''
if __name__ == "__main__":
@ -426,10 +444,21 @@ if __name__ == "__main__":
# append the example subfolders depending on the installed packages
if 'MOLECULE' in packages:
example_subfolders.append('../../examples/micelle')
# peptide thermo_style as multi
#example_subfolders.append('../../examples/peptide')
#if 'ASPHERE' in packages:
# example_subfolders.append('../../examples/ASPHERE/ellipsoid')
#if 'AMOEBA' in packages:
# example_subfolders.append('../../examples/amoeba')
if 'BODY' in packages:
example_subfolders.append('../../examples/body')
if 'DIELECTRIC' in packages:
example_subfolders.append('../../examples/PACKAGES/dielectric')
if 'COLLOID' in packages:
example_subfolders.append('../../examples/colloid')
@ -438,48 +467,64 @@ if __name__ == "__main__":
if 'MANYBODY' in packages:
example_subfolders.append('../../examples/tersoff')
example_subfolders.append('../../examples/vashishta')
if 'RIGID' in packages:
example_subfolders.append('../../examples/rigid')
if inplace_input == True:
# save current working dir
p = subprocess.run("pwd", shell=True, text=True, capture_output=True)
pwd = p.stdout.split('\n')[0]
pwd = os.path.abspath(pwd)
print("Working directory: " + pwd)
# change dir to a folder under examples/
# change dir to a folder under examples/, need to use os.chdir()
# TODO: loop through the subfolders under examples/, depending on the installed packages
total_tests = 0
passed_tests = 0
for directory in example_subfolders:
p = subprocess.run("pwd", shell=True, text=True, capture_output=True)
print("\nEntering " + directory)
os.chdir(directory)
# create a symbolic link to the lammps binary at the present directory
cmd_str = "ln -s " + lmp_binary + " lmp"
os.system(cmd_str)
if os.path.isfile("lmp") == False:
cmd_str = "ln -s " + lmp_binary + " lmp"
os.system(cmd_str)
cmd_str = "ls in.*"
p = subprocess.run(cmd_str, shell=True, text=True, capture_output=True)
input_list = p.stdout.split('\n')
input_list.remove('')
print("List of input scripts:")
print(input_list)
print(f"List of input scripts: {input_list}")
total_tests += len(input_list)
# iterate through the input scripts
iterate(input_list, config)
num_passed = iterate(input_list, config)
passed_tests += num_passed
# unlink the symbolic link
cmd_str = "unlink lmp"
os.system(cmd_str)
# get back to the working dir
cmd_str = "cd " + pwd
os.system(cmd_str)
os.chdir(pwd)
else:
# or using the input scripts in the working directory
input_list=['in.lj', 'in.rhodo', 'in.eam']
iterate(input_list, config)
total_tests = len(input_list)
passed_tests = iterate(input_list, config)
print("Summary:")
print(f" - {passed_tests} passed / {total_tests} tests")