Tested with more example subfolders

tools/regression-tests/run_tests.py

@@ -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]
+    print(f"Comparing thermo output from log.lammps with the reference log {thermo_ref_file}")
-    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}")
     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"
+      if os.path.isfile("lmp") == False:
-      os.system(cmd_str)
+        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(f"List of input scripts: {input_list}")
-      print(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.chdir(pwd)
-      os.system(cmd_str)
+
 
   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")