1. Change storing out file from csearch-crest

aqme/csearch/crest.py

@@ -251,6 +251,7 @@ def xtb_opt_main(
 
     xyzoutall = str(dat_dir) + "/" + name_no_path + "_conformers.xyz"
 
+    # CREST sampling
     if self.args.program.lower() == "crest":
         self.args.log.write(f"\no  Starting CREST sampling")
         if constrained_opt:
@@ -287,12 +288,12 @@ def xtb_opt_main(
 
         run_command(command, f"/{dat_dir}/{name_no_path}.out")
 
-        # get number of n_atoms
         try:
             natoms = open("crest_best.xyz").readlines()[0].strip()
         except FileNotFoundError:
                 self.args.log.write(f"\nx  CREST optimization failed! This might be caused by different reasons. For example, this might happen if you're using metal complexes without specifying any kind of template in the complex_type option (i.e. squareplanar).\n")
 
+        # CREGEN sorting
         if self.args.cregen and int(natoms) != 1:
             self.args.log.write(f"\no  Starting CREGEN sorting")
             command = ["crest", "crest_best.xyz", "--cregen", "crest_conformers.xyz"]

aqme/utils.py

@@ -33,17 +33,12 @@
 
 def run_command(command, outfile):
     """
-    Runs the subprocess command and outputs to the necessary output file
+    Runs the subprocess command and saves the results in an output file (not shown in the terminal)
     """
 
-    p2 = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=subprocess.DEVNULL)
-    txt = [line.decode("utf-8") for line in p2.stdout]
-    p2.stdout.close()
-
-    with open(outfile, "w") as f:
-        for line in txt:
-            f.write(line)
-    f.close()
+    output = open(outfile, "w")
+    subprocess.run(command, stdout=output, stderr=subprocess.DEVNULL)
+    output.close()
 
 
 def periodic_table():