Some modification in the cluster

Author: mesonepigreco

Modules/Cluster.py

@@ -223,6 +223,11 @@ def __init__(self, hostname=None, pwd=None, extra_options="", workdir = "",
         # Useful if the cluster has a limit for the maximum number of jobs allowed.
         self.batch_size = 1000
 
+        # This could be a function that generates for each input file additional
+        # text in the submission file.
+        # Usefull if you want to copy things in a different directory to run the calculation on the cluster.
+        self.additional_script_parameters = None
+
 
         # Allow to setup additional custom extra parameters
         self.custom_params = {}
@@ -426,9 +431,11 @@ def batch_submission(self, list_of_structures, calc, indices,
         new_mpicmd  = self.mpi_cmd.replace("NPROC", str(self.n_cpu))
         results = [None] * N_structs
         submitted = []
+        submission_labels = []
         for i in range(N_structs):
             # Prepare a typical label
             lbl = label + "_" + str(indices[i])
+            submission_labels.append(lbl)
 
             atm = list_of_structures[i].get_ase_atoms()
             atm.set_calculator(calc)
@@ -521,10 +528,20 @@ def batch_submission(self, list_of_structures, calc, indices,
 
         # Go to the working directory
         submission += "cd " + self.workdir + "\n"
+
+        # If any, apply the extra text before and after the calculation
+        other_input = ""
+        other_output = ""
+        if self.additional_script_parameters is not None:
+            other_input, other_output = self.additional_script_parameters(submission_labels)
+
+        submission += other_input
 
         # Use the xargs trick
         #submission += "xargs -d " + r"'\n'" + " -L1 -P%d -a %s -- bash -c\n" % (n_togheder, 
         submission += app_list 
+
+        submission += other_output
 
         # Copy the submission script
         sub_fpath = "%s/%s.sh" % (self.local_workdir, label + "_" + str(indices[0]))