--- a/build_file.py	Fri Feb 03 15:39:07 2023 +0000
+++ b/build_file.py	Tue Jul 18 13:26:20 2023 +0000
@@ -1,6 +1,7 @@
 import json
 import re
 import sys
+from typing import List
 
 from muspinsim import MuSpinInput
 
@@ -395,21 +396,63 @@
     return err_found
 
 
+def append_template_file(
+    template_path: str,
+    mu_params: dict,
+    file_contents: List[str]
+):
+    """
+    Loads an input file generated using muspinsim-gen and appends its contents
+    to what has already been created from config. Also ensures that the spins
+    are appended correctly.
+    """
+    # Check if we have already defined spins in the file
+    spins_line = None
+    spins_line_index = None
+    if ("spins" in mu_params):
+        # Find the current line definition in the file
+        # In the format 'spins\n e\n'
+        for i, line in enumerate(file_contents):
+            if line.startswith("spins"):
+                spins_line = line.split("\n")[1].strip()
+                spins_line_index = i
+        if spins_line_index is not None:
+            del file_contents[spins_line_index]
+
+    # Append the template file's contents
+    with open(template_path, encoding="utf-8") as template_file:
+        for line in template_file:
+            # Append the spins if needed
+            if line.startswith("spins") and spins_line is not None:
+                next_line = template_file.readline().strip()
+                file_contents += f"spins\n    {next_line} {spins_line}\n"
+            else:
+                file_contents += line
+
+
 def main():
     """
     Entry point
     """
     input_json_path = sys.argv[1]
-    mu_params = json.load(open(input_json_path, "r", encoding="utf-8"))
+    mu_input_params = json.load(open(input_json_path, "r", encoding="utf-8"))
+
+    out_file_name = mu_input_params["out_file_prefix"].strip().replace(
+        " ", "_")
 
-    out_file_name = mu_params["out_file_prefix"].strip().replace(" ", "_")
+    # Check if using a template
+    template_path = None
+    if (mu_input_params["use_structure_file_conditional"]
+            ["use_structure_file"]) == "true":
+        template_path = "muspinsim_gen_out.in"
 
     # combine all sections
     mu_params = {
-        **mu_params["spins"],
-        **mu_params["interaction_params"],
-        **mu_params["experiment_params"],
-        **mu_params["fitting_params"]["fitting_options"],
+        **mu_input_params["use_structure_file_conditional"]["spins"],
+        ** (mu_input_params["use_structure_file_conditional"]
+            ["interaction_params"]),
+        **mu_input_params["experiment_params"],
+        **mu_input_params["fitting_params"]["fitting_options"],
     }
 
     # get experiment parameters
@@ -430,6 +473,10 @@
     if parse_dict(parse_func_dict, mu_params, file_contents):
         sys.exit(1)
 
+    # Load and append the template if specified
+    if template_path is not None:
+        append_template_file(template_path, mu_params, file_contents)
+
     write_file("outfile.in", file_contents)
 
     try: