Revert "Do not skip first step when logging energy and xyz"

This reverts commit 046bfaf.

emle/calculator.py

@@ -1033,6 +1033,7 @@ def run(self, path=None):
         # Log energies to file.
         if (
             self._energy_frequency > 0
+            and not self._is_first_step
             and self._step % self._energy_frequency == 0
         ):
             with open(self._energy_file, "a+") as f:
@@ -1067,8 +1068,11 @@ def run(self, path=None):
                 f.write("\n")
 
         # Increment the step counter.
-        self._step += 1
-        _logger.info(f"Step: {self._step}")
+        if self._is_first_step:
+            self._is_first_step = False
+        else:
+            self._step += 1
+            _logger.info(f"Step: {self._step}")
 
     def _calculate_energy_and_gradients(
         self,