From c6ffa2c646833fc9b36349d4b4ecf97da893ad68 Mon Sep 17 00:00:00 2001
From: Pierre Beaujean <pierreb24@gmail.com>
Date: Wed, 10 Jan 2024 14:44:32 +0100
Subject: [PATCH] append to existing file

---
 nachos/bake.py        | 14 +++++++++++++-
 nachos/core/baking.py | 22 ++++++++++++++++++++--
 2 files changed, 33 insertions(+), 3 deletions(-)

diff --git a/nachos/bake.py b/nachos/bake.py
index d14eb2d..bdf7c6e 100644
--- a/nachos/bake.py
+++ b/nachos/bake.py
@@ -7,6 +7,7 @@
 
 from qcip_tools import derivatives_g, derivatives
 from qcip_tools.chemistry_files import helpers, PropertyNotDefined, PropertyNotPresent
+from qcip_tools.chemistry_files.chemistry_datafile import ChemistryDataFile, BadChemistryDataFile
 
 import nachos
 from nachos.core import files, baking
@@ -110,6 +111,9 @@ def get_arguments_parser():
         type=treat_romberg_arg,
         help='Bypass detection and force a value in the triangle. Must be of the form `k;m`.')
 
+    arguments_parser.add_argument(
+        '-a', '--append', action='store_true', help='Append to existing H5 file')
+
     return arguments_parser
 
 
@@ -144,8 +148,16 @@ def main():
     storage = files.ComputationalResults(recipe, directory=recipe_directory)
     storage.read(args.data)
 
+    original_cf = ChemistryDataFile()
+    if args.append:
+        with open(args.output) as f:
+            try:
+                original_cf.read(f)
+            except BadChemistryDataFile as e:
+                return exit_failure('Cannot append data to `{}`: {}'.format(args.output, e))
+
     # go and bake
-    baker = baking.Baker(recipe, storage, directory=recipe_directory)
+    baker = baking.Baker(recipe, storage, directory=recipe_directory, original_cf=original_cf)
     only = None
 
     if args.only:
diff --git a/nachos/core/baking.py b/nachos/core/baking.py
index 0d3835b..bb43987 100644
--- a/nachos/core/baking.py
+++ b/nachos/core/baking.py
@@ -13,6 +13,14 @@ class BadBaking(Exception):
     pass
 
 
+def _equal_molecules_or_raise(mol1, mol2):
+    """Compare two geometries
+    """
+
+    if [a.symbol for a in mol1] != [a.symbol for a in mol2]:
+        raise BadBaking('not the same geometries: atomic symbols are different')
+
+
 class Baker:
     """Baker class to finally perform the numerical differentiation
 
@@ -22,9 +30,11 @@ class Baker:
     :type storage: nachos.core.files.ComputationalResults
     :param directory: working directory
     :type directory: str
+    :param original_cf: Originak chemistry file to append to
+    :type original_cf: qcip_tools.chemistry_files.chemistry_datafile.ChemistryDataFile
     """
 
-    def __init__(self, recipe, storage, directory='.'):
+    def __init__(self, recipe, storage, directory='.', original_cf=None):
         self.recipe = recipe
 
         if not os.path.isdir(directory):
@@ -33,6 +43,14 @@ def __init__(self, recipe, storage, directory='.'):
         self.directory = directory
         self.storage = storage
 
+        if original_cf is not None:
+            _equal_molecules_or_raise(self.recipe.geometry, original_cf.molecule)
+            self.original_cf = original_cf
+        else:
+            self.original_cf = chemistry_datafile.ChemistryDataFile.from_molecule(
+                self.recipe.geometry, 'nachos ND result'
+            )
+
         if self.storage.check() != ([], []):
             raise BadBaking('The storage (h5 file) does not fulfill the recipe!')
 
@@ -73,7 +91,7 @@ def bake(self, only=None, out=sys.stdout, verbosity_level=0, copy_zero_field_bas
             raise BadBaking('no differentiation requested!')
 
         bases.sort(key=lambda a: a[1], reverse=True)
-        f = chemistry_datafile.ChemistryDataFile.from_molecule(self.recipe.geometry, 'nachos ND result')
+        f = self.original_cf
         dof = 3 * len(self.recipe.geometry)
 
         if copy_zero_field_basis: