From 4224d6adbb9c5b48ef4cd6f949e69bc6e9218148 Mon Sep 17 00:00:00 2001
From: Carlo Antonio Pignedoli <c.pignedoli@gmail.com>
Date: Thu, 12 Sep 2024 13:59:21 +0000
Subject: [PATCH] modified to allow nics calculations

---
 aiida_gaussian/calculations/gaussian.py |  5 +++-
 aiida_gaussian/parsers/gaussian.py      | 33 ++++++++++++++++++++++---
 2 files changed, 33 insertions(+), 5 deletions(-)

diff --git a/aiida_gaussian/calculations/gaussian.py b/aiida_gaussian/calculations/gaussian.py
index 2067894..0f7c610 100644
--- a/aiida_gaussian/calculations/gaussian.py
+++ b/aiida_gaussian/calculations/gaussian.py
@@ -170,7 +170,10 @@ def prepare_for_submission(self, folder):
         input_string = GaussianCalculation._render_input_string_from_params(
             self.inputs.parameters.get_dict(), pmg_structure
         )
-
+        # for NICS replace X0+ with Bq
+        if "nmr" in self.inputs.parameters.get_dict()['route_parameters']:
+            input_string = input_string.replace("X0+", "Bq")
+            
         with open(folder.get_abs_path(self.INPUT_FILE), "w") as out_file:
             out_file.write(input_string)
 
diff --git a/aiida_gaussian/parsers/gaussian.py b/aiida_gaussian/parsers/gaussian.py
index 68f4898..533b681 100644
--- a/aiida_gaussian/parsers/gaussian.py
+++ b/aiida_gaussian/parsers/gaussian.py
@@ -53,7 +53,7 @@ def _parse_log(self, log_file_string, inputs):
             return self.exit_codes.ERROR_OUTPUT_PARSING
 
         property_dict.update(self._parse_electron_numbers(log_file_string))
-
+        
         # set output nodes
         self.out("output_parameters", Dict(dict=property_dict))
 
@@ -78,7 +78,7 @@ def _parse_electron_numbers(self, log_file_string):
             return {"num_electrons": [int(e) for e in find_el.groups()]}
         else:
             return {}
-
+            
     def _parse_log_cclib(self, log_file_string):
 
         data = cclib.io.ccread(io.StringIO(log_file_string))
@@ -176,7 +176,9 @@ def _parse_log(self, log_file_string, inputs):
 
         if property_dict is None:
             return self.exit_codes.ERROR_OUTPUT_PARSING
-
+        # parse nics
+        property_dict.update(self._parse_nics(log_file_string))
+        
         property_dict.update(self._parse_electron_numbers(log_file_string))
 
         # Add spin expectations in property_dict
@@ -198,7 +200,30 @@ def _parse_log(self, log_file_string, inputs):
             return exit_code
 
         return None
-
+    def _parse_nics(self,log_file_string):
+
+        sigma = []
+
+        def extract_values(line):
+            parts = line.split()
+            return np.array([parts[1], parts[3], parts[5]], dtype=float)
+
+        lines = log_file_string.splitlines()
+        i_line = 0
+        while i_line < len(lines):
+            if "Bq   Isotropic" in lines[i_line]:
+                s = np.zeros((3, 3))
+                s[0] = extract_values(lines[i_line + 1])
+                s[1] = extract_values(lines[i_line + 2])
+                s[2] = extract_values(lines[i_line + 3])
+                sigma.append(s)
+                i_line += 4
+            else:
+                i_line += 1
+        if len(sigma) == 0:
+            return {}
+        return {'nics':np.array(sigma)}
+    
     def _parse_log_spin_exp(self, log_file_string):
         """Parse spin expectation values"""