Bugfix: handling of configurations and gradients

* The code handled configurations incorrectly.This has been fixed.
* The gradients were not output correctly, causing problems in e.g the Structure
  and Thermochemistry steps.
* Changed logging at the INFO level to DEBUG to clean up the output of geomeTRIC.

HISTORY.rst

@@ -1,6 +1,12 @@
 =======
 History
 =======
+2024.2.7 -- Bugfix: handling of configurations and gradients
+    * The code handled configurations incorrectly.This has been fixed.
+    * The gradients were not output correctly, causing problems in e.g the Structure
+      and Thermochemistry steps.
+    * Changed logging at the INFO level to DEBUG to clean up the output of geomeTRIC.
+
 2024.10.15 -- Bugfix: error if used in a loop and previous directories deleted.
    * The code crashed if called with a loop in the flowchart, and the last directory of
      a previous loop iteration was deleted before running the next iteration.

torchani_step/SEAMM_TorchANI.py_template

@@ -319,8 +319,8 @@ class TorchANI:
                             if need_gradients:
                                 dE = dE_stack.mean(dim=0).tolist()
                                 dE_stdev = dE_stack.std(dim=0).tolist()
-                                results["gradients"] = dE
-                                results["gradients, stdev"] = dE_stdev
+                                results["gradients"] = dE[0]
+                                results["gradients, stdev"] = dE_stdev[0]
 
                             configuration["results"]["data"].append(results)
 

torchani_step/energy.py

@@ -248,7 +248,7 @@ def analyze(self, indent="", **kwargs):
         )
 
         # Get the appropriate system/configuration for the new coordinates
-        system, configuration = self.get_system_configuration(P)
+        system, configuration = self.get_system_configuration(None)
 
         schema = kwargs["schema"]
         step_no = kwargs["step_no"]
@@ -263,9 +263,6 @@ def analyze(self, indent="", **kwargs):
         # The model chemistry
         self.model = f"ANI/{P['model']}"
 
-        # Get the appropriate system/configuration
-        system, configuration = self.get_system_configuration(P)
-
         have_stdev = False
         for system in schema["systems"]:
             system_name = system["name"]

torchani_step/torchani.py

@@ -174,15 +174,17 @@ def description_text(self, P=None):
                 text += __(node.description_text(), indent=3 * " ").__str__()
             except Exception as e:
                 print(f"Error describing torchani flowchart: {e} in {node}")
-                logger.critical(f"Error describing torchani flowchart: {e} in {node}")
+                self.logger.critical(
+                    f"Error describing torchani flowchart: {e} in {node}"
+                )
                 raise
             except:  # noqa: E722
                 print(
                     "Unexpected error describing torchani flowchart: {} in {}".format(
                         sys.exc_info()[0], str(node)
                     )
                 )
-                logger.critical(
+                self.logger.critical(
                     "Unexpected error describing torchani flowchart: {} in {}".format(
                         sys.exc_info()[0], str(node)
                     )
@@ -240,7 +242,7 @@ def run(self):
             schema, indent=4, cls=CompactJSONEncoder, sort_keys=True
         )
         files = {"input.json": input_data}
-        logger.info("input.json:\n" + files["input.json"])
+        self.logger.debug("input.json:\n" + files["input.json"])
         executor = self.flowchart.executor
 
         # Read configuration file for TorchANI if it exists
@@ -292,7 +294,7 @@ def run(self):
             "stderr.txt",
         ]
 
-        self.logger.info(f"{cmd=}")
+        self.logger.debug(f"{cmd=}")
 
         result = executor.run(
             cmd=cmd,
@@ -308,9 +310,9 @@ def run(self):
             self.logger.error("There was an error running TorchANI")
             return None
 
-        logger.debug("\n" + pprint.pformat(result))
+        self.logger.debug("\n" + pprint.pformat(result))
 
-        logger.info("stdout:\n" + result["stdout"])
+        self.logger.debug("stdout:\n" + result["stdout"])
         if "stderr.txt" in result and "data" in result["stderr.txt"]:
             if result["stderr.txt"]["data"] != "":
                 lines = result["stderr.txt"]["data"].splitlines()
@@ -324,7 +326,7 @@ def run(self):
                         continue
                     tmp.append(line)
                 if len(tmp) > 0:
-                    logger.warning("stderr:\n" + "\n".join(tmp))
+                    self.logger.warning("stderr:\n" + "\n".join(tmp))
 
         lines = result["output.json"]["data"].splitlines()
         line = lines[0]