Merge pull request #5 from chemle/feature_logging

Add support for basic error logging

README.md

@@ -109,7 +109,7 @@ emle-server --backend torchani
 When using the `orca` backend, you will also need to specify the path to the
 *real* `orca` exectubale using the `--orca-path` command-line argument, or the
 `EMLE_ORCA_PATH` environment variable. (To check that EMLE is running, look for
-an `emle_log.txt` file in the working directory, where. The input for `orca` will
+a log or settings  file in the working directory.) The input for `orca` will
 be taken from the `&orc` section of the `sander` configuration file, so use this
 to specify the method, etc.
 
@@ -206,11 +206,19 @@ are electron charge.
 
 ## Logging
 
-Energies can be written to a log file using the `--log` command-line argument or
-the `EMLE_LOG` environment variable. This should be an integer specifying the
-frequency at which energies are written. (The default is 1, i.e. every step
-is logged.) The output will look something like the following, where the
-columns specify the current step, the in vacuo energy and the total energy.
+Energies can be written to a file using the `--energy-file` command-line argument
+or the `EMLE_ENERGY_FILE` environment variable. The frequency of logging can be
+specified using `--energy-frequency` or `EMLE_ENERGY_FREQUENCY`. This should be an
+integer specifying the frequency at which energies are written. (The default is
+0, which means that energies aren't logged.) The output will look something like
+the following, where the columns specify the current step, the in vacuo energy
+and the total energy.
+
+General log messages are written to the file specified by the `--log-file` or
+`EMLE_LOG_FILE` options. (By default, no log file is used and diagnostic messages
+are written to `sys.stderr`.) The log level can be adjusted by using the
+`--log-level` or `EMLE_LOG_LEVEL` options. For performance, the default log level
+is set to `ERROR`.
 
 ```
 #     Step            E_vac (Eh)            E_tot (Eh)
@@ -288,9 +296,10 @@ Alternatively, if two values are passed then these will be used as initial and
 final values of λ, with the additional `--interpolate-steps` option specifying
 the number of steps (calls to the server) over which λ will be linearly
 interpolated. (This can also be specified using the `EMLE_INTERPOLATE_STEPS`
-environment variable.) In this case the `emle_log.txt` file will contain output
-similar to that shown below. The columns specify the current step, the current
-λ value, the energy at the current λ value, and the pure MM and EMLE energies.
+environment variable.) In this case the energy file (if written) will contain
+output similar to that shown below. The columns specify the current step, the
+current λ value, the energy at the current λ value, and the pure MM and EMLE
+energies.
 
 ```
 #     Step                     λ             E(λ) (Eh)           E(λ=0) (Eh)           E(λ=1) (Eh)

bin/emle-server

@@ -69,9 +69,12 @@ external_backend = os.getenv("EMLE_EXTERNAL_BACKEND")
 plugin_path = os.getenv("EMLE_PLUGIN_PATH")
 device = os.getenv("EMLE_DEVICE")
 try:
-    log = int(os.getenv("EMLE_LOG"))
+    energy_frequency = int(os.getenv("EMLE_ENERGY_FREQUENCY"))
 except:
-    log = 1
+    energy_frequency = 0
+energy_file = os.getenv("EMLE_energy_file")
+log_level = os.getenv("EMLE_LOG_LEVEL")
+log_file = os.getenv("EMLE_LOG_FILE")
 save_settings = os.getenv("EMLE_SAVE_SETTINGS")
 orca_template = os.getenv("EMLE_ORCA_TEMPLATE")
 deepmd_model = os.getenv("EMLE_DEEPMD_MODEL")
@@ -131,7 +134,10 @@ env = {
     "orca_path": orca_path,
     "restart": restart,
     "orca_template": orca_template,
-    "log": log,
+    "energy_frequency": energy_frequency,
+    "energy_file": energy_file,
+    "log_level": log_level,
+    "log_file": log_file,
     "save_settings": save_settings,
 }
 
@@ -275,11 +281,30 @@ parser.add_argument(
     required=False,
 )
 parser.add_argument(
-    "--log",
+    "--energy-frequency",
     type=int,
     help="The frequency of logging energies to file",
     required=False,
 )
+parser.add_argument(
+    "--energy-file",
+    type=str,
+    help="The file to log energies to",
+    required=False,
+)
+parser.add_argument(
+    "--log-level",
+    type=str,
+    help="The logging level",
+    choices=["TRACE", "DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"],
+    required=False,
+)
+parser.add_argument(
+    "--log-file",
+    type=str,
+    help="The file to log to",
+    required=False,
+)
 parser.add_argument(
     "--save-settings",
     action=argparse.BooleanOptionalAction,