Initial Implementation of Logs

.gitignore

@@ -1,5 +1,9 @@
+*.log
+*.log.backup
+
 *.pyc
 
 .idea/
 
 simfiles
+

crystalpol/__main__.py

@@ -4,10 +4,15 @@ from crystalpol.shared.config import Config
 from yaml.loader import SafeLoader
 import yaml
 
+from pathlib import Path
 import setproctitle
 import argparse
+import logging
+import sys
 import os
 
+from crystalpol.shared.utils import weekday_date_time
+from crystalpol.shared.utils.log import Log
 
 __VERSION = "v0.0.1"
 os.nice(+19)
@@ -47,6 +52,16 @@ def main():
     )
     args = parser.parse_args()
 
+    log_file = Path("run.log")
+    if log_file.exists():
+        log_file.rename(log_file.with_suffix(".log.backup"))
+
+    logging.basicConfig(
+        filename=args.outfile,
+        format='%(message)s',
+        level=logging.INFO
+    )
+
     try:
         with open(args.config) as file:
             data = yaml.load(file, Loader=SafeLoader)
@@ -54,6 +69,8 @@ def main():
     except IOError:
         raise RuntimeError('Invalid or Missing Config File.')
 
+    Log.make_header(__VERSION, data.get('crystal_pol'))
+
     pol = Polarization(args.infile, args.outfile, config)
     pol.run()
 

crystalpol/polarization.py

@@ -6,10 +6,12 @@ from crystalpol.shared.system.atom import Atom
 from crystalpol.shared.config import Config
 from crystalpol.gaussian import Gaussian
 
-from typing import List
+from typing import List, Tuple
 
 import sys
 
+from crystalpol.shared.utils.log import Log
+
 
 class Polarization:
     __slots__ = ('geom_file', 'outfile', 'config', 'gaussian', 'crystal')
@@ -30,12 +32,20 @@ class Polarization:
         self.read_crystal()
 
         cycle = 1
-        charge_diff = sys.float_info.max
+        max_charge_diff = sys.float_info.max
-        while charge_diff > self.config.charge_tolerance:
+        while max_charge_diff > self.config.charge_tolerance:
 
-            charge_diff = self.update_crystal_charges(
+            max_charge_diff, charge_diff = self.update_crystal_charges(
                 self.gaussian.run(cycle, self.crystal),
             )
+
+            Log.make_run(
+                cycle,
+                max_charge_diff,
+                charge_diff,
+                self.crystal
+            )
+
             cycle += 1
 
     def read_crystal(self) -> None:
@@ -49,7 +59,7 @@ class Polarization:
         for molecule in molecules:
             self.crystal.add_cell([molecule])
 
-    def update_crystal_charges(self, charges: List[float]) -> float:
+    def update_crystal_charges(self, charges: List[float]) -> Tuple[float, list]:
 
         charge_diff = []
 
@@ -60,7 +70,9 @@ class Polarization:
                         charge_diff.append(abs(atom.chg - charges[index]))
                     atom.chg = charges[index]
 
-        return abs(max(charge_diff, key=abs)) if charge_diff else sys.float_info.max
+        max_charge_diff = abs(max(charge_diff, key=abs)) if charge_diff else sys.float_info.max
+
+        return max_charge_diff, charge_diff
 
     def _get_molecules_from_lines(self, lines: List[str]) -> List[Molecule]:
         if (len(lines) % self.config.n_atoms) == 0:

crystalpol/shared/utils/__init__.py

@@ -0,0 +1,5 @@
+import time
+
+
+def weekday_date_time():
+    return time.strftime("%A, %d %b %Y at %H:%M:%S")

crystalpol/shared/utils/log.py

@@ -0,0 +1,45 @@
+import sys
+
+from crystalpol.shared.config import Config
+
+import logging
+
+from crystalpol.shared.utils import weekday_date_time
+
+
+class Log:
+    @staticmethod
+    def make_header(version: str, config_dict: dict):
+        logging.info(
+            f"##########################################################################################\n"
+            f"##############             Welcome to CRYSTALPOL version {version}             ##############\n"
+            f"##########################################################################################\n"
+        )
+        logging.info(f"Your python version is {sys.version}\n")
+        logging.info(f"Program started on {weekday_date_time()}\n")
+
+        logging.info("------------------------------------------------------------------------------------------")
+        logging.info("                   CRYSTALPOL variables being used in this run:                           ")
+        logging.info("------------------------------------------------------------------------------------------\n")
+        for key, value in config_dict.items():
+            logging.info(f"\t{key} = {(key if key else 'Not set')}")
+
+        logging.info("------------------------------------------------------------------------------------------")
+        logging.info(f"                                      RUN Results:                                       ")
+        logging.info("------------------------------------------------------------------------------------------\n")
+
+    @staticmethod
+    def make_run(cycle, max_charge_diff, charge_diff, crystal):
+        logging.info(f"cycle: {cycle}")
+        logging.info(f"\nMax charge diff: {max_charge_diff}")
+        logging.info(f"Charge Diff: {charge_diff}\n")
+
+        logging.info("------------------------------------------------------------------------------------------")
+        logging.info(f"             S             rx             ry             rz             chg              ")
+        logging.info("------------------------------------------------------------------------------------------")
+        for atom in crystal[0][0]:
+            logging.info(f"             {atom.symbol}        {atom.rx}        {atom.ry}        {atom.rz}        {atom.chg}    ")
+
+        logging.info("\n------------------------------------------------------------------------------------------\n")
+
+