Merge pull request #61 from robinzyb/devel

move print to logger

README.md

@@ -39,7 +39,8 @@ pip install .
 # Feature Request
 Any advice is welcome. If you would like to request a new feature, please open an issue in github and upload example input and output files.
 
-
+# Developer
+set environment variable CP2KDATA_LOG_LEVEL to DEBUG to get the complete information.
 
 
 

cp2kdata/dpdata_plugin.py

@@ -1,10 +1,15 @@
+from .log import get_logger
+import numpy as np
+
 from dpdata.unit import EnergyConversion, LengthConversion, ForceConversion, PressureConversion
 from dpdata.format import Format
+
 from . import Cp2kOutput
 from .block_parser.converge import parse_e_f_converge
-import numpy as np
-from cp2kdata.block_parser.md_xyz import parse_pos_xyz_from_wannier
-import os
+from .block_parser.md_xyz import parse_pos_xyz_from_wannier
+
+logger = get_logger(__name__)
+
 
 AU_TO_EV = EnergyConversion("hartree", "eV").value()
 AU_TO_ANG = LengthConversion("bohr", "angstrom").value()
@@ -13,9 +18,9 @@
 
 WRAPPER = "--- You are parsing data using package Cp2kData ---"
 VIRIAL_WRN = (
-    "Virial Parsing using cp2kdata as plug in for dpdata\n"
-    "was not multiplied by volume before cp2kdata v0.6.4\n"
-    "please check the cp2kdata version and the virial.npy\n"
+    "Virial Parsing using cp2kdata as plug in for dpdata "
+    "was not multiplied by volume before cp2kdata v0.6.4 "
+    "please check the cp2kdata version and the virial.npy"
     )
 
 
@@ -28,7 +33,7 @@ def from_labeled_system(self, file_name, **kwargs):
         true_symbols = kwargs.get('true_symbols', False)
 
         # -- start parsing --
-        print(WRAPPER)
+        logger.debug(WRAPPER)
         converge_info = parse_e_f_converge(file_name)
         if not converge_info.converge:
             data = {
@@ -61,11 +66,11 @@ def from_labeled_system(self, file_name, **kwargs):
         data['forces'] = cp2k_e_f.atomic_forces_list * AU_TO_EV/AU_TO_ANG
         if cp2k_e_f.has_stress():
             # note that virial = stress * volume
-            print(VIRIAL_WRN)
+            logger.warning(VIRIAL_WRN)
             volume = np.linalg.det(data['cells'][0])
             data['virials'] = cp2k_e_f.stress_tensor_list*volume/EV_ANG_m3_TO_GPa
 
-        print(WRAPPER)
+        logger.debug(WRAPPER)
         return data
 
 
@@ -81,7 +86,7 @@ def from_labeled_system(self, file_name, restart: bool=None, **kwargs):
         cp2k_output_name = kwargs.get('cp2k_output_name', None)
 
         # -- start parsing --
-        print(WRAPPER)
+        logger.debug(WRAPPER)
 
         cp2kmd = Cp2kOutput(output_file=cp2k_output_name,
                             run_type="MD",
@@ -130,26 +135,26 @@ def from_labeled_system(self, file_name, restart: bool=None, **kwargs):
         data['forces'] = cp2kmd.atomic_forces_list * AU_TO_EV/AU_TO_ANG
         if cp2kmd.has_stress():
             # note that virial = stress * volume
-            print(VIRIAL_WRN)
+            logger.warning(VIRIAL_WRN)
             # the shape of cells should be (num_frames, 3, 3)
             # the np.linalg.det() function can handle this and return (num_frames,)
             volumes = np.linalg.det(data['cells'])
             volumes = volumes[:, np.newaxis, np.newaxis]
             data['virials'] = cp2kmd.stress_tensor_list*volumes/EV_ANG_m3_TO_GPa
 
-        print(WRAPPER)
+        logger.debug(WRAPPER)
         return data
 
 
 def get_chemical_symbols_from_cp2kdata(cp2koutput, true_symbols):
     if cp2koutput.atomic_kind is None:
-        print("Missing the atomic kind informations, atom names are true chemical symbols.")
+        logger.debug("Missing the atomic kind informations, atom names are true chemical symbols.")
         chemical_symbols = cp2koutput.get_chemical_symbols()
     elif true_symbols:
-        print("You have manually true_symbols=True, atom names are true chemical symbols.")
+        logger.debug("You have manually true_symbols=True, atom names are true chemical symbols.")
         chemical_symbols = cp2koutput.get_chemical_symbols()
     else:
-        print("Atom names are fake chemical symbols as you set in cp2k input.")
+        logger.debug("Atom names are fake chemical symbols as you set in cp2k input.")
         chemical_symbols = cp2koutput.get_chemical_symbols_fake()
     chemical_symbols = np.array(chemical_symbols)
     return chemical_symbols

cp2kdata/log.py

@@ -0,0 +1,13 @@
+import logging
+import os
+
+level_name = os.environ.get('CP2KDATA_LOG_LEVEL', 'INFO')
+level = logging._nameToLevel.get(level_name, logging.INFO)
+
+# format to include timestamp and module
+logging.basicConfig(format='%(asctime)s %(levelname)-8s %(name)-40s: %(message)s', level=level)
+# suppress transitions logging
+# logging.getLogger('transitions.core').setLevel(logging.WARNING)
+
+def get_logger(name=None):
+    return logging.getLogger(name)

cp2kdata/utils.py

@@ -1,13 +1,17 @@
 """
 this script put misc function here.
 """
-from ase.geometry.analysis import Analysis
-from ase.io import read, write
 #from cp2kdata import Cp2kOutput
 import numpy as np
 import os
 import shutil
 
+from ase.geometry.analysis import Analysis
+from ase.io import read, write
+
+from .log import get_logger
+
+logger = get_logger(__name__)
 # frequently used unit convertion
 au2eV = 27.211386245988
 au2A = 0.529177210903
@@ -75,7 +79,7 @@ def printtbox(arg):
     print("--> CP2KDATA: {0}".format(arg))
 
 def format_logger(info, filename):
-    print(f"Parsing {info:10} from {filename}")
+    logger.debug(f"Parsing {info:10} from {filename}")
 
 def file_content(file, num):
     # read a specific line of file or return the block