From ce58ded8619ed8466bf506b7decee14003d22cb1 Mon Sep 17 00:00:00 2001
From: Mikkel Strange <mikst@fysik.dtu.dk>
Date: Wed, 28 Sep 2016 16:57:05 +0200
Subject: [PATCH] more polishing
---
parser/parser-atk/atkio.py | 5 +++
parser/parser-atk/parser_calculator.py | 38 +++++++++++++++-------
parser/parser-atk/parser_configurations.py | 3 +-
3 files changed, 32 insertions(+), 14 deletions(-)
diff --git a/parser/parser-atk/atkio.py b/parser/parser-atk/atkio.py
index db4f935..b85f85f 100644
--- a/parser/parser-atk/atkio.py
+++ b/parser/parser-atk/atkio.py
@@ -19,6 +19,11 @@ class Reader:
self.calculator_x[gid] = parse_calculator(self.f, calc_name)
def initialize(self):
+ """Read the names of the variables in the netcdf file for
+ configurations and calculators and setup
+ the finger print table which maps between calculated
+ quantities and configurations.
+ """
self.conf_names = self._read_configuration_names()
self.calc_names = self._read_calculator_names()
self.finger_print_table = self._read_finger_print_table()
diff --git a/parser/parser-atk/parser_calculator.py b/parser/parser-atk/parser_calculator.py
index 804ddeb..bf1ae00 100644
--- a/parser/parser-atk/parser_calculator.py
+++ b/parser/parser-atk/parser_calculator.py
@@ -9,15 +9,18 @@ SphericalSymmetric = 'SphericalSymmetric'
LDA = type('LDA', (object,), {'PZ': 'LDA.PZ',
- 'PW': 'LDA.PW'})()
+ 'PW': 'LDA.PW',
+ 'RPA': 'LDA.RPA'})()
GGA = type('GGA', (object,), {'PBE': 'GGA.PBE',
'RPBE': 'GGA.RPBE',
- 'PW91': 'GGA.PW91'})()
+ 'PW91': 'GGA.PW91',
+ 'PBES': 'GGA.PBES'})()
ptable = {name: symbol for symbol, name in zip(data.chemical_symbols,
data.atomic_names)}
PeriodicTable = type('PeriodicTable', (object,), ptable)()
+
Preconditioner = type('Preconditioner', (object,), {'Off': 'Off',
'On': 'On'})
@@ -28,11 +31,14 @@ Preconditioner = type('Preconditioner', (object,), {'Off': 'Off',
# class LCAOCalculator(object):
# def __init__(self, basis_set=None, ...)
#
-# is easily done, but a bit more work at the moment
+# is easily done, but a bit more work at the moment...
#
def init(self, *args, **kwargs):
+ #if len(args)>0:
+ # print(*args)
+ #assert len(args) == 0
self.args = args
- for key, value in kwargs.iteritems():
+ for key, value in kwargs.items():
setattr(self, key, value)
@@ -42,23 +48,31 @@ clss = ['LCAOCalculator', 'BasisSet', 'ConfinedOrbital', 'CheckpointHandler',
'NumericalAccuracyParameters', 'MonkhorstPackGrid',
'NormConservingPseudoPotential', 'AnalyticalSplit', 'ConfinedOrbital',
'PolarizationOrbital', 'PulayMixer']
+
for cls in clss:
code = cls + ' = type("' + cls + '", (object,)' + ', {"__init__": init})'
exec(code)
-def parse_calculator(fd, conf='BulkConfiguration_gID000', verbose=False):
- """conf: the configuratio the calcualtor refers to
+def parse_calculator(fd, calcname):
+ """calc: the configuratio the calcualtor refers to
+ The name of the calculator in the nc-file is
+ conf_calculator, fx BulkConfiguration_gID000_calculator
"""
- code = fd.variables[conf + '_calculator'].data[:].copy()
+ code = fd.variables[calcname].data[:].copy()
code = code.tostring().decode("utf-8")
- s = re.search('\s*(?P<name>[0-9a-zA-Z_]+)\s*=\s*LCAOCalculator\(', code)
- name = s.group('name')
+ if 1:
+ print(code)
+ #s = re.search('\s*(?P<name>[0-9a-zA-Z_]+)\s*=\s*LCAOCalculator\(', code)
+ #name = s.group('name')
exec(code)
- calc = (locals()[name])
- return calc
+ for obj in locals().values():
+ if isinstance(obj, LCAOCalculator):
+ return obj
+ assert 0, 'No calculator found'
if __name__ == '__main__':
from scipy.io.netcdf import netcdf_file
fd = netcdf_file('Water.nc', 'r')
- calc = parse_calculator(fd)
+ calc = parse_calculator(fd, 'BulkConfiguration_gID000_calculator')
+ print(dir(calc))
diff --git a/parser/parser-atk/parser_configurations.py b/parser/parser-atk/parser_configurations.py
index b0d4b4d..4181a1f 100644
--- a/parser/parser-atk/parser_configurations.py
+++ b/parser/parser-atk/parser_configurations.py
@@ -15,7 +15,6 @@ Silicon = type('Silicon', (object,), {})
Silicon.symbol = 'Si'
-
class UnitCell:
def __init__(self, a, b, c, origin=None):
self.cell = [a, b, c]
@@ -64,5 +63,5 @@ if __name__ == '__main__':
import re
from scipy.io.netcdf import netcdf_file
fd = netcdf_file('Water.nc', 'r')
- atoms = parse_configuration(fd, verbose=True)
+ atoms = parse_configuration(fd, 'BulkConfiguration_gID000', verbose=True)
print(atoms)
--
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