From dc09cfb3ed7667ef65b5727c710ab11a339b5c79 Mon Sep 17 00:00:00 2001
From: Mikkel Strange <mikst@fysik.dtu.dk>
Date: Sun, 18 Sep 2016 13:40:16 +0200
Subject: [PATCH] small changes
---
parser/parser-atk/atkio2.py | 71 ++++++++++++----------
parser/parser-atk/parser_configurations.py | 4 +-
2 files changed, 40 insertions(+), 35 deletions(-)
diff --git a/parser/parser-atk/atkio2.py b/parser/parser-atk/atkio2.py
index 34d62a1..8b34c55 100644
--- a/parser/parser-atk/atkio2.py
+++ b/parser/parser-atk/atkio2.py
@@ -2,7 +2,7 @@ from copy import copy
from scipy.io.netcdf import netcdf_file
from parser_configurations import parse_configuration as p_conf
from parser_calculator import parse_calculator as p_calc
-
+import re
class X:
def __init__(self, name=None):
@@ -20,19 +20,28 @@ class Reader:
self.CommonConcepts = X('CommonConcepts')
self.CommonConcepts.Configurations = X('Configurations')
- if 1:
- gIDs = []
- for k in self.f.dimensions.keys():
- if '_gID' not in k:
- continue
- i = k.index('_gID')
- gID = int(k[i+4: i+7])
- if gID not in gIDs:
- gIDs.append(gID)
-
- self.gIDs = gIDs
+ gIDs = []
+ for k in self.f.dimensions.keys():
+ if '_gID' not in k:
+ continue
+ i = k.index('_gID')
+ gID = int(k[i+4: i+7])
+ if gID not in gIDs:
+ gIDs.append(gID)
+
+ self.gIDs = gIDs
+ pm = re.compile('MoleculeConfiguration(?P<gid>_gID[0-9][0-9][0-9])$')
+ pb = re.compile('BulkConfiguration(?P<gid>_gID[0-9][0-9][0-9])$')
+ for key in self.f.variables.keys():
+ s = re.search(pm, key)
+ if s is not None:
+ self.conf_gID = s.group('gid')
+ break
+ s = re.search(pb, key)
+ if s is not None:
+ self.conf_gID = s.group('gid')
+ break
- self.conf_gID = '_gID000'
self.atk_version = self.f.version[4:].decode('utf-8')
self.finger_prints = [x.split(':') for x in
self.f.fingerprint_table.\
@@ -58,17 +67,7 @@ class Reader:
self.wave_functions = X('wave_functions')
def extract_calculator(self):
- #p_calc(self)
- # dummy until p_calc stops crashing!
- name = self.CommonConcepts.Configurations.name + self.conf_gID
- self.calculator = p_calc(self.f, name)
-# self.calculator = X('calculator')
-# self.calculator.basis = 'dzp'
-# self.calculator.method = 'DFT'
-# self.calculator.xc = 'LDA'
-# self.calculator.charge = 0
-# self.calculator.temp = 300.0 # icp
-# self.calculator.dens_tolerance = 0.0001 # icp
+ self.calculator = p_calc(self.f, self.conf_name)
def extract_bandstructure(self):
self.wave_functions = X('wave_functions')
@@ -115,15 +114,21 @@ class Reader:
ham.e_tot = ham.e_kin + ham.e_xc + ham.e_hartree + ham.e_S
def extract_common_concepts(self):
- if 'BulkConfiguration_gID000_dimension' in self.f.dimensions.keys():
- self.CommonConcepts.Configurations = X('BulkConfiguration')
- elif 'MoleculeConfiguration_gID000_dimension' in \
- self.f.dimensions.keys():
- self.CommonConcepts.Configurations = X('MoleculeConfiguration')
- else:
- assert 0, 'Not a Bulk or Molecule configurations found!'
-
- self.atoms = p_conf(self.f, self.CommonConcepts.Configurations.name)
+ pm = re.compile('MoleculeConfiguration(?P<gid>_gID[0-9][0-9][0-9])$')
+ pb = re.compile('BulkConfiguration(?P<gid>_gID[0-9][0-9][0-9])$')
+ for key in self.f.variables.keys():
+ s = re.search(pm, key)
+ if s is not None:
+ self.conf_gID = s.group('gid')
+ self.conf_name = s.group()
+ break
+ s = re.search(pb, key)
+ if s is not None:
+ self.conf_gID = s.group('gid')
+ self.conf_name = s.group()
+ break
+ print(self.conf_name)
+ self.atoms = p_conf(self.f, self.conf_name)
if __name__ == '__main__':
import sys
diff --git a/parser/parser-atk/parser_configurations.py b/parser/parser-atk/parser_configurations.py
index 839720a..b0d4b4d 100644
--- a/parser/parser-atk/parser_configurations.py
+++ b/parser/parser-atk/parser_configurations.py
@@ -47,8 +47,8 @@ class BulkConfiguration:
self.atoms = atoms
-def parse_configuration(fd, conftype='BulkConfiguration', verbose=False):
- code = fd.variables[conftype + '_gID000'].data[:].copy()
+def parse_configuration(fd, confname, verbose=False):
+ code = fd.variables[confname].data[:].copy()
code = code.tostring().decode("utf-8")
s = re.search('\s*(?P<name>[0-9a-zA-Z_]+)\s*=\s*BulkConfiguration\(', code)
name = s.group('name')
--
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