From 883d1b7736f28f9e51d8d4d18900eb0f1a02f8d5 Mon Sep 17 00:00:00 2001
From: Ask Hjorth Larsen <asklarsen@gmail.com>
Date: Mon, 4 Jul 2016 20:20:22 +0200
Subject: [PATCH] move files around
---
.../parser-siesta/H2O}/0_NORMAL_EXIT | 0
.../parser-siesta/H2O}/BASIS_ENTHALPY | 0
.../parser-siesta/H2O}/BASIS_HARRIS_ENTHALPY | 0
{H2O => parser/parser-siesta/H2O}/CLOCK | 0
.../parser-siesta/H2O}/FORCE_STRESS | 0
{H2O => parser/parser-siesta/H2O}/H.ion | 0
{H2O => parser/parser-siesta/H2O}/H.ion.xml | 0
{H2O => parser/parser-siesta/H2O}/H.psf | 0
.../parser-siesta/H2O}/INPUT_TMP.95611 | 0
.../parser-siesta/H2O}/NON_TRIMMED_KP_LIST | 0
{H2O => parser/parser-siesta/H2O}/O.ion | 0
{H2O => parser/parser-siesta/H2O}/O.ion.xml | 0
{H2O => parser/parser-siesta/H2O}/O.psf | 0
.../parser-siesta/H2O}/fdf-95611.log | 0
{H2O => parser/parser-siesta/H2O}/h2o.BONDS | 0
.../parser-siesta/H2O}/h2o.BONDS_FINAL | 0
{H2O => parser/parser-siesta/H2O}/h2o.DM | Bin
{H2O => parser/parser-siesta/H2O}/h2o.EIG | 0
{H2O => parser/parser-siesta/H2O}/h2o.FA | 0
{H2O => parser/parser-siesta/H2O}/h2o.KP | 0
.../parser-siesta/H2O}/h2o.ORB_INDX | 0
.../parser-siesta/H2O}/h2o.STRUCT_OUT | 0
{H2O => parser/parser-siesta/H2O}/h2o.XV | 0
{H2O => parser/parser-siesta/H2O}/h2o.alloc | 0
{H2O => parser/parser-siesta/H2O}/h2o.fdf | 0
{H2O => parser/parser-siesta/H2O}/h2o.xml | 0
{H2O => parser/parser-siesta/H2O}/out | 0
parser/parser-siesta/parser.py | 24 ++++++++++++++++++
parser/parser-siesta/setup_paths.py | 6 +++++
parser/parser-siesta/util.py | 20 +++++++++++++++
30 files changed, 50 insertions(+)
rename {H2O => parser/parser-siesta/H2O}/0_NORMAL_EXIT (100%)
rename {H2O => parser/parser-siesta/H2O}/BASIS_ENTHALPY (100%)
rename {H2O => parser/parser-siesta/H2O}/BASIS_HARRIS_ENTHALPY (100%)
rename {H2O => parser/parser-siesta/H2O}/CLOCK (100%)
rename {H2O => parser/parser-siesta/H2O}/FORCE_STRESS (100%)
rename {H2O => parser/parser-siesta/H2O}/H.ion (100%)
rename {H2O => parser/parser-siesta/H2O}/H.ion.xml (100%)
rename {H2O => parser/parser-siesta/H2O}/H.psf (100%)
rename {H2O => parser/parser-siesta/H2O}/INPUT_TMP.95611 (100%)
rename {H2O => parser/parser-siesta/H2O}/NON_TRIMMED_KP_LIST (100%)
rename {H2O => parser/parser-siesta/H2O}/O.ion (100%)
rename {H2O => parser/parser-siesta/H2O}/O.ion.xml (100%)
rename {H2O => parser/parser-siesta/H2O}/O.psf (100%)
rename {H2O => parser/parser-siesta/H2O}/fdf-95611.log (100%)
rename {H2O => parser/parser-siesta/H2O}/h2o.BONDS (100%)
rename {H2O => parser/parser-siesta/H2O}/h2o.BONDS_FINAL (100%)
rename {H2O => parser/parser-siesta/H2O}/h2o.DM (100%)
rename {H2O => parser/parser-siesta/H2O}/h2o.EIG (100%)
rename {H2O => parser/parser-siesta/H2O}/h2o.FA (100%)
rename {H2O => parser/parser-siesta/H2O}/h2o.KP (100%)
rename {H2O => parser/parser-siesta/H2O}/h2o.ORB_INDX (100%)
rename {H2O => parser/parser-siesta/H2O}/h2o.STRUCT_OUT (100%)
rename {H2O => parser/parser-siesta/H2O}/h2o.XV (100%)
rename {H2O => parser/parser-siesta/H2O}/h2o.alloc (100%)
rename {H2O => parser/parser-siesta/H2O}/h2o.fdf (100%)
rename {H2O => parser/parser-siesta/H2O}/h2o.xml (100%)
rename {H2O => parser/parser-siesta/H2O}/out (100%)
create mode 100644 parser/parser-siesta/parser.py
create mode 100644 parser/parser-siesta/setup_paths.py
create mode 100644 parser/parser-siesta/util.py
diff --git a/H2O/0_NORMAL_EXIT b/parser/parser-siesta/H2O/0_NORMAL_EXIT
similarity index 100%
rename from H2O/0_NORMAL_EXIT
rename to parser/parser-siesta/H2O/0_NORMAL_EXIT
diff --git a/H2O/BASIS_ENTHALPY b/parser/parser-siesta/H2O/BASIS_ENTHALPY
similarity index 100%
rename from H2O/BASIS_ENTHALPY
rename to parser/parser-siesta/H2O/BASIS_ENTHALPY
diff --git a/H2O/BASIS_HARRIS_ENTHALPY b/parser/parser-siesta/H2O/BASIS_HARRIS_ENTHALPY
similarity index 100%
rename from H2O/BASIS_HARRIS_ENTHALPY
rename to parser/parser-siesta/H2O/BASIS_HARRIS_ENTHALPY
diff --git a/H2O/CLOCK b/parser/parser-siesta/H2O/CLOCK
similarity index 100%
rename from H2O/CLOCK
rename to parser/parser-siesta/H2O/CLOCK
diff --git a/H2O/FORCE_STRESS b/parser/parser-siesta/H2O/FORCE_STRESS
similarity index 100%
rename from H2O/FORCE_STRESS
rename to parser/parser-siesta/H2O/FORCE_STRESS
diff --git a/H2O/H.ion b/parser/parser-siesta/H2O/H.ion
similarity index 100%
rename from H2O/H.ion
rename to parser/parser-siesta/H2O/H.ion
diff --git a/H2O/H.ion.xml b/parser/parser-siesta/H2O/H.ion.xml
similarity index 100%
rename from H2O/H.ion.xml
rename to parser/parser-siesta/H2O/H.ion.xml
diff --git a/H2O/H.psf b/parser/parser-siesta/H2O/H.psf
similarity index 100%
rename from H2O/H.psf
rename to parser/parser-siesta/H2O/H.psf
diff --git a/H2O/INPUT_TMP.95611 b/parser/parser-siesta/H2O/INPUT_TMP.95611
similarity index 100%
rename from H2O/INPUT_TMP.95611
rename to parser/parser-siesta/H2O/INPUT_TMP.95611
diff --git a/H2O/NON_TRIMMED_KP_LIST b/parser/parser-siesta/H2O/NON_TRIMMED_KP_LIST
similarity index 100%
rename from H2O/NON_TRIMMED_KP_LIST
rename to parser/parser-siesta/H2O/NON_TRIMMED_KP_LIST
diff --git a/H2O/O.ion b/parser/parser-siesta/H2O/O.ion
similarity index 100%
rename from H2O/O.ion
rename to parser/parser-siesta/H2O/O.ion
diff --git a/H2O/O.ion.xml b/parser/parser-siesta/H2O/O.ion.xml
similarity index 100%
rename from H2O/O.ion.xml
rename to parser/parser-siesta/H2O/O.ion.xml
diff --git a/H2O/O.psf b/parser/parser-siesta/H2O/O.psf
similarity index 100%
rename from H2O/O.psf
rename to parser/parser-siesta/H2O/O.psf
diff --git a/H2O/fdf-95611.log b/parser/parser-siesta/H2O/fdf-95611.log
similarity index 100%
rename from H2O/fdf-95611.log
rename to parser/parser-siesta/H2O/fdf-95611.log
diff --git a/H2O/h2o.BONDS b/parser/parser-siesta/H2O/h2o.BONDS
similarity index 100%
rename from H2O/h2o.BONDS
rename to parser/parser-siesta/H2O/h2o.BONDS
diff --git a/H2O/h2o.BONDS_FINAL b/parser/parser-siesta/H2O/h2o.BONDS_FINAL
similarity index 100%
rename from H2O/h2o.BONDS_FINAL
rename to parser/parser-siesta/H2O/h2o.BONDS_FINAL
diff --git a/H2O/h2o.DM b/parser/parser-siesta/H2O/h2o.DM
similarity index 100%
rename from H2O/h2o.DM
rename to parser/parser-siesta/H2O/h2o.DM
diff --git a/H2O/h2o.EIG b/parser/parser-siesta/H2O/h2o.EIG
similarity index 100%
rename from H2O/h2o.EIG
rename to parser/parser-siesta/H2O/h2o.EIG
diff --git a/H2O/h2o.FA b/parser/parser-siesta/H2O/h2o.FA
similarity index 100%
rename from H2O/h2o.FA
rename to parser/parser-siesta/H2O/h2o.FA
diff --git a/H2O/h2o.KP b/parser/parser-siesta/H2O/h2o.KP
similarity index 100%
rename from H2O/h2o.KP
rename to parser/parser-siesta/H2O/h2o.KP
diff --git a/H2O/h2o.ORB_INDX b/parser/parser-siesta/H2O/h2o.ORB_INDX
similarity index 100%
rename from H2O/h2o.ORB_INDX
rename to parser/parser-siesta/H2O/h2o.ORB_INDX
diff --git a/H2O/h2o.STRUCT_OUT b/parser/parser-siesta/H2O/h2o.STRUCT_OUT
similarity index 100%
rename from H2O/h2o.STRUCT_OUT
rename to parser/parser-siesta/H2O/h2o.STRUCT_OUT
diff --git a/H2O/h2o.XV b/parser/parser-siesta/H2O/h2o.XV
similarity index 100%
rename from H2O/h2o.XV
rename to parser/parser-siesta/H2O/h2o.XV
diff --git a/H2O/h2o.alloc b/parser/parser-siesta/H2O/h2o.alloc
similarity index 100%
rename from H2O/h2o.alloc
rename to parser/parser-siesta/H2O/h2o.alloc
diff --git a/H2O/h2o.fdf b/parser/parser-siesta/H2O/h2o.fdf
similarity index 100%
rename from H2O/h2o.fdf
rename to parser/parser-siesta/H2O/h2o.fdf
diff --git a/H2O/h2o.xml b/parser/parser-siesta/H2O/h2o.xml
similarity index 100%
rename from H2O/h2o.xml
rename to parser/parser-siesta/H2O/h2o.xml
diff --git a/H2O/out b/parser/parser-siesta/H2O/out
similarity index 100%
rename from H2O/out
rename to parser/parser-siesta/H2O/out
diff --git a/parser/parser-siesta/parser.py b/parser/parser-siesta/parser.py
new file mode 100644
index 0000000..83766fb
--- /dev/null
+++ b/parser/parser-siesta/parser.py
@@ -0,0 +1,24 @@
+from __future__ import print_function
+import sys
+import setup_paths
+
+from nomadcore.simple_parser import mainFunction, SimpleMatcher as SM
+from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
+from nomadcore.unit_conversion.unit_conversion \
+ import register_userdefined_quantity
+
+
+arg = sys.argv[1]
+
+infoFileDescription = SM(
+ name='root',
+ weak=True,
+ startReStr='',
+ fixedStartValues={'program_name': 'siesta'},
+ sections=['section_run'],
+ subFlags=SM.SubFlags.Sequenced,
+ subMatchers=[
+ SM(r'Siesta Version: (?P<program_version>\S*)')
+ ])
+
+
diff --git a/parser/parser-siesta/setup_paths.py b/parser/parser-siesta/setup_paths.py
new file mode 100644
index 0000000..e0a0fb0
--- /dev/null
+++ b/parser/parser-siesta/setup_paths.py
@@ -0,0 +1,6 @@
+import sys, os, os.path
+baseDir = os.path.dirname(os.path.abspath(__file__))
+commonDir = os.path.normpath(os.path.join(baseDir,"../../../../python-common/common/python"))
+
+if not commonDir in sys.path:
+ sys.path.insert(0, commonDir)
diff --git a/parser/parser-siesta/util.py b/parser/parser-siesta/util.py
new file mode 100644
index 0000000..6b0f4fc
--- /dev/null
+++ b/parser/parser-siesta/util.py
@@ -0,0 +1,20 @@
+OCT_ENERGY_UNIT_NAME = 'usrOctEnergyUnit'
+f_num = r'[-+]?(\d*\.\d+|\d+\.\d*)' # e.g.: 0.7 1. -.1
+e_num = r'[-+]?\d*\.\d+[EeDd][-+]\d*' # e.g.: -7.642e-300
+i_num = r'[-+\d]*'
+
+def numpattern(id, unit=None, pattern=f_num):
+ if unit is None:
+ pat = r'(?P<%(id)s>%(pattern)s)'
+ else:
+ pat = r'(?P<%(id)s__%(unit)s>%(pattern)s)'
+ return pat % dict(id=id, unit=unit, pattern=pattern)
+
+def pat(meta, regex):
+ return '(?P<%s>%s)' % (meta, regex)
+def word(meta):
+ return pat(meta, regex=r'\S*')
+def integer(meta):
+ return pat(meta, regex=i_num)
+def floating(meta):
+ return pat(meta, regex='%s|%s' % (f_num, e_num))
--
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