diff --git a/parser/parser-siesta/check.sh b/parser/parser-siesta/check.sh
index d98ff510ab81ea05fd59c63004a074a116ef3895..866138698f44116fe1891777a2645056e698bb19 100755
--- a/parser/parser-siesta/check.sh
+++ b/parser/parser-siesta/check.sh
@@ -1,9 +1,9 @@
#!/bin/bash
-python main.py test/H2O/out --annotate > test/H2O/json 2>&1
-python main.py test/H2O-relax/out --annotate > test/H2O-relax/json 2>&1
-python main.py test/Al-bulk/out --annotate > test/Al-bulk/json 2>&1
-python main.py test/Al-slab/out --annotate > test/Al-slab/json 2>&1
-python main.py test/MgO/out --annotate > test/MgO/json 2>&1
-python main.py test/smeagol-Au-leads/Au.out --annotate > test/smeagol-Au-leads/json 2>&1
-python main.py test/smeagol-Au-scregion/Au.out --annotate > test/smeagol-Au-scregion/json 2>&1
+python main.py test/H2O/out --annotate 2>&1 | tee test/H2O/json
+python main.py test/H2O-relax/out --annotate 2>&1 | tee test/H2O-relax/json
+python main.py test/Al-bulk/out --annotate 2>&1 | tee test/Al-bulk/json
+python main.py test/Al-slab/out --annotate 2>&1 | tee test/Al-slab/json
+python main.py test/MgO/out --annotate 2>&1 | tee test/MgO/json
+python main.py test/smeagol-Au-leads/Au.out --annotate 2>&1 | tee test/smeagol-Au-leads/json
+python main.py test/smeagol-Au-scregion/Au.out --annotate 2>&1 | tee test/smeagol-Au-scregion/json
diff --git a/parser/parser-siesta/main.py b/parser/parser-siesta/main.py
index c949578b42f81c8a0604c012b61afd2007274bcd..32f2d5f998a4cf8edfa74fbea2c81243162487f9 100644
--- a/parser/parser-siesta/main.py
+++ b/parser/parser-siesta/main.py
@@ -3,6 +3,7 @@ import os
import sys
import setup_paths
from glob import glob
+import re
import numpy as np
from ase.data import chemical_symbols
@@ -30,8 +31,6 @@ def siesta_energy(title, meta, **kwargs):
return SM(r'siesta:\s*%s\s*=\s*(?P<%s__eV>\S+)' % (title, meta),
name=meta, **kwargs)
-import re
-
def line_iter(fd, linepattern = re.compile(r'\s*([^#]+)')):
# Strip off comments and whitespace, return only non-empty strings
for line in fd:
@@ -89,123 +88,6 @@ def get_input_metadata(inputvars_file, use_new_format):
return inputvars, blocks
-def ArraySM(header, row, build, **kwargs):
-
- class LineBuf:
- def __init__(self):
- self.lines = []
-
- def adhoc_addrow(self, parser):
- line = parser.fIn.readline()
- self.lines.append(line)
-
- def _build_array(self, parser):
- build(parser.backend.superBackend, self.lines)
- self.lines = []
-
- linebuf = LineBuf()
- sm = SM(header,
- name=kwargs.pop('name', 'startarray'),
- required=True,
- subFlags=SM.SubFlags.Sequenced,
- subMatchers=[
- SM(row, name='array', repeats=True,
- forwardMatch=True,
- adHoc=linebuf.adhoc_addrow, required=True),
- SM(r'', endReStr='', adHoc=linebuf._build_array, name='endarray',
- forwardMatch=True)
- ],
- **kwargs)
- return sm
-
-
-def errprint(func):
- def wrapper(backend, lines):
- try:
- func(backend, lines)
- except Exception:
- print('Error in %s: %d lines' % (func.__name__,
- len(lines)))
- for line in lines:
- print(line, file=sys.stderr)
- raise
- return wrapper
-
-def tokenize(lines):
- return np.array([line.split() for line in lines], object)
-
-
-#@errprint
-#def build_cell(backend, lines):
-# cell = tokenize(lines).astype(float)
-# backend.addArrayValues('simulation_cell', convert_unit(cell, 'angstrom'))
-
-@errprint
-def get_forces(backend, lines):
- if len(lines) == 0:
- # Siesta sometimes, stupidly, writes a Forces header.
- # It then proceeds to not write any forces.
- # Thus we ignore that silliness
- return
- forces = tokenize(lines)[:, 1:].astype(float)
- assert forces.shape[1] == 3, forces.shape
- backend.addArrayValues('atom_forces', convert_unit(forces, 'eV/angstrom'))
-
-@errprint
-def get_stress(backend, lines):
- stress = tokenize(lines)[:, 1:].astype(float)
- assert stress.shape == (3, 3)
- backend.addArrayValues('stress_tensor', convert_unit(stress, 'eV/angstrom**3'))
-
-@errprint
-def get_dipole(backend, lines):
- assert len(lines) == 1
- dipole = tokenize(lines)[:, -3:].astype(float)
- # Hmm. There is no common metadata for dipole moment for some reason.
- #print('dipole', dipole)
-
-#def get_array(metaname, dtype, istart=0, iend=None, unit=None):
-# @errprint
-# def buildarray(backend, lines):
-# arr = tokenize(lines)
-# if iend is None:
-# arr = arr[:, istart:]
-# else:
-# arr = arr[:, istart:iend]
-# arr = arr.astype(dtype)
-# if unit is not None:
-# arr = convert_unit(arr, unit)
-# backend.addArrayValues(metaname, arr)
-# return buildarray
-def get_array(metaname, dtype=float, istart=0, iend=None, unit=None,
- storage=None):
- @errprint
- def buildarray(backend, lines):
- arr = tokenize(lines)
- if iend is None:
- arr = arr[:, istart:]
- else:
- arr = arr[:, istart:iend]
- arr = arr.astype(dtype)
- if unit is not None:
- arr = convert_unit(arr, unit)
- if storage is not None:
- storage[metaname] = arr
- else:
- backend.addArrayValues(metaname, arr)
- return buildarray
-
-
-
-@errprint
-def add_positions_and_labels(backend, lines):
- matrix = tokenize(lines)
- positions = matrix[:, 1:4].astype(float)
- labels = np.array([chemical_symbols[i] for i in matrix[:, 5].astype(int)])
- backend.addArrayValues('atom_positions', convert_unit(positions, 'bohr'))
- backend.addArrayValues('atom_labels', labels)
-
-
"""
%block PAO.Basis # Define Basis set
O 2 # Species label, number of l-shells
@@ -439,6 +321,9 @@ class SiestaContext(object):
for key, value in meta.items():
backend.addArrayValues(key, value)
+ backend.addArrayValues('configuration_periodic_dimensions',
+ np.ones(3, bool))
+
assert len(self.data) == 0, self.data
def onClose_section_run(self, backend, gindex, section):
@@ -665,9 +550,6 @@ mainFileDescription = SM(
r'',
name='root',
#weak=True,
- #fixedStartValues={'program_name': 'siesta',
- # 'program_basis_set_type': 'numeric AOs',
- # 'configuration_periodic_dimensions': np.ones(3, bool)},
sections=['section_run'],
subMatchers=[
get_header_matcher(),