Commit ce07a7cc authored by Carl Poelking's avatar Carl Poelking
Browse files

XML parsing.

parent 12e80786
......@@ -66,18 +66,20 @@ def parse(output_file_name):
jbe.startedParsingSession(output_file_name, parser_info)
base_dir = os.path.dirname(os.path.abspath(output_file_name))
terminal = LibAtomsParser(osio)
terminal_trj = LibAtomsTrajectory(osio)
terminal_trj.ParseOutput(output_file_name)
out = terminal
terminal_gap = LibAtomsGapParser(osio)
terminal_gap.ParseOutput(output_file_name)
terminal_trj = terminal_gap.trj
osio << "Start parsing ..." << osio.endl
osio << "Base directory = '%s'" % base_dir << osio.endl
gap = terminal_gap
trj = terminal_trj
log("Start parsing ...")
log("Base directory = '%s'" % base_dir)
with open_section(jbe, 'section_run') as gid_run:
push(jbe, trj, 'program_name')
push(jbe, trj, 'program_version')
push(jbe, gap, 'program_name')
push(jbe, gap, 'program_version', key2='GAP_params.svn_version')
jbe.finishedParsingSession("ParseSuccess", None)
return
......
......@@ -8,6 +8,7 @@ import os
import sys
import re
import numpy as np
import xml.dom.minidom
try:
import ase
......@@ -17,6 +18,36 @@ except ImportError:
HAVE_ASE = False
pass
def XmlGetUnique(root, tag):
nodes = XmlGetAll(root, tag)
if len(nodes) > 1:
raise ValueError("More than one node with tag '%s'" % tag)
return nodes[0]
def XmlGetAll(root, tag):
nodes = root.getElementsByTagName(tag)
ret_nodes = []
for node in nodes:
if node.localName != None: ret_nodes.append(node)
return ret_nodes
def XmlGetChildDict(root):
tag_child = {}
for child in root.childNodes:
if child.localName == None: continue
if not child.localName in tag_child:
tag_child[child.localName] = []
tag_child[child.localName].append(child)
return tag_child
def XmlGetAttributes(root):
return root.attributes
def XmlGetText(root):
return root.firstChild.nodeValue
class LibAtomsParser(object):
def __init__(self, log=None):
self.log = log
......@@ -33,7 +64,7 @@ class LibAtomsParser(object):
return self
def As(self, typ=None):
if typ == None:
typ = type(self.selected_data_item)
return self.selected_data_item
return typ(self.selected_data_item)
def SummarizeKeyDefaults(self):
if not self.log: return
......@@ -140,15 +171,125 @@ class LibAtomsParser(object):
self.Set('program_version', 'n/a')
return
class LibAtomsGapParser(LibAtomsParser):
def __init__(self, log=None):
super(LibAtomsGapParser, self).__init__(log)
self.logtag = 'gap-xml'
self.trj = None
return
def ParseOutput(self, output_file):
self.Set('program_name', 'libAtoms')
dom = xml.dom.minidom.parse(output_file)
root = XmlGetUnique(dom, 'GAP_params')
# Child keys should be: ['gpSparse', 'command_line', 'GAP_data', 'XYZ_data']
#print(list(child_nodes.keys()))
child_nodes = XmlGetChildDict(root)
# 'GAP_params'
atts = XmlGetAttributes(root)
keys = ['label', 'svn_version']
for key in keys:
self.Set('GAP_params.%s' % key, atts[key].value) # TODO Handle look-up errors
# 'GAP_params/GAP_data'
key = 'GAP_data'
if key in child_nodes:
node = child_nodes[key][0]
atts = XmlGetAttributes(node)
keys = ['do_core', 'e0']
for key in keys:
self.Set('GAP_data.%s' % key, atts[key].value) # TODO Handle look-up errors
# 'GAP_params/command_line'
key = 'command_line'
if key in child_nodes:
node = child_nodes[key][0]
text = XmlGetText(node)
self.Set('command_line.command_line', text)
# 'GAP_params/gpSparse'
key = 'gpSparse'
if key in child_nodes:
node = child_nodes[key][0]
atts = XmlGetAttributes(node)
keys = ['n_coordinate']
for key in keys:
self.Set('gpSparse.%s' % key, atts[key].value) # TODO Handle look-up errors
# GAP_params/gpSparse/gpCoordinates
gp_coord_node = XmlGetUnique(node, 'gpCoordinates')
gp_coord_child_nodes = XmlGetChildDict(gp_coord_node)
gp_coord_node_att = XmlGetAttributes(gp_coord_node)
for key in gp_coord_node_att.keys():
self.Set('gpCoordinates.%s' % key, gp_coord_node_att[key].value)
# 'GAP_params/gpSparse/gpCoordinates/theta
key = 'theta'
if key in gp_coord_child_nodes:
node = gp_coord_child_nodes[key][0]
text = XmlGetText(node).strip()
self.Set('gpCoordinates.%s' % key, text)
# 'GAP_params/gpSparse/gpCoordinates/descriptor
key = 'descriptor'
if key in gp_coord_child_nodes:
node = gp_coord_child_nodes[key][0]
text = XmlGetText(node).strip()
self.Set('gpCoordinates.%s' % key, text)
# 'GAP_params/gpSparse/gpCoordinates/descriptor
key = 'permutation'
if key in gp_coord_child_nodes:
node = gp_coord_child_nodes[key][0]
att = XmlGetAttributes(node)
text = XmlGetText(node).strip()
self.Set('gpCoordinates.perm.%s' % key, text)
self.Set('gpCoordinates.perm.i', att['i'].value)
# 'GAP_params/gpSparse/gpCoordinates/sparseX
key = 'sparseX'
if key in gp_coord_child_nodes:
n_sparseX = self['gpCoordinates.n_sparseX'].As(int)
n_dim = self['gpCoordinates.dimensions'].As(int)
sparseX_filename = self['gpCoordinates.sparseX_filename'].As(str)
# Read alpha coefficients
nodes = gp_coord_child_nodes[key]
alpha_cutoff = np.zeros((n_sparseX, 2), dtype='float64')
for i,node in enumerate(nodes):
att = XmlGetAttributes(node)
alpha_cutoff[i,0] = float(att["alpha"].value)
alpha_cutoff[i,1] = float(att["sparseCutoff"].value)
self.Set('gpCoordinates.alpha', alpha_cutoff)
# Read descriptor matrix
X_matrix = np.loadtxt(sparseX_filename)
assert X_matrix.shape[0] == n_sparseX*n_dim
# i-th row of X-matrix stores X-vector of config i
X_matrix = X_matrix.reshape((n_dim, n_sparseX))
self.Set('gpCoordinates.sparseX', X_matrix)
# 'GAP_params/XYZ_data'
key = 'XYZ_data'
if key in child_nodes:
node = child_nodes[key][0]
text = XmlGetText(node)
trj_file = 'lib-atoms-gap.from-xml.xyz'
ofs = open(trj_file, 'w')
for child in node.childNodes:
if child.nodeValue == None: continue
ln = child.nodeValue.strip(' \n')
if ln == '': continue
ofs.write(ln+'\n')
ofs.close()
self.trj = LibAtomsTrajectory(self.log)
self.trj.ParseOutput(trj_file)
return
class LibAtomsTrajectory(LibAtomsParser):
def __init__(self, log=None):
super(LibAtomsTrajectory, self).__init__(log)
self.ase_configs = None
self.frames = []
self.logtag = 'trj'
def ParseOutput(self, output_file):
if self.log:
self.log << self.log.mg << "libAtomsParser::ParseOutput ..." << self.log.endl
if HAVE_ASE:
read_fct = ase.io.read
read_fct_args = { 'index':':' }
......@@ -156,11 +297,9 @@ class LibAtomsTrajectory(LibAtomsParser):
raise NotImplementedError("None-ASE read function requested, but not yet available.")
read_fct = None
read_fct_args = None
# PARSE CONFIGURATIONS
self.ase_configs = read_fct(output_file, **read_fct_args)
self.LoadAseConfigs(self.ase_configs)
self.Set('program_name', 'libAtoms')
self.Set('program_version', 'n/a')
return
......@@ -169,7 +308,7 @@ class LibAtomsTrajectory(LibAtomsParser):
frame = LibAtomsFrame(self.log)
frame.LoadAseConfig(config)
self.frames.append(frame)
if self.log: log << "Loaded %d configurations" % len(self.frames) << log.endl
if self.log: self.log << "Loaded %d configurations" % len(self.frames) << self.log.endl
return
class LibAtomsFrame(LibAtomsParser):
......
......@@ -425,7 +425,7 @@ class ShellInterface(object):
try:
height, width = os.popen('stty size', 'r').read().split()
width = int(width)
leftright = ((width - len(title)-2) // 2
leftright = ((width - len(title)-2)) // 2
except ValueError:
leftright = 40
return trim*leftright + " " + title + " " + trim*leftright
......
......@@ -21,7 +21,7 @@ object LibAtomsParser extends SimpleExternalParserGenerator(
)) :: Nil
),
mainFileTypes = Seq("text/.*"),
mainFileRe = """ ll """.r,
mainFileRe = """\s*<GAP_params\s""".r,
cmd = Seq(DefaultPythonInterpreter.pythonExe(), "${envDir}/parsers/lib-atoms/parser/parser-lib-atoms/libAtomsParser.py",
"${mainFilePath}"),
resList = Seq(
......
......@@ -5,10 +5,10 @@ import org.specs2.mutable.Specification
object LibAtomsParserSpec extends Specification {
"LibAtomsParserTest" >> {
"test with json-events" >> {
ParserRun.parse(LibAtomsParser, "parsers/lib-atoms/test/lib-atoms-tungsten/tungsten_gap_6.xyz", "json-events") must_== ParseResult.ParseSuccess
ParserRun.parse(LibAtomsParser, "parsers/lib-atoms/test/lib-atoms-gap-test/gp.xml", "json-events") must_== ParseResult.ParseSuccess
}
"test with json" >> {
ParserRun.parse(LibAtomsParser, "parsers/lib-atoms/test/lib-atoms-tungsten/tungsten_gap_6.xyz", "json") must_== ParseResult.ParseSuccess
ParserRun.parse(LibAtomsParser, "parsers/lib-atoms/test/lib-atoms-gap-test/gp.xml", "json") must_== ParseResult.ParseSuccess
}
}
}
<GAP_2013_5_30_60_14_20_28_943>
<Potential label="GAP_2013_5_30_60_14_20_28_943" init_args="IP GAP"/>
<GAP_params label="GAP_2013_5_30_60_14_20_28_943" svn_version="11610">
<GAP_data do_core="F" e0="-9.19483512529700064"/>
<gpSparse label="GAP_2013_5_30_60_14_20_28_943" n_coordinate="1">
<gpCoordinates label="GAP_2013_5_30_60_14_20_28_9431" dimensions="1576" signal_variance="1.00000000000000000" signal_mean="0.00000000000000000" sparsified="T" n_permutations="1" covariance_type="2" n_sparseX="100" sparseX_filename="gp.xml.sparseX.GAP_2013_5_30_60_14_20_28_9431">
<theta> 0.40000000000000000E+01 </theta>
<descriptor>soap l_max=14 n_max=14 atom_sigma=0.5 zeta=4 cutoff=5.0 cutoff_transition_width=1.0 delta=1.0 f0=0.0 covariance_type=dot_product sparse_method=kmeans n_sparseX=100</descriptor>
<permutation i="1">1 </permutation>
<sparseX i="1" alpha="65.26379993425908310" sparseCutoff="1.00000000000000000"/>
<sparseX i="2" alpha="-68.10615573030179348" sparseCutoff="1.00000000000000000"/>
<sparseX i="3" alpha="29.79792500462039939" sparseCutoff="1.00000000000000000"/>
<sparseX i="4" alpha="-69.20000063321749906" sparseCutoff="1.00000000000000000"/>
<sparseX i="5" alpha="34.70560465153286600" sparseCutoff="1.00000000000000000"/>
<sparseX i="6" alpha="14.73902282206444347" sparseCutoff="1.00000000000000000"/>
<sparseX i="7" alpha="145.98088827553172564" sparseCutoff="1.00000000000000000"/>
<sparseX i="8" alpha="-214.48560863169950608" sparseCutoff="1.00000000000000000"/>
<sparseX i="9" alpha="188.76203414507153866" sparseCutoff="1.00000000000000000"/>
<sparseX i="10" alpha="328.30693311531888412" sparseCutoff="1.00000000000000000"/>
<sparseX i="11" alpha="-45.07262758953340409" sparseCutoff="1.00000000000000000"/>
<sparseX i="12" alpha="262.61453539816164948" sparseCutoff="1.00000000000000000"/>
<sparseX i="13" alpha="33.71275025741536524" sparseCutoff="1.00000000000000000"/>
<sparseX i="14" alpha="11.22612656130687192" sparseCutoff="1.00000000000000000"/>
<sparseX i="15" alpha="-151.90457764740870061" sparseCutoff="1.00000000000000000"/>
<sparseX i="16" alpha="-322.83249470027510597" sparseCutoff="1.00000000000000000"/>
<sparseX i="17" alpha="-331.31794678743472105" sparseCutoff="1.00000000000000000"/>
<sparseX i="18" alpha="-32.27242232862548832" sparseCutoff="1.00000000000000000"/>
<sparseX i="19" alpha="-189.98876444330406343" sparseCutoff="1.00000000000000000"/>
<sparseX i="20" alpha="-51.45432577054576484" sparseCutoff="1.00000000000000000"/>
<sparseX i="21" alpha="-312.48248955523706627" sparseCutoff="1.00000000000000000"/>
<sparseX i="22" alpha="-310.06137399899478169" sparseCutoff="1.00000000000000000"/>
<sparseX i="23" alpha="-125.74820546688276579" sparseCutoff="1.00000000000000000"/>
<sparseX i="24" alpha="-133.14664218937750206" sparseCutoff="1.00000000000000000"/>
<sparseX i="25" alpha="254.52945034173043837" sparseCutoff="1.00000000000000000"/>
<sparseX i="26" alpha="-180.78595624249396678" sparseCutoff="1.00000000000000000"/>
<sparseX i="27" alpha="-240.01397361445319234" sparseCutoff="1.00000000000000000"/>
<sparseX i="28" alpha="-232.57681730239985995" sparseCutoff="1.00000000000000000"/>
<sparseX i="29" alpha="-188.93211675918988135" sparseCutoff="1.00000000000000000"/>
<sparseX i="30" alpha="-328.49096171895257612" sparseCutoff="1.00000000000000000"/>
<sparseX i="31" alpha="-3.92264322378805108" sparseCutoff="1.00000000000000000"/>
<sparseX i="32" alpha="-57.03806049019905799" sparseCutoff="1.00000000000000000"/>
<sparseX i="33" alpha="-197.10597940928562366" sparseCutoff="1.00000000000000000"/>
<sparseX i="34" alpha="-213.61988089062185736" sparseCutoff="1.00000000000000000"/>
<sparseX i="35" alpha="-140.91014116967943437" sparseCutoff="1.00000000000000000"/>
<sparseX i="36" alpha="-116.01749045373561842" sparseCutoff="1.00000000000000000"/>
<sparseX i="37" alpha="-99.98124633019918406" sparseCutoff="1.00000000000000000"/>
<sparseX i="38" alpha="-319.73530293084553477" sparseCutoff="1.00000000000000000"/>
<sparseX i="39" alpha="-23.99121832196087922" sparseCutoff="1.00000000000000000"/>
<sparseX i="40" alpha="-159.54690639218952697" sparseCutoff="1.00000000000000000"/>
<sparseX i="41" alpha="-471.66640452792773885" sparseCutoff="1.00000000000000000"/>
<sparseX i="42" alpha="-2211.37346143270815446" sparseCutoff="1.00000000000000000"/>
<sparseX i="43" alpha="631.12310821544178907" sparseCutoff="1.00000000000000000"/>
<sparseX i="44" alpha="-145.00080119692779590" sparseCutoff="1.00000000000000000"/>
<sparseX i="45" alpha="249.51130659671196099" sparseCutoff="1.00000000000000000"/>
<sparseX i="46" alpha="-200.86462281811793673" sparseCutoff="1.00000000000000000"/>
<sparseX i="47" alpha="-85.19374760072962260" sparseCutoff="1.00000000000000000"/>
<sparseX i="48" alpha="-88.10062098178126178" sparseCutoff="1.00000000000000000"/>
<sparseX i="49" alpha="397.83673966023235380" sparseCutoff="1.00000000000000000"/>
<sparseX i="50" alpha="241.23006826522262713" sparseCutoff="1.00000000000000000"/>
<sparseX i="51" alpha="533.35509189242441153" sparseCutoff="1.00000000000000000"/>
<sparseX i="52" alpha="731.71250810978233403" sparseCutoff="1.00000000000000000"/>
<sparseX i="53" alpha="796.36530096001149559" sparseCutoff="1.00000000000000000"/>
<sparseX i="54" alpha="303.75427399352145130" sparseCutoff="1.00000000000000000"/>
<sparseX i="55" alpha="-89.34347724755534159" sparseCutoff="1.00000000000000000"/>
<sparseX i="56" alpha="-635.06950653957767372" sparseCutoff="1.00000000000000000"/>
<sparseX i="57" alpha="-359.20143113561385917" sparseCutoff="1.00000000000000000"/>
<sparseX i="58" alpha="-304.08756252895580019" sparseCutoff="1.00000000000000000"/>
<sparseX i="59" alpha="-273.53035880759773590" sparseCutoff="1.00000000000000000"/>
<sparseX i="60" alpha="-259.86061614050657909" sparseCutoff="1.00000000000000000"/>
<sparseX i="61" alpha="-343.71636916412012397" sparseCutoff="1.00000000000000000"/>
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<sparseX i="69" alpha="-111.92064433857494521" sparseCutoff="1.00000000000000000"/>
<sparseX i="70" alpha="-290.71160850550450050" sparseCutoff="1.00000000000000000"/>
<sparseX i="71" alpha="-530.59879373802482405" sparseCutoff="1.00000000000000000"/>
<sparseX i="72" alpha="-726.75848544323287115" sparseCutoff="1.00000000000000000"/>
<sparseX i="73" alpha="-719.39381889268145187" sparseCutoff="1.00000000000000000"/>
<sparseX i="74" alpha="-47.34856901761477133" sparseCutoff="1.00000000000000000"/>
<sparseX i="75" alpha="-637.24744199274596212" sparseCutoff="1.00000000000000000"/>
<sparseX i="76" alpha="-388.67437392604762181" sparseCutoff="1.00000000000000000"/>
<sparseX i="77" alpha="311.12613684926481028" sparseCutoff="1.00000000000000000"/>
<sparseX i="78" alpha="200.47970766249866870" sparseCutoff="1.00000000000000000"/>
<sparseX i="79" alpha="198.05225351390151900" sparseCutoff="1.00000000000000000"/>
<sparseX i="80" alpha="-413.44824095658469787" sparseCutoff="1.00000000000000000"/>
<sparseX i="81" alpha="-391.07321954151808541" sparseCutoff="1.00000000000000000"/>
<sparseX i="82" alpha="-525.93815824174112095" sparseCutoff="1.00000000000000000"/>
<sparseX i="83" alpha="242.70079110437475833" sparseCutoff="1.00000000000000000"/>
<sparseX i="84" alpha="1077.97349479399440497" sparseCutoff="1.00000000000000000"/>
<sparseX i="85" alpha="936.17262576597704538" sparseCutoff="1.00000000000000000"/>
<sparseX i="86" alpha="240.86049415737548429" sparseCutoff="1.00000000000000000"/>
<sparseX i="87" alpha="152.78097085229072150" sparseCutoff="1.00000000000000000"/>
<sparseX i="88" alpha="60.26900138883726044" sparseCutoff="1.00000000000000000"/>
<sparseX i="89" alpha="45.97381262976676908" sparseCutoff="1.00000000000000000"/>
<sparseX i="90" alpha="17.40119056651742468" sparseCutoff="1.00000000000000000"/>
<sparseX i="91" alpha="25.48636500685580941" sparseCutoff="1.00000000000000000"/>
<sparseX i="92" alpha="-49.32987233746940348" sparseCutoff="1.00000000000000000"/>
<sparseX i="93" alpha="24.24508964596141070" sparseCutoff="1.00000000000000000"/>
<sparseX i="94" alpha="24.43613086751934205" sparseCutoff="1.00000000000000000"/>
<sparseX i="95" alpha="-20.23532082155766787" sparseCutoff="1.00000000000000000"/>
<sparseX i="96" alpha="-55.45940094552515376" sparseCutoff="1.00000000000000000"/>
<sparseX i="97" alpha="-84.90455411131105734" sparseCutoff="1.00000000000000000"/>
<sparseX i="98" alpha="-175.82239181095036429" sparseCutoff="1.00000000000000000"/>
<sparseX i="99" alpha="-32.35949098045956163" sparseCutoff="1.00000000000000000"/>
<sparseX i="100" alpha="-31.39563016941585261" sparseCutoff="1.00000000000000000"/>
</gpCoordinates>
</gpSparse>
<command_line><![CDATA[ at_file=teach.xyz descriptor_str={soap l_max=14 n_max=14 atom_sigma=0.5 zeta=4 cutoff=5.0 cutoff_transition_width=1.0 delta=1.0 f0=0.0 covariance_type=dot_product sparse_method=kmeans n_sparseX=100} do_sparse default_sigma={0.001 0.1 0.1} config_type_sigma={slice_sample:0.0001:0.01:0.01} e0=-9.19483512529700 sparse_jitter=1.0e-6 energy_parameter_name=energy force_parameter_name=force virial_parameter_name=virial config_type_parameter_name=config_type gp_file=gp.xml sparseX_separate_file=T rnd_seed=666]]></command_line>
<XYZ_data>
<![CDATA[1]]>
<![CDATA[config_type=slice_sample energy=-1.119483512529700E+01 virial="-5.703978934983333E-03 -0.000000000000000E+00 -0.000000000000000E+00 -0.000000000000000E+00 -5.703978934983293E-03 -0.000000000000000E+00 -0.000000000000000E+00 -0.000000000000000E+00 -5.703978934983333E-03" Lattice="3.180500495732849E+00 0.000000000000000E+00 0.000000000000000E+00 0.000000000000000E+00 3.180500495732849E+00 0.000000000000000E+00 1.590250242866424E+00 1.590250242866424E+00 1.590250242866424E+00" Properties=species:S:1:pos:R:3:force:R:3:Z:I:1]]>
<![CDATA[W 0.000000000000000E+00 0.000000000000000E+00 0.000000000000000E+00 0.000000000000000E+00 0.000000000000000E+00 0.000000000000000E+00 74]]>
<![CDATA[1]]>
<![CDATA[config_type=slice_sample energy=-1.112699059894089E+01 virial="-2.173033363987340E+00 -0.000000000000000E+00 5.815487283233488E-01 -0.000000000000000E+00 -8.450069889252690E-01 -0.000000000000000E+00 5.815487283233488E-01 -0.000000000000000E+00 -8.762406533705639E-01" Lattice="3.333535977556725E+00 0.000000000000000E+00 0.000000000000000E+00 0.000000000000000E+00 3.180500495732849E+00 0.000000000000000E+00 1.590250242866424E+00 1.590250242866424E+00 1.590250242866424E+00" Properties=species:S:1:pos:R:3:force:R:3:Z:I:1]]>
<![CDATA[W 0.000000000000000E+00 0.000000000000000E+00 0.000000000000000E+00 0.000000000000000E+00 0.000000000000000E+00 0.000000000000000E+00 74]]>
<![CDATA[1]]>
<![CDATA[config_type=slice_sample energy=-1.113328168095495E+01 virial="-2.191716281389271E+00 2.010072565263313E-01 3.761463865110470E-01 2.010072565263313E-01 -8.730663227844153E-01 2.824513167776501E-02 3.761463865110470E-01 2.824513167776501E-02 -8.827530442147667E-01" Lattice="3.333535977556725E+00 0.000000000000000E+00 0.000000000000000E+00 -5.319854411024297E-02 3.180500495732849E+00 0.000000000000000E+00 1.590250242866424E+00 1.590250242866424E+00 1.590250242866424E+00" Properties=species:S:1:pos:R:3:force:R:3:Z:I:1]]>
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