Skip to content
GitLab
Commit d1803f6e authored by Mohamed, Fawzi Roberto (fawzi)'s avatar Mohamed, Fawzi Roberto (fawzi)
Browse files

Making band structure normalizer compile...

parent fb2a7938
Hide whitespace changes
Inline Side-by-side
src/main/scala/eu/nomad_lab/normalizers/BandStructureNormalizer.scala
View file @ d1803f6e
......@@ -8,7 +8,9 @@ import eu.nomad_lab.normalize.ExternalNormalizerGenerator
import eu.nomad_lab.meta
import eu.nomad_lab.query
import eu.nomad_lab.resolve._
import eu.nomad_lab.ref.NomadUri
import eu.nomad_lab.h5.EmitJsonVisitor
import eu.nomad_lab.h5.SectionH5
import eu.nomad_lab.h5.H5EagerScanner
import eu.nomad_lab.parsers.ExternalParserWrapper
import eu.nomad_lab.JsonUtils
......@@ -30,7 +32,7 @@ object BandStructureNormalizer extends ExternalNormalizerGenerator(
)) :: Nil
),
context = "calculation_context",
filter = query.CompiledQuery(query.QueryExpression("section_k_band and not section_k_band_normalized"), meta.KnownMetaInfoEnvs.all),
filter = query.CompiledQuery(query.QueryExpression("section_k_band" /*" and not section_k_band_normalized" */ ), meta.KnownMetaInfoEnvs.all),
cmd = Seq(DefaultPythonInterpreter.pythonExe(), "${envDir}/normalizers/band-structure/normalizer/normalizer-band-structure/normalizer_band_structure.py",
"${context}", "${archivePath}"),
resList = Seq(
......@@ -91,98 +93,108 @@ object BandStructureNormalizer extends ExternalNormalizerGenerator(
refE match {
case Some(e) =>
writeOut(s""",
| "$refEName": ${e.mkString("[",",","]")}""".stripMargin)
| "$refEName": ${e.mkString("[", ",", "]")}""".stripMargin)
case None => ()
}
}
b.parentSection.map{ singleConf: SectionH5 =>
val eFermi = singleConf.maybeValue("energy_reference_fermi")(_.seqDoubleValue)
b.parentSection.foreach { singleConf: SectionH5 =>
val eFermi = singleConf.maybeValue("energy_reference_fermi").map(_.seqDoubleValue())
writeOutRefE("energy_reference_fermi", eFermi)
val eVbTop = singleConf.maybeValue("energy_reference_highest_occupied").map(_.seqDoubleValue)
val eVbTop = singleConf.maybeValue("energy_reference_highest_occupied").map(_.seqDoubleValue())
writeOutRefE("energy_reference_highest_occupied", eVbTop)
var contextsToGiveBack = Seq()
var contextsToGiveBack: Seq[ResolvedRef] = Seq()
try {
// get DOS
val dosInfo: Option[(Option[Seq[Double]], Option[Seq[Double]], SectionH5)] = b.parentSection.map{ singleConf: SectionH5 =>
// try locally
val dosColl = singleConf.subSectionCollection("section_dos")
if (dosColl.length > 0) {
if (dosColl.length > 1)
logging.warn(s"multiple dos in $singleConf, using first")
Some(eFermi, eVbTop, dosColl(0))
} else {
// look in archive
val sysIdx = singleConf.maybeValue("single_configuration_calculation_to_system_ref").map( _.longValue )
val sys = singleConf.parentSection.map{ run: SectionH5 =>
run.sectionTable("section_system")(sysIdx)
}
sys.maybeValue("configuration_raw_gid").map( _.stringValue) match {
case Some(confId) =>
val possibleDosScanOp = new query.CollectUrisScanOp(
context = "section_single_configuration_calculation",
filter = query.CompiledQuery(query.QueryExpression("section_dos and configuration_raw_gid = \"$confId\"")),
metaInfoEnv0 = None)
val evaluator = new query.DirectArchiveScanner(
archiveSet = archiveSet,
archive = c.archive,
scanOp = possibleDosScanOp
)
evaluator.run()
val uris = possibleDosScanOp.uris
evaluator.cleanup()
if (uris.length > 0) {
if (uris.length > 1) {
logger.warn(s"found multiple DoS potentially matching to $b in archive: $uris, shoudl check method more carefully, skipping for now...")
None
} else {
val dosCtx = resolve.resolveInArchiveSet(archiveSet, NomadUri(uris(0)).toRef)
contextsToGiveBack += dosCtx
dosCtx match {
case Section(_,dosSingleConf) =>
val dosEVbTop = dosSingleConf.maybeValue("energy_reference_highest_occupied").map(_.doubleValue)
val dosEFermi = dosSingleConf.maybeValue("energy_reference_fermi").map(_.doubleValue)
if (dosCollection.length > 0) {
if (dosCollection.length > 1)
logger.warn(s"multiple dos in $singleConf, using first")
Some(dosEFermi, dosEVbTop, dosColl(0))
} else {
logger.warn(s"query error, expected a section_dos in $dosSingleConf")
None
// get DOS
val dosInfo: Option[(Option[Seq[Double]], Option[Seq[Double]], SectionH5)] = b.parentSection match {
case None => None
case Some(singleConf) =>
// try locally
val dosColl = singleConf.subSectionCollection("section_dos")
if (dosColl.length > 0) {
if (dosColl.length > 1)
logger.warn(s"multiple dos in $singleConf, using first")
Some(eFermi, eVbTop, dosColl(0))
} else {
// look in archive
singleConf.maybeValue("single_configuration_calculation_to_system_ref").map(_.longValue) match {
case None => None
case Some(sysIdx) =>
singleConf.parentSection.map { run: SectionH5 =>
run.table.subSectionTable("section_system")(sysIdx)
} match {
case None => None
case Some(sys) =>
sys.maybeValue("configuration_raw_gid").map(_.stringValue) match {
case Some(confId) =>
val possibleDosScanOp = new query.CollectUrisScanOp(
context = "section_single_configuration_calculation",
filter = query.CompiledQuery(query.QueryExpression("section_dos and configuration_raw_gid = \"$confId\""), meta.KnownMetaInfoEnvs.all),
metaInfoEnv0 = None
)
val evaluator = new query.DirectArchiveScanner(
archiveSet = archiveSet,
archive = c.archive,
scanOp = possibleDosScanOp
)
evaluator.run()
val uris = possibleDosScanOp.uris
evaluator.cleanup()
if (uris.length > 0) {
if (uris.length > 1) {
logger.warn(s"found multiple DoS potentially matching to $b in archive: $uris, should check method more carefully, skipping for now...")
None
} else {
val dosCtx = Resolver.resolveInArchiveSet(archiveSet, NomadUri(uris(0)).toRef)
contextsToGiveBack = contextsToGiveBack :+ dosCtx
dosCtx match {
case Section(_, dosSingleConf) =>
val dosEVbTop = dosSingleConf.maybeValue("energy_reference_highest_occupied").map(_.seqDoubleValue())
val dosEFermi = dosSingleConf.maybeValue("energy_reference_fermi").map(_.seqDoubleValue())
val dosCollection = dosSingleConf.subSectionCollection("section_dos")
if (dosCollection.length > 0) {
if (dosCollection.length > 1)
logger.warn(s"multiple dos in $singleConf, using first")
Some((dosEFermi, dosEVbTop, dosColl(0)))
} else {
logger.warn(s"query error, expected a section_dos in $dosSingleConf")
None
}
case _ =>
logger.warn(s"query error, expected valid section as result of query, not ${dosCtx.uriString}")
None
}
}
} else {
None
}
case None =>
logger.warn(s"Could not find configuration_raw_gid for configuration of band structure $b, search of DoS failed.")
None
}
case _ =>
logger.warn(s"query error, expected valid section as result of query, not ${dosCtx.uriString}")
None
}
}
} else {
None
}
case None =>
logger.warn(s"Could not find configuration_raw_gid for configuration of band structure $b, search of DoS failed.")
None
}
}
}
}
}
dosInfo match {
case Some((dFermi, dVBTop, dos)) =>
writeOut(""",
dosInfo match {
case Some((dFermi, dVBTop, dos)) =>
writeOut(""",
| "dos": {
| "section_dos":""".stripMargin)
scanner.scanResolvedRef(Section(archiveSet, dos), visitor)
writeOutRefE("energy_reference_fermi", dFermi)
writeOutRefE("energy_reference_highest_occupied", dVBTop)
writeOut("\n }")
case None => ()
}
scanner.scanResolvedRef(Section(archiveSet, dos), visitor)
writeOutRefE("energy_reference_fermi", dFermi)
writeOutRefE("energy_reference_highest_occupied", dVBTop)
writeOut("\n }")
case None => ()
}
} finally {
for (ctx <- contextsToGiveBack)
ctx.giveBack()
}
writeOut("\n}")
}
flush()
}
writeOut("]\n")
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment