From b6fab8c3f1694d666d5cf6e5802166b48cab045b Mon Sep 17 00:00:00 2001
From: lopa <pardini@physik.hu-berlin.de>
Date: Thu, 28 Jun 2018 15:20:48 +0200
Subject: [PATCH] BSE exciton
---
.../exciting_parser_XS_input.py | 24 ++--
parser/parser-exciting/exciting_parser_xs.py | 107 ++++++++++++++++++
parser/parser-exciting/parser_exciting.py | 92 ++++++++++++++-
.../eu/nomad_lab/parsers/ExcitingParser.scala | 1 +
4 files changed, 211 insertions(+), 13 deletions(-)
create mode 100644 parser/parser-exciting/exciting_parser_xs.py
diff --git a/parser/parser-exciting/exciting_parser_XS_input.py b/parser/parser-exciting/exciting_parser_XS_input.py
index f6561d3..54472c7 100644
--- a/parser/parser-exciting/exciting_parser_XS_input.py
+++ b/parser/parser-exciting/exciting_parser_XS_input.py
@@ -49,10 +49,10 @@ class InputHandler(xml.sax.handler.ContentHandler):
# self.vkloffScrDum = "-1.0 -1.0 -1.0"
self.screening = "none"
self.bse = "none"
- self.screentype = "full"
+# self.screentype = "full"
############ BSE variables################
self.aresbse = "True"
- self.bsetype = "singlet"
+# self.bsetype = "singlet"
self.lmaxdielt = 14
self.nstlbse = [0, 0, 0, 0] ######## DA FARE
self.nstlbseDum = [0, 0, 0, 0] ######## DA FARE
@@ -193,11 +193,11 @@ class InputHandler(xml.sax.handler.ContentHandler):
self.rgkmaxScr = attrs.getValue('rgkmax')
except:
self.rgkmaxSrc = 0.0
- try:
- self.screentype = attrs.getValue('screentype')
- self.backend.addValue("x_exciting_xs_screening_type", int(self.screentype))
- except:
- self.backend.addValue("x_exciting_xs_screening_type", self.screentype)
+# try:
+# self.screentype = attrs.getValue('screentype')
+# self.backend.addValue("x_exciting_xs_screening_type", int(self.screentype))
+# except:
+# self.backend.addValue("x_exciting_xs_screening_type", self.screentype)
# self.aresbse = "true"
# self.bsetype = "singlet"
@@ -222,11 +222,11 @@ class InputHandler(xml.sax.handler.ContentHandler):
self.backend.addValue("x_exciting_xs_bse_antiresonant", self.aresbse)
except:
self.backend.addValue("x_exciting_xs_bse_antiresonant", self.aresbse)
- try:
- self.bsetype = attrs.getValue('bsetype')
- self.backend.addValue("x_exciting_xs_bse_type", self.bsetype)
- except:
- self.backend.addValue("x_exciting_xs_bse_type", self.bsetype)
+# try:
+# self.bsetype = attrs.getValue('bsetype')
+# self.backend.addValue("x_exciting_xs_bse_type", self.bsetype)
+# except:
+# self.backend.addValue("x_exciting_xs_bse_type", self.bsetype)
try:
self.lmaxdielt = attrs.getValue('lmaxdielt')
self.backend.addValue("x_exciting_xs_bse_angular_momentum_cutoff", int(self.lmaxdielt))
diff --git a/parser/parser-exciting/exciting_parser_xs.py b/parser/parser-exciting/exciting_parser_xs.py
new file mode 100644
index 0000000..8453bf4
--- /dev/null
+++ b/parser/parser-exciting/exciting_parser_xs.py
@@ -0,0 +1,107 @@
+# Copyright 2017-2018 Lorenzo Pardini
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from builtins import object
+import setup_paths
+import xml.sax
+from nomadcore.simple_parser import mainFunction, CachingLevel
+from nomadcore.simple_parser import SimpleMatcher as SM
+from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
+from nomadcore.unit_conversion import unit_conversion
+import os, sys, json, logging
+
+################################################################
+# This is the subparser for the exciting GW output
+################################################################
+
+
+class XSParser(object):
+ """context for wien2k In2 parser"""
+
+ def __init__(self):
+ pass
+# self.excitonEnergys = []
+# self.vertexLabels = []
+# self.vertexNum = 0
+# self.parser = None
+# self.secSingleConfIndex = None
+
+ def startedParsing(self, path, parser):
+ """called when parsing starts"""
+ self.parser = parser
+ # allows to reset values if the same superContext is used to parse different files
+# self.initialize_values()
+
+ def parseExciton(self, excFile, backend, excNum, excEn, excBindEn, osclStr, transCoeff):
+# if dftSingleConfigurationGindex is not None:
+# backend.openNonOverlappingSection("section_calculation_to_calculation_refs")
+# backend.addValue("calculation_to_calculation_ref", dftSingleConfigurationGindex)
+# backend.addValue("calculation_to_calculation_kind", "starting_point")
+# backend.closeNonOverlappingSection("section_calculation_to_calculation_refs")
+# logging.error("GW onClose_section_single_configuration_calculation")
+ with open(excFile) as g:
+ while 1:
+ s = g.readline()
+ if not s: break
+ s = s.strip()
+ s = s.split()
+ if s[0] != "#":
+ excNum[-1].append(int(s[0]))
+ excEn[-1].append(float(s[1]))
+ excBindEn[-1].append(float(s[2]))
+ osclStr[-1].append(float(s[3]))
+ transCoeff[-1][0].append(float(s[4]))
+ transCoeff[-1][1].append(float(s[5]))
+
+# print("s===",excNum)
+# if len(st) == 3:
+
+# if len(s) >= 40:
+
+# print("vaaa")
+# self.gmaxvr = float(gmaxvr[0])
+# self.unitCellVol = float(unitCellVol[0])
+# backend.openNonOverlappingSection("section_single_configuration_calculation")
+# if dftSingleConfigurationGindex is not None:
+# backend.openNonOverlappingSection("section_calculation_to_calculation_refs")
+# backend.addValue("calculation_to_calculation_ref", dftSingleConfigurationGindex)
+# backend.addValue("calculation_to_calculation_kind", "starting_point")
+# backend.closeNonOverlappingSection("section_calculation_to_calculation_refs")
+#
+# dirPath = os.path.dirname(gwFile)
+# if os.access(os.path.join(dirPath, "EVALQP.DAT"), os.F_OK):
+ # eigvalGWFile = os.path.join(dirPath, "EVALQP.DAT")
+# elif os.access(os.path.join(dirPath, "EVALQP.TXT"), os.F_OK):
+# eigvalGWFile = os.path.join(dirPath, "EVALQP.TXT")
+ # else:
+# pass
+# dosGWFile = os.path.join(dirPath, "TDOS-QP.OUT")
+ # bandCarbGWFile = os.path.join(dirPath, "bandstructure-qp.dat")
+ # bandBorGWFile = os.path.join(dirPath, "BAND-QP.OUT")
+ # vertexGWFile = os.path.join(dirPath, "BANDLINES.OUT")
+ # vertexLabGWFile = os.path.join(dirPath, "bandstructure.xml")
+ # selfCorGWFile = os.path.join(dirPath, "SELFC.DAT")
+ # inputFile = os.path.join(dirPath, "input.xml")
+ # inputgw1File = os.path.join(dirPath, "input-gw.xml")
+# inputgw2File = os.path.join(dirPath, "input_gw.xml")
+
+def get_cachingLevelForMetaName(metaInfoEnv, CachingLvl):
+ cachingLevelForMetaName = {}
+# 'section_single_configuration_calculation': CachingLvl
+# }
+# cachingLevelForMetaName["gw_fundamental_gap"] = CachingLevel.Cache
+# cachingLevelForMetaName["gw_optical_gap"] = CachingLevel.Cache
+# cachingLevelForMetaName["gw_fermi_energy"] = CachingLevel.Cache
+ return cachingLevelForMetaName
+
diff --git a/parser/parser-exciting/parser_exciting.py b/parser/parser-exciting/parser_exciting.py
index 2f2f298..dadf2aa 100644
--- a/parser/parser-exciting/parser_exciting.py
+++ b/parser/parser-exciting/parser_exciting.py
@@ -23,7 +23,7 @@ from nomadcore.caching_backend import CachingLevel
from nomadcore.unit_conversion import unit_conversion
from nomadcore.unit_conversion.unit_conversion import convert_unit_function
import os, sys, json, exciting_parser_dos,exciting_parser_bandstructure, exciting_parser_gw, exciting_parser_GS_input
-import exciting_parser_XS_input
+import exciting_parser_XS_input, exciting_parser_xs
from ase import Atoms
import logging
@@ -69,6 +69,10 @@ class ExcitingParserContext(object):
self.dummy = 0
self.i=0
self.clathrates = False
+ self.bsetype = None
+ self.screentype = None
+ self.tensorComp = []
+ self.excitonEnergies = []
# self.volumeOptIndex = 0
def onOpen_section_run(self, backend, gIndex, section):
@@ -227,6 +231,11 @@ class ExcitingParserContext(object):
break
if os.path.exists(xsFile):
+ excNum = []
+ excEn = []
+ excBindEn = []
+ osclStr = []
+ transCoeff = []
# print("BSE!!!")
# if os.path.exists(inputgwFile):
inputXSFile = os.path.join(dirPath, "input.xml")
@@ -238,10 +247,91 @@ class ExcitingParserContext(object):
backend.addValue("method_to_method_ref", self.secMethodIndex)
backend.addValue("method_to_method_kind", "starting_point")
backend.closeNonOverlappingSection("section_method_to_method_refs")
+
+ for files in os.listdir(dirPath):
+ if files[0:11] == "EXCITON_BSE":
+ dummyBse = files[11:13]
+# self.tensorComp = files[-6:-4]
+ self.tensorComp.append(files[-6:-4])
+
+ if dummyBse == 'si':
+ self.bsetype = 'singlet'
+# name = "EXCITON_BSE" + self.bsetype
+ elif dummyBse == 'tr':
+ self.bsetype = 'triplet'
+ elif dummyBse == 'RP':
+ self.bsetype = 'RPA'
+ elif dummyBse == 'IP':
+ self.bsetype = 'IP'
+ name = "EXCITON_BSE" + self.bsetype + '_SCR'
+ if files[len(name):len(name)+4] == 'full':
+ self.screentype = 'full'
+ elif files[len(name):len(name)+4] == 'diag':
+ self.screentype = 'diag'
+ elif files[len(name):len(name)+4] == 'noin':
+ self.screentype = 'noinvdiag'
+ elif files[len(name):len(name)+4] == 'long':
+ self.screentype = 'longrange'
+
+ backend.addValue("x_exciting_xs_screening_type", self.screentype)
+ backend.addValue("x_exciting_xs_bse_type", self.bsetype)
+# print("===", self.tensorComp[0])
with open(inputXSFile) as f:
exciting_parser_XS_input.parseInput(f, backend, self.rgkmax)
backend.closeSection("section_method",selfXSSetGIndex)
+ numberOfComponents = len(self.tensorComp)
+
+ backend.openNonOverlappingSection("section_single_configuration_calculation")
+ if self.secSingleConfIndex is not None:
+ backend.openNonOverlappingSection("section_calculation_to_calculation_refs")
+ backend.addValue("calculation_to_calculation_ref", self.secSingleConfIndex)
+ backend.addValue("calculation_to_calculation_kind", "starting_point")
+ backend.closeNonOverlappingSection("section_calculation_to_calculation_refs")
+
+ for i in range(numberOfComponents):
+ excNum.append([])
+ excEn.append([])
+ excBindEn.append([])
+ osclStr.append([])
+ transCoeff.append([[],[]])
+ outputXSFile = os.path.join(dirPath, "EXCITON_BSE" + self.bsetype + '_SCR' + self.screentype + "_OC" + self.tensorComp[i] + ".OUT")
+ with open(outputXSFile) as g:
+ xsParser = exciting_parser_xs.XSParser()
+ xsParser.parseExciton(outputXSFile, backend, excNum, excEn, excBindEn, osclStr, transCoeff) #, dftMethodSectionGindex = self.secMethodIndex,
+# dftSingleConfigurationGindex = self.secSingleConfIndex)
+# backend.addvalue("x_exciting_xs_bse_number_of_components",numberOfComponents)
+# backend.addvalue("x_exciting_xs_bse_number_of_excitons",len(excNum))
+ backend.addValue("x_exciting_xs_bse_exciton_energies",excEn)
+# print("===",excBindEn)
+ backend.closeNonOverlappingSection("section_single_configuration_calculation")
+
+
+# print(outputXSFile)
+
+# for files in os.listdir(dirPath):
+# if files[0:11] == "EXCITON_BSE":
+# dummyBse = files[11:13]
+# dummyTenCom = files[-6:-4]
+# if dummyBse == 'si':
+# self.bsetype = 'singlet'
+## name = "EXCITON_BSE" + self.bsetype
+# elif dummyBse == 'tr':
+# self.bsetype = 'triplet'
+# elif dummyBse == 'RP':
+# self.bsetype = 'RPA'
+# elif dummyBse == 'IP':
+# self.bsetype = 'IP'
+# name = "EXCITON_BSE" + self.bsetype + '_SCR'
+# if files[len(name):len(name)+4] == 'full':
+# self.screentype = 'full'
+# elif files[len(name):len(name)+4] == 'diag':
+# self.screentype = 'diag'
+# elif files[len(name):len(name)+4] == 'noin':
+# self.screentype = 'noinvdiag'
+# elif files[len(name):len(name)+4] == 'long':
+# self.screentype = 'longrange'
+# print("===",self.screentype)
###########################TEST#############################
diff --git a/src/main/scala/eu/nomad_lab/parsers/ExcitingParser.scala b/src/main/scala/eu/nomad_lab/parsers/ExcitingParser.scala
index 12ae532..2198d04 100644
--- a/src/main/scala/eu/nomad_lab/parsers/ExcitingParser.scala
+++ b/src/main/scala/eu/nomad_lab/parsers/ExcitingParser.scala
@@ -49,6 +49,7 @@ object ExcitingParser extends SimpleExternalParserGenerator(
"parser-exciting/exciting_parser_input.py",
"parser-exciting/exciting_parser_GS_input.py",
"parser-exciting/exciting_parser_XS_input.py",
+ "parser-exciting/exciting_parser_xs.py",
"parser-exciting/setup_paths.py",
"nomad_meta_info/public.nomadmetainfo.json",
"nomad_meta_info/common.nomadmetainfo.json",
--
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