From 0f0e1e13a7677bf566e31867cdd64bdc466c1b65 Mon Sep 17 00:00:00 2001
From: lopa <pardini@physik.hu-berlin.de>
Date: Fri, 8 Jun 2018 17:55:46 +0200
Subject: [PATCH] Added support for Quantum Espresso (strain)
---
parser/parser-elastic/out | 7498 +++++++++++++++++++++++
parser/parser-elastic/parser_elastic.py | 150 +-
2 files changed, 7541 insertions(+), 107 deletions(-)
create mode 100644 parser/parser-elastic/out
diff --git a/parser/parser-elastic/out b/parser/parser-elastic/out
new file mode 100644
index 0000000..9f86b51
--- /dev/null
+++ b/parser/parser-elastic/out
@@ -0,0 +1,7498 @@
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diff --git a/parser/parser-elastic/parser_elastic.py b/parser/parser-elastic/parser_elastic.py
index 8fb6604..aec2eb2 100644
--- a/parser/parser-elastic/parser_elastic.py
+++ b/parser/parser-elastic/parser_elastic.py
@@ -58,69 +58,54 @@ class SampleContext(object):
backend.addValue('program_version', '1.0')
def onClose_section_system(self, backend, gIndex, section):
+# print("quiiiii")
backend.addArrayValues('configuration_periodic_dimensions', np.asarray([True, True, True]))
self.SGN = int(section["x_elastic_space_group_number"][0])
mainFile = self.parser.fIn.fIn.name
dirPath = os.path.dirname(mainFile) #####exciting sbt -> zip file#### YES ?????????? sure???? check first OKOKOKKO
- self.mainFile = self.parser.fIn.name #####exciting sbt -> zip file#### YES
- self.mainFilePath = self.mainFile[0:-12] #####exciting sbt -> zip file#### YES
+ self.mainFile = self.parser.fIn.name
+ self.mainFilePath = self.mainFile[0:-12]
# print("self.mainFileUri=",self.mainFileUri)
# dirPath = self.mainFileUri[0:-12] #####exciting LOCAL HOME or from NOMAD URI nmd:// ####### YES OKOKOKOK
-# print("dirPath=",dirPath)
+# print("os.listdir(dirPath)=",os.listdir(dirPath))
# for files in os.listdir(self.mainFilePath):
for files in os.listdir(dirPath):
if files[-3:] == "xml":
inputFile = files
+# print("Exself.mainFilePath=",self.mainFilePath)
+# print("inputFile=",inputFile)
os.chdir(self.mainFilePath)
with open(inputFile) as f:
elastic_parser_input_exciting.parseInput(f, backend)
elif files[-6:] == "struct":
inputFile = files
+# print("Wiself.mainFilePath=",self.mainFilePath)
+# print("inputFile=",inputFile)
os.chdir(self.mainFilePath)
-# structSuperContext = elastic_parser_input_wien2k.Wien2kStructContext()
-# structParser = AncillaryParser(
-# fileDescription = elastic_parser_input_wien2k.buildStructureMatchers(),
-# parser = self.parser,
-# cachingLevelForMetaName = elastic_parser_input_wien2k.get_cachingLevelForMetaName(self.metaInfoEnv, CachingLevel.PreOpenedIgnore),
-# superContext = structSuperContext)
with open(inputFile) as g:
while 1:
s = g.readline()
if not s: break
s = s.strip()
-# print("s===",s)
-# structParser.parseFile(fIn)
-# elastic_parser_input_wien2k.parseInput(f, backend)
-#
-# if os.path.exists(fName):
-# structSuperContext = wien2k_parser_struct.Wien2kStructContext()
-# structParser = AncillaryParser(
-# fileDescription = wien2k_parser_struct.buildStructureMatchers(),
-# parser = self.parser,
-# cachingLevelForMetaName = wien2k_parser_struct.get_cachingLevelForMetaName(self.metaInfoEnv, CachingLevel.PreOpenedIgnore),
-# superContext = structSuperContext)
-#
-# with open(fName) as fIn:
-# structParser.parseFile(fIn)
-#####come era prima di wien pass
-#####come era prima di wien os.chdir(self.mainFilePath)
-# os.chdir(dirPath)
-#####come era prima di wien with open(inputFile) as f:
-#####come era prima di wien elastic_parser_input.parseInput(f, backend)
-# print(os.listdir(dirPath))
-# if os.path.exist([-3:]) == "xml":
-# inputFile = os.path.exist()
-# inputFile = os.path.join(dirPath, "input.xml")
-# print("inputFile=",inputFile)
+ elif files[-3:] == ".in":
+ if files != "ElaStic_2nd.in":
+ inputFile = files
+# print("Esself.mainFilePath=",self.mainFilePath)
+# print("inputFile=",inputFile)
+ os.chdir(self.mainFilePath)
+ with open(inputFile) as g:
+ while 1:
+ s = g.readline()
+ if not s: break
+ s = s.strip()
def onClose_section_method(self, backend, gIndex, section):
+# print("quoooo")
ha_per_joule = convert_unit(1, "hartree", "J")
giga = 10**9
elCode = section['x_elastic_code']
elasticGIndex = backend.openSection("section_single_configuration_calculation")
-# self.mainFile = self.parser.fIn.name #####exciting sbt -> zip file#### NO
-# self.mainFilePath = self.mainFile[0:-12] #####exciting sbt -> zip file#### NO
- self.mainFilePath = self.mainFileUri[0:-12] #####exciting LOCAL HOME or from NOMAD URI nmd:// ####### NO
+ self.mainFilePath = self.mainFileUri[0:-12]
mdr = float(section['x_elastic_max_lagrangian_strain'][0])
ordr = int(section['x_elastic_elastic_constant_order'][0])
nds = int(section['x_elastic_number_of_distorted_structures'][0])
@@ -166,35 +151,37 @@ class SampleContext(object):
elif elCode[0] == 'WIEN':
ext_uri.append(self.mainFilePath + 'Dst0' + str(j) + '/Dst0' + str(j) + '_0' + str(i) + '/Dst0'+ str(j) + '_0' + str(i) + '_Converged.scf')
# pass
- elif elCode[0] == 'ESPRESSO':
- pass
+ elif elCode[0] == 'QUANTUM':
+ ext_uri.append(self.mainFilePath + 'Dst0' + str(j) + '/Dst0' + str(j) + '_0' + str(i) + '/Dst0'+ str(j) + '_0' + str(i) + '.out')
#####################above: to be repeated below for the wien2k and QE################
else:
if elCode[0] == 'exciting':
ext_uri.append(self.mainFilePath + 'Dst0' + str(j) + '/Dst0' + str(j) + '_' + str(i) + '/INFO.OUT')
elif elCode[0] == 'WIEN':
ext_uri.append(self.mainFilePath + 'Dst0' + str(j) + '/Dst0' + str(j) + '_' + str(i) + '/Dst0' + str(j) + '_' + str(i) + '_Converged.scf')
+ elif elCode[0] == 'QUANTUM':
+ ext_uri.append(self.mainFilePath + 'Dst0' + str(j) + '/Dst0' + str(j) + '_' + str(i) + '/Dst0' + str(j) + '_' + str(i) + '.out')
else:
if (i<10):
if elCode[0] == 'exciting':
ext_uri.append(self.mainFilePath + 'Dst' + str(j) + '/Dst' + str(j) + '_0' + str(i) + '/INFO.OUT')
elif elCode[0] == 'WIEN':
ext_uri.append(self.mainFilePath + 'Dst' + str(j) + '/Dst' + str(j) + '_0' + str(i) + '/Dst' + str(j) + '_0' + str(i) + '_Converged.scf')
+ elif elCode[0] == 'QUANTUM':
+ ext_uri.append(self.mainFilePath + 'Dst' + str(j) + '/Dst' + str(j) + '_0' + str(i) + '/Dst' + str(j) + '_0' + str(i) + '.out')
else:
if elCode[0] == 'exciting':
ext_uri.append(self.mainFilePath + 'Dst' + str(j) + '/Dst' + str(j) + '_' + str(i) + '/INFO.OUT')
elif elCode[0] == 'WIEN':
ext_uri.append(self.mainFilePath + 'Dst' + str(j) + '/Dst' + str(j) + '_' + str(i) +'/Dst' + str(j) + '_' + str(i) + '_Converged.scf')
+ elif elCode[0] == 'QUANTUM':
+ ext_uri.append(self.mainFilePath + 'Dst' + str(j) + '/Dst' + str(j) + '_' + str(i) +'/Dst' + str(j) + '_' + str(i) + '.out')
for ref in ext_uri:
refGindex = backend.openSection("section_calculation_to_calculation_refs")
backend.addValue("calculation_to_calculation_external_url", ref)
backend.addValue("calculation_to_calculation_kind", "source_calculation")
backend.closeSection("section_calculation_to_calculation_refs", refGindex)
-# backend.closeSection("section_run")
-# backend.closeSection("section_calculation_to_calculation_refs", refGindex)
-# backend.closeSection("section_single_configuration_calculation", singlGindex)
-
##############ADDED ABOVE####################
energy = []
@@ -221,21 +208,6 @@ class SampleContext(object):
cur_dir = os.getcwd()
# print("cur_dir=", cur_dir)
-
-# my_file_exc = '/' + Dstn+'-Energy.dat'
-# my_file_wien = '/' +Dstn+'_Energy.dat'
-# my_file_exciting = Path('my_file_exc')
-# my_file_wien2k = Path('my_file_wien')
-
-# print("my_file_exc=",my_file_exc)
-# print("my_file_wien=",my_file_wien)
-# print("my_file_exciting=",my_file_exciting)
-# print("my_file_wien2k=",my_file_wien2k)
-# cur_dir = os.getcwd()
-# print("cur_dir=", cur_dir)
-# print(my_file_exciting.exists())
-# print(my_file_wien2k.exists())
-
# print("elCode[0]=",elCode[0])
if elCode[0] == 'exciting':
# print("ooooooooooexciting")
@@ -267,16 +239,6 @@ class SampleContext(object):
os.chdir('../')
except:
pass
-# while 1:
-# s = f.readline()
-# if not s: break
-# s = s.strip()
-# dummy_eta, dummy_energy = s.split()
-## print("dummy_eta=",dummy_eta)
-## print("dummy_energy=",dummy_energy)
-# eta[-1].append(float(dummy_eta))
-# energy[-1].append(float(dummy_energy)*ha_per_joule)
-# os.chdir('../')
elif elCode[0] == 'WIEN':
# print("oooooooooooowien2k")
@@ -287,6 +249,20 @@ class SampleContext(object):
s = s.strip()
dummy_eta, dummy_energy = s.split()
# print("dummy_eta=",dummy_eta)
+# print("dummy_energy=",dummy_energy)
+ eta[-1].append(float(dummy_eta))
+ energy[-1].append(float(dummy_energy)*ha_per_joule)
+ os.chdir('../')
+
+ elif elCode[0] == 'QUANTUM':
+# print("oooooooooooowien2k")
+ f = open(Dstn+'_Energy.dat', 'r')
+ while 1:
+ s = f.readline()
+ if not s: break
+ s = s.strip()
+ dummy_eta, dummy_energy = s.split()
+# print("dummy_eta=",dummy_eta)
# print("dummy_energy=",dummy_energy)
eta[-1].append(float(dummy_eta))
energy[-1].append(float(dummy_energy)*ha_per_joule)
@@ -295,37 +271,6 @@ class SampleContext(object):
else:
os.chdir('../')
-# try: # WIEN2k
-# f = open(Dstn+'_Energy.dat', 'r')
-# while 1:
-# s = f.readline()
-# if not s: break
-# s = s.strip()
-# dummy_eta, dummy_energy = s.split()
-# print("dummy_eta=",dummy_eta)
-# print("dummy_energy=",dummy_energy)
-# eta[-1].append(float(dummy_eta))
-# energy[-1].append(float(dummy_energy)*ha_per_joule)
-# os.chdir('../')
-# except FileNotFoundError:
-# os.chdir('../')
-
- # try: # exciting
- # f = open(Dstn+'-Energy.dat', 'r')
- # while 1:
- # s = f.readline()
- # if not s: break
-# s = s.strip()
-# dummy_eta, dummy_energy = s.split()
- # print("dummy_eta=",dummy_eta)
- # print("dummy_energy=",dummy_energy)
- # eta[-1].append(float(dummy_eta))
- # energy[-1].append(float(dummy_energy)*ha_per_joule)
- # os.chdir('../')
- # except FileNotFoundError:
- # os.chdir('../')
-# os.chdir('../')
-# print("and now?",os.getcwd())
defTyp = []
f = open('Distorted_Parameters','r')
@@ -344,15 +289,6 @@ class SampleContext(object):
defTyp[-1].append(s[i])
f.close()
-# backend.addValue("x_elastic_deformation_types", defTyp)
-# backend.addValue("x_elastic_number_of_deformations", defNum)
-# backend.addValue("x_elastic_energy_strain_eta_values", eta)
-# backend.addValue("x_elastic_energy_strain_energy_values", energy)
-# backend.closeSection("x_elastic_section_single_configuration_calculation", elasticGIndex)
-
-# my_file = Path("Energy-vs-Strain")
-# print("ooooo",my_file.exists())
-# print("oooooooo ", os.listdir())
prova = os.listdir('.')
# print("prova= ",prova)
if 'Energy-vs-Strain' in prova:
--
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