Skip to content
Snippets Groups Projects
Commit 900abe68 authored by Pardini, Lorenzo (lopa)'s avatar Pardini, Lorenzo (lopa)
Browse files

added elastic parser

parent e2749be7
Branches
Tags
No related merge requests found
Show whitespace changes
Inline Side-by-side
parser/parser-elastic/parser_elastic.py
+ 79
− 373
View file @ 900abe68
#!/usr/bin/env python
from sys import stdin
from numpy import *
from math import *
import numpy as np
import subprocess
import warnings
import os.path
import shutil
import copy
import math
import sys
import os
#def __init__(self):
# self.energy = []
# self.eta = []
os.chdir('../../test/examples/elastic')
#INFO=open('../../test/examples/elastic/INFO_ElaStic', 'r')
INFO=open('INFO_ElaStic', 'r')
l1 = INFO.readline()
ordr= int(l1.split()[-1])
l2 = INFO.readline()
mthd= l2.split()[-1]
l3 = INFO.readline()
cod = l3.split()[-1]
l4 = INFO.readline()
SGN = int(l4.split()[-1])
l5 = INFO.readline()
V0 = float(l5.split()[-2])
l6 = INFO.readline()
mdr = float(l6.split()[-1])
l7 = INFO.readline()
NoP = int(l7.split()[-1])
INFO.close()
'''
###### The number of independent elastic constants is calculated and then checked ######
###### whether it corresponds to the number of "Dst--" folders ######
#
if (1 <= SGN and SGN <= 2): # Triclinic
LC = 'N'
if (ordr == 2): ECs = 21
if (ordr == 3): ECs = 56
elif(3 <= SGN and SGN <= 15): # Monoclinic
LC = 'M'
if (ordr == 2): ECs = 13
if (ordr == 3): ECs = 32
elif(16 <= SGN and SGN <= 74): # Orthorhombic
LC = 'O'
if (ordr == 2): ECs = 9
if (ordr == 3): ECs = 20
elif(75 <= SGN and SGN <= 88): # Tetragonal II
LC = 'TII'
if (ordr == 2): ECs = 7
if (ordr == 3): ECs = 16
elif(89 <= SGN and SGN <= 142): # Tetragonal I
LC = 'TI'
if (ordr == 2): ECs = 6
if (ordr == 3): ECs = 12
elif(143 <= SGN and SGN <= 148): # Rhombohedral II
LC = 'RII'
if (ordr == 2): ECs = 7
if (ordr == 3): ECs = 20
elif(149 <= SGN and SGN <= 167): # Rhombohedral I
LC = 'RI'
if (ordr == 2): ECs = 6
if (ordr == 3): ECs = 14
elif(168 <= SGN and SGN <= 176): # Hexagonal II
LC = 'HII'
if (ordr == 2): ECs = 5
if (ordr == 3): ECs = 12
elif(177 <= SGN and SGN <= 194): # Hexagonal I
LC = 'HI'
if (ordr == 2): ECs = 5
if (ordr == 3): ECs = 10
elif(195 <= SGN and SGN <= 206): # Cubic II
LC = 'CII'
if (ordr == 2): ECs = 3
if (ordr == 3): ECs = 8
elif(207 <= SGN and SGN <= 230): # Cubic I
LC = 'CI'
if (ordr == 2): ECs = 3
if (ordr == 3): ECs = 6
'''
i = 1
while 1:
if (i<10):
Dstn = 'Dst0'+ str(i)
if (os.path.exists(Dstn) == True):
i += 1
else:
break
else:
Dstn = 'Dst' + str(i)
if (os.path.exists(Dstn) == True):
i += 1
else:
break
defNum = i - 1
ECs = defNum
#if defNum != ECs:
# print("Error")
energy = []
eta = []
for j in range(1, ECs+1):
if (j<10):
Dstn = 'Dst0'+ str(j)
eta.append([])
energy.append([])
else:
Dstn = 'Dst' + str(i)
eta.append([])
energy.append([])
os.chdir(Dstn)
f = open(Dstn+'-Energy.dat', 'r')
while 1:
s = f.readline()
print("s=",s)
if not s: break
s = s.strip()
dummy_eta, dummy_energy = s.split()
eta[-1].append(float(dummy_eta))
energy[-1].append(float(dummy_energy))
os.chdir('../')
defTyp = []
f = open('Distorted_Parameters','r')
while 1:
s = f.readline()
if not s: break
s = s.strip()
if 'Lagrangian' in s:
defTyp.append([])
s = s.split("(")
s = s[-1].split(")")
s = s[0].split(",")
for i in range(0,6):
s[i] = s[i].strip()
if s[i] == '0.0':
defTyp[-1].append(float(s[i]))
elif s[i] == 'eta':
defTyp[-1].append(mdr)
elif s[i] == '2eta':
defTyp[-1].append(2.0*mdr)
elif s[i] == '-eta':
defTyp[-1].append(-mdr)
elif s[i] == '.5eta':
defTyp[-1].append(0.5*mdr)
elif s[i] == '-2eta':
defTyp[-1].append(-2.0*mdr)
elif s[i] == '3eta':
defTyp[-1].append(3.0*mdr)
elif s[i] == '4eta':
defTyp[-1].append(4.0*mdr)
elif s[i] == '5eta':
defTyp[-1].append(5.0*mdr)
elif s[i] == '6eta':
defTyp[-1].append(6.0*mdr)
elif s[i] == '-3eta':
defTyp[-1].append(-3.0*mdr)
elif s[i] == '-5eta':
defTyp[-1].append(-5.0*mdr)
elif s[i] == '-6eta':
defTyp[-1].append(-6.0*mdr)
elif s[i] == '-4eta':
defTyp[-1].append(-4.0*mdr)
f.close()
os.chdir('Energy-vs-Strain')
d2E6_val = []
d2E4_val = []
d2E2_val = []
d2E6_eta = []
d2E4_eta = []
d2E2_eta = []
d2E_val_tot = []
d2E_eta_tot = []
for i in range(1, ECs+1):
d2E_val_tot.append([])
d2E_eta_tot.append([])
if (i<10):
Dstn = 'Dst0'+ str(i) + '_d2E.dat'
f = open (Dstn,'r')
while 1:
s = f.readline()
if not s: break
s = s.strip()
if "order" in s.split():
d2E_val_tot[-1].append([])
d2E_eta_tot[-1].append([])
elif len(s) >= 30:
d2E_eta, d2E_values = s.split()
d2E_val_tot[-1][-1].append(float(d2E_values))
d2E_eta_tot[-1][-1].append(float(d2E_eta))
f.close()
else:
Dstn = 'Dst' + str(i) + '_d2E.dat'
f = open (Dstn,'r')
while 1:
s = f.readline()
if not s: break
s = s.strip()
if "order" in s.split():
d2E_val_tot[-1].append([])
d2E_eta_tot[-1].append([])
elif len(s) >= 30:
d2E_eta, d2E_values = s.split()
d2E_val_tot[-1][-1].append(float(d2E_values))
d2E_eta_tot[-1][-1].append(float(d2E_eta))
f.close()
d2E6_val.append(d2E_val_tot[i-1][0])
d2E4_val.append(d2E_val_tot[i-1][1])
d2E2_val.append(d2E_val_tot[i-1][2])
d2E6_eta.append(d2E_eta_tot[i-1][0])
d2E4_eta.append(d2E_eta_tot[i-1][1])
d2E2_eta.append(d2E_eta_tot[i-1][2])
CrossVal6_val = []
CrossVal4_val = []
CrossVal2_val = []
CrossVal_val_tot = []
CrossVal6_eta = []
CrossVal4_eta = []
CrossVal2_eta = []
CrossVal_eta_tot = []
for i in range(1, ECs+1):
CrossVal_val_tot.append([])
CrossVal_eta_tot.append([])
if (i<10):
DstnCV = 'Dst0'+ str(i) + '_CVe.dat'
f = open (DstnCV,'r')
while 1:
s = f.readline()
if not s: break
s = s.strip()
if "order" in s.split():
CrossVal_val_tot[-1].append([])
CrossVal_eta_tot[-1].append([])
elif len(s) >= 20 and s.split()[0] != '#':
CrossVal_eta, CrossVal_values = s.split()
CrossVal_val_tot[-1][-1].append(float(CrossVal_values))
CrossVal_eta_tot[-1][-1].append(float(CrossVal_eta))
f.close()
else:
DstnCV = 'Dst' + str(i) + '_CVe.dat'
f = open (Dstn,'r')
while 1:
s = f.readline()
if not s: break
s = s.strip()
if "order" in s.split():
CrossVal_val_tot[-1].append([])
CrossVal_eta_tot[-1].append([])
elif len(s) >= 20 and s.split()[0] != '#':
CrossVal_eta, CrossVal_values = s.split()
CrossVal_val_tot[-1][-1].append(float(CrossVal_values))
CrossVal_val_tot[-1][-1].append(float(CrossVal_values))
f.close()
CrossVal6_val.append(CrossVal_val_tot[i-1][0])
CrossVal4_val.append(CrossVal_val_tot[i-1][1])
CrossVal2_val.append(CrossVal_val_tot[i-1][2])
CrossVal6_eta.append(CrossVal_eta_tot[i-1][0])
CrossVal4_eta.append(CrossVal_eta_tot[i-1][1])
CrossVal2_eta.append(CrossVal_eta_tot[i-1][2])
os.chdir('../')
f = open ('ElaStic_'+str(ordr)+'nd.in','r')
etaEC = []
fitEC = []
for i in range(1, ECs+1):
s = f.readline()
s = s.strip()
dummy, etaEC_dummy, fitEC_dummy = s.split()
etaEC.append(etaEC_dummy)
fitEC.append(fitEC_dummy)
f = open ('ElaStic_'+str(ordr)+'nd.out','r')
allMat = [[],[],[],[],[],[]]
voigtMat = [[],[],[],[],[],[]]
ECMat = [[],[],[],[],[],[]]
complMat = [[],[],[],[],[],[]]
while 1:
s = f.readline()
if not s: break
s = s.strip()
s = s.split()
if len(s) == 1:
try: float(s[0])
except ValueError:
continue
else:
EC_eigen = float(s[0])
elif "B_V" in s:
B_V = float(s[5])
elif "G_V" in s:
G_V = float(s[5])
elif "B_R" in s:
B_R = float(s[5])
elif "G_R" in s:
G_R = float(s[5])
elif "B_H" in s:
B_H = float(s[5])
elif "G_H" in s:
G_H = float(s[5])
elif "E_V" in s:
E_V = float(s[5])
elif "nu_V" in s:
nu_V = float(s[5])
elif "E_R" in s:
E_R = float(s[5])
elif "nu_R" in s:
nu_R = float(s[5])
elif "E_H" in s:
E_H = float(s[5])
elif "nu_H" in s:
nu_H = float(s[5])
elif len(s) == 6 and s[0] != "Elastic" and s[0] != "Eigenvalues":
for i in range(0,6):
allMat[i].append(s[i])
elif "AVR" in s:
AVR = float(s[6])
f.close()
for i in range(0,6):
voigtMat[i] = allMat[i][0:6]
ECMat[i] = allMat[i][6:12]
complMat[i] = allMat[i][12:18]
for i in range(0,6):
for j in range(0,6):
ECMat[i][j] = float(ECMat[i][j])
complMat[i][j] = float(complMat[i][j])
from builtins import object
import setup_paths
from nomadcore.simple_parser import mainFunction
from nomadcore.simple_parser import SimpleMatcher as SM
from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
import os, sys, json
class SampleContext(object):
"""context for the sample parser"""
def __init__(self):
self.parser = None
def initialize_values(self):
"""allows to reset values if the same superContext is used to parse different files"""
pass
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()
# description of the input
mainFileDescription = \
SM(name = 'root',
weak = False,
startReStr = "",
subMatchers = [
SM(name = 'input',
# weak = True,
# startReStr = r"\s*Order of elastic constants\s*=\s*[0-9]",
startReStr = "",
# endReStr = r"\*sNumber of distorted structures\*s=\s*(?P<x_elastic_number_of_disordered_structures>[0-9]+)",
repeats = False,
required = False,
forwardMatch = False,
sections = ['section_run'],
subMatchers = [
SM(r"\s*Order of elastic constants\s*=\s*(?P<x_elastic_elastic_constant_order>[0-9]+)"),
SM(r"\s*Method of calculation\s*=\s*(?P<x_elastic_calculation_method>[-a-zA-Z]+)"),
SM(r"\s*DFT code name\s*=\s*(?P<x_elastic_code>[-a-zA-Z]+)"),
SM(r"\s*Space-group number\s*=\s*(?P<x_elastic_space_group_number>[0-9]+)"),
SM(r"\s*Volume of equilibrium unit cell\s*=\s*(?P<x_elastic_unit_cell_volume>[-0-9.]+)\s*\[a.u\^3\]"),
SM(r"\s*Maximum Lagrangian strain\s*=\s*(?P<x_elastic_max_lagrangian_strain>[0-9.]+)"),
SM(r"\s*Number of distorted structures\s*=\s*(?P<x_elastic_number_of_disordered_structures>[0-9]+)")
])
])
#mainFileDescription = SM(name = 'root',
# startReStr = Order of elastic constants\*s=\s*(?P<x_elastic_elastic_constant_order>[0-9]+)"",
# subMatchers = [
# SM(name = 'newRun',
# startReStr = "",
# sections = ['section_run'],
# subMatchers = [
# SM(r"\*sOrder of elastic constants\*s=\s*(?P<x_elastic_elastic_constant_order>[0-9]+)"),
# SM(r"\*sMethod of calculation\*s=\s*(?P<x_elastic_calculation_method>[-a-zA-Z]+)"),
# SM(r"\*sDFT code name\*s=\s*(?P<x_elastic_code>[-a-zA-Z]+)"),
# SM(r"\*sSpace-group number\*s=\s*(?P<x_elastic_space_group_number>[0-9]+)"),
# SM(r"\*sVolume of equilibrium unit cell\*s=\s*(?P<x_elastic_unit_cell_volume>[-0-9]+)\*s\[a.u\^3\]"),
# SM(r"\*sMaximum Lagrangian strain\*s=\s*(?P<x_elastic_max_lagrangian_strain>[0-9.]+)"),
# SM(r"\*sNumber of distorted structures\*s=\s*(?P<x_elastic_number_of_disordered_structures>[0-9]+)")
# ])
# ])
# loading metadata from nomad-meta-info/meta_info/nomad_meta_info/fhi_aims.nomadmetainfo.json
parserInfo = {
"name": "elastic_parser",
"version": "1.0"
}
metaInfoPath = os.path.normpath(os.path.join(os.path.dirname(os.path.abspath(__file__)),"../../../../nomad-meta-info/meta_info/nomad_meta_info/elastic.nomadmetainfo.json"))
metaInfoEnv, warnings = loadJsonFile(filePath = metaInfoPath, dependencyLoader = None, extraArgsHandling = InfoKindEl.ADD_EXTRA_ARGS, uri = None)
if __name__ == "__main__":
superContext = SampleContext()
mainFunction(mainFileDescription, metaInfoEnv, parserInfo, superContext = superContext)
src/main/scala/eu/nomad_lab/parsers/ElasticParser.scala
+ 3
− 5
View file @ 900abe68
......@@ -21,14 +21,12 @@ object ElasticParser extends SimpleExternalParserGenerator(
)) :: Nil
),
mainFileTypes = Seq("text/.*"),
mainFileRe = """\s*=================================================+\s*
\s*\|\s*EXCITING\s(?<version>\S*) started\s*=
(?:\s*\|\sversion hash id:\s*(?<hashId>\S*)\s*=)?""".r,
cmd = Seq(DefaultPythonInterpreter.pythonExe(), "${envDir}/parsers/exciting/parser/parser-exciting/parser_exciting.py",
mainFileRe = """\s*Order of elastic constants\s*=\s*[0-9]+\s*""".r,
cmd = Seq(DefaultPythonInterpreter.pythonExe(), "${envDir}/parsers/elastic/parser/parser-elastic/parser_elastic.py",
"--uri", "${mainFileUri}", "${mainFilePath}"),
resList = Seq(
"parser-elastic/parser_elastic.py",
"parser-exciting/setup_paths.py",
"parser-elastic/setup_paths.py",
"nomad_meta_info/public.nomadmetainfo.json",
"nomad_meta_info/common.nomadmetainfo.json",
"nomad_meta_info/meta_types.nomadmetainfo.json",
......
src/test/scala/eu/nomad_lab/parsers/ElasticParserSpec.scala
+ 3
− 3
View file @ 900abe68
......@@ -4,12 +4,12 @@ import org.specs2.mutable.Specification
object ElasticParserSpec extends Specification {
"ElasticParserTestSpin" >> {
"ElasticParserTest" >> {
"test with json-events" >> {
ParserRun.parse(ElasticParser, "parsers/elastic/test/examples/elastic/INFO.OUT", "json-events") must_== ParseResult.ParseSuccess
ParserRun.parse(ElasticParser, "parsers/elastic/test/examples/elastic/INFO_ElaStic", "json-events") must_== ParseResult.ParseSuccess
}
"test with json" >> {
ParserRun.parse(ElasticParser, "parsers/elastic/test/examples/elastic/INFO.OUT", "json") must_== ParseResult.ParseSuccess
ParserRun.parse(ElasticParser, "parsers/elastic/test/examples/elastic/INFO_ElaStic", "json") must_== ParseResult.ParseSuccess
}
}
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Please register or to comment