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Commit 4d3635a6 authored by Pardini, Lorenzo (lopa)'s avatar Pardini, Lorenzo (lopa)
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added specific parsing for Clathrates

parent f3d9e730
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parser/parser-exciting/parser_exciting.py
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# Copyright 2017-2018 Lorenzo Pardini
# Copyright 2016-2018 The NOMAD Developers Group
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
......@@ -11,7 +11,8 @@
# 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.
#
# Main author and maintainer: Lorenzo Pardini <loren.pard@gmail.com>
from builtins import object
import setup_paths
import numpy as np
......@@ -29,6 +30,13 @@ class ExcitingParserContext(object):
def __init__(self):
self.parser = None
# self.mainFileUri = sys.argv[1] #exciting !!!!!!LOCAL HOME!!!!!!!! OKOKOKOK
self.mainFileUri = sys.argv[2] #exciting !!! FOR NOMAD URI nmd:// or sbt -> zip file!!!!!!!! OKOKKOOK
self.mainFilePath = None
self.mainFile = None
self.volumeCubOpt = False
self.volumeOpt = False
self.volumeCubOptIndex = 0
def initialize_values(self):
self.metaInfoEnv = self.parser.parserBuilder.metaInfoEnv
......@@ -57,6 +65,62 @@ class ExcitingParserContext(object):
self.frameSequence = []
self.samplingGIndex = 0
self.dummy = 0
self.i=0
self.clathrates = False
# self.volumeOptIndex = 0
def onOpen_section_run(self, backend, gIndex, section):
# self.i=self.i+1
# print("self.i=",self.i)
curDir = os.getcwd()
mainFile = self.parser.fIn.fIn.name #####exciting sbt -> zip filei r from NOMAD URI nmd:// #### YES ?????????? sure???? check first OKOKOKKO
self.mainFilePath = os.path.dirname(mainFile) #####exciting sbt -> zip file#### YES ?????????? sure???? check first OKOKOKKO
# self.mainFilePath = self.mainFileUri[0:-9] #####exciting LOCAL HOME ####### YES OKOKOKOK
# print("self.mainFilePath===",self.mainFilePath)
os.chdir(self.mainFilePath)
os.chdir('../')
# self.i=self.i+1
# print("self.i=",self.i)
# self.volumeOptIndex = 0
# for root, dirs, files in os.walk('.'):
# if root == '.':
# for directory in dirs:
# if directory[-4:-1]==
# print("root=",root)
# print("dirs=",dirs)
# print("files=",files)
#####volume optimization for simple cubic systems########
if 'INFO_VOL' in os.listdir('.'):
self.volumeOpt = True
# print("self.volumeOpt=",self.volumeOpt)
with open('INFO_VOL') as g:
while 1:
s = g.readline()
if not s: break
s = s.strip()
else:
for files in os.listdir('.'):
# print("files=",files)
# backend.addValue("x_exciting_dummy2", files)
if files[0:7] == 'rundir-':
self.volumeCubOptIndex+=1
os.chdir(curDir)
# curDir = os.getcwd()
# dirPath = self.mainFileUri[0:-9]
# os.chdir(dirPath)
# os.chdir('../')
# i = 0
# for files in os.listdir('.'):
# if files[0:7] == 'rundir-':
# i+=1
# if i>1:
# self.volumeOpt = True
# optGindex = backend.openSection("section_method")
# print("optGindex=",optGindex)
# backend.addValue("x_exciting_volume_optimization", self.volumeOpt)
# backend.closeSection("section_method", optGindex)
# os.chdir(curDir)
def onOpen_section_sampling_method(self, backend, gIndex, section):
self.secSamplingMethodIndex = gIndex
......@@ -67,6 +131,36 @@ class ExcitingParserContext(object):
def onOpen_section_system(self, backend, gIndex, section):
self.secSystemIndex = gIndex
curDir = os.getcwd()
mainFile = self.parser.fIn.fIn.name #####exciting sbt -> zip file or from NOMAD URI nmd:// #### YES ?????????? sure???? check first OKOKOKKO
self.mainFilePath = os.path.dirname(mainFile) #####exciting sbt -> zip file#### YES ?????????? sure???? check first OKOKOKKO
# self.mainFilePath = self.mainFileUri[0:-9] #####exciting LOCAL HOME####### YES OKOKOKOK
# print("self.mainFilePath===",self.mainFilePath)
os.chdir(self.mainFilePath)
# print("listdir=",os.listdir('.'))
if 'str.out' in os.listdir('.'):
self.clathrates = True
backend.addValue("x_exciting_clathrates", True)
clathrate_labels = []
clathrate_coordinates = []
with open('str.out') as g:
while 1:
s = g.readline()
if not s: break
s = s.strip()
s = s.split()
if len(s) == 4:
# print("s=",s[0],float(s[0]))
clathrate_coordinates.append([float(s[0]),float(s[1]),float(s[2])])
clathrate_labels.append(s[3])
# print("clathrate_coordinates=",clathrate_coordinates)
backend.addArrayValues("x_exciting_clathrates_atom_coordinates", np.asarray(clathrate_coordinates))
backend.addValue("x_exciting_clathrates_atom_labels", clathrate_labels)
else:
backend.addValue("x_exciting_clathrates", False)
# backend.addArrayValues("x_exciting_clathrates_atom_coordinates", np.array(clathrate_coordinates))
# backend.addValue("x_exciting_clathrates_atom_labels", clathrate_labels)
os.chdir(curDir)
def onOpen_section_single_configuration_calculation(self, backend, gIndex, section):
if self.secSingleConfIndex is None:
......@@ -84,6 +178,25 @@ class ExcitingParserContext(object):
def onClose_section_run(self, backend, gIndex, section):
self.secRunIndex = gIndex
# backend.addValue("x_exciting_dummy", self.volumeOptIndex)
########### VOLUME OPTIMIZATION #########################
# curDir = os.getcwd()
## mainFile = self.parser.fIn.fIn.name #####exciting sbt -> zip file#### YES ?????????? sure???? check first OKOKOKKO
## dirPath = os.path.dirname(mainFile) #####exciting sbt -> zip file#### YES ?????????? sure???? check first OKOKOKKO
# dirPath = self.mainFileUri[0:-9] #####exciting LOCAL HOME or from NOMAD URI nmd:// ####### YES OKOKOKOK
# os.chdir(dirPath)
# os.chdir('../')
# self.volumeOptIndex = 0
# for files in os.listdir('.'):
# if files[0:7] == 'rundir-':
# self.volumeOptIndex+=1
######################independent from above#################
if self.volumeCubOptIndex>1:
self.volumeCubOpt = True
optGindex = backend.openSection("section_method")
backend.addValue("x_exciting_volume_optimization", self.volumeCubOpt)
backend.closeSection("section_method", optGindex)
# os.chdir(curDir)
def onClose_x_exciting_section_geometry_optimization(self, backend, gIndex, section):
"""Trigger called when x_abinit_section_dataset is closed.
......@@ -194,6 +307,30 @@ class ExcitingParserContext(object):
backend.addValue('single_configuration_to_calculation_method_ref', self.secMethodIndex)
backend.addValue('single_configuration_calculation_to_system_ref', self.secSystemIndex)
# print("self.samplingMethod=",self.samplingMethod)
####################VOLUME TEST BEGIN################################
ext_uri = []
# backend.addValue("x_exciting_dummy=",self.volumeOptIndex)
# backend.addValue("x_exciting_dummy", self.volumeOptIndex)
if self.volumeCubOptIndex > 1:
for j in range(1, self.volumeCubOptIndex):
if (j<10):
ext_uri.append(self.mainFilePath[0:-9] + 'rundir-0' + str(j) + '/INFO.OUT')
# backend.addValue("x_exciting_dummy2", ext_uri[-1])
# print("ext_uri===",ext_uri)
else:
ext_uri.append(self.mainFilePath[0:-9] + 'rundir-' + str(j) + '/INFO.OUT')
# backend.addValue("x_exciting_dummy2", ext_uri[-1])
# print("ext_uri===",ext_uri)
# backend.addArrayValues("x_exciting_dummy2", np.asarray(ext_uri))
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)
####################VOLUME TEST END############################
if self.samplingMethod == "geometry_optimization":
self.geometryForceThreshold = section["x_exciting_geometry_optimization_threshold_force"][0]
forceX = section["x_exciting_geometry_atom_forces_x"]
......@@ -399,6 +536,7 @@ class ExcitingParserContext(object):
self.secSystemDescriptionIndex = gIndex
if self.atom_pos and self.cell_format[0] == 'cartesian':
# print("self.atom_pos=",self.atom_pos)
backend.addArrayValues('atom_positions', np.asarray(self.atom_pos))
elif self.atom_pos and self.cell_format[0] == 'lattice':
# print("aaaself.atom_pos=",self.atom_pos)
......@@ -408,6 +546,7 @@ class ExcitingParserContext(object):
self.atom_pos = atoms.get_positions()
backend.addArrayValues('atom_positions', np.asarray(self.atom_pos))
if self.atom_labels is not None:
# print("aaaself.atom_labels=",self.atom_labels)
backend.addArrayValues('atom_labels', np.asarray(self.atom_labels))
self.atom_labels = []
......@@ -427,10 +566,11 @@ class ExcitingParserContext(object):
pass
def onClose_x_exciting_section_atoms_group(self, backend, gIndex, section):
# print("start.self.atom_labels=",self.atom_labels)
fromB = unit_conversion.convert_unit_function("bohr", "m")
formt = section['x_exciting_atom_position_format']
if self.atom_pos is not None: self.atom_pos = []
if self.atom_labels is not None: self.atom_labels = []
# if self.atom_pos is not None: self.atom_pos = []
# if self.atom_labels is not None: self.atom_labels = []
self.cell_format = formt
pos = [section['x_exciting_geometry_atom_positions_' + i] for i in ['x', 'y', 'z']]
# print("pos=",pos)
......@@ -439,6 +579,7 @@ class ExcitingParserContext(object):
if pl[1] != natom or pl[2] != natom:
raise Exception("invalid number of atoms in various components %s" % pl)
for i in range(natom):
# print("nattom=",natom)
# print("i=",i)
# print("natom=",natom)
# print("[pos[0][i]=",pos[0][i])
......@@ -457,7 +598,10 @@ class ExcitingParserContext(object):
# print("section['x_exciting_geometry_atom_labels']=",section['x_exciting_geometry_atom_labels'])
# print("self.samplingMethod[0]=",self.samplingMethod)
if self.samplingMethod is not "geometry_optimization":
# print("prima=",self.atom_labels)
self.atom_labels = self.atom_labels + (section['x_exciting_geometry_atom_labels'] * natom)
# print("self.atom_labels=",self.atom_labels)
# print("section['x_exciting_geometry_atom_labels']=",section['x_exciting_geometry_atom_labels'])
else:
self.atom_labels = self.atom_labels + section['x_exciting_geometry_atom_labels']
# print("self.atom_labels_dopodopo=",self.atom_labels)
......@@ -465,16 +609,56 @@ class ExcitingParserContext(object):
def onClose_section_method(self, backend, gIndex, section):
if gIndex == self.secMethodIndex:
backend.addValue('electronic_structure_method', "DFT")
energy_thresh = section["x_exciting_scf_threshold_energy_change"][0]
potential_thresh = section["x_exciting_scf_threshold_potential_change_list"][0]
charge_thresh = section["x_exciting_scf_threshold_charge_change_list"][0]
try:
energy_thresh = section["x_exciting_scf_threshold_energy_change"][0]
except:
pass
try:
potential_thresh = section["x_exciting_scf_threshold_potential_change_list"][0]
except:
pass
try:
charge_thresh = section["x_exciting_scf_threshold_charge_change_list"][0]
except:
pass
if section["x_exciting_scf_threshold_force_change_list"]:
force_thresh = section["x_exciting_scf_threshold_force_change_list"][0]
backend.addValue('x_exciting_scf_threshold_force_change', force_thresh)
backend.addValue('scf_threshold_energy_change', energy_thresh)
backend.addValue('x_exciting_scf_threshold_potential_change', potential_thresh)
backend.addValue('x_exciting_scf_threshold_charge_change', charge_thresh)
# backend.addValue('x_exciting_scf_threshold_force_change', force_thresh)
try:
backend.addValue('x_exciting_scf_threshold_force_change', force_thresh)
except:
pass
try:
backend.addValue('scf_threshold_energy_change', energy_thresh)
except:
pass
try:
backend.addValue('x_exciting_scf_threshold_potential_change', potential_thresh)
except:
pass
try:
backend.addValue('x_exciting_scf_threshold_charge_change', charge_thresh)
except:
pass
##########BELOW VOLUME OPTIMIZATION######################
# if self.volumeOptIndex>1:
# self.volumeOpt = True
# optGindex = backend.openSection("section_method")
# backend.addValue("x_exciting_volume_optimization", self.volumeOpt)
# backend.closeSection("section_method", optGindex)
#
# ext_uri = []
# backend.addValue("x_exciting_dummy", self.volumeOptIndex)
# if self.volumeOptIndex > 1:
# for j in range(1, self.volumeOptIndex):
# if (j<10):
# ext_uri.append(self.mainFilePath[0:-9] + 'rundir-0' + str(j) + '/INFO.OUT')
# else:
# ext_uri.append(self.mainFilePath[0:-9] + 'rundir-' + str(j) + '/INFO.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)
mainFileDescription = \
SM(name = "root matcher",
......@@ -587,6 +771,7 @@ mainFileDescription = \
SM(r"\s*Wall time \(seconds\)\s*:\s*(?P<x_exciting_time_scf_iteration>[-0-9.]+)"),
SM(r"\s*RMS change in effective potential \(target\)\s*:\s*(?P<x_exciting_effective_potential_convergence_scf_iteration__hartree>[0-9]+\.[0-9]*([E]?[-]?[0-9]+))\s*\(\s*(?P<x_exciting_scf_threshold_potential_change_list__hartree>[0-9]\.[0-9]*([E]?[-]?[0-9]+))\)"),
SM(r"\s*Absolute change in total energy\s*\(target\)\s*:\s*(?P<x_exciting_energy_convergence_scf_iteration>[0-9]+\.[0-9]*([E]?[-]?[0-9]+))\s*\(\s*(?P<x_exciting_scf_threshold_energy_change__hartree>[0-9]\.[0-9]*([E]?[-]?[0-9]+))\)"),
SM(r"\s*Absolute change in total energy\s*\(target\)\s*\:\s*\s*\(\s*[0-9]+\.[0-9]+\s*[0-9]+\.[0-9]+\s*[0-9]+\.[0-9]+\s*\)\s*avg =\s*[0-9]+\.[0-9]+\s*\(\s*(?P<x_exciting_scf_threshold_energy_change__hartree>[0-9.]+E?[-][0-9]+)\s*\)"),
SM(r"\s*Charge distance\s*\(target\)\s*:\s*(?P<x_exciting_charge_convergence_scf_iteration>[0-9]\.[0-9]*([E]?[-]?[0-9]+))\s*\(\s*(?P<x_exciting_scf_threshold_charge_change_list>[0-9]\.[0-9]*([E]?[-]?[0-9]+))\)"),
SM(r"\s*Abs. change in max-nonIBS-force\s*\(target\)\s*:\s*(?P<x_exciting_force_convergence_scf_iteration>[0-9]\.[0-9]*([E]?[-]?[0-9]+))\s*\(\s*(?P<x_exciting_scf_threshold_force_change_list>[0-9]\.[0-9]*([E]?[-]?[0-9]+))\)")
]),
......
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