added codes

Author: yomichi

.gitignore

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+### https://raw.github.com/github/gitignore/5db84d2431ce5209d252112fdc377c0f17d5078b/Python.gitignore
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+
+### https://raw.github.com/github/gitignore/5db84d2431ce5209d252112fdc377c0f17d5078b/Global/macOS.gitignore
+
+# General
+.DS_Store
+.AppleDouble
+.LSOverride
+
+# Icon must end with two \r
+Icon
+
+# Thumbnails
+._*
+
+# Files that might appear in the root of a volume
+.DocumentRevisions-V100
+.fseventsd
+.Spotlight-V100
+.TemporaryItems
+.Trashes
+.VolumeIcon.icns
+.com.apple.timemachine.donotpresent
+
+# Directories potentially created on remote AFP share
+.AppleDB
+.AppleDesktop
+Network Trash Folder
+Temporary Items
+.apdisk
+
+
+### https://raw.github.com/github/gitignore/5db84d2431ce5209d252112fdc377c0f17d5078b/Global/Windows.gitignore
+
+# Windows thumbnail cache files
+Thumbs.db
+ehthumbs.db
+ehthumbs_vista.db
+
+# Dump file
+*.stackdump
+
+# Folder config file
+[Dd]esktop.ini
+
+# Recycle Bin used on file shares
+$RECYCLE.BIN/
+
+# Windows Installer files
+*.cab
+*.msi
+*.msix
+*.msm
+*.msp
+
+# Windows shortcuts
+*.lnk
+
+
+### https://raw.github.com/github/gitignore/5db84d2431ce5209d252112fdc377c0f17d5078b/Global/Linux.gitignore
+
+*~
+
+# temporary files which can be created if a process still has a handle open of a deleted file
+.fuse_hidden*
+
+# KDE directory preferences
+.directory
+
+# Linux trash folder which might appear on any partition or disk
+.Trash-*
+
+# .nfs files are created when an open file is removed but is still being accessed
+.nfs*
+
+
+### https://raw.github.com/github/gitignore/5db84d2431ce5209d252112fdc377c0f17d5078b/Global/Vim.gitignore
+
+# Swap
+[._]*.s[a-v][a-z]
+[._]*.sw[a-p]
+[._]s[a-rt-v][a-z]
+[._]ss[a-gi-z]
+[._]sw[a-p]
+
+# Session
+Session.vim
+
+# Temporary
+.netrwhist
+*~
+# Auto-generated tag files
+tags
+# Persistent undo
+[._]*.un~
+
+
+### https://raw.github.com/github/gitignore/5db84d2431ce5209d252112fdc377c0f17d5078b/Global/Emacs.gitignore
+
+# -*- mode: gitignore; -*-
+*~
+\#*\#
+/.emacs.desktop
+/.emacs.desktop.lock
+*.elc
+auto-save-list
+tramp
+.\#*
+
+# Org-mode
+.org-id-locations
+*_archive
+
+# flymake-mode
+*_flymake.*
+
+# eshell files
+/eshell/history
+/eshell/lastdir
+
+# elpa packages
+/elpa/
+
+# reftex files
+*.rel
+
+# AUCTeX auto folder
+/auto/
+
+# cask packages
+.cask/
+dist/
+
+# Flycheck
+flycheck_*.el
+
+# server auth directory
+/server/
+
+# projectiles files
+.projectile
+
+# directory configuration
+.dir-locals.el
+
+

docs/sphinx/en/build/html/.nojekyll abics/__init__.pydocs/sphinx/en/build/html/.nojekyll renamed to abics/__init__.py

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+from .default_observer import *

abics/applications/__init__.py

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+from .base_solver import SolverBase
+from collections import namedtuple
+import numpy as np
+from pymatgen import Structure
+import os
+import sys,shutil,io
+
+class aenetSolver(SolverBase):
+    """
+    This class defines the aenet solver.
+    """
+
+    def __init__(self, path_to_solver):
+        """
+        Initialize the solver.
+
+        Parameters
+        ----------
+        path_to_solver : str
+                      Path to the solver.
+        """
+        super(aenetSolver, self).__init__(path_to_solver)
+        self.path_to_solver = path_to_solver
+        self.input = aenetSolver.Input()
+        self.output = aenetSolver.Output()
+
+    def name(self):
+        return "aenet"
+
+    class Input(object):
+        def __init__(self):
+            self.base_info = None
+            self.pos_info = None
+
+        def from_directory(self, base_input_dir):
+            # set information of base_input and pos_info from files in base_input_dir
+            self.base_info = os.path.abspath(base_input_dir)
+            self.pos_info = open('{}/structure.xsf'.format(base_input_dir), 'r').read()
+
+        def update_info_by_structure(self, structure, seldyn_arr=None):
+            self.pos_info = structure.to('XSF')
+
+        def update_info_from_files(self, output_dir, rerun):
+            print('rerun not implemented. Something has gone wrong')
+            sys.exit(1)
+            
+        def write_input(self, output_dir):
+            # Write input files
+            if self.base_info is None:
+                raise AttributeError("Fail to set base_info.")
+            os.makedirs(output_dir, exist_ok=True)
+            for fname in os.listdir(self.base_info):
+                shutil.copy('{}/{}'.format(self.base_info, fname), output_dir)
+            with open('{}/structure.xsf'.format(output_dir), 'w') as f:
+                f.write(self.pos_info)
+
+        def cl_args(self, nprocs, nthreads, output_dir):
+            # Specify command line arguments
+            return ['{}/predict.in'.format(output_dir),]
+
+    class Output(object):
+
+        def get_results(self, output_dir):
+            # Read results from files in output_dir and calculate values
+            Phys = namedtuple("PhysVaules", ("energy", "structure"))
+            structure = Structure.from_file('{}/structure.xsf'.format(output_dir))
+            with open('{}/stdout'.format(output_dir)) as f:
+                lines = f.read()
+                fi_io = io.StringIO(lines)
+                line = fi_io.readline()
+            if 'optimized' in lines:
+                while 'optimized' not in line:
+                    line = fi_io.readline()
+                for i in range(4):
+                    fi_io.readline()
+                for i in range(len(structure)):
+                    xyz = [float(x) for x in fi_io.readline().split()[1:4]]
+                    structure.replace(i, structure[i].species, coords = xyz,
+                                      coords_are_cartesian = True)
+            while 'Total energy' not in line:
+                line = fi_io.readline()
+            energy = line.split()[-2]
+            return Phys(np.float64(energy), structure)
+
+    def solver_run_schemes(self):
+        return ('subprocess')
+