#Copyright Aksyonov D.A
from __future__ import division, unicode_literals, absolute_import
import os, math, re, sys
import numpy as np
from collections import Iterable
import shutil, gzip
import traceback
from contextlib import contextmanager
try:
from six import string_types
except:
print('Warning! six module was not found, I use only str and basestring as string_types; errors can be expected')
try:
string_types = basestring #for python 2.7
except NameError:
string_types = str # for python 3
from siman import header
from siman.header import printlog
[docs]class TracePrints(object):
def __init__(self):
self.stdout = sys.stdout
[docs] def write(self, s):
self.stdout.write("Writing %r\n" % s)
traceback.print_stack(file=self.stdout)
[docs]def angle(v1, v2):
#in degrees
return math.acos(np.dot(v1, v2) / (np.linalg.norm(v1) * np.linalg.norm(v2))) / math.pi * 180
[docs]def normal(v1, v2):
#normal to two vectors
return np.cross(v1, v2)
[docs]def get_mismatch(a, b):
"""
relative mistmatch between the lattice vectors a and b
"""
a = np.array(a)
b = np.array(b)
return np.linalg.norm(b) / np.linalg.norm(a) - 1
[docs]def get_vector(a, b):
a = np.array(a)
b = np.array(b)
vec = np.subtract(a,b)
return vec
[docs]def get_vec(a, b):
a = np.array(a)
b = np.array(b)
l = np.linalg.norm(a-b)
return l
[docs]def vec_l(vec):
#length of vector
l = np.linalg.norm(vec)
return l
[docs]def red_prec(value, precision = 100.):
#
a = value * precision
return round(a)/1./precision
[docs]def return_xred(xr, shift = 0):
# return reduced values to [0-shift, 1-shift] range or
#
bob = 0-shift; upb = 1-shift;
for j in 0,1,2:
if xr[j] < bob:
xr[j] = xr[j] - int(xr[j]) + 1 #allows to account that xr can be more than 2
if xr[j] >= upb:
xr[j] = xr[j] - int(xr[j])
return xr
[docs]def is_list_like(obj):
return not isinstance(obj, string_types) and isinstance(obj, Iterable)
[docs]def is_string_like(s):
return isinstance(s, string_types)
[docs]def list2string(ilist, joiner = ' '):
#' '.join(['{:}']*len(lis)).format(*lis)
return joiner.join(np.array(ilist).astype(str))
[docs]def merge_dics(dic1, dic2):
"""
return dic
"""
dic_new = dic1.copy()
dic_new.update(dic2)
return dic_new
[docs]def cat_files(files, output_file):
#files (list) - file names
#
with open(output_file,'wb') as wfd:
for f in files:
with open(f,'rb') as fd:
shutil.copyfileobj(fd, wfd, 1024*1024*10)
return
[docs]def grep_file(string, file, reverse = False):
#reverse(bool) - read file in reversed order - require upload to memory
out = ''
lines = []
with open(file, 'rb') as f:
text = f.read().decode(errors='replace')
# lines = f.readlines()
lines = str(text).split('\n')
# for line in text:
# print(text)
# print(lines)
if reverse:
f = reversed(lines)
for line in f:
# print(line)
if string in line:
out = line
return str(out.strip() )
[docs]def gunzip_file(filename):
printlog('unzipping file', filename)
with open(filename[:-3], 'wb') as f_out:
with gzip.open(filename, 'rb') as f_in:
shutil.copyfileobj(f_in, f_out)
return
[docs]def makedir(path, renew_folder=False):
"""
*path* - path to some file
Make dirname(path) directory if it does not exist
"""
import shutil as S
dirname = os.path.dirname(path)
if renew_folder and os.path.exists(dirname): S.rmtree(path)
else: pass
if dirname and not os.path.exists(dirname):
os.makedirs(dirname)
printlog("Directory", dirname, " was created", imp = 'y')
return
[docs]def latex_chem(formula):
""" """
# print(formula)
if '$' not in formula:
formula =re.sub("([0-9]{1,3})", "$_{\\1}$", formula)
return formula
[docs]def latex_spg(spg):
# print(spg)
# spg = spg.replace('_1', '$_1$')
spg = spg.replace('p', 'P')
if '-' in spg:
pos = spg.find('-')
dig = spg[pos+1]
spg = spg.replace('-'+dig, '\\bar{'+dig+'}')
spg = '$'+spg+'$'
return spg
[docs]def bash_chk_file_cmd(file):
#bash returns empty string if file exist
return " [ -e "+ file +""" ] || echo "NO" ; """
# def find_transition_atom(elements):
# #return list of unique transition elements
# for elements
[docs]def get_common_chemical_base(st1,st2):
from difflib import SequenceMatcher
s1 = st1.get_reduced_formula()
s2 = st2.get_reduced_formula()
match = SequenceMatcher(None, s1, s2).find_longest_match(0, len(s1), 0, len(s2))
base = s1[match.a: match.a + match.size]
return latex_chem(base)
[docs]def b2s(b):
#bool to vasp str
if b:
s = 'T'
else:
s = 'F'
return s
[docs]def is_unique(d, dist, prec = 0.001):
"""
check if d is unique within the provided precision in the given list dist
return 1 if unique, else 0
"""
if len(dist)>0:
if min([abs(d-d1) for d1 in dist])>prec:
out = 1
else:
out = 0
else:
out = 1
return out
[docs]def calc_ngkpt(recip, kspacing):
to_ang_local = 1
N_from_kspacing = []
for i in 0, 1, 2:
N_from_kspacing.append( math.ceil( (np.linalg.norm(recip[i]) / to_ang_local) / kspacing) )
return N_from_kspacing
[docs]def setting_sshpass(cl = None, clust = None):
"""
Creates some variables for sshpass mode
cl (Caluculation) - object, should contain cluster dict, has higher priority
clust (dict) - cluster dicts
"""
if cl and hasattr(cl , 'cluster'):
clust = cl.cluster
# print(clust.get('sshpass'))
if clust and clust.get('sshpass') is True:
printlog('setting sshpass to True', imp = '')
header.sshpass = clust['sshpass']
header.path2pass = clust.get('path2pass')
else:
header.sshpass = None
header.path2pass = None
# def format_str():
[docs]@contextmanager
def cwd(path):
"""
Alows to change working directory inside
with cwd():
expression
"""
oldpwd=os.getcwd()
os.chdir(path)
try:
yield
finally:
os.chdir(oldpwd)
[docs]def block_print():
"""
Blocks standard output. It may be used in functions that do not have silent mode.
"""
sys.stdout = open(os.devnull, 'w')
[docs]def enable_print():
"""
Enables standard output. It may be used in functions that do not have silent mode.
"""
sys.stdout = sys.__stdout__