mirror of https://gitlab.com/QEF/q-e.git
Convert to Python3 and minor improvements
This commit is contained in:
Eisuke Kawashima
parent
9d2fe65012
commit
493d0e6340
|
|
@ -1,13 +1,15 @@
|
|||
#
|
||||
# Script to automatically add status and error message to ALLOCATE and DEALLOCATE in
|
||||
# Fortran files.
|
||||
#
|
||||
# Script to automatically add status and error message to ALLOCATE and DEALLOCATE in
|
||||
# Fortran files.
|
||||
#
|
||||
# Author: S. Ponce
|
||||
# Date: Sept. 2019
|
||||
#
|
||||
|
||||
from __future__ import print_function
|
||||
import numpy as np
|
||||
|
||||
|
||||
# File name
|
||||
file_name = 'elphel2_shuffle.f90'
|
||||
|
||||
|
|
@ -18,7 +20,7 @@ with open(file_name,'r') as F:
|
|||
#tmp = lines.split()
|
||||
if len(tmp_split) < 1:
|
||||
continue
|
||||
#
|
||||
#
|
||||
#print tmp_split[0][0:9]
|
||||
if tmp_split[0] == 'SUBROUTINE':
|
||||
for ii in np.arange(len(tmp)):
|
||||
|
|
@ -28,7 +30,7 @@ with open(file_name,'r') as F:
|
|||
end = ii
|
||||
|
||||
name_sub = str(tmp[start+2:end])
|
||||
|
||||
|
||||
if tmp_split[0] == 'FUNCTION':
|
||||
for ii in np.arange(len(tmp)):
|
||||
if tmp[ii] == 'N' and tmp[ii+1] == ' ':
|
||||
|
|
@ -47,19 +49,18 @@ with open(file_name,'r') as F:
|
|||
if tmp[ii] == ')':
|
||||
final = ii
|
||||
#print 'start ',start
|
||||
print str(tmp[0:start-9])+'ALLOCATE('+str(tmp[start:final])+', STAT = ierr)'
|
||||
print str(tmp[0:start-9])+'IF (ierr /= 0) CALL errore(\''+str(name_sub)+'\', \'Error allocating '+str(tmp[start:end])+'\', 1)'
|
||||
print('{}ALLOCATE({}, STAT = ierr)'.format(tmp[0:start-9], tmp[start:final]))
|
||||
print("{}IF (ierr /= 0) CALL errore('{}', 'Error allocating {}', 1)".format(
|
||||
tmp[0:start-9], name_sub, tmp[start:end]
|
||||
))
|
||||
elif tmp_split[0][0:11] == 'DEALLOCATE(':
|
||||
for ii in np.arange(len(tmp)):
|
||||
if tmp[ii] == '(':
|
||||
start = ii
|
||||
if tmp[ii] == ')':
|
||||
end = ii
|
||||
print str(tmp[0:start-10])+'DEALLOCATE('+str(tmp[start+1:end])+', STAT = ierr)'
|
||||
print str(tmp[0:start-10])+'IF (ierr /= 0) CALL errore(\''+str(name_sub)+'\', \'Error deallocating '+str(tmp[start+1:end])+'\', 1)'
|
||||
print('{}DEALLOCATE({}, STAT = ierr)'.format(tmp[0:start-10], tmp[start+1:end]))
|
||||
print("{}IF (ierr /= 0) CALL errore('{}', 'Error deallocating {}', 1)".format(
|
||||
tmp[0:start-10], name_sub, tmp[start+1:end]))
|
||||
else:
|
||||
print str(lines),
|
||||
|
||||
|
||||
|
||||
|
||||
print(lines, end='')
|
||||
|
|
|
|||
|
|
@ -1,11 +1,13 @@
|
|||
#!/usr/bin/python
|
||||
#!/usr/bin/env python3
|
||||
#
|
||||
# Post-processing script from of PH data in format used by EPW
|
||||
# 14/07/2015 - Creation of the script - Samuel Ponce
|
||||
# 14/03/2018 - Automatically reads the number of q-points - Michael Waters
|
||||
# 14/03/2018 - Detect if SOC is included in the calculation - Samuel Ponce
|
||||
# 14/03/2018 - Detect if SOC is included in the calculation - Samuel Ponce
|
||||
# 13/11/2018 - Write dyn files in xml format for SOC case - Shunhong Zhang (USTC)
|
||||
#
|
||||
#
|
||||
from __future__ import print_function
|
||||
from builtins import input
|
||||
import numpy as np
|
||||
import os
|
||||
from xml.dom import minidom
|
||||
|
|
@ -14,12 +16,12 @@ from xml.dom import minidom
|
|||
def dyn2xml(prefix):
|
||||
ndyn=int(os.popen('head -2 {0}.dyn0|tail -1'.format(prefix)).read())
|
||||
for idyn in range(1,ndyn+1):
|
||||
print '{0}.dyn{1} to {0}.dyn_q{1}.xml'.format(prefix,idyn)
|
||||
print('{0}.dyn{1} to {0}.dyn_q{1}.xml'.format(prefix, idyn))
|
||||
dynmat=dyn(prefix,idyn)
|
||||
dynmat._write_xml()
|
||||
def get_geom_info():
|
||||
if os.path.isfile('ph.out')==False:
|
||||
print 'cannot extract geometry info from ph.out'
|
||||
if not os.path.isfile('ph.out'):
|
||||
print('cannot extract geometry info from ph.out')
|
||||
return 1
|
||||
else:
|
||||
volm=float(os.popen('grep -a volume ph.out 2>/dev/null|tail -1').readline().split()[-2])
|
||||
|
|
@ -47,7 +49,7 @@ class dyn(object):
|
|||
self._at=np.zeros((3,3),float)
|
||||
self._bg=np.zeros((3,3),float)
|
||||
try: self._volm,self._at,self._bg = get_geom_info()
|
||||
except: print 'warning: lattice info not found'
|
||||
except Exception: print('warning: lattice info not found')
|
||||
for i in range(0, 4):
|
||||
f.readline()
|
||||
self._species=[];
|
||||
|
|
@ -215,7 +217,7 @@ def hasSOC(prefix):
|
|||
xmldoc = minidom.parse(fname)
|
||||
item = xmldoc.getElementsByTagName('spinorbit')[0]
|
||||
lSOC = item.childNodes[0].data
|
||||
|
||||
|
||||
return lSOC
|
||||
|
||||
# Check if the calculation was done in sequential
|
||||
|
|
@ -225,11 +227,11 @@ def isSEQ(prefix):
|
|||
lseq = True
|
||||
else:
|
||||
lseq = False
|
||||
|
||||
|
||||
return lseq
|
||||
|
||||
|
||||
# Enter the number of irr. q-points
|
||||
user_input = raw_input('Enter the prefix used for PH calculations (e.g. diam)\n')
|
||||
user_input = input('Enter the prefix used for PH calculations (e.g. diam)\n')
|
||||
prefix = str(user_input)
|
||||
|
||||
# Test if SOC
|
||||
|
|
@ -237,14 +239,14 @@ SOC = hasSOC(prefix)
|
|||
|
||||
# If SOC detected, but dyn is not in XML and we want to convert it
|
||||
if SOC=='true':
|
||||
user_input = raw_input('Calculation with SOC detected. Do you want to convert dyn in XML format [y/n]?\n')
|
||||
user_input = input('Calculation with SOC detected. Do you want to convert dyn in XML format [y/n]?\n')
|
||||
if str(user_input) == 'y':
|
||||
dyn2xml(prefix)
|
||||
os.system('mv {0}.dyn*.xml save'.format(prefix))
|
||||
|
||||
# If no SOC detected, do you want to convert into XML format
|
||||
# If no SOC detected, do you want to convert into XML format
|
||||
if SOC=='false':
|
||||
user_input = raw_input('Calculation without SOC detected. Do you want to convert to xml anyway [y/n]?\n')
|
||||
user_input = input('Calculation without SOC detected. Do you want to convert to xml anyway [y/n]?\n')
|
||||
if str(user_input) == 'y':
|
||||
SOC = 'true'
|
||||
dyn2xml(prefix)
|
||||
|
|
@ -258,7 +260,7 @@ if True: # this gets the nqpt from the outputfiles
|
|||
|
||||
else:
|
||||
# Enter the number of irr. q-points
|
||||
user_input = raw_input('Enter the number of irreducible q-points\n')
|
||||
user_input = input('Enter the number of irreducible q-points\n')
|
||||
nqpt = user_input
|
||||
try:
|
||||
nqpt = int(user_input)
|
||||
|
|
@ -293,7 +295,7 @@ for iqpt in np.arange(1,nqpt+1):
|
|||
else:
|
||||
os.system('cp _ph0/'+prefix+'.q_'+str(iqpt)+'/'+prefix+'.dvscf save/'+prefix+'.dvscf_q'+label)
|
||||
os.system('rm _ph0/'+prefix+'.q_'+str(iqpt)+'/*wfc*' )
|
||||
|
||||
|
||||
else:
|
||||
# Case with SOC
|
||||
if SOC == 'true':
|
||||
|
|
@ -316,4 +318,3 @@ for iqpt in np.arange(1,nqpt+1):
|
|||
else:
|
||||
os.system('cp _ph0/'+prefix+'.q_'+str(iqpt)+'/'+prefix+'.dvscf1 save/'+prefix+'.dvscf_q'+label)
|
||||
os.system('rm _ph0/'+prefix+'.q_'+str(iqpt)+'/*wfc*' )
|
||||
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
#!/usr/bin/python
|
||||
#!/usr/bin/env python3
|
||||
#
|
||||
# Post-processing script from of PH data in format used by EPW
|
||||
# 14/07/2015 - Creation of the script - Samuel Ponce
|
||||
|
|
|
|||
|
|
@ -1,15 +1,16 @@
|
|||
#
|
||||
# 14/07/2015 Samuel Ponce
|
||||
#
|
||||
from __future__ import print_function
|
||||
import numpy as np
|
||||
|
||||
i=0
|
||||
for ii in np.arange(0.5,0.0,-1.0/200):
|
||||
print str(ii)+' 0.0 0.0 '+str(1.0/201)
|
||||
i +=1
|
||||
i = 0
|
||||
for ii in np.arange(0.5, 0.0, -1.0 / 200):
|
||||
print('{0} 0.0 0.0 {1}'.format(ii, 1.0 / 201))
|
||||
i += 1
|
||||
|
||||
for ii in np.arange(0.0,0.5+1.0/200,1.0/200):
|
||||
print str(ii)+' '+str(ii)+' 0.0 '+str(1.0/201)
|
||||
i +=1
|
||||
for ii in np.arange(0.0, 0.5 + 1.0 / 200, 1.0 / 200):
|
||||
print('{0} {0} 0.0 {1}'.format(ii, 1.0 / 201))
|
||||
i += 1
|
||||
|
||||
print i
|
||||
print(i)
|
||||
|
|
|
|||
|
|
@ -1,20 +1,19 @@
|
|||
#
|
||||
# Post-processing script QE --> EPW
|
||||
# Post-processing script QE --> EPW
|
||||
# 14/07/2015 - Samuel Ponce
|
||||
#
|
||||
|
||||
from builtins import input
|
||||
import numpy as np
|
||||
import os
|
||||
|
||||
# Enter the number of irr. q-points
|
||||
user_input = raw_input('Enter the prefix used for PH calculations (e.g. diam)\n')
|
||||
prefix = str(user_input)
|
||||
# Enter the number of irr. q-points
|
||||
prefix = input('Enter the prefix used for PH calculations (e.g. diam)\n')
|
||||
|
||||
# Enter the number of irr. q-points
|
||||
user_input = raw_input('Enter the number of irreducible q-points\n')
|
||||
nqpt = user_input
|
||||
# Enter the number of irr. q-points
|
||||
nqpt = input('Enter the number of irreducible q-points\n')
|
||||
try:
|
||||
nqpt = int(user_input)
|
||||
nqpt = int(nqpt)
|
||||
except ValueError:
|
||||
raise Exception('The value you enter is not an integer!')
|
||||
|
||||
|
|
@ -30,4 +29,3 @@ for iqpt in np.arange(1,nqpt+1):
|
|||
else:
|
||||
os.system('cp _ph0/'+prefix+'.q_'+str(iqpt)+'/'+prefix+'.dvscf1 save/'+prefix+'.dvscf_q'+label)
|
||||
os.system('rm _ph0/'+prefix+'.q_'+str(iqpt)+'/*wfc*' )
|
||||
|
||||
|
|
|
|||
|
|
@ -1,20 +1,19 @@
|
|||
#
|
||||
# Post-processing script QE --> EPW
|
||||
# Post-processing script QE --> EPW
|
||||
# 14/07/2015 - Samuel Ponce
|
||||
#
|
||||
|
||||
from builtins import input
|
||||
import numpy as np
|
||||
import os
|
||||
|
||||
# Enter the number of irr. q-points
|
||||
user_input = raw_input('Enter the prefix used for PH calculations (e.g. diam)\n')
|
||||
prefix = str(user_input)
|
||||
# Enter the number of irr. q-points
|
||||
prefix = input('Enter the prefix used for PH calculations (e.g. diam)\n')
|
||||
|
||||
# Enter the number of irr. q-points
|
||||
user_input = raw_input('Enter the number of irreducible q-points\n')
|
||||
nqpt = user_input
|
||||
# Enter the number of irr. q-points
|
||||
nqpt = input('Enter the number of irreducible q-points\n')
|
||||
try:
|
||||
nqpt = int(user_input)
|
||||
nqpt = int(nqpt)
|
||||
except ValueError:
|
||||
raise Exception('The value you enter is not an integer!')
|
||||
|
||||
|
|
@ -30,4 +29,3 @@ for iqpt in np.arange(1,nqpt+1):
|
|||
else:
|
||||
os.system('cp _ph0/'+prefix+'.q_'+str(iqpt)+'/'+prefix+'.dvscf1 save/'+prefix+'.dvscf_q'+label)
|
||||
os.system('rm _ph0/'+prefix+'.q_'+str(iqpt)+'/*wfc*' )
|
||||
|
||||
|
|
|
|||
|
|
@ -1,20 +1,19 @@
|
|||
#
|
||||
# Post-processing script QE --> EPW
|
||||
# Post-processing script QE --> EPW
|
||||
# 14/07/2015 - Samuel Ponce
|
||||
#
|
||||
|
||||
from builtins import input
|
||||
import numpy as np
|
||||
import os
|
||||
|
||||
# Enter the number of irr. q-points
|
||||
user_input = raw_input('Enter the prefix used for PH calculations (e.g. diam)\n')
|
||||
prefix = str(user_input)
|
||||
# Enter the number of irr. q-points
|
||||
prefix = input('Enter the prefix used for PH calculations (e.g. diam)\n')
|
||||
|
||||
# Enter the number of irr. q-points
|
||||
user_input = raw_input('Enter the number of irreducible q-points\n')
|
||||
nqpt = user_input
|
||||
# Enter the number of irr. q-points
|
||||
nqpt = input('Enter the number of irreducible q-points\n')
|
||||
try:
|
||||
nqpt = int(user_input)
|
||||
nqpt = int(nqpt)
|
||||
except ValueError:
|
||||
raise Exception('The value you enter is not an integer!')
|
||||
|
||||
|
|
@ -30,4 +29,3 @@ for iqpt in np.arange(1,nqpt+1):
|
|||
else:
|
||||
os.system('cp _ph0/'+prefix+'.q_'+str(iqpt)+'/'+prefix+'.dvscf1 save/'+prefix+'.dvscf_q'+label)
|
||||
os.system('rm _ph0/'+prefix+'.q_'+str(iqpt)+'/*wfc*' )
|
||||
|
||||
|
|
|
|||
|
|
@ -1,20 +1,19 @@
|
|||
#
|
||||
# Post-processing script QE --> EPW
|
||||
# Post-processing script QE --> EPW
|
||||
# 14/07/2015 - Samuel Ponce
|
||||
#
|
||||
|
||||
from builtins import input
|
||||
import numpy as np
|
||||
import os
|
||||
|
||||
# Enter the number of irr. q-points
|
||||
user_input = raw_input('Enter the prefix used for PH calculations (e.g. diam)\n')
|
||||
prefix = str(user_input)
|
||||
# Enter the number of irr. q-points
|
||||
prefix = input('Enter the prefix used for PH calculations (e.g. diam)\n')
|
||||
|
||||
# Enter the number of irr. q-points
|
||||
user_input = raw_input('Enter the number of irreducible q-points\n')
|
||||
nqpt = user_input
|
||||
# Enter the number of irr. q-points
|
||||
nqpt = input('Enter the number of irreducible q-points\n')
|
||||
try:
|
||||
nqpt = int(user_input)
|
||||
nqpt = int(nqpt)
|
||||
except ValueError:
|
||||
raise Exception('The value you enter is not an integer!')
|
||||
|
||||
|
|
@ -30,4 +29,3 @@ for iqpt in np.arange(1,nqpt+1):
|
|||
else:
|
||||
os.system('cp _ph0/'+prefix+'.q_'+str(iqpt)+'/'+prefix+'.dvscf1 save/'+prefix+'.dvscf_q'+label)
|
||||
os.system('rm _ph0/'+prefix+'.q_'+str(iqpt)+'/*wfc*' )
|
||||
|
||||
|
|
|
|||
|
|
@ -1,20 +1,19 @@
|
|||
#
|
||||
# Post-processing script QE --> EPW
|
||||
# Post-processing script QE --> EPW
|
||||
# 14/07/2015 - Samuel Ponce
|
||||
#
|
||||
|
||||
from builtins import input
|
||||
import numpy as np
|
||||
import os
|
||||
|
||||
# Enter the number of irr. q-points
|
||||
user_input = raw_input('Enter the prefix used for PH calculations (e.g. diam)\n')
|
||||
prefix = str(user_input)
|
||||
# Enter the number of irr. q-points
|
||||
prefix = input('Enter the prefix used for PH calculations (e.g. diam)\n')
|
||||
|
||||
# Enter the number of irr. q-points
|
||||
user_input = raw_input('Enter the number of irreducible q-points\n')
|
||||
nqpt = user_input
|
||||
# Enter the number of irr. q-points
|
||||
nqpt = input('Enter the number of irreducible q-points\n')
|
||||
try:
|
||||
nqpt = int(user_input)
|
||||
nqpt = int(nqpt)
|
||||
except ValueError:
|
||||
raise Exception('The value you enter is not an integer!')
|
||||
|
||||
|
|
@ -30,4 +29,3 @@ for iqpt in np.arange(1,nqpt+1):
|
|||
else:
|
||||
os.system('cp _ph0/'+prefix+'.q_'+str(iqpt)+'/'+prefix+'.dvscf1 save/'+prefix+'.dvscf_q'+label)
|
||||
os.system('rm _ph0/'+prefix+'.q_'+str(iqpt)+'/*wfc*' )
|
||||
|
||||
|
|
|
|||
|
|
@ -1,20 +1,19 @@
|
|||
#
|
||||
# Post-processing script QE --> EPW
|
||||
# Post-processing script QE --> EPW
|
||||
# 14/07/2015 - Samuel Ponce
|
||||
#
|
||||
|
||||
from builtins import input
|
||||
import numpy as np
|
||||
import os
|
||||
|
||||
# Enter the number of irr. q-points
|
||||
user_input = raw_input('Enter the prefix used for PH calculations (e.g. diam)\n')
|
||||
prefix = str(user_input)
|
||||
# Enter the number of irr. q-points
|
||||
prefix = input('Enter the prefix used for PH calculations (e.g. diam)\n')
|
||||
|
||||
# Enter the number of irr. q-points
|
||||
user_input = raw_input('Enter the number of irreducible q-points\n')
|
||||
nqpt = user_input
|
||||
# Enter the number of irr. q-points
|
||||
nqpt = input('Enter the number of irreducible q-points\n')
|
||||
try:
|
||||
nqpt = int(user_input)
|
||||
nqpt = int(nqpt)
|
||||
except ValueError:
|
||||
raise Exception('The value you enter is not an integer!')
|
||||
|
||||
|
|
@ -30,4 +29,3 @@ for iqpt in np.arange(1,nqpt+1):
|
|||
else:
|
||||
os.system('cp _ph0/'+prefix+'.q_'+str(iqpt)+'/'+prefix+'.dvscf1 save/'+prefix+'.dvscf_q'+label)
|
||||
os.system('rm _ph0/'+prefix+'.q_'+str(iqpt)+'/*wfc*' )
|
||||
|
||||
|
|
|
|||
|
|
@ -1,3 +1,4 @@
|
|||
from __future__ import print_function
|
||||
import re, sys
|
||||
|
||||
info = """
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
#! /usr/bin/python
|
||||
#!/usr/bin/env python3
|
||||
|
||||
###### SUM STATES #######
|
||||
# Python script for summing and ploting the data from the Density Of States
|
||||
|
|
@ -31,17 +31,17 @@
|
|||
# ni.pdos_atm#1\(Ni\)_wfc#2\(d\) -t "Example PP/02" -xr -6 2
|
||||
#
|
||||
#
|
||||
# The procedure for obtaining the DOS files is explained
|
||||
# The procedure for obtaining the DOS files is explained
|
||||
# i.e. in (espresso-dir)/PP/examples/example02/
|
||||
#
|
||||
#
|
||||
# Author: Dr. Julen Larrucea
|
||||
# University of Bremen,
|
||||
# Bremen Centre for Computational Materials Science, HMI Group
|
||||
# julenl [at] gmail.com or larrucea [at] hmi.uni-bremen.de
|
||||
#
|
||||
# This file is distributed under the terms of the GNU General Public
|
||||
# This file is distributed under the terms of the GNU General Public
|
||||
# License. See the file `License'
|
||||
# in the root directory of the present distribution,
|
||||
# in the root directory of the present distribution,
|
||||
# or http://www.gnu.org/copyleft/gpl.txt .
|
||||
#######################
|
||||
|
||||
|
|
@ -60,7 +60,7 @@ min_y,max_y="",""
|
|||
output_file_name="sum_dos.out"
|
||||
prt="no"
|
||||
|
||||
print " #### sum_states.py version "+str(version)+" #### "
|
||||
print(" #### sum_states.py version {} #### ".format(version))
|
||||
|
||||
|
||||
# Check if X11, mathplotlib and gnuplot are available
|
||||
|
|
@ -89,14 +89,14 @@ if len(sys.argv)>1:
|
|||
if option=="t":
|
||||
graphtitle= sys.argv[sys.argv.index('-t')+1]
|
||||
if option=="xr":
|
||||
min_x,max_x= float(sys.argv[sys.argv.index('-xr')+1]),float(sys.argv[sys.argv.index('-xr')+2])
|
||||
min_x,max_x= float(sys.argv[sys.argv.index('-xr')+1]),float(sys.argv[sys.argv.index('-xr')+2])
|
||||
if option=="yr":
|
||||
min_y,max_y= float(sys.argv[sys.argv.index('-yr')+1]),float(sys.argv[sys.argv.index('-yr')+2])
|
||||
min_y,max_y= float(sys.argv[sys.argv.index('-yr')+1]),float(sys.argv[sys.argv.index('-yr')+2])
|
||||
if option=="v":
|
||||
print "sum_dos.py version: "+version
|
||||
print("sum_dos.py version:", version)
|
||||
sys.exit()
|
||||
if option=="h":
|
||||
print '''
|
||||
print('''
|
||||
-o QE output file name (for grepping Fermi E)
|
||||
-s Selection of atoms for summing the DOSes. "*" for all, *1*Fe*d* for first Fe atom " (def. "*")
|
||||
-p Print output to a file and aditionaly provide an output name (def. no output and "sum_dos.out")
|
||||
|
|
@ -105,8 +105,8 @@ if len(sys.argv)>1:
|
|||
-yr set min and max y value for the axes in the graph
|
||||
-h print this help
|
||||
-v print version
|
||||
Example: sum_states.py --s sys.pdos_atm#4\(Fe2\)_wfc#2\(d\) -t "Wustite LDA+U single Fe" -xr -9 4
|
||||
'''
|
||||
Example: sum_states.py --s sys.pdos_atm#4\(Fe2\)_wfc#2\(d\) -t "Wustite LDA+U single Fe" -xr -9 4
|
||||
''')
|
||||
sys.exit()
|
||||
|
||||
|
||||
|
|
@ -116,13 +116,13 @@ if len(os.popen('echo $DISPLAY').read()) > 1:
|
|||
try:
|
||||
from pylab import *
|
||||
mplplot="yes"
|
||||
print "pylab imported"
|
||||
print("pylab imported")
|
||||
except:
|
||||
print "There is no mathplotlib installed. Using gnuplot."
|
||||
print("There is no mathplotlib installed. Using gnuplot.")
|
||||
mplplot="no"
|
||||
prt="yes"
|
||||
else:
|
||||
print "No X11. Trying to plot on terminal"
|
||||
print("No X11. Trying to plot on terminal")
|
||||
graphic_plot="no"
|
||||
if prog_gnuplot=="no":
|
||||
prt="yes"
|
||||
|
|
@ -132,7 +132,7 @@ else:
|
|||
if pwout == "":
|
||||
for filen in filter(os.path.isfile, os.listdir('.')):
|
||||
if "Program PWSCF" in linecache.getline(filen, 2):
|
||||
print "Using " + filen + " as pw.x output. You can specify another one with the -o option."
|
||||
print("Using " + filen + " as pw.x output. You can specify another one with the -o option.")
|
||||
pwout=filen
|
||||
|
||||
# Parse Fermi energy from the pw.x output
|
||||
|
|
@ -140,35 +140,32 @@ if pwout!="":
|
|||
try:
|
||||
os.popen("grep -a 'the Fermi energy is' "+pwout ).read()
|
||||
fermi=float(os.popen("grep -a 'the Fermi energy is' "+pwout ).read().split()[4])
|
||||
print "Fermi energy = ", fermi, "a.u."
|
||||
print("Fermi energy = ", fermi, "a.u.")
|
||||
except:
|
||||
print "WARNING: No Fermi energy found. Using 0 e.V. instead"
|
||||
print("WARNING: No Fermi energy found. Using 0 e.V. instead")
|
||||
fermi=0
|
||||
else:
|
||||
print "WARNING: No pw.x output found. Using E Fermi = 0 e.V."
|
||||
print("WARNING: No pw.x output found. Using E Fermi = 0 e.V.")
|
||||
fermi=0
|
||||
|
||||
# List of all DOS files to add
|
||||
# List of all DOS files to add
|
||||
dosfiles=[]
|
||||
for dfile in os.listdir('.'):
|
||||
if fnmatch.fnmatch(dfile, selat):
|
||||
dosfiles.append(dfile)
|
||||
dosfiles.append(dfile)
|
||||
if len(dosfiles)==0:
|
||||
print "ERROR: Provide a (list of) valid DOS file(s)"
|
||||
print("ERROR: Provide a (list of) valid DOS file(s)")
|
||||
sys.exit()
|
||||
|
||||
print "dosfiles list: ",
|
||||
for dosfile in dosfiles:
|
||||
print dosfile,
|
||||
print ""
|
||||
print("dosfiles list:", " ".join(dosfiles))
|
||||
|
||||
# Check wetter we have k-solved DOS
|
||||
if open(dosfiles[0],'r').readline().split()[1]=="E":
|
||||
ksolved="no"
|
||||
print "no ksolved"
|
||||
print("no ksolved")
|
||||
elif open(dosfiles[0],'r').readline().split()[1]=="ik":
|
||||
ksolved="yes"
|
||||
print "ksolved"
|
||||
print("ksolved")
|
||||
|
||||
# Sum over all k-points and files
|
||||
mat=[] # matrix with total sum of ldos
|
||||
|
|
@ -191,28 +188,28 @@ for i in range(len(dosfiles)):
|
|||
elif ik == k and k > 1:
|
||||
oldmat.append([float(line.split()[1]),float(line.split()[2]),float(line.split()[3])])
|
||||
elif len(line) < 5 and k > 1: #if blank line, sum k-frame to the total
|
||||
for j in range(len(oldmat)):
|
||||
for j in range(len(oldmat)):
|
||||
mati[j]=[mati[j][0],mati[j][1]+oldmat[j][1],mati[j][2]+oldmat[j][2]]
|
||||
|
||||
if mat == []: # if it is the first dos file, copy total matrix (mat) = the first dos files's data
|
||||
mat=mati[:]
|
||||
else:
|
||||
for j in range(len(mati)): # if it is not the first file, sum values
|
||||
mat[j]=[mat[j][0],mat[j][1]+mati[j][1],mat[j][2]+mati[j][2]]
|
||||
mat[j]=[mat[j][0],mat[j][1]+mati[j][1],mat[j][2]+mati[j][2]]
|
||||
|
||||
|
||||
print "...ploting..."
|
||||
print("...ploting...")
|
||||
|
||||
|
||||
if prt=="yes":
|
||||
out=open(output_file_name,"w")
|
||||
x,y1,y2=[],[],[]
|
||||
x,y1,y2=[],[],[]
|
||||
for i in mat:
|
||||
x.append(i[0]-fermi)
|
||||
y1.append(i[1])
|
||||
y2.append(-i[2])
|
||||
if prt=="yes": # print to a file
|
||||
print>>out, i[0]-fermi, i[1], i[2]
|
||||
print(i[0] - fermi, i[1], i[2], file=out)
|
||||
if prt=="yes":
|
||||
out.close()
|
||||
|
||||
|
|
@ -222,7 +219,7 @@ if graphic_plot=="yes":
|
|||
if mplplot=="yes":
|
||||
plot(x,y1,linewidth=1.0)
|
||||
plot(x,y2,linewidth=1.0)
|
||||
print min(y2),max(y1)
|
||||
print(min(y2), max(y1))
|
||||
plt.title(graphtitle)
|
||||
plt.xlabel('E (eV)')
|
||||
plt.ylabel('States')
|
||||
|
|
@ -231,15 +228,13 @@ if graphic_plot=="yes":
|
|||
plt.fill(x,y1,color='0.8')
|
||||
plt.fill(x,y2,color='0.9')
|
||||
if min_x and max_x:
|
||||
fromx,tox=min_x,max_x
|
||||
fromx, tox = min_x, max_x
|
||||
plt.axis([fromx, tox, min(y2), max(y1)])
|
||||
show()
|
||||
show()
|
||||
elif mplplot=="no" and prog_gnuplot=="yes": # If no mathplotlib available, use gnuplot
|
||||
os.system("echo \"plot '"+ output_file_name + "' using ($1-"+str(fermi)+"):2 w l, '' u ($1"+str(fermi)+"):3 w l\" | gnuplot -persist")
|
||||
os.system("""echo "plot '{0}' using ($1-{1}):2 w l, '' u ($1-{1}):3 w l" | gnuplot -persist""".format(
|
||||
output_file_name, fermi))
|
||||
elif graphic_plot=="no": # If no X forwarding available, show graph in terminal
|
||||
if prog_gnuplot=="yes":
|
||||
os.system("echo \"set terminal dumb; plot '"+ output_file_name + "' using ($1-"+str(fermi)+"):2 w l, '' u ($1-"+str(fermi)+"):3 w l\" | gnuplot -persist")
|
||||
|
||||
|
||||
|
||||
|
||||
os.system("""echo "set terminal dumb; plot '{0}' using ($1-{1}):2 w l, '' u ($1-{1}):3 w l" | gnuplot -persist""".format(
|
||||
output_file_name, fermi))
|
||||
|
|
|
|||
|
|
@ -1,20 +1,25 @@
|
|||
from __future__ import print_function
|
||||
import sys
|
||||
import subprocess as sp
|
||||
|
||||
have_yaml = True
|
||||
try:
|
||||
import yaml
|
||||
except:
|
||||
have_yaml = False
|
||||
|
||||
try:
|
||||
from StringIO import StringIO
|
||||
except ImportError:
|
||||
from io import BytesIO as StringIO
|
||||
have_yaml = False
|
||||
|
||||
try:
|
||||
from io import StringIO
|
||||
except ImportError:
|
||||
try:
|
||||
from StringIO import StringIO
|
||||
except ImportError:
|
||||
from io import BytesIO as StringIO
|
||||
|
||||
|
||||
print("\n\n This is a helper tool to check the details of your GPU before configuring QE.\n\n")
|
||||
print("""Remeber to load CUDA environemt and run this on the COMPUTE NODE
|
||||
if you are not sure that the frontend node shares
|
||||
print("""Remeber to load CUDA environemt and run this on the COMPUTE NODE
|
||||
if you are not sure that the frontend node shares
|
||||
the same configuration as the backend nodes\n\n""")
|
||||
|
||||
|
||||
|
|
@ -52,13 +57,11 @@ else:
|
|||
minor = str(5 if int(minor)>=5 else 0)
|
||||
if 'major' in line:
|
||||
_, major = line.split(':')
|
||||
|
||||
|
||||
if minor != "" and major != "":
|
||||
print("Compute capabilities for dev {}: {}.{}".format(str(devnum), major.strip(),minor.strip()))
|
||||
conf_cc=major.strip()+minor.strip()
|
||||
minor = ""; major = ""; devnum += 1
|
||||
|
||||
|
||||
print("\n If all compute capabilities match, configure QE with:")
|
||||
print("./configure --with-cuda=$CUDA_HOME --with-cuda-cc={} --with-cuda-runtime={}\n".format(conf_cc, conf_rt))
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -1,8 +1,9 @@
|
|||
from __future__ import print_function
|
||||
import numpy as np
|
||||
|
||||
#1) Run dev-tools/mem_counter inside EPW/src
|
||||
#2) compile UtilXlib/mem_counter.f90 with -D__DEBUG flag
|
||||
#3) Run EPW
|
||||
#3) Run EPW
|
||||
#4) grep ' allocating' epw1.out > alloc.txt
|
||||
#5) grep 'deallocating' epw1.out > dealloc.txt
|
||||
#6) Run this script after having changed the correct allocation lengths
|
||||
|
|
@ -37,18 +38,18 @@ with open('dealloc.txt','r') as R:
|
|||
deall_found = [ False ] * dealloc_len
|
||||
|
||||
for ii in np.arange(alloc_len):
|
||||
print ii,' / ',alloc_len
|
||||
print(ii, ' / ', alloc_len)
|
||||
name = alloc_name[ii]
|
||||
|
||||
|
||||
found = False
|
||||
for jj in np.arange(dealloc_len):
|
||||
if name == dealloc_name[jj]:
|
||||
if (alloc_size[ii] == dealloc_size[jj] and deall_found[jj]==False ) :
|
||||
if alloc_size[ii] == dealloc_size[jj] and not deall_found[jj]:
|
||||
# We found the corresponding all/deall pair
|
||||
deall_found[jj] = True
|
||||
found = True
|
||||
break
|
||||
if (found == False):
|
||||
if not found:
|
||||
with open('mem_analyse.out','a') as O:
|
||||
O.write('We did not find a maching pair in '+str(alloc_sub[ii])+'\n')
|
||||
O.write('Allocate: '+str(name)+' '+str(alloc_size[ii])+'\n')
|
||||
|
|
@ -56,6 +57,3 @@ for ii in np.arange(alloc_len):
|
|||
# print 'We did not find a maching pair in ', alloc_sub[ii]
|
||||
# print 'Allocate: ',name,' ',alloc_size[ii]
|
||||
# print 'Deallocate: ',dealloc_name[jj],' ',dealloc_size[jj]
|
||||
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -24,6 +24,7 @@ for file in *.bkp; do cp $file ${file%.bkp}; done
|
|||
|
||||
"""
|
||||
|
||||
from __future__ import print_function
|
||||
import os, sys, re
|
||||
from shutil import copyfile
|
||||
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
#!/usr/bin/env python
|
||||
#!/usr/bin/env python3
|
||||
|
||||
# (C) 2010 Norbert Nemec
|
||||
#
|
||||
|
|
|
|||
|
|
@ -1,9 +1,9 @@
|
|||
#! /usr/bin/python -tt
|
||||
#!/usr/bin/env python3
|
||||
|
||||
from __future__ import absolute_import
|
||||
from __future__ import division
|
||||
from __future__ import print_function
|
||||
|
||||
from builtins import input
|
||||
from getpass import getpass
|
||||
from smtplib import SMTP
|
||||
|
||||
|
|
@ -14,7 +14,6 @@ name and password would allow to send e-mail through it.
|
|||
"""
|
||||
|
||||
|
||||
|
||||
SMTP_HOST = 'smtp.gmail.com:587'
|
||||
LOCAL_HOST = ''
|
||||
|
||||
|
|
@ -28,12 +27,12 @@ def main():
|
|||
|
||||
# server.ehlo()
|
||||
# print(server.ehlo())
|
||||
|
||||
|
||||
server.starttls()
|
||||
|
||||
print(server.ehlo(LOCAL_HOST))
|
||||
|
||||
user = raw_input('user: ')
|
||||
user = input('user: ')
|
||||
password = getpass('password: ')
|
||||
|
||||
print(server.login(user, password))
|
||||
|
|
@ -41,17 +40,17 @@ def main():
|
|||
fromaddr = 'testfarmqef@gmail.com'
|
||||
toaddrs = 'samuel.pon@gmail.com'
|
||||
msg = "\r\n".join([
|
||||
"From: testfarmqef@gmail.com",
|
||||
"To: samuel.pon@gmail.com",
|
||||
"Subject: Buildbot",
|
||||
"",
|
||||
"Why, oh why"
|
||||
])
|
||||
"From: testfarmqef@gmail.com",
|
||||
"To: samuel.pon@gmail.com",
|
||||
"Subject: Buildbot",
|
||||
"",
|
||||
"Why, oh why"
|
||||
])
|
||||
|
||||
|
||||
server.sendmail(fromaddr, toaddrs, msg)
|
||||
server.sendmail(fromaddr, toaddrs, msg)
|
||||
server.close()
|
||||
|
||||
|
||||
if __name__ == '__main__':
|
||||
main()
|
||||
|
||||
|
|
|
|||
|
|
@ -1,20 +1,19 @@
|
|||
#
|
||||
# Post-processing script QE --> EPW
|
||||
# Post-processing script QE --> EPW
|
||||
# 14/07/2015 - Samuel Ponce
|
||||
#
|
||||
|
||||
from builtins import input
|
||||
import numpy as np
|
||||
import os
|
||||
|
||||
# Enter the number of irr. q-points
|
||||
user_input = raw_input('Enter the prefix used for PH calculations (e.g. diam)\n')
|
||||
prefix = str(user_input)
|
||||
# Enter the number of irr. q-points
|
||||
prefix = input('Enter the prefix used for PH calculations (e.g. diam)\n')
|
||||
|
||||
# Enter the number of irr. q-points
|
||||
user_input = raw_input('Enter the number of irreducible q-points\n')
|
||||
nqpt = user_input
|
||||
# Enter the number of irr. q-points
|
||||
nqpt = input('Enter the number of irreducible q-points\n')
|
||||
try:
|
||||
nqpt = int(user_input)
|
||||
nqpt = int(nqpt)
|
||||
except ValueError:
|
||||
raise Exception('The value you enter is not an integer!')
|
||||
|
||||
|
|
@ -30,5 +29,3 @@ for iqpt in np.arange(1,nqpt+1):
|
|||
else:
|
||||
os.system('cp _ph0/'+prefix+'.q_'+str(iqpt)+'/'+prefix+'.dvscf1 save/'+prefix+'.dvscf_q'+label)
|
||||
os.system('rm -f _ph0/'+prefix+'.q_'+str(iqpt)+'/*wfc*')
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -1,11 +1,12 @@
|
|||
from __future__ import print_function
|
||||
import numpy as np
|
||||
|
||||
tot = 0
|
||||
tot = 0
|
||||
|
||||
for ii in np.arange(0,1,0.25):
|
||||
for jj in np.arange(0,1,0.25):
|
||||
for kk in np.arange(0,1,0.25):
|
||||
print ii,' ',jj,' ',kk,' ',1.0/64
|
||||
for ii in np.arange(0, 1, 0.25):
|
||||
for jj in np.arange(0, 1, 0.25):
|
||||
for kk in np.arange(0, 1, 0.25):
|
||||
print(ii, ' ', jj, ' ', kk, ' ', 1.0 / 64)
|
||||
tot += 1
|
||||
|
||||
print tot
|
||||
print(tot)
|
||||
|
|
|
|||
|
|
@ -1,20 +1,19 @@
|
|||
#
|
||||
# Post-processing script QE --> EPW
|
||||
# Post-processing script QE --> EPW
|
||||
# 14/07/2015 - Samuel Ponce
|
||||
#
|
||||
|
||||
from builtins import input
|
||||
import numpy as np
|
||||
import os
|
||||
|
||||
# Enter the number of irr. q-points
|
||||
user_input = raw_input('Enter the prefix used for PH calculations (e.g. diam)\n')
|
||||
prefix = str(user_input)
|
||||
# Enter the number of irr. q-points
|
||||
prefix = input('Enter the prefix used for PH calculations (e.g. diam)\n')
|
||||
|
||||
# Enter the number of irr. q-points
|
||||
user_input = raw_input('Enter the number of irreducible q-points\n')
|
||||
nqpt = user_input
|
||||
# Enter the number of irr. q-points
|
||||
nqpt = input('Enter the number of irreducible q-points\n')
|
||||
try:
|
||||
nqpt = int(user_input)
|
||||
nqpt = int(nqpt)
|
||||
except ValueError:
|
||||
raise Exception('The value you enter is not an integer!')
|
||||
|
||||
|
|
@ -28,4 +27,3 @@ for iqpt in np.arange(1,nqpt+1):
|
|||
else:
|
||||
os.system('cp _ph0/'+prefix+'.q_'+str(iqpt)+'/'+prefix+'.dvscf1 save/'+prefix+'.dvscf_q'+label)
|
||||
os.system('rm -f _ph0/'+prefix+'.q_'+str(iqpt)+'/*wfc*')
|
||||
|
||||
|
|
|
|||
|
|
@ -26,6 +26,7 @@ documentation for further details.'''
|
|||
# copyright: (c) 2012 James Spencer
|
||||
# license: modified BSD; see LICENSE for more details
|
||||
|
||||
from __future__ import print_function
|
||||
import glob
|
||||
import optparse
|
||||
import os
|
||||
|
|
|
|||
|
|
@ -8,6 +8,7 @@ A framework for regression testing numerical programs.
|
|||
:license: modified BSD; see LICENSE for more details.
|
||||
'''
|
||||
|
||||
from __future__ import print_function
|
||||
import glob
|
||||
import os
|
||||
import pipes
|
||||
|
|
|
|||
|
|
@ -8,6 +8,7 @@ Parse jobconfig and userconfig ini files.
|
|||
:license: modified BSD; see LICENSE for more details.
|
||||
'''
|
||||
|
||||
from __future__ import print_function
|
||||
import copy
|
||||
import glob
|
||||
import os
|
||||
|
|
|
|||
|
|
@ -8,6 +8,7 @@ Custom exceptions. Initialise signal handler for the interrupt signal.
|
|||
:license: modified BSD; see LICENSE for more details.
|
||||
'''
|
||||
|
||||
from __future__ import print_function
|
||||
import signal
|
||||
import sys
|
||||
|
||||
|
|
|
|||
|
|
@ -8,6 +8,7 @@ Classes and functions for comparing data.
|
|||
:license: modified BSD; see LICENSE for more details.
|
||||
'''
|
||||
|
||||
from __future__ import print_function
|
||||
import re
|
||||
import sys
|
||||
import warnings
|
||||
|
|
|
|||
|
|
@ -4,6 +4,7 @@ simple script to mark as CDATA all text contained in PP_INPUTFILE element. It
|
|||
avoids any issue related to the presence on XML reserved characters in that
|
||||
section.
|
||||
"""
|
||||
from __future__ import print_function
|
||||
from subprocess import Popen, PIPE
|
||||
from xml.etree import cElementTree as eT
|
||||
import os
|
||||
|
|
|
|||
Loading…
Reference in New Issue