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EZFIO
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Python3. 

Version:2.0.0

Version:2.0.1
This commit is contained in:
Anthony Scemama 2020-01-27 11:32:17 +01:00
parent 9cc4b60f79
commit 7e6be9ab45
15 changed files with 83 additions and 84 deletions
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2
Bash/ezfio.sh
View File

@ -7,7 +7,7 @@ EZFIO_ROOT=$( cd $(dirname "${BASH_SOURCE}")/.. ; pwd -P )
function _ezfio_py()
{
python2 ${EZFIO_ROOT}/Python/ezfio.py "$@"
python3 ${EZFIO_ROOT}/Python/ezfio.py "$@"
}

18
README.rst
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@ -180,7 +180,7 @@ Create a file named ``create_input.py`` with:
.. code-block:: python
#!/usr/bin/python2
#!/usr/bin/python3
import sys
EZFIO = "./EZFIO" # Put here the absolute path to the EZFIO directory
@ -195,17 +195,17 @@ Create a file named ``create_input.py`` with:
Molecule = []
for line in input.splitlines():
new_list = map(eval,line.split())
new_list = list(map(eval,line.split()))
Molecule.append(new_list)
# Create the mass array
mass = map( lambda x: x[0], Molecule )
# print mass
mass = [ x[0] for x in Molecule ]
# print(mass)
# [16.0, 1.0, 1.0]
# Create the coord array
coord = map( lambda x: (x[1], x[2], x[3]), Molecule )
# print coord
coord = [ (x[1], x[2], x[3]) for x in Molecule ]
# print(coord)
# [(0.0, 0.222396, 0.0), (1.436494, -0.88966, 0.0), (-1.436494, -0.88966, 0.0)]
# Select the EZFIO file
@ -217,13 +217,13 @@ Create a file named ``create_input.py`` with:
ezfio.molecule_coord = coord
# Check that the total mass is correct:
print ezfio.properties_mass # Should give 18.
print(ezfio.properties_mass) # Should give 18.
Execute the script:
.. code-block:: bash
$ python2 create_input.py
$ python3 create_input.py
18.0
The printed mass is correct, and a new directory (``Water``) was created
@ -364,7 +364,7 @@ Here is the same script as the Python script, but using Bash
#!/bin/bash
source EZFIO/Bash/ezfio.sh
source EZFIO/Bash/ezfio.sh # Put correct path here
# Select the EZFIO file
ezfio set_file Water

16
bin/archive_ezfio.py
View File

@ -1,9 +1,9 @@
#!/usr/bin/env python2
#!/usr/bin/env python3
import sys
import os
sys.path = [ os.path.dirname(__file__)+"/../Python" ]+sys.path
import cPickle as pickle
import pickle as pickle
import zlib
from ezfio import ezfio_obj, ezfio
@ -20,7 +20,7 @@ def main():
sys.argv.remove("-v")
if len(sys.argv) == 1:
print "syntax: %s <EZFIO_Filename>"%(sys.argv[0])
print(("syntax: %s <EZFIO_Filename>"%(sys.argv[0])))
sys.exit(1)
ezfio_filename = sys.argv[1]
while ezfio_filename[-1] == "/":
@ -28,21 +28,19 @@ def main():
ezfio.set_filename(ezfio_filename)
get_functions = filter(
lambda x: x.startswith("has_"),
ezfio_obj.__dict__.keys() )
get_functions = [x for x in list(ezfio_obj.__dict__.keys()) if x.startswith("has_")]
d = {}
for f in get_functions:
f_name = f[4:]
try:
exec """d['%s'] = ezfio.%s"""%(f_name,f_name)
exec("""d['%s'] = ezfio.%s"""%(f_name,f_name))
except:
if do_verbose:
print "%-40s [%5s]"%(f_name, "Empty")
print(("%-40s [%5s]"%(f_name, "Empty")))
else:
if do_verbose:
print "%-40s [%5s]"%(f_name, " OK ")
print(("%-40s [%5s]"%(f_name, " OK ")))
dump = zlib.compress(pickle.dumps(d))
file = open(ezfio_filename+".ezar","w")

14
bin/unarchive_ezfio.py
View File

@ -1,9 +1,9 @@
#!/usr/bin/env python2
#!/usr/bin/env python3
import sys
import os
sys.path = [ os.path.dirname(__file__)+"/../Python" ]+sys.path
import cPickle as pickle
import pickle as pickle
import zlib
from ezfio import ezfio_obj, ezfio
@ -15,7 +15,7 @@ ezfio.error = f
def main():
if len(sys.argv) == 1:
print "syntax: %s <EZFIO_Archive.ezar>"%(sys.argv[0])
print(("syntax: %s <EZFIO_Archive.ezar>"%(sys.argv[0])))
sys.exit(1)
ezfio_filename = sys.argv[1].split(".ezar")[0]
@ -27,7 +27,7 @@ def main():
d = pickle.loads(zlib.decompress(dump))
set_functions = d.keys()
set_functions = list(d.keys())
nerrors_old = len(d)+1
nerrors = nerrors_old+1
@ -37,15 +37,15 @@ def main():
failed = []
for f_name in set_functions:
try:
exec """ezfio.%s = d['%s']"""%(f_name,f_name)
exec("""ezfio.%s = d['%s']"""%(f_name,f_name))
except:
nerrors += 1
failed.append(f_name)
if nerrors != 0:
print "Unarchive failed:"
print("Unarchive failed:")
for i in failed:
print i
print(i)
sys.exit(1)
if __name__ == "__main__":

4
git-tools/commit-msg
View File

@ -1,4 +1,4 @@
#!/usr/bin/python2
#!/usr/bin/python3
import os,sys
ROOT = os.path.dirname(__file__)+'/../../'
@ -6,7 +6,7 @@ file = open(ROOT+'version','r')
lines = file.readlines()
file.close()
file = open(sys.argv[1],'a')
print >>file, 'Version:'+lines[0].split('=')[1]
print('Version:'+lines[0].split('=')[1], file=file)
file.close()

4
git-tools/post-commit
View File

@ -1,4 +1,4 @@
#!/usr/bin/python2
#!/usr/bin/python3
import os
ROOT = os.path.dirname(__file__)+'/../../'
@ -6,7 +6,7 @@ ROOT = os.path.dirname(__file__)+'/../../'
file = open(ROOT+'version','r') ;
lines = file.readlines() ;
file.close() ;
v = map(int,lines[0].split('=')[1].split('.'));
v = list(map(int,lines[0].split('=')[1].split('.')));
v[2] += 1
lines[0] = "VERSION=%d.%d.%d\n"%tuple(v)

2
make.config
View File

@ -6,4 +6,4 @@ FC ?= gfortran -g -ffree-line-length-none -fPIC # -fopenmp
FCFLAGS ?= -fPIC
AR ?= ar
RANLIB ?= ranlib
PYTHON ?= python2
PYTHON ?= python3

27
src/ezfio-head.py
View File

@ -25,10 +25,11 @@
import os, sys
import time
import cStringIO as StringIO
import io as StringIO
from gzip import GzipFile
import tempfile
import threading
from functools import reduce
def version(x):
b = [int(i) for i in x.split('.')]
@ -40,7 +41,7 @@ def size(x):
def flatten(l):
res = []
for i in l:
if hasattr(i, "__iter__") and not isinstance(i, basestring):
if hasattr(i, "__iter__") and not isinstance(i, str):
res.extend(flatten(i))
else:
res.append(i)
@ -149,18 +150,18 @@ class ezfio_obj(object):
except OSError:
pass
file = open(path.strip()+'/.version','w')
print >>file,self.version
print(self.version, file=file)
file.close()
def error(self,where,txt):
print '------------------------------------------------------------'
print 'EZFIO File : '+self.filename
print 'EZFIO Error in : '+where.strip()
print '------------------------------------------------------------'
print ''
print txt.strip()
print ''
print '------------------------------------------------------------'
print('------------------------------------------------------------')
print('EZFIO File : '+self.filename)
print('EZFIO Error in : '+where.strip())
print('------------------------------------------------------------')
print('')
print(txt.strip())
print('')
print('------------------------------------------------------------')
raise IOError
def get_filename(self):
@ -233,7 +234,7 @@ echo %s > %s/ezfio/library"""%(filename,filename,self.LIBRARY,filename))
indices = []
values = []
for i in xrange(isize):
for i in range(isize):
try:
line = self.file.readline().split()
except:
@ -250,7 +251,7 @@ echo %s > %s/ezfio/library"""%(filename,filename,self.LIBRARY,filename))
if self.buffer_rank == -1:
self.error('write_buffer','No buffered file is open.')
for i in xrange(isize):
for i in range(isize):
for j in indices[i]:
self.file.write("%4d "%(j,))
self.file.write("%24.15e\n"%(values[i],))

6
src/ezfio-tail.py
View File

@ -32,7 +32,7 @@ def main():
try:
EZFIO_FILE = os.environ["EZFIO_FILE"]
except KeyError:
print "EZFIO_FILE not defined"
print("EZFIO_FILE not defined")
return 1
ezfio.set_file(EZFIO_FILE)
@ -42,7 +42,7 @@ def main():
try:
f = getattr(ezfio,command)
except AttributeError:
print "{0} not found".format(command)
print("{0} not found".format(command))
return 1
if command.startswith('has'):
@ -67,7 +67,7 @@ def main():
except NameError:
data = text
except:
print "Syntax Error"
print("Syntax Error")
return 1
if data is None:
data = "None"

32
src/groups.py
View File

@ -34,26 +34,26 @@ file = open("../version","r")
v = file.readline()
file.close()
v = v.split('=')[1].strip()
print >>file_py, """
print("""
def get_version(self):
return '%s'
version = property(fset=None,fget=get_version)
"""%(v)
"""%(v), file=file_py)
import sys
for group in groups.keys():
print path%{ 'group' : group }
print >>file_py, path_py%{ 'group' : group }
for group in list(groups.keys()):
print(path%{ 'group' : group })
print(path_py%{ 'group' : group }, file=file_py)
for var,type,dims,command in groups[group]:
command_py = command
dims_py = str(dims)
for g in groups.keys():
for g in list(groups.keys()):
command_py = command_py.replace(g,'self.'+g)
dims_py = dims_py.replace(g,'self.'+g)
var = var.lower()
group = group.lower()
strdims = tuple(map(lambda x: '('+str(x)+')',dims))
strdims = tuple(['('+str(x)+')' for x in dims])
strdims = str(strdims).replace("'","")
if len(dims) == 1:
strdims = strdims[:-2]+")"
@ -76,8 +76,8 @@ for group in groups.keys():
'var': var,
'group': group,
'dims': strdims}
print attributes%d
print >>file_py, attributes_py%d
print(attributes%d)
print(attributes_py%d, file=file_py)
else:
d = { 'type': type,
'var': var,
@ -88,15 +88,15 @@ for group in groups.keys():
'expr_py': command_py}
buffer = calculated%d
buffer = re.sub(r"at\((.*),(.*)\)",r'\1(\2)',buffer)
print buffer
print >>file_py, calculated_py%d
print(buffer)
print(calculated_py%d, file=file_py)
elif type == "buffered":
d = { 'group': group,
'var': var,
'dims_py': dims_py,
'dims': dims }
print buffered%d
print >>file_py, buffered_py%d
print(buffered%d)
print(buffered_py%d, file=file_py)
else:
dims_loop = ''
copy_loop = ''
@ -119,7 +119,7 @@ for group in groups.keys():
copy_loop = copy_loop[:-1]%{'var': var,'group': group} + ")\n"
for k,d in enumerate(dims):
copy_loop += (len(dims)-k-1)*" "+" enddo\n"
for g in groups.keys():
for g in list(groups.keys()):
dims_loop_py = dims_loop_py.replace(" "+g,' self.'+g)
dims_loop_py = dims_loop_py.replace("*"+g,'*self.'+g)
dims_loop_py = dims_loop_py.replace("/"+g,'/self.'+g)
@ -140,7 +140,7 @@ for group in groups.keys():
'dims_loop_py': dims_loop_py,
'copy_loop': copy_loop,
'declar_loop' : declar_loop}
print attributes_arr%d
print >>file_py, attributes_arr_py%d
print(attributes_arr%d)
print(attributes_arr_py%d, file=file_py)
file_py.close()

4
src/groups_templates.py
View File

@ -345,7 +345,7 @@ attributes_py = """
attributes_arr_py = """
def get_%(group)s_%(var)s(self):
rank = %(rank)s
dims = range(rank)
dims = list(range(rank))
%(dims_loop_py)s
dim_max = 1
for d in dims:
@ -359,7 +359,7 @@ attributes_arr_py = """
def set_%(group)s_%(var)s(self,%(var)s):
rank = %(rank)s
dims = range(rank)
dims = list(range(rank))
%(dims_loop_py)s
dim_max = 1
for d in dims:

2
src/libezfio_file.irp.f
View File

@ -184,6 +184,6 @@ subroutine ezfio_finish()
BEGIN_SHELL [ /usr/bin/env python3 ]
import os
from zlib import crc32
print ' call irp_finalize_%s'%(str(abs(crc32(os.getcwd()))))
print(' call irp_finalize_%s'%(str(abs(crc32(os.getcwd().encode())))))
END_SHELL
end

18
src/libezfio_util.irp.f
View File

@ -300,11 +300,11 @@ end function
! Build Python functions
"""
for t in format.keys():
print template_nowrite%{ 'type_short' : t_short(t), 'type' : t, 'fmt':format[t][0] }
print(template_nowrite%{ 'type_short' : t_short(t), 'type' : t, 'fmt':format[t][0] })
if not t.startswith("character"):
print template_write%{ 'type_short' : t_short(t), 'type' : t, 'fmt':format[t][0] }
print(template_write%{ 'type_short' : t_short(t), 'type' : t, 'fmt':format[t][0] })
if t != "logical":
print template_no_logical%{ 'type_short' : t_short(t), 'type' : t, 'fmt':format[t][0] }
print(template_no_logical%{ 'type_short' : t_short(t), 'type' : t, 'fmt':format[t][0] })
template_py = """
def read_%(type_short)s(self,dir,fil):
@ -331,7 +331,7 @@ template_py = """
l_filename += [ dir.strip()+'/'+fil ]
dat = conv(dat)
file = open(l_filename[0],'w')
print >>file,'%(fmt)s'%%(dat,)
print('%(fmt)s'%%(dat,), file=file)
file.close()
os.rename(l_filename[0],l_filename[1])
@ -371,13 +371,13 @@ template_py = """
file.write("\\n")
dat = flatten(dat)
for i in xrange(dim_max):
for i in range(dim_max):
file.write("%(fmt)s\\n"%%(dat[i],))
file.flush()
buffer = file.getvalue()
file.close()
file = GzipFile(filename=l_filename[0],mode='wb')
file.write(buffer)
file.write(buffer.encode())
file.close()
os.rename(l_filename[0],l_filename[1])
except:
@ -387,16 +387,16 @@ template_py = """
file_py = open("libezfio_util-gen.py","w")
for t in format.keys():
print >>file_py, template_py%{ 'type_short' : t_short(t), 'type' : t, 'fmt':format[t][1] }
print (template_py%{ 'type_short' : t_short(t), 'type' : t, 'fmt':format[t][1] }, file=file_py)
import os
command = "'echo %s > '//libezfio_filename//'/ezfio/last_library'"
cwd = os.getcwd()
cwd = cwd.split('src')[:-1]
cwd = '/'.join(cwd)
print >>file_py, """
print("""
LIBRARY = "%s"
"""%cwd
"""%cwd,file=file_py)
file_py.close()

16
src/read_config.py
View File

@ -31,7 +31,7 @@ import os, sys
lines = []
for filename in [ '../config/'+i for i in os.listdir('../config')]:
file = open(filename,'r')
lines += map(lambda x: (x,filename), file.readlines())
lines += [(x,filename) for x in file.readlines()]
try:
if lines[-1] != '':
lines.append( ('', filename) )
@ -51,7 +51,7 @@ for line, filename in lines:
groups[group] = my_list
elif line[0] != ' ': # New group
group = line.strip()
if group in groups.keys():
if group in list(groups.keys()):
my_list = groups[group]
else:
my_list = []
@ -76,12 +76,12 @@ for line, filename in lines:
my_list.append(tuple(buffer))
except:
import sys, time
print >>sys.stderr, ''
print >>sys.stderr, '*'*80
print >>sys.stderr, 'Error in EZFIO config file '+filename+' :'
print >>sys.stderr, line
print >>sys.stderr, '*'*80
print >>sys.stderr, ''
print('', file=sys.stderr)
print('*'*80, file=sys.stderr)
print('Error in EZFIO config file '+filename+' :', file=sys.stderr)
print(line, file=sys.stderr)
print('*'*80, file=sys.stderr)
print('', file=sys.stderr)
time.sleep(3)
sys.exit(1)

2
version
View File

@ -1 +1 @@
VERSION=2.0
VERSION=2.0.1