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Python 3 compatibility for log commands in tools/python

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This commit is contained in:
ali
2022-02-21 17:25:13 -06:00
committed by Axel Kohlmeyer
parent c68015ca87
commit 58eb331b08
3 changed files with 61 additions and 52 deletions
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4
tools/python/log2txt.py
View File

@ -10,13 +10,15 @@
# if no columns listed, all columns are included
# Author: Steve Plimpton (Sandia), sjplimp at sandia.gov
from __future__ import print_function
import sys,os
path = os.environ["LAMMPS_PYTHON_TOOLS"]
sys.path.append(path)
from log import log
if len(sys.argv) < 3:
raise StandardError, "Syntax: log2txt.py log.lammps data.txt X Y ..."
raise Exception("Syntax: log2txt.py log.lammps data.txt X Y ...")
logfile = sys.argv[1]
datafile = sys.argv[2]

5
tools/python/logplot.py
View File

@ -1,4 +1,4 @@
#!/usr/bin/env python -i
#!/usr/bin/env python
# Script: logplot.py
# Purpose: use GnuPlot to plot two columns from a LAMMPS log file
@ -15,7 +15,7 @@ from log import log
from gnu import gnu
if len(sys.argv) != 4:
raise StandardError, "Syntax: logplot.py log.lammps X Y"
raise Exception("Syntax: logplot.py log.lammps X Y")
logfile = sys.argv[1]
xlabel = sys.argv[2]
@ -25,4 +25,3 @@ lg = log(logfile)
x,y = lg.get(xlabel,ylabel)
g = gnu()
g.plot(x,y)
print "Type Ctrl-D to exit Python"

104
tools/python/pizza/log.py
View File

@ -6,6 +6,8 @@
# certain rights in this software. This software is distributed under
# the GNU General Public License.
from __future__ import print_function
# log tool
oneline = "Read LAMMPS log files and extract thermodynamic data"
@ -64,7 +66,7 @@ class log:
# --------------------------------------------------------------------
def __init__(self,*list):
def __init__(self,*arglist):
self.nvec = 0
self.names = []
self.ptr = {}
@ -72,18 +74,18 @@ class log:
# flist = list of all log file names
words = list[0].split()
words = arglist[0].split()
self.flist = []
for word in words: self.flist += glob.glob(word)
if len(self.flist) == 0 and len(list) == 1:
raise StandardError,"no log file specified"
if len(self.flist) == 0 and len(arglist) == 1:
raise Exception("no log file specified")
if len(list) == 1:
if len(arglist) == 1:
self.increment = 0
self.read_all()
else:
if len(self.flist) > 1:
raise StandardError,"can only incrementally read one log file"
raise Exception("can only incrementally read one log file")
self.increment = 1
self.eof = 0
@ -92,24 +94,23 @@ class log:
def read_all(self):
self.read_header(self.flist[0])
if self.nvec == 0: raise StandardError,"log file has no values"
if self.nvec == 0: raise Exception("log file has no values")
# read all files
for file in self.flist: self.read_one(file)
print
# sort entries by timestep, cull duplicates
self.data.sort(self.compare)
self.data.sort(key=(lambda elem: elem[0]))
self.cull()
self.nlen = len(self.data)
print "read %d log entries" % self.nlen
print("read %d log entries" % self.nlen)
# --------------------------------------------------------------------
def next(self):
if not self.increment: raise StandardError,"cannot read incrementally"
if not self.increment: raise Exception("cannot read incrementally")
if self.nvec == 0:
try: open(self.flist[0],'r')
@ -124,12 +125,12 @@ class log:
def get(self,*keys):
if len(keys) == 0:
raise StandardError, "no log vectors specified"
raise Exception( "no log vectors specified" )
map = []
colmap = []
for key in keys:
if self.ptr.has_key(key):
map.append(self.ptr[key])
if key in self.ptr:
colmap.append(self.ptr[key])
else:
count = 0
for i in range(self.nvec):
@ -137,15 +138,15 @@ class log:
count += 1
index = i
if count == 1:
map.append(index)
colmap.append(index)
else:
raise StandardError, "unique log vector %s not found" % key
raise Exception( "unique log vector %s not found" % key)
vecs = []
for i in range(len(keys)):
vecs.append(self.nlen * [0])
for j in xrange(self.nlen):
vecs[i][j] = self.data[j][map[i]]
for j in range(self.nlen):
vecs[i][j] = self.data[j][colmap[i]]
if len(keys) == 1: return vecs[0]
else: return vecs
@ -154,10 +155,10 @@ class log:
def write(self,filename,*keys):
if len(keys):
map = []
colmap = []
for key in keys:
if self.ptr.has_key(key):
map.append(self.ptr[key])
if key in self.ptr:
colmap.append(self.ptr[key])
else:
count = 0
for i in range(self.nvec):
@ -165,17 +166,25 @@ class log:
count += 1
index = i
if count == 1:
map.append(index)
colmap.append(index)
else:
raise StandardError, "unique log vector %s not found" % key
raise Exception( "unique log vector %s not found" % key)
else:
map = range(self.nvec)
colmap = range(self.nvec)
f = open(filename,"w")
for i in xrange(self.nlen):
for j in xrange(len(map)):
print >>f,self.data[i][map[j]],
print >>f
# write col names from dict in the right order
colnames = [k for j in colmap for k,v in self.ptr.items() if v == j]
for j in range(len(colnames)):
print(colnames[j], file=f, end=" ")
print("\n", file=f, end="")
# write data
for i in range(self.nlen):
for j in range(len(colmap)):
print(self.data[i][colmap[j]],file=f,end=" "),
print("\n",file=f,end="")
f.close()
# --------------------------------------------------------------------
@ -243,18 +252,18 @@ class log:
# --------------------------------------------------------------------
def read_one(self,*list):
def read_one(self,*arglist):
# if 2nd arg exists set file ptr to that value
# if 2nd arg exists set file ptr io that value
# read entire (rest of) file into txt
file = list[0]
file = arglist[0]
if file[-3:] == ".gz":
f = popen("%s -c %s" % (PIZZA_GUNZIP,file),'rb')
else:
f = open(file,'rb')
if len(list) == 2: f.seek(list[1])
if len(arglist) == 2: f.seek(arglist[1])
txt = f.read()
if file[-3:] == ".gz": eof = 0
else: eof = f.tell()
@ -270,12 +279,12 @@ class log:
# set start = position in file to start looking for next chunk
# rewind eof if final entry is incomplete
s1 = txt.find(self.firststr,start)
s2 = txt.find("Loop time of",start+1)
s1 = txt.find(self.firststr.encode('utf-8'),start)
s2 = txt.find("Loop time of".encode('utf-8'),start+1)
if s1 >= 0 and s2 >= 0 and s1 < s2: # found s1,s2 with s1 before s2
if self.style == 2:
s1 = txt.find("\n",s1) + 1
s1 = txt.find("\n".encode('utf-8'),s1) + 1
elif s1 >= 0 and s2 >= 0 and s2 < s1: # found s1,s2 with s2 before s1
s1 = 0
elif s1 == -1 and s2 >= 0: # found s2, but no s1
@ -284,25 +293,25 @@ class log:
elif s1 >= 0 and s2 == -1: # found s1, but no s2
last = 1
if self.style == 1:
s2 = txt.rfind("\n--",s1) + 1
s2 = txt.rfind("\n--".encode('utf-8'),s1) + 1
else:
s1 = txt.find("\n",s1) + 1
s2 = txt.rfind("\n",s1) + 1
s1 = txt.find("\n".encode('utf-8'),s1) + 1
s2 = txt.rfind("\n".encode('utf-8'),s1) + 1
eof -= len(txt) - s2
elif s1 == -1 and s2 == -1: # found neither
# could be end-of-file section
# or entire read was one chunk
if txt.find("Loop time of",start) == start: # end of file, so exit
if txt.find("Loop time of".encode('utf-8'),start) == start: # end of file, so exit
eof -= len(txt) - start # reset eof to "Loop"
break
last = 1 # entire read is a chunk
s1 = 0
if self.style == 1:
s2 = txt.rfind("\n--",s1) + 1
s2 = txt.rfind("\n--".encode('utf-8'),s1) + 1
else:
s2 = txt.rfind("\n",s1) + 1
s2 = txt.rfind("\n".encode('utf-8'),s1) + 1
eof -= len(txt) - s2
if s1 == s2: break
@ -313,24 +322,23 @@ class log:
# parse each entry for numeric fields, append to data
if self.style == 1:
sections = chunk.split("\n--")
sections = chunk.split("\n--".encode('utf-8'))
pat1 = re.compile("Step\s*(\S*)\s")
pat2 = re.compile("=\s*(\S*)")
for section in sections:
word1 = [re.search(pat1,section).group(1)]
word2 = re.findall(pat2,section)
words = word1 + word2
self.data.append(map(float,words))
self.data.append(list(map(float,words)))
else:
lines = chunk.split("\n")
lines = chunk.split("\n".encode('utf-8'))
for line in lines:
words = line.split()
self.data.append(map(float,words))
self.data.append(list(map(float,words)))
# print last timestep of chunk
print int(self.data[len(self.data)-1][0]),
print(int(self.data[len(self.data)-1][0]),)
sys.stdout.flush()
return eof