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make dump.py files consistent and improve python 2/3 portability

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This commit is contained in:
Axel Kohlmeyer
2022-08-17 16:15:03 -04:00
parent 1b979be939
commit 7b9b056c98
3 changed files with 86 additions and 79 deletions
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70
python/examples/pizza/dump.py
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@ -148,6 +148,7 @@ d.extra(data) extract bond/tri/line list from data
# 12/09, David Hart (SNL): allow use of NumPy or Numeric
# 03/17, Richard Berger (Temple U): improve Python 3 compatibility,
# simplify read_snapshot by using reshape
# 08/22, Axel Kohlmeyer (Temple U): remove Numeric, more Python 2/3 compatibility
# ToDo list
# try to optimize this line in read_snap: words += f.readline().split()
@ -189,16 +190,26 @@ import sys, re, glob, types
from os import popen
from math import * # any function could be used by set()
try:
import numpy as np
oldnumeric = False
except:
import Numeric as np
oldnumeric = True
import numpy as np
try: from DEFAULTS import PIZZA_GUNZIP
except: PIZZA_GUNZIP = "gunzip"
# --------------------------------------------------------------------
# wrapper to convert old style comparision function to key function
def cmp2key(oldcmp):
class keycmp:
def __init__(self, obj, *args):
self.obj = obj
def __lt__(self, other):
return oldcmp(self.obj,other.obj) < 0
def __gt__(self, other):
return oldcmp(self.obj,other.obj) > 0
def __eq__(self, other):
return oldcmp(self.obj,other.obj) == 0
return keycmp
# Class definition
class dump:
@ -251,7 +262,7 @@ class dump:
snap = self.read_snapshot(f)
while snap:
self.snaps.append(snap)
print(snap.time,end='')
print(snap.time,end=' ')
sys.stdout.flush()
snap = self.read_snapshot(f)
@ -260,7 +271,7 @@ class dump:
# sort entries by timestep, cull duplicates
self.snaps.sort(self.compare_time)
self.snaps.sort(key=cmp2key(self.compare_time))
self.cull()
self.nsnaps = len(self.snaps)
print("read %d snapshots" % self.nsnaps)
@ -288,9 +299,9 @@ class dump:
# if snapshots are scaled, unscale them
if (not self.names.has_key("x")) or \
(not self.names.has_key("y")) or \
(not self.names.has_key("z")):
if (not "x" in self.names) or \
(not "y" in self.names) or \
(not "z" in self.names):
print("no unscaling could be performed")
elif self.nsnaps > 0:
if self.scaled(self.nsnaps-1): self.unscale()
@ -346,13 +357,13 @@ class dump:
try:
snap = Snap()
item = f.readline()
snap.time = int(f.readline().decode().split()[0]) # just grab 1st field
snap.time = int(f.readline().split()[0]) # just grab 1st field
item = f.readline()
snap.natoms = int(f.readline().decode())
snap.natoms = int(f.readline())
snap.aselect = np.zeros(snap.natoms)
item = f.readline().decode()
item = f.readline()
words = f.readline().split()
snap.xlo,snap.xhi = float(words[0]),float(words[1])
words = f.readline().split()
@ -360,7 +371,7 @@ class dump:
words = f.readline().split()
snap.zlo,snap.zhi = float(words[0]),float(words[1])
item = f.readline().decode()
item = f.readline()
if len(self.names) == 0:
words = item.split()[2:]
if len(words):
@ -374,15 +385,12 @@ class dump:
else: self.names[words[i]] = i
if snap.natoms:
words = f.readline().decode().split()
words = f.readline().split()
ncol = len(words)
for i in range(1,snap.natoms):
words += f.readline().decode().split()
words += f.readline().split()
floats = map(float,words)
if oldnumeric:
atom_data = np.array(list(floats),np.Float)
else:
atom_data = np.array(list(floats),np.float)
atom_data = np.array(list(floats),np.float)
snap.atoms = atom_data.reshape((snap.natoms, ncol))
else:
@ -572,10 +580,10 @@ class dump:
def names2str(self):
ncol = len(self.snaps[0].atoms[0])
pairs = self.names.items()
values = self.names.values()
str = ""
for i in range(ncol):
if i in values: str += pairs[values.index(i)][0] + ' '
for p in pairs:
if p[1] == i: str += p[0] + ' '
return str
# --------------------------------------------------------------------
@ -618,7 +626,7 @@ class dump:
else: f = open(file,"a")
for snap in self.snaps:
if not snap.tselect: continue
print(snap.time,end='')
print(snap.time,end=' ')
sys.stdout.flush()
if header:
@ -653,7 +661,7 @@ class dump:
if len(self.snaps): namestr = self.names2str()
for snap in self.snaps:
if not snap.tselect: continue
print(snap.time,end='')
print(snap.time,end=' ')
sys.stdout.flush()
file = root + "." + str(snap.time)
@ -707,7 +715,7 @@ class dump:
list = re.findall(pattern,eq)
lhs = list[0][1:]
if not self.names.has_key(lhs):
if not lhs in self.names:
self.newcolumn(lhs)
for item in list:
@ -727,7 +735,7 @@ class dump:
def setv(self,colname,vec):
print("Setting ...")
if not self.names.has_key(colname):
if not colname in self.names:
self.newcolumn(colname)
icol = self.names[colname]
@ -765,7 +773,7 @@ class dump:
def spread(self,old,n,new):
iold = self.names[old]
if not self.names.has_key(new): self.newcolumn(new)
if not new in self.names: self.newcolumn(new)
inew = self.names[new]
min,max = self.minmax(old)
@ -858,8 +866,7 @@ class dump:
self.map(ncol+1,str)
for snap in self.snaps:
atoms = snap.atoms
if oldnumeric: newatoms = np.zeros((snap.natoms,ncol+1),np.Float)
else: newatoms = np.zeros((snap.natoms,ncol+1),np.float)
newatoms = np.zeros((snap.natoms,ncol+1),np.float)
newatoms[:,0:ncol] = snap.atoms
snap.atoms = newatoms
@ -1018,8 +1025,7 @@ class dump:
# convert values to int and absolute value since can be negative types
if oldnumeric: bondlist = np.zeros((nbonds,4),np.Int)
else: bondlist = np.zeros((nbonds,4),np.int)
bondlist = np.zeros((nbonds,4),np.int)
ints = [abs(int(value)) for value in words]
start = 0
stop = 4