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convert tabs to spaces, remove extra spaces, fix comments

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This commit is contained in:
danielque
2023-08-09 16:49:09 +02:00
parent 633058e1ab
commit d560b34214
47 changed files with 1263 additions and 1266 deletions
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32
src/ldump.py
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@ -3,7 +3,7 @@
#
# Copyright (2005) Sandia Corporation. Under the terms of Contract
# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
# certain rights in this software. This software is distributed under
# certain rights in this software. This software is distributed under
# the GNU General Public License.
# ldump tool
@ -12,14 +12,14 @@ oneline = "Read dump files with line segment info"
docstr = """
l = ldump("dump.one") read in one or more dump files
l = ldump("dump.1 dump.2.gz") can be gzipped
l = ldump("dump.*") wildcard expands to multiple files
l = ldump("dump.*",0) two args = store filenames, but don't read
l = ldump("dump.1 dump.2.gz") can be gzipped
l = ldump("dump.*") wildcard expands to multiple files
l = ldump("dump.*",0) two args = store filenames, but don't read
incomplete and duplicate snapshots are deleted
no column name assignment is performed
time = l.next() read next snapshot from dump files
time = l.next() read next snapshot from dump files
used with 2-argument constructor to allow reading snapshots one-at-a-time
snapshot will be skipped only if another snapshot has same time stamp
@ -43,7 +43,7 @@ time,box,atoms,bonds,tris,lines = l.viz(index) return list of viz objects
lines = id,type,x1,y1,z1,x2,y2,z2 for each line as 2d array
id,type are from associated atom
l.owrap(...) wrap lines to same image as their atoms
l.owrap(...) wrap lines to same image as their atoms
owrap() is called by dump tool's owrap()
useful for wrapping all molecule's atoms/lines the same so it is contiguous
@ -100,7 +100,7 @@ class ldump:
for word in words: self.flist += glob.glob(word)
if len(self.flist) == 0 and len(list) == 1:
raise StandardError,"no ldump file specified"
if len(list) == 1:
self.increment = 0
self.read_all()
@ -155,15 +155,15 @@ class ldump:
snap = self.read_snapshot(f)
if not snap:
self.nextfile += 1
if self.nextfile == len(self.flist): return -1
if self.nextfile == len(self.flist): return -1
f.close()
self.eof = 0
continue
self.eof = 0
continue
self.eof = f.tell()
f.close()
try:
self.findtime(snap.time)
continue
continue
except: break
self.snaps.append(snap)
@ -175,7 +175,7 @@ class ldump:
# --------------------------------------------------------------------
# read a single snapshot from file f
# return snapshot or 0 if failed
def read_snapshot(self,f):
try:
snap = Snap()
@ -216,7 +216,7 @@ class ldump:
# --------------------------------------------------------------------
# map atom column names
def map(self,*pairs):
if len(pairs) % 2 != 0:
raise StandardError, "ldump map() requires pairs of mappings"
@ -263,7 +263,7 @@ class ldump:
del self.snaps[i]
else:
i += 1
# --------------------------------------------------------------------
# return list of lines to viz for snapshot isnap
# if called with flag, then index is timestep, so convert to snapshot index
@ -291,7 +291,7 @@ class ldump:
# create line list from id,type,end1x,end1y,end2x,end2y
# don't add line if all 4 values are 0 since not a line
lines = []
for i in xrange(snap.natoms):
atom = snap.atoms[i]
@ -322,7 +322,7 @@ class ldump:
# idump = index of my line I in dump's atoms
# jdump = atom J in dump's atoms that atom I was owrapped on
# delx,dely = offset applied to atom I and thus to line I
for i in xrange(snap.natoms):
tag = atoms[i][id]
idump = idsdump[tag]