ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15358 f3b2605a-c512-4ea7-a41b-209d697bcdaa

Browse Source
This commit is contained in:
sjplimp
2016-07-22 22:57:54 +00:00
parent 2f936d5e56
commit 778f4d338c
22 changed files with 694 additions and 246 deletions
Download Patch File Download Diff File Expand all files Collapse all files

232
python/examples/pizza/dump.py
View File

@ -6,6 +6,10 @@
# certain rights in this software. This software is distributed under
# the GNU General Public License.
# for python3 compatibility
from __future__ import print_function
# dump tool
oneline = "Read, write, manipulate dump files and particle attributes"
@ -179,7 +183,7 @@ d.extra(data) extract bond/tri/line list from data
# Imports and external programs
import sys, commands, re, glob, types
import sys, re, glob, types
from os import popen
from math import * # any function could be used by set()
@ -220,7 +224,7 @@ class dump:
self.flist = []
for word in words: self.flist += glob.glob(word)
if len(self.flist) == 0 and len(list) == 1:
raise StandardError,"no dump file specified"
raise StandardError("no dump file specified")
if len(list) == 1:
self.increment = 0
@ -245,19 +249,19 @@ class dump:
snap = self.read_snapshot(f)
while snap:
self.snaps.append(snap)
print snap.time,
print(snap.time,end='')
sys.stdout.flush()
snap = self.read_snapshot(f)
f.close()
print
print()
# sort entries by timestep, cull duplicates
self.snaps.sort(self.compare_time)
self.cull()
self.nsnaps = len(self.snaps)
print "read %d snapshots" % self.nsnaps
print("read %d snapshots" % self.nsnaps)
# select all timesteps and atoms
@ -266,36 +270,36 @@ class dump:
# set default names for atom columns if file wasn't self-describing
if len(self.snaps) == 0:
print "no column assignments made"
print("no column assignments made")
elif len(self.names):
print "assigned columns:",self.names2str()
print("assigned columns:",self.names2str())
elif self.snaps[0].atoms == None:
print "no column assignments made"
print("no column assignments made")
elif len(self.snaps[0].atoms[0]) == 5:
self.map(1,"id",2,"type",3,"x",4,"y",5,"z")
print "assigned columns:",self.names2str()
print("assigned columns:",self.names2str())
elif len(self.snaps[0].atoms[0]) == 8:
self.map(1,"id",2,"type",3,"x",4,"y",5,"z",6,"ix",7,"iy",8,"iz")
print "assigned columns:",self.names2str()
print("assigned columns:",self.names2str())
else:
print "no column assignments made"
print("no column assignments made")
# 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")):
print "no unscaling could be performed"
print("no unscaling could be performed")
elif self.nsnaps > 0:
if self.scaled(self.nsnaps-1): self.unscale()
else: print "dump is already unscaled"
else: print("dump is already unscaled")
# --------------------------------------------------------------------
# read next snapshot from list of files
def next(self):
if not self.increment: raise StandardError,"cannot read incrementally"
if not self.increment: raise StandardError("cannot read incrementally")
# read next snapshot in current file using eof as pointer
# if fail, try next file
@ -307,15 +311,15 @@ class dump:
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
# select the new snapshot with all its atoms
@ -324,7 +328,7 @@ class dump:
snap = self.snaps[self.nsnaps]
snap.tselect = 1
snap.nselect = snap.natoms
for i in xrange(snap.natoms): snap.aselect[i] = 1
for i in range(snap.natoms): snap.aselect[i] = 1
self.nsnaps += 1
self.nselect += 1
@ -370,14 +374,14 @@ class dump:
if snap.natoms:
words = f.readline().split()
ncol = len(words)
for i in xrange(1,snap.natoms):
for i in range(1,snap.natoms):
words += f.readline().split()
floats = map(float,words)
if oldnumeric: atoms = np.zeros((snap.natoms,ncol),np.Float)
else: atoms = np.zeros((snap.natoms,ncol),np.float)
start = 0
stop = ncol
for i in xrange(snap.natoms):
for i in range(snap.natoms):
atoms[i] = floats[start:stop]
start = stop
stop += ncol
@ -413,7 +417,7 @@ class dump:
def map(self,*pairs):
if len(pairs) % 2 != 0:
raise StandardError, "dump map() requires pairs of mappings"
raise StandardError("dump map() requires pairs of mappings")
for i in range(0,len(pairs),2):
j = i + 1
self.names[pairs[j]] = pairs[i]-1
@ -430,15 +434,15 @@ class dump:
self.nsnaps -= 1
ndel += 1
else: i += 1
print "%d snapshots deleted" % ndel
print "%d snapshots remaining" % self.nsnaps
print("%d snapshots deleted" % ndel)
print("%d snapshots remaining" % self.nsnaps)
# --------------------------------------------------------------------
# scale coords to 0-1 for all snapshots or just one
def scale(self,*list):
if len(list) == 0:
print "Scaling dump ..."
print("Scaling dump ...")
x = self.names["x"]
y = self.names["y"]
z = self.names["z"]
@ -466,7 +470,7 @@ class dump:
def unscale(self,*list):
if len(list) == 0:
print "Unscaling dump ..."
print("Unscaling dump ...")
x = self.names["x"]
y = self.names["y"]
z = self.names["z"]
@ -493,7 +497,7 @@ class dump:
# wrap coords from outside box to inside
def wrap(self):
print "Wrapping dump ..."
print("Wrapping dump ...")
x = self.names["x"]
y = self.names["y"]
@ -515,7 +519,7 @@ class dump:
# unwrap coords from inside box to outside
def unwrap(self):
print "Unwrapping dump ..."
print("Unwrapping dump ...")
x = self.names["x"]
y = self.names["y"]
@ -537,7 +541,7 @@ class dump:
# wrap coords to same image as atom ID stored in "other" column
def owrap(self,other):
print "Wrapping to other ..."
print("Wrapping to other ...")
id = self.names["id"]
x = self.names["x"]
@ -554,9 +558,9 @@ class dump:
zprd = snap.zhi - snap.zlo
atoms = snap.atoms
ids = {}
for i in xrange(snap.natoms):
for i in range(snap.natoms):
ids[atoms[i][id]] = i
for i in xrange(snap.natoms):
for i in range(snap.natoms):
j = ids[atoms[i][iother]]
atoms[i][x] += (atoms[i][ix]-atoms[j][ix])*xprd
atoms[i][y] += (atoms[i][iy]-atoms[j][iy])*yprd
@ -570,7 +574,7 @@ class dump:
pairs = self.names.items()
values = self.names.values()
str = ""
for i in xrange(ncol):
for i in range(ncol):
if i in values: str += pairs[values.index(i)][0] + ' '
return str
@ -581,12 +585,12 @@ class dump:
def sort(self,*list):
if len(list) == 0:
print "Sorting selected snapshots ..."
print("Sorting selected snapshots ...")
id = self.names["id"]
for snap in self.snaps:
if snap.tselect: self.sort_one(snap,id)
elif type(list[0]) is types.StringType:
print "Sorting selected snapshots by %s ..." % list[0]
print("Sorting selected snapshots by %s ..." % list[0])
id = self.names[list[0]]
for snap in self.snaps:
if snap.tselect: self.sort_one(snap,id)
@ -602,7 +606,7 @@ class dump:
atoms = snap.atoms
ids = atoms[:,id]
ordering = np.argsort(ids)
for i in xrange(len(atoms[0])):
for i in range(len(atoms[0])):
atoms[:,i] = np.take(atoms[:,i],ordering)
# --------------------------------------------------------------------
@ -614,33 +618,33 @@ class dump:
else: f = open(file,"a")
for snap in self.snaps:
if not snap.tselect: continue
print snap.time,
print(snap.time,end='')
sys.stdout.flush()
if header:
print >>f,"ITEM: TIMESTEP"
print >>f,snap.time
print >>f,"ITEM: NUMBER OF ATOMS"
print >>f,snap.nselect
print >>f,"ITEM: BOX BOUNDS"
print >>f,snap.xlo,snap.xhi
print >>f,snap.ylo,snap.yhi
print >>f,snap.zlo,snap.zhi
print >>f,"ITEM: ATOMS",namestr
print("ITEM: TIMESTEP",file=f)
print(snap.time,file=f)
print("ITEM: NUMBER OF ATOMS",file=f)
print(snap.nselect,file=f)
print("ITEM: BOX BOUNDS",file=f)
print(snap.xlo,snap.xhi,file=f)
print(snap.ylo,snap.yhi,file=f)
print(snap.zlo,snap.zhi,file=f)
print("ITEM: ATOMS",namestr,file=f)
atoms = snap.atoms
nvalues = len(atoms[0])
for i in xrange(snap.natoms):
for i in range(snap.natoms):
if not snap.aselect[i]: continue
line = ""
for j in xrange(nvalues):
for j in range(nvalues):
if (j < 2):
line += str(int(atoms[i][j])) + " "
else:
line += str(atoms[i][j]) + " "
print >>f,line
print(line,file=f)
f.close()
print "\n%d snapshots" % self.nselect
print("\n%d snapshots" % self.nselect)
# --------------------------------------------------------------------
# write one dump file per snapshot from current selection
@ -649,34 +653,34 @@ class dump:
if len(self.snaps): namestr = self.names2str()
for snap in self.snaps:
if not snap.tselect: continue
print snap.time,
print(snap.time,end='')
sys.stdout.flush()
file = root + "." + str(snap.time)
f = open(file,"w")
print >>f,"ITEM: TIMESTEP"
print >>f,snap.time
print >>f,"ITEM: NUMBER OF ATOMS"
print >>f,snap.nselect
print >>f,"ITEM: BOX BOUNDS"
print >>f,snap.xlo,snap.xhi
print >>f,snap.ylo,snap.yhi
print >>f,snap.zlo,snap.zhi
print >>f,"ITEM: ATOMS",namestr
print("ITEM: TIMESTEP",file=f)
print(snap.time,file=f)
print("ITEM: NUMBER OF ATOMS",file=f)
print(snap.nselect,file=f)
print("ITEM: BOX BOUNDS",file=f)
print(snap.xlo,snap.xhi,file=f)
print(snap.ylo,snap.yhi,file=f)
print(snap.zlo,snap.zhi,file=f)
print("ITEM: ATOMS",namestr,file=f)
atoms = snap.atoms
nvalues = len(atoms[0])
for i in xrange(snap.natoms):
for i in range(snap.natoms):
if not snap.aselect[i]: continue
line = ""
for j in xrange(nvalues):
for j in range(nvalues):
if (j < 2):
line += str(int(atoms[i][j])) + " "
else:
line += str(atoms[i][j]) + " "
print >>f,line
print(line,file=f)
f.close()
print "\n%d snapshots" % self.nselect
print("\n%d snapshots" % self.nselect)
# --------------------------------------------------------------------
# find min/max across all selected snapshots/atoms for a particular column
@ -688,7 +692,7 @@ class dump:
for snap in self.snaps:
if not snap.tselect: continue
atoms = snap.atoms
for i in xrange(snap.natoms):
for i in range(snap.natoms):
if not snap.aselect[i]: continue
if atoms[i][icol] < min: min = atoms[i][icol]
if atoms[i][icol] > max: max = atoms[i][icol]
@ -698,7 +702,7 @@ class dump:
# set a column value via an equation for all selected snapshots
def set(self,eq):
print "Setting ..."
print("Setting ...")
pattern = "\$\w*"
list = re.findall(pattern,eq)
@ -715,14 +719,14 @@ class dump:
for snap in self.snaps:
if not snap.tselect: continue
for i in xrange(snap.natoms):
if snap.aselect[i]: exec ceq
for i in range(snap.natoms):
if snap.aselect[i]: exec(ceq)
# --------------------------------------------------------------------
# set a column value via an input vec for all selected snapshots/atoms
def setv(self,colname,vec):
print "Setting ..."
print("Setting ...")
if not self.names.has_key(colname):
self.newcolumn(colname)
icol = self.names[colname]
@ -730,10 +734,10 @@ class dump:
for snap in self.snaps:
if not snap.tselect: continue
if snap.nselect != len(vec):
raise StandardError,"vec length does not match # of selected atoms"
raise StandardError("vec length does not match # of selected atoms")
atoms = snap.atoms
m = 0
for i in xrange(snap.natoms):
for i in range(snap.natoms):
if snap.aselect[i]:
atoms[i][icol] = vec[m]
m += 1
@ -746,12 +750,12 @@ class dump:
icol = self.names[col]
id = self.names["id"]
ids = {}
for i in xrange(self.snaps[istep].natoms):
for i in range(self.snaps[istep].natoms):
ids[self.snaps[istep].atoms[i][id]] = i
for snap in self.snaps:
if not snap.tselect: continue
atoms = snap.atoms
for i in xrange(snap.natoms):
for i in range(snap.natoms):
if not snap.aselect[i]: continue
j = ids[atoms[i][id]]
atoms[i][icol] = self.snaps[istep].atoms[j][icol]
@ -765,14 +769,14 @@ class dump:
inew = self.names[new]
min,max = self.minmax(old)
print "min/max = ",min,max
print("min/max = ",min,max)
gap = max - min
invdelta = n/gap
for snap in self.snaps:
if not snap.tselect: continue
atoms = snap.atoms
for i in xrange(snap.natoms):
for i in range(snap.natoms):
if not snap.aselect[i]: continue
ivalue = int((atoms[i][iold] - min) * invdelta) + 1
if ivalue > n: ivalue = n
@ -796,7 +800,7 @@ class dump:
def atom(self,n,*list):
if len(list) == 0:
raise StandardError, "no columns specified"
raise StandardError("no columns specified")
columns = []
values = []
for name in list:
@ -809,11 +813,11 @@ class dump:
for snap in self.snaps:
if not snap.tselect: continue
atoms = snap.atoms
for i in xrange(snap.natoms):
for i in range(snap.natoms):
if atoms[i][id] == n: break
if atoms[i][id] != n:
raise StandardError, "could not find atom ID in snapshot"
for j in xrange(ncol):
raise StandardError("could not find atom ID in snapshot")
for j in range(ncol):
values[j][m] = atoms[i][columns[j]]
m += 1
@ -827,7 +831,7 @@ class dump:
snap = self.snaps[self.findtime(n)]
if len(list) == 0:
raise StandardError, "no columns specified"
raise StandardError("no columns specified")
columns = []
values = []
for name in list:
@ -836,9 +840,9 @@ class dump:
ncol = len(columns)
m = 0
for i in xrange(snap.natoms):
for i in range(snap.natoms):
if not snap.aselect[i]: continue
for j in xrange(ncol):
for j in range(ncol):
values[j][m] = snap.atoms[i][columns[j]]
m += 1
@ -887,7 +891,7 @@ class dump:
def iterator(self,flag):
start = 0
if flag: start = self.iterate + 1
for i in xrange(start,self.nsnaps):
for i in range(start,self.nsnaps):
if self.snaps[i].tselect:
self.iterate = i
return i,self.snaps[i].time,1
@ -912,7 +916,7 @@ class dump:
# need Numeric/Numpy mode here
atoms = []
for i in xrange(snap.natoms):
for i in range(snap.natoms):
if not snap.aselect[i]: continue
atom = snap.atoms[i]
atoms.append([atom[id],atom[type],atom[x],atom[y],atom[z]])
@ -927,7 +931,7 @@ class dump:
bonds = []
if self.bondflag:
alist = {}
for i in xrange(len(atoms)): alist[int(atoms[i][0])] = i
for i in range(len(atoms)): alist[int(atoms[i][0])] = i
for bond in self.bondlist:
try:
i = alist[bond[2]]
@ -953,9 +957,9 @@ class dump:
# --------------------------------------------------------------------
def findtime(self,n):
for i in xrange(self.nsnaps):
for i in range(self.nsnaps):
if self.snaps[i].time == n: return i
raise StandardError, "no step %d exists" % n
raise StandardError("no step %d exists" % n)
# --------------------------------------------------------------------
# return maximum box size across all selected snapshots
@ -982,7 +986,7 @@ class dump:
for snap in self.snaps:
if not snap.tselect: continue
atoms = snap.atoms
for i in xrange(snap.natoms):
for i in range(snap.natoms):
if not snap.aselect[i]: continue
if atoms[i][icol] > max: max = atoms[i][icol]
return int(max)
@ -1004,11 +1008,11 @@ class dump:
nbonds = int(f.readline())
item = f.readline()
if not re.search("BONDS",item):
raise StandardError, "could not read bonds from dump file"
raise StandardError("could not read bonds from dump file")
words = f.readline().split()
ncol = len(words)
for i in xrange(1,nbonds):
for i in range(1,nbonds):
words += f.readline().split()
f.close()
@ -1019,7 +1023,7 @@ class dump:
ints = [abs(int(value)) for value in words]
start = 0
stop = 4
for i in xrange(nbonds):
for i in range(nbonds):
bondlist[i] = ints[start:stop]
start += ncol
stop += ncol
@ -1027,7 +1031,7 @@ class dump:
self.bondflag = 1
self.bondlist = bondlist
except:
raise StandardError,"could not read from bond dump file"
raise StandardError("could not read from bond dump file")
# request bonds from data object
@ -1043,7 +1047,7 @@ class dump:
self.bondflag = 1
self.bondlist = bondlist
except:
raise StandardError,"could not extract bonds from data object"
raise StandardError("could not extract bonds from data object")
# request tris/lines from cdata object
@ -1057,7 +1061,7 @@ class dump:
self.lineflag = 1
self.linelist = lines
except:
raise StandardError,"could not extract tris/lines from cdata object"
raise StandardError("could not extract tris/lines from cdata object")
# request tris from mdump object
@ -1066,10 +1070,10 @@ class dump:
self.triflag = 2
self.triobj = arg
except:
raise StandardError,"could not extract tris from mdump object"
raise StandardError("could not extract tris from mdump object")
else:
raise StandardError,"unrecognized argument to dump.extra()"
raise StandardError("unrecognized argument to dump.extra()")
# --------------------------------------------------------------------
@ -1103,7 +1107,7 @@ class tselect:
snap.tselect = 1
data.nselect = len(data.snaps)
data.aselect.all()
print "%d snapshots selected out of %d" % (data.nselect,data.nsnaps)
print("%d snapshots selected out of %d" % (data.nselect,data.nsnaps))
# --------------------------------------------------------------------
@ -1115,7 +1119,7 @@ class tselect:
data.snaps[i].tselect = 1
data.nselect = 1
data.aselect.all()
print "%d snapshots selected out of %d" % (data.nselect,data.nsnaps)
print("%d snapshots selected out of %d" % (data.nselect,data.nsnaps))
# --------------------------------------------------------------------
@ -1124,7 +1128,7 @@ class tselect:
for snap in data.snaps:
snap.tselect = 0
data.nselect = 0
print "%d snapshots selected out of %d" % (data.nselect,data.nsnaps)
print("%d snapshots selected out of %d" % (data.nselect,data.nsnaps))
# --------------------------------------------------------------------
@ -1140,7 +1144,7 @@ class tselect:
snap.tselect = 0
data.nselect -= 1
data.aselect.all()
print "%d snapshots selected out of %d" % (data.nselect,data.nsnaps)
print("%d snapshots selected out of %d" % (data.nselect,data.nsnaps))
# --------------------------------------------------------------------
@ -1149,14 +1153,14 @@ class tselect:
snaps = data.snaps
cmd = "flag = " + teststr.replace("$t","snaps[i].time")
ccmd = compile(cmd,'','single')
for i in xrange(data.nsnaps):
for i in range(data.nsnaps):
if not snaps[i].tselect: continue
exec ccmd
exec(ccmd)
if not flag:
snaps[i].tselect = 0
data.nselect -= 1
data.aselect.all()
print "%d snapshots selected out of %d" % (data.nselect,data.nsnaps)
print("%d snapshots selected out of %d" % (data.nselect,data.nsnaps))
# --------------------------------------------------------------------
# atom selection class
@ -1173,12 +1177,12 @@ class aselect:
if len(args) == 0: # all selected timesteps
for snap in data.snaps:
if not snap.tselect: continue
for i in xrange(snap.natoms): snap.aselect[i] = 1
for i in range(snap.natoms): snap.aselect[i] = 1
snap.nselect = snap.natoms
else: # one timestep
n = data.findtime(args[0])
snap = data.snaps[n]
for i in xrange(snap.natoms): snap.aselect[i] = 1
for i in range(snap.natoms): snap.aselect[i] = 1
snap.nselect = snap.natoms
# --------------------------------------------------------------------
@ -1201,29 +1205,29 @@ class aselect:
if len(args) == 0: # all selected timesteps
for snap in data.snaps:
if not snap.tselect: continue
for i in xrange(snap.natoms):
for i in range(snap.natoms):
if not snap.aselect[i]: continue
exec ccmd
exec(ccmd)
if not flag:
snap.aselect[i] = 0
snap.nselect -= 1
for i in xrange(data.nsnaps):
for i in range(data.nsnaps):
if data.snaps[i].tselect:
print "%d atoms of %d selected in first step %d" % \
(data.snaps[i].nselect,data.snaps[i].natoms,data.snaps[i].time)
print("%d atoms of %d selected in first step %d" % \
(data.snaps[i].nselect,data.snaps[i].natoms,data.snaps[i].time))
break
for i in xrange(data.nsnaps-1,-1,-1):
for i in range(data.nsnaps-1,-1,-1):
if data.snaps[i].tselect:
print "%d atoms of %d selected in last step %d" % \
(data.snaps[i].nselect,data.snaps[i].natoms,data.snaps[i].time)
print("%d atoms of %d selected in last step %d" % \
(data.snaps[i].nselect,data.snaps[i].natoms,data.snaps[i].time))
break
else: # one timestep
n = data.findtime(args[0])
snap = data.snaps[n]
for i in xrange(snap.natoms):
for i in range(snap.natoms):
if not snap.aselect[i]: continue
exec ccmd
exec(ccmd)
if not flag:
snap.aselect[i] = 0
snap.nselect -= 1