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start porting some LAMMPS python module examples to python3 with compatibility to python2

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This commit is contained in:
Axel Kohlmeyer
2016-07-19 16:59:57 -04:00
parent ec9c9a235a
commit 21ea3ccfb7
18 changed files with 148 additions and 109 deletions
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72
python/examples/pizza/dump.py
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@ -179,6 +179,8 @@ d.extra(data) extract bond/tri/line list from data
# Imports and external programs
from __future__ import print_function
import sys, commands, re, glob, types
from os import popen
from math import * # any function could be used by set()
@ -324,7 +326,7 @@ 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 +372,14 @@ 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
@ -554,9 +556,9 @@ 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 +572,7 @@ 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
@ -602,7 +604,7 @@ 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)
# --------------------------------------------------------------------
@ -630,10 +632,10 @@ class dump:
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:
@ -666,10 +668,10 @@ class dump:
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:
@ -688,7 +690,7 @@ 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]
@ -715,7 +717,7 @@ class dump:
for snap in self.snaps:
if not snap.tselect: continue
for i in xrange(snap.natoms):
for i in range(snap.natoms):
if snap.aselect[i]: exec ceq
# --------------------------------------------------------------------
@ -733,7 +735,7 @@ class dump:
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 +748,12 @@ 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]
@ -772,7 +774,7 @@ 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
ivalue = int((atoms[i][iold] - min) * invdelta) + 1
if ivalue > n: ivalue = n
@ -809,11 +811,11 @@ 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):
for j in range(ncol):
values[j][m] = atoms[i][columns[j]]
m += 1
@ -836,9 +838,9 @@ 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 +889,7 @@ 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 +914,7 @@ 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 +929,7 @@ 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]]
@ -953,7 +955,7 @@ 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
@ -982,7 +984,7 @@ 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)
@ -1008,7 +1010,7 @@ class dump:
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 +1021,7 @@ 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
@ -1149,7 +1151,7 @@ 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
if not flag:
@ -1173,12 +1175,12 @@ 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
# --------------------------------------------------------------------
@ -1201,18 +1203,18 @@ 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
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)
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)
@ -1221,7 +1223,7 @@ class aselect:
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
if not flag:

10
python/examples/pizza/gnu.py
View File

@ -87,7 +87,7 @@ g.curve(N,'r') set color of curve N
import types, os
try: from DEFAULTS import PIZZA_GNUPLOT
except: PIZZA_GNUPLOT = "gnuplot"
except: PIZZA_GNUPLOT = "gnuplot -p"
try: from DEFAULTS import PIZZA_GNUTERM
except: PIZZA_GNUTERM = "x11"
@ -133,7 +133,7 @@ class gnu:
self.export(file,linear,vectors[0])
self.figures[self.current-1].ncurves = 1
else:
if len(vectors) % 2: raise StandardError,"vectors must come in pairs"
if len(vectors) % 2: raise StandardError("vectors must come in pairs")
for i in range(0,len(vectors),2):
file = self.file + ".%d.%d" % (self.current,i/2+1)
self.export(file,vectors[i],vectors[i+1])
@ -167,11 +167,11 @@ class gnu:
def export(self,filename,*vectors):
n = len(vectors[0])
for vector in vectors:
if len(vector) != n: raise StandardError,"vectors must be same length"
if len(vector) != n: raise StandardError("vectors must be same length")
f = open(filename,'w')
nvec = len(vectors)
for i in xrange(n):
for j in xrange(nvec):
for i in range(n):
for j in range(nvec):
print >>f,vectors[j][i],
print >>f
f.close()