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python 3 compatibility for src/*.py files

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move imports to top of files
add from __future__ import
commands module -> subprocesses module
print statement -> print() function
exec statement -> exec() function
xrange -> range
map() -> list(map())
StandardError -> Exception
integer division: / -> //
x.has_key(y) -> y in x
sort(): use functools.cmp_to_key
type(x) is y -> isinstance(x, y)
raw_input -> input
change variable names 'list' to avoid clashes with list class
This commit is contained in:
danielque
2023-08-10 13:19:02 +02:00
parent d560b34214
commit 597e606bde
34 changed files with 1463 additions and 1352 deletions
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25
src/chain.py
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@ -8,6 +8,12 @@
# chain tool
# Imports and external programs
from __future__ import print_function, division, absolute_import
import math
from data import data
oneline = "Create bead-spring chains for LAMMPS input"
docstr = """
@ -52,11 +58,6 @@ c.write("data.file") write out all built chains to LAMMPS data file
# xlo,ylo,zlo = -xyz prd / 2
# xhi,yhi,zhi = x,y,zprd /2
# Imports and external programs
import math
from data import data
# Class definition
class chain:
@ -92,12 +93,12 @@ class chain:
self.zlo = -self.zprd/2.0
self.zhi = self.zprd/2.0
print "Simulation box: %g by %g by %g" % (self.xprd,self.yprd,self.zprd)
print("Simulation box: %g by %g by %g" % (self.xprd,self.yprd,self.zprd))
# --------------------------------------------------------------------
def build(self,n,nper):
for ichain in xrange(n):
for ichain in range(n):
atoms = []
bonds = []
id_atom_prev = id_mol_prev = id_bond_prev = 0
@ -107,7 +108,7 @@ class chain:
if len(self.bonds):
id_bond_prev = self.bonds[-1][0]
for imonomer in xrange(nper):
for imonomer in range(nper):
if imonomer == 0:
x = self.xlo + self.random()*self.xprd
y = self.ylo + self.random()*self.yprd
@ -146,7 +147,7 @@ class chain:
if idmol > nper/2:
idmol = nper - imonomer
else:
raise StandardError,"chain ID is not a valid value"
raise Exception("chain ID is not a valid value")
atoms.append([idatom,idmol,self.mtype,x,y,z,ix,iy,iz])
if imonomer:
@ -160,8 +161,8 @@ class chain:
def write(self,file):
if len(self.atoms) != self.n:
raise StandardError,"%d monomers instead of requested %d" % \
(len(self.atoms),self.n)
raise Exception("%d monomers instead of requested %d" % \
(len(self.atoms),self.n))
list = [atom[2] for atom in self.atoms]
atypes = max(list)
@ -229,7 +230,7 @@ class chain:
# --------------------------------------------------------------------
def random(self):
k = self.seed/IQ
k = self.seed//IQ
self.seed = IA*(self.seed-k*IQ) - IR*k
if self.seed < 0:
self.seed += IM