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convert tabs to spaces, remove extra spaces, fix comments

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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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28
src/chain.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.
# chain tool
@ -12,11 +12,11 @@ oneline = "Create bead-spring chains for LAMMPS input"
docstr = """
c = chain(N,rho) setup box with N monomers at reduced density rho
c = chain(N,rho,1,1,2) x,y,z = aspect ratio of box (def = 1,1,1)
c = chain(N,rho,1,1,2) x,y,z = aspect ratio of box (def = 1,1,1)
c.seed = 48379 set random # seed (def = 12345)
c.mtype = 2 set type of monomers (def = 1)
c.btype = 1 set type of bonds (def = 1)
c.mtype = 2 set type of monomers (def = 1)
c.btype = 1 set type of bonds (def = 1)
c.blen = 0.97 set length of bonds (def = 0.97)
c.dmin = 1.02 set min dist from i-1 to i+1 site (def = 1.02)
@ -24,11 +24,11 @@ c.id = "chain" set molecule ID to chain # (default)
c.id = "end1" set molecule ID to count from one end of chain
c.id = "end2" set molecule ID to count from either end of chain
c.build(100,10) create 100 chains, each of length 10
c.build(100,10) create 100 chains, each of length 10
can be invoked multiple times interleaved with different settings
must fill box with total of N monomers
c.write("data.file") write out all built chains to LAMMPS data file
"""
@ -60,7 +60,7 @@ from data import data
# Class definition
class chain:
# --------------------------------------------------------------------
def __init__(self,n,rhostar,*list):
@ -112,7 +112,7 @@ class chain:
x = self.xlo + self.random()*self.xprd
y = self.ylo + self.random()*self.yprd
z = self.zlo + self.random()*self.zprd
ix = iy = iz = 0
ix = iy = iz = 0
else:
restriction = True
while restriction:
@ -134,7 +134,7 @@ class chain:
dz = z - atoms[-2][5]
if math.sqrt(dx*dx + dy*dy + dz*dz) <= self.dmin:
restriction = True
x,y,z,ix,iy,iz = self.pbc(x,y,z,ix,iy,iz)
idatom = id_atom_prev + imonomer + 1
if self.id == "chain":
@ -147,12 +147,12 @@ class chain:
idmol = nper - imonomer
else:
raise StandardError,"chain ID is not a valid value"
atoms.append([idatom,idmol,self.mtype,x,y,z,ix,iy,iz])
if imonomer:
bondid = id_bond_prev + imonomer
bondid = id_bond_prev + imonomer
bonds.append([bondid,self.btype,idatom-1,idatom])
self.atoms += atoms
self.bonds += bonds
@ -186,7 +186,7 @@ class chain:
lines = []
for i in range(atypes): lines.append("%d 1.0\n" % (i+1))
d.sections["Masses"] = lines
lines = []
for atom in self.atoms:
line = "%d %d %d %g %g %g %d %d %d\n" % \
@ -194,7 +194,7 @@ class chain:
atom[6], atom[7], atom[8])
lines.append(line)
d.sections["Atoms"] = lines
lines = []
for bond in self.bonds:
line = "%d %d %d %d\n" % (bond[0], bond[1], bond[2], bond[3])