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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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116
src/patch.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.
# patch tool
@ -13,10 +13,10 @@ oneline = "Create patchy Lennard-Jones particles for LAMMPS input"
docstr = """
p = patch(vfrac) setup box with a specified volume fraction
p = patch(vfrac,1,1,2) x,y,z = aspect ratio of box (def = 1,1,1)
p.seed = 48379 set random # seed (def = 12345)
p.randomized = 0 1 = choose next particle randomly, 0 = as generated
p.dim = 2 set dimension of created box (def = 3)
p.seed = 48379 set random # seed (def = 12345)
p.randomized = 0 1 = choose next particle randomly, 0 = as generated
p.dim = 2 set dimension of created box (def = 3)
p.blen = 0.97 set length of tether bonds (def = 0.97)
p.dmin = 1.02 set min r from i-1 to i+1 tether site (def = 1.02)
p.lattice = [Nx,Ny,Nz] generate Nx by Ny by Nz lattice of particles
@ -25,7 +25,7 @@ p.lattice = [Nx,Ny,Nz] generate Nx by Ny by Nz lattice of particles
lattice = [0,0,0] = generate N particles randomly, default
p.build(100,"hex2",1,2,3) create 100 "hex2" particles with types 1,2,3
can be invoked multiple times
keywords:
c60hex2: diam,1,2,3 = C-60 with 2 hex patches and ctr part, types 1,2,3
@ -46,7 +46,7 @@ p.build(100,"hex2",1,2,3) create 100 "hex2" particles with types 1,2,3
from Alo to Ahi and Blo to Bhi, line type m
linetri: Alo,Ahi,Blo,Bhi,m = 3-line 2d triangle with random base
from Alo to Ahi and height Blo to Bhi, type m
p.write("data.patch") write out system to LAMMPS data file
"""
@ -69,7 +69,7 @@ from data import data
# Class definition
class patch:
# --------------------------------------------------------------------
def __init__(self,vfrac,*list):
@ -179,7 +179,7 @@ class patch:
#xp[0] = 1; xp[1] = 0; xp[2] = 0
#yp[0] = 0; yp[1] = 1; yp[2] = 0
#zp[0] = 0; zp[1] = 0; zp[2] = 1
# random origin or lattice site for new particle
if latflag == 0:
@ -195,15 +195,15 @@ class patch:
zorig = self.zlo + iz*self.zprd/self.lattice[2]
#xorig = 0; yorig = 0; zorig = 0
# unpack bonds in molecule before atoms so idatom = all previous atoms
for bond in molecule[1]:
idbond += 1
bonds.append([idbond,bond[0],bond[1]+idatom+1,bond[2]+idatom+1])
# unpack triples in molecule as displacements from associated atom
for triple in molecule[2]: triples.append(triple)
# unpack atoms in molecule
@ -223,7 +223,7 @@ class patch:
ix = iy = iz = 0
x,y,z,ix,iy,iz = self.pbc(x,y,z,ix,iy,iz)
atoms.append([idatom,idmol,atom[0],x,y,z,ix,iy,iz])
elif self.style == "tri":
for i,atom in enumerate(molecule[0]):
idatom += 1
@ -239,7 +239,7 @@ class patch:
if not triples: triflag = 0
else: triflag = 1
atoms.append([idatom,idmol,atom[0],triflag,mass,x,y,z,ix,iy,iz])
if triflag:
triple = triples[i]
xtri = triple[0]
@ -272,7 +272,7 @@ class patch:
list = [atom[2] for atom in atoms]
atypes = max(list)
d = data()
d.title = "LAMMPS data file for Nanoparticles"
d.headers["atoms"] = len(atoms)
@ -345,7 +345,7 @@ class patch:
if self.lattice[0]*self.lattice[1] != len(self.molecules):
raise StandardError,"lattice inconsistent with # of molecules"
else: latflag = 0
idatom = idbond = idmol = 0
atoms = []
bonds = []
@ -357,10 +357,10 @@ class patch:
if self.randomized: i = int(self.random()*len(self.molecules))
else: i = 0
molecule = self.molecules.pop(i)
idmol += 1
segments = []
# xp[2],yp[2] = randomly oriented, normalized basis vectors
# xp is in random direction
# yp is (0,0,1) crossed into xp
@ -387,15 +387,15 @@ class patch:
xorig = self.xlo + ix*self.xprd/self.lattice[0]
yorig = self.ylo + iy*self.yprd/self.lattice[1]
zorig = 0.0
# unpack bonds in molecule before atoms so idatom = all previous atoms
for bond in molecule[1]:
idbond += 1
bonds.append([idbond,bond[0],bond[1]+idatom+1,bond[2]+idatom+1])
# unpack segments in molecule as displacements from associated atom
for segment in molecule[3]: segments.append(segment)
# unpack atoms in molecule
@ -445,7 +445,7 @@ class patch:
segment[2],segment[3],tmp = \
self.pbc_near(segment[2],segment[3],0,x,y,z)
lines.append([idatom] + segment)
# create the data file
list = [atom[2] for atom in atoms]
@ -464,7 +464,7 @@ class patch:
d.headers["zlo zhi"] = (self.zlo,self.zhi)
# atoms section of data file
records = []
if self.style == "molecular":
for atom in atoms:
@ -502,7 +502,7 @@ class patch:
# --------------------------------------------------------------------
# adjust x,y,z to be inside periodic box
def pbc(self,x,y,z,ix,iy,iz):
if x < self.xlo:
x += self.xprd
@ -526,7 +526,7 @@ class patch:
# --------------------------------------------------------------------
# adjust xnew,ynew,znew to be near x,y,z in periodic sense
def pbc_near(self,xnew,ynew,znew,x,y,z):
if x-xnew > 0.5*self.xprd: xnew += self.xprd
elif xnew-x > 0.5*self.xprd: xnew -= self.xprd
@ -540,7 +540,7 @@ class patch:
# params = diam,type1,type2,type3
# type1 = type of non-patch atoms, type2 = type of patch atoms
# type3 = type of center-of-sphere atom
def c60hex2(self,*params):
template = BUCKY_60
diam = params[0]
@ -549,19 +549,19 @@ class patch:
atoms = make_sphere(template,diam,params[1],patches)
volume = 4.0/3.0 * pi * diam*diam*diam/8
return atoms,[],[],[],volume
# --------------------------------------------------------------------
# params = diam,type1,type2
# type1 = type of large center atom, type2 = type of hex patch atoms
def hex2(self,*params):
diam = params[0]
type1 = params[1]
type2 = params[2]
atoms = []
atoms.append([type1,0.0,0.0,0.0])
atoms.append(atom_on_sphere(diam,type2,0.5*diam,0.0,0.0))
atoms.append(atom_on_sphere(diam,type2,0.5*diam,1.0,0.0))
atoms.append(atom_on_sphere(diam,type2,0.5*diam,-1.0,0.0))
@ -580,19 +580,19 @@ class patch:
volume = 4.0/3.0 * pi * diam*diam*diam/8
return atoms,[],[],[],volume
# --------------------------------------------------------------------
# params = diam,type1,type2
# type1 = type of large center atom, type2 = type of hex patch atoms
def hex4(self,*params):
diam = params[0]
type1 = params[1]
type2 = params[2]
atoms = []
atoms.append([type1,0.0,0.0,0.0])
atoms.append(atom_on_sphere(diam,type2,0.5*diam,0.0,0.0))
atoms.append(atom_on_sphere(diam,type2,0.5*diam,1.0,0.0))
atoms.append(atom_on_sphere(diam,type2,0.5*diam,-1.0,0.0))
@ -632,13 +632,13 @@ class patch:
# params = diam,nring,type1,type2
# nring = # of particles in ring
# type1 = type of large center atom, type2 = type of ring atoms
def ring(self,*params):
diam = params[0]
nring = params[1]
type1 = params[2]
type2 = params[3]
atoms = []
atoms.append([type1,0.0,0.0,0.0])
@ -655,7 +655,7 @@ class patch:
# m12,m12type = length of tethers on each side of ball (m12 = 0 = no tether)
# set three types of bonds:
# 1 = big to small, 2 = small to small, 3 = across two tethers
def ball(self,*params):
diam = params[0]
m1 = params[1]
@ -684,14 +684,14 @@ class patch:
if i == 0: bonds.append([1,0,1+m1])
else: bonds.append([2,1+m1+i-1,1+m1+i])
if m1 and m2: bonds.append([3,1,m1+1])
volume = 4.0/3.0 * pi * diam*diam*diam/8 + (m1+m2)*pi/6.0
return atoms,bonds,[],[],volume
# --------------------------------------------------------------------
# params = type1,type2
# type1 = type of 1/3 layers, type2 = type of middle layer
def tri5(self,*params):
template = TRI5_HOLLOW
nlayer = 3
@ -724,12 +724,12 @@ class patch:
ntype = params[3]
m1type = params[4]
m2type = params[5]
atoms = []
for i in range(n):
x,y,z = i*self.blen,0.0,0.0
atoms.append([ntype,x,y,z])
if m1: atoms += tether(m1,m1type,self.blen,self.dmin,
atoms[n-2],atoms[n-1],self.random)
if m2: atoms += tether(m2,m2type,self.blen,self.dmin,
@ -742,7 +742,7 @@ class patch:
for i in range(m2):
if i == 0: bonds.append([1,0,n+m1])
else: bonds.append([1,n+m1+i-1,n+m1+i])
volume = (n+m1+m2) * pi / 6.0
return atoms,bonds,[],[],volume
@ -750,7 +750,7 @@ class patch:
# params = nsize,m1,m2,m3,ntype,m1type,m2type,m3type
# nsize,ntype = size,type of triangle center
# m123,m123type = length of tethers on each corner (m123 = 0 = no tether)
def tri(self,*params):
nsize = params[0]
m1 = params[1]
@ -760,7 +760,7 @@ class patch:
m1type = params[5]
m2type = params[6]
m3type = params[7]
atoms = []
for i in range(nsize):
n = nsize - i
@ -794,7 +794,7 @@ class patch:
# params = m1,m2,m3,m4,m5,m6,ntype,m1type,m2type,m3type,m4type,m5type,m6type
# ntype = type of hex center
# m123456,m123456type = length of tethers on each corner (m = 0 = no tether)
def hex(self,*params):
m1 = params[0]
m2 = params[1]
@ -809,7 +809,7 @@ class patch:
m4type = params[10]
m5type = params[11]
m6type = params[12]
atoms = []
atoms.append([ntype,0.0,0.0,0.0])
atoms.append([ntype,self.blen,0.0,0.0])
@ -818,7 +818,7 @@ class patch:
atoms.append([ntype,-self.blen/2.0,self.blen*sqrt(3.0)/2.0,0.0])
atoms.append([ntype,self.blen/2.0,-self.blen*sqrt(3.0)/2.0,0.0])
atoms.append([ntype,-self.blen/2.0,-self.blen*sqrt(3.0)/2.0,0.0])
n = len(atoms)
if m1: atoms += tether(m1,m1type,self.blen,self.dmin,
atoms[0],atoms[1],self.random)
@ -864,7 +864,7 @@ class patch:
def dimer(self,*params):
sep = params[0]
type = params[1]
atoms = []
x,y,z = 0.0,0.0,0.0
atoms.append([type,x,y,z])
@ -887,7 +887,7 @@ class patch:
if n % 2 == 0:
raise StandardError, "N in patch::star2d is not odd"
middle = n/2
atoms = []
x,y,z = 0.0,0.0,0.0
atoms.append([type,x,y,z])
@ -919,7 +919,7 @@ class patch:
height = (m-1) * sep
width = (n-1) * sep
atoms = []
for i in range(n):
x,y,z = i*sep,0.0,0.0
@ -941,7 +941,7 @@ class patch:
# params = a,type
# a = edge length of tet
# type = type of each vertex in tet
def tritet(self,*params):
a = params[0]
type = params[1]
@ -985,7 +985,7 @@ class patch:
# Blo to Bhi = bounds of edge length in y of box
# Clo to Chi = bounds of edge length in y of box
# type = type of each vertex in rectangular box
def tribox(self,*params):
alo = params[0]
ahi = params[1]
@ -994,7 +994,7 @@ class patch:
clo = params[4]
chi = params[5]
type = params[6]
a = alo + self.random()*(ahi-alo)
b = blo + self.random()*(bhi-blo)
c = clo + self.random()*(chi-clo)
@ -1063,7 +1063,7 @@ class patch:
# Alo to Ahi = bounds of edge length in x of rectangle
# Blo to Bhi = bounds of edge length in y of rectangle
# type = type of each line segment in rectangle
def linebox(self,*params):
alo = float(params[0])
ahi = float(params[1])
@ -1073,7 +1073,7 @@ class patch:
a = alo + self.random()*(ahi-alo)
b = blo + self.random()*(bhi-blo)
atoms = []
segments = []
@ -1099,7 +1099,7 @@ class patch:
# Alo to Ahi = bounds of base length in x of triangle
# Blo to Bhi = bounds of heigth in y of isosceles triangle
# type = type of each line segment in triangle
def linetri(self,*params):
alo = float(params[0])
ahi = float(params[1])
@ -1109,7 +1109,7 @@ class patch:
base = alo + self.random()*(ahi-alo)
ht = blo + self.random()*(bhi-blo)
atoms = []
segments = []
@ -1208,7 +1208,7 @@ TRI5_HOLLOW = ((0,0,0),(1,0,0),(2,0,0),(3,0,0),(4,0,0),
(1.0,2*sqrt(3)/2,0),(3.0,2*sqrt(3)/2,0),
(1.5,3*sqrt(3)/2,0),(2.5,3*sqrt(3)/2,0),
(2.0,4*sqrt(3)/2,0))
SIMPLE_7 = ((0,0,0),(1,0,0),(-1,0,0),(0,1,0),(0,-1,0),(0,0,1),(0,0,-1))
# C60 with added center point at end