def load(fullfilename):
#TODO move this splitting to within Material so the extension can
#automatically be the default prefix...then move it into structure
filedir, fileprefix, fileext = path_split(fullfilename)
from vimm.Material import Material
from vimm.Atom import Atom
from vimm.Cell import Cell
material = Material(fileprefix)
material.format = fileext
pkl_file = open(fullfilename, 'rb')
structure = pickle.load(pkl_file)
first_run = 1
if first_run:
first_run = 0
else:
material.new_geo()
for structureAtom in structure:
material.add_atom(Atom(structureAtom.Z, structureAtom.xyz_cartn))
aVec, bVec, cVec = structure.lattice.base
cell = Cell(aVec, bVec, cVec)
material.set_cell(cell)
material.bonds_from_distance()
return material
def load(fullfilename):
filedir, fileprefix, fileext = path_split(fullfilename)
material = Material(fileprefix)
file = open(fullfilename, 'r')
line = file.readline()
title = line.strip()
line = file.readline()
title2 = line.strip()
line = file.readline()
title3 = line.strip()
line = file.readline()
natoms = int(line[:3])
nbonds = int(line[3:6])
# Note: I'm skipping the H information here, which is
# typically given in fields 5-
for i in range(natoms):
line = file.readline()
words = line.split()
xyz = array(map(float, words[:3]))
sym = cleansym(words[3])
atno = sym2no[sym]
material.add_atom(Atom(atno, xyz, sym, sym + str(i)))
atoms = material.get_atoms()
for i in range(nbonds):
line = file.readline()
words = line.split()
# bond order is the third field, which I'm ignoring
iat, jat, iorder = map(int, words[:3])
material.add_bond(Bond(atoms[iat - 1], atoms[jat - 1], iorder))
return material
def load(fullfilename):
filedir, fileprefix, fileext = path_split(fullfilename)
material=Material(fileprefix)
file=open(fullfilename, 'r')
first_run = 1
while 1:
line = file.readline()
if not line: break
words = line.split()
nat = int(words[0])
comment = file.readline()
if first_run:
first_run = 0
else:
material.new_geo()
for i in range(nat):
line = file.readline()
words=line.split()
sym=cleansym(words[0])
atno = sym2no[sym]
xyz = array(map(float,words[1:4]))
material.add_atom(Atom(atno, xyz, sym, sym+str(i)))
material.bonds_from_distance()
return material
def load(fullfilename):
filedir, fileprefix, fileext = path_split(fullfilename)
material = Material(fileprefix)
file = open(fullfilename, 'r')
atoms = []
bfs = []
orbs = []
mode = None
for line in file.readlines():
if atpat.search(line): mode = 'atoms'
elif bfpat.search(line): mode = 'bfs'
elif orbpat.search(line): mode = 'orbs'
elif mode == 'atoms': atoms.append(line)
elif mode == 'bfs': bfs.append(line)
elif mode == 'orbs': orbs.append(line)
else: print '? ', line,
for line in atoms:
words = line.split()
if len(words) < 6: continue
atno = int(words[2])
xyz = map(float, words[3:6])
material.add_atom(Atom(atno, array(xyz)))
material.bonds_from_distance()
material.geo.basis = parse_basis(bfs)
material.geo.orbs = parse_orbs(orbs)
return material
def load(fullfilename):
filedir, fileprefix, fileext = path_split(fullfilename)
material = Material(fileprefix)
file = open(fullfilename, 'r')
nwchem_options = {}
geo_pat = re.compile("\s*No\.\s*Tag\s*Charge")
molchg_pat = re.compile("\s*Charge\s*:\s*")
multip_pat = re.compile("\s*Spin multiplicity:\s*")
geos = []
while 1:
line = file.readline()
if not line: break
if geo_pat.search(line):
geo = get_geo(file)
geos.append(geo)
elif molchg_pat.search(line):
words = string.split(line)
nwchem_options['molchg'] = int(words[2])
elif multip_pat.search(line):
words = string.split(line)
nwchem_options['multip'] = int(words[2])
# end of main infinite loop
file.close()
print "Loading %d geometries" % len(geos)
for igeo in range(len(geos)):
if igeo: material.new_geo()
for (atno, xyz) in geos[igeo]:
material.add_atom(Atom(atno, xyz))
if len(material.geo.atoms) < 200: material.bonds_from_distance()
material.nwchem_options = nwchem_options
return material
def add_the_unit_cell(material, buffer):
name = material.get_name()
cell = material.get_cell()
atoms = material.get_atom_list()
if cell: return material # Don't do anything for now
newname = "%s_cell" % name
newmaterial = Material(newname)
if not buffer: buffer = 2. # Can still set to a small value like 0.01
xmin, xmax, ymin, ymax, zmin, zmax = bbox_atoms(atoms, buffer)
for atom in atoms:
atno = atom.get_atno()
xyz = atom.get_position()
xyznew = array((xyz[0] - xmin, xyz[1] - ymin, xyz[2] - zmin))
newmaterial.add_atom(Atom(atno, xyznew))
newmaterial.set_cell(
Cell((xmax - xmin, 0, 0), (0, ymax - ymin, 0), (0, 0, zmax - zmin)))
opts = getattr(material, "seqquest_options", {})
if opts: newmaterial.seqquest_options = opts.copy()
opts = getattr(material, "socorro_options", {})
if opts: newmaterial.socorro_options = opts.copy()
newmaterial.bonds_from_distance()
return newmaterial
def load(fullfilename):
filedir, fileprefix, fileext = path_split(fullfilename)
material=Material(fileprefix)
file=open(fullfilename, 'r')
first_run = 1
while 1:
line = file.readline()
if not line: break
if not geostart.search(line): continue
if first_run:
first_run = 0
else:
material.new_geo()
i = 1
while 1:
line = file.readline()
if geoend.search(line): break
match = atpat.match(line)
sym = match.group(1)
x = float(match.group(2))
y = float(match.group(3))
z = float(match.group(4))
sym=cleansym(sym)
atno = sym2no[sym]
xyz = array((x,y,z))
material.add_atom(Atom(atno, xyz, sym, sym+str(i)))
i += 1
material.bonds_from_distance()
return material
def load(fullfilename):
filedir, fileprefix, fileext = path_split(fullfilename)
material = Material(fileprefix)
file = open(fullfilename, 'r')
line = file.readline()
title = line.strip()
line = file.readline()
natoms, nbonds = map(int, line.split())
for i in range(natoms):
line = file.readline()
words = line.split()
xyz = array(map(float, words[:3]))
sym = cleansym(words[3])
atno = sym2no[sym]
material.add_atom(Atom(atno, xyz, sym, sym + str(i)))
atoms = material.get_atoms()
for i in range(nbonds):
line = file.readline()
words = line.split()
# I think order is the third one, but I'm not sure
iat, jat, iorder = map(int, words[:3])
material.add_bond(Bond(atoms[iat - 1], atoms[jat - 1], iorder))
return material
def load(fullfilename):
filedir, fileprefix, fileext = path_split(fullfilename)
material = Material(fileprefix)
file = open(fullfilename, 'r')
first_run = True
while 1:
line = file.readline()
if not line: break
words = line.split()
nat = int(words[0])
comment = file.readline()
ax, ay, az, bx, by, bz, cx, cy, cz = [
float(i) for i in comment.split()
]
cell = Cell((ax, ay, az), (bx, by, bz), (cx, cy, cz))
if first_run:
first_run = False
else:
material.new_geo()
material.set_cell(cell)
for i in range(nat):
line = file.readline()
words = line.split()
sym = cleansym(words[0])
atno = sym2no[sym]
xyz = array(map(float, words[1:4]))
material.add_atom(Atom(atno, xyz, sym, sym + str(i)))
material.bonds_from_distance()
return material
def build_the_alkane(n):
atoms = alkanebuilder(n)
if not n: n = 1
nc = 2 * n + 2
nh = 2 * nc + 2
material = Material("C%dH%d" % (nc, nh))
for atno, xyz in atoms:
material.add_atom(Atom(atno, xyz))
material.bonds_from_distance()
return material
def build_the_crystal(crystal_type, sym1, sym2, a, c_a):
uc, atoms = builders[crystal_type](a, c_a, sym1, sym2)
material = Material(crystal_type.replace(' ', '_'))
for sym, (x, y, z) in atoms:
atno = sym2no[sym]
material.add_atom(Atom(atno, array((x, y, z))))
cell = Cell(uc[0], uc[1], uc[2])
material.set_cell(cell)
material.bonds_from_distance()
return material
def build_the_crystal_from_db(crystal_type):
uc, atoms = crystal_type_dict[crystal_type]
material = Material(crystal_type.replace(' ', '_'))
for sym, (x, y, z) in atoms:
atno = sym2no[sym]
material.add_atom(Atom(atno, array((x, y, z)), sym))
cell = Cell(uc[0], uc[1], uc[2])
material.set_cell(cell)
material.bonds_from_distance()
return material
def parse_cart(lines):
material = Material("vimm")
for line in lines:
words = line.split()
if not words: continue
sym = str(words[0])
atno = sym2no[sym]
xyz = array(map(float, words[1:4]))
material.add_atom(Atom(atno, xyz, sym, sym))
material.bonds_from_distance()
return material
def load(fullfilename):
filedir, fileprefix, fileext = path_split(fullfilename)
material=Material(fileprefix)
file=open(fullfilename, 'r')
hatpat = re.compile('HETATM')
atpat = re.compile('^ATOM')
conpat = re.compile('^CONECT')
ordpat = re.compile('^ORDER')
endpat = re.compile('^END')
ucpat = re.compile('^CRYSTX')
bonds = {}
orders = {}
iat = 0
for line in open(fullfilename):
if hatpat.search(line) or atpat.search(line):
d1,i,d2,d3,d4,d5,x,y,z,attype,d6,d7,q = read(line,atom_format)
xyz = array([x,y,z])
sym = cleansym(attype)
atno = sym2no[sym]
atom = Atom(atno,xyz,sym,sym+str(iat))
atom.fftype = attype # save just in case
material.add_atom(atom)
iat += 1
elif conpat.search(line):
ats = map(int,line[6:].split())
index = ats[0]-1
bonds[index] = [atj-1 for atj in ats[1:]]
orders[index] = [1]*(len(ats)-1)
elif ordpat.search(line):
ords = map(int,line[6:].split())
index = ords[0]-1
orders[index] = ords[1:]
elif ucpat.search(line):
words = line.split()
a,b,c,alpha,beta,gamma = map(float,words[1:7])
axyz,bxyz,cxyz = abcabg2abc(a,b,c,alpha,beta,gamma)
cell = Cell(axyz,bxyz,cxyz)
material.set_cell(cell)
atoms = material.get_atoms()
#print len(atoms)," atoms loaded"
for iat in bonds.keys():
bond_partners = bonds[iat]
bond_orders = orders[iat]
for jat,ij_order in zip(bond_partners,bond_orders):
if jat > iat: material.add_bond(Bond(atoms[iat],atoms[jat],
ij_order))
return material
def load(fullfilename):
filedir, fileprefix, fileext = path_split(fullfilename)
material=Material(fileprefix)
try:
from matter.Structure import Structure
st = Structure()
st.read(fullfilename)
for i,atom in enumerate(st):
Z = atom.Z
xyz_cartn = atom.xyz_cartn
sym = atom.symbol
material.add_atom(Atom(Z, xyz_cartn, sym, sym+str(i)))
material.bonds_from_distance()
lvs = st.lattice.base
cell = Cell(lvs[0],lvs[1],lvs[2])
material.set_cell(cell)
return material
except:
print 'Vimm needs matter package from pypi to open cif files'
return
def load(fullfilename):
filedir, fileprefix, fileext = path_split(fullfilename)
material = Material(fileprefix)
parser = CMLParser()
geos = parser.process(fullfilename)
molecule = geos[0]
atoms = molecule.atoms
cell = molecule.cell
nat = len(atoms)
for i in range(nat):
sym, pos = atoms[i]
pos = array(pos)
atno = sym2no[sym]
material.add_atom(Atom(atno, pos, sym, sym + str(i)))
if cell:
the_cell = Cell(cell[0], cell[1], cell[2])
material.set_cell(the_cell)
material.bonds_from_distance()
return material
def build_the_supercell(material, ass, bss, css):
if ass == 1 and bss == 1 and css == 1:
return material
name = material.get_name()
cell = material.get_cell()
atomlist = material.get_atom_list()
axyz = cell.axyz
bxyz = cell.bxyz
cxyz = cell.cxyz
newname = "%s%d%d%d" % (name, ass, bss, css)
newmaterial = Material(newname)
naxyz = ass * axyz
nbxyz = bss * bxyz
ncxyz = css * cxyz
for atom in atomlist:
atno = atom.get_atno()
sym = atom.get_symbol()
xyz = atom.get_position()
for i in range(ass):
for j in range(bss):
for k in range(css):
xyznew = xyz + i * axyz + j * bxyz + k * cxyz
newmaterial.add_atom(Atom(atno, xyznew, sym))
newmaterial.set_cell(Cell(naxyz, nbxyz, ncxyz))
opts = getattr(material, "seqquest_options", {})
if opts: newmaterial.seqquest_options = opts.copy()
opts = getattr(material, "socorro_options", {})
if opts: newmaterial.socorro_options = opts.copy()
newmaterial.bonds_from_distance()
return newmaterial
def load(fullfilename):
filedir, fileprefix, fileext = path_split(fullfilename)
material=Material(fileprefix)
curresnum = None
curres = None
locator = None
residues = []
for line in open(fullfilename):
tag = line[:6].strip()
if tag == 'ATOM' or tag == 'HETATM':
loctag = line[16:17].strip()
resnum = int(line[22:26])
modifyer = line[26].strip()
restag = line[18:21].strip()
x = float(line[30:38])
y = float(line[38:46])
z = float(line[46:54])
xyz = array([x,y,z])
try:
sym = line[13:15].strip()
sym = symconv[sym]
atno = sym2no[sym]
except:
sym = line[12:15].strip()
atno = sym2no[sym]
if loctag:
if not locator: locator = loctag
if loctag and loctag != locator: continue
if modifyer: continue # skip residue #25B if we already have #25
material.add_atom(Atom(atno,xyz))
elif tag == 'CRYST1':
words = line.split()
a,b,c,alpha,beta,gamma = map(float,words[1:7])
#finish
material.bonds_from_distance()
return material
def load(fullfilename,**kwargs):
# Keyword args
VERBOSE = kwargs.get('VERBOSE',False)
filedir, fileprefix, fileext = path_split(fullfilename)
material=Material(fileprefix)
# Pass 1: check ndtset
ndtset = 0
natom = 0
ntypat = 0
dt = 1
iter = abinit_tokenizer(open(fullfilename),**kwargs)
while 1:
try:
word = iter.next()
except:
break
if word == 'ndtset':
ndtset = int(iter.next())
if ndtset > 1:
print "Multiple data sets found. Reading only the first"
# If you want to select a particular data set, pop
# up a dialog box here and ask which one you
# want to load.
# Also need to put code in here so that you don't
# get the dialog box twice, such as dt_selected
# boolean
elif word == 'natom':
natom = int(iter.next())
elif word == 'ntypat':
ntypat = int(iter.next())
# Pass 2: get remaining info
xangst = None
xred = None
xcart = None
znucl = None
typat = None
rprim = None
acell = None
angdeg = None
iter = abinit_tokenizer(open(fullfilename),**kwargs)
while 1:
try:
word = iter.next()
except:
break
if word == 'xangst' or word == 'xangst%d' % dt:
xangst = get_natom3(iter,natom)
elif word == 'xred' or word == 'xred%d' % dt:
xred = get_natom3(iter,natom)
elif word == 'xcart' or word == 'xcart%d' % dt:
xcart = get_natom3(iter,natom)
elif word == 'znucl':
znucl = [int(float(i)) for i in nextn(iter,ntypat)]
elif word == 'typat':
typat = [int(i) for i in nextn(iter,natom)]
elif word == 'acell' or word == 'acell%d' % dt:
acell = [float(i) for i in nextn(iter,3)]
elif word == 'rprim' or word == 'rprim%d' % dt:
rprim = [float(i) for i in nextn(iter,9)]
elif word == 'angdeg' or word == 'angdeg%d' % dt:
angdeg = [float(i) for i in nextn(iter,3)]
# Done parsing
if VERBOSE:
print "natom = ",natom
print "ntypat = ",ntypat
print "znucl = ",znucl
print "typat = ",typat
print "xcart = ",xcart
print "xred = ",xred
print "xangst = ",xangst
print "acel = ",acell
print "rprim = ",rprim
print "angdeg = ",angdeg
# Build the unit cell. Precedence is rprim > angdeg
if not acell: acell = [1,1,1]
acell = [bohr2ang*i for i in acell] # Convert acell to Angstrom
if rprim:
ax,ay,az,bx,by,bz,cx,cy,cz = rprim
cell = Cell( (acell[0]*ax,acell[0]*ay,acell[0]*az),
(acell[1]*bx,acell[1]*by,acell[1]*bz),
(acell[2]*cx,acell[2]*cy,acell[2]*cz))
else:
if not angdeg:
angdeg = [90.,90.,90.]
axyz,bxyz,cxyz = abcabg2abc(acell[0],acell[1],acell[2],
angdeg[0],angdeg[1],angdeg[2])
cell = Cell(axyz,bxyz,cxyz)
material.set_cell(cell)
# Build the atom list. Precedence is xred > xangst > xcart
if xred:
A,B,C = cell.abc()
for i in range(natom):
atno = znucl[typat[i-1]-1]
xr,yr,zr = xred[i]
xyz = xr*A + yr*B + zr*C
material.add_atom(Atom(atno,xyz))
elif xangst:
for i in range(natom):
atno = znucl[typat[i-1]-1]
material.add_atom(Atom(atno,xangst[i]))
elif xcart:
for i in range(natom):
atno = znucl[typat[i-1]-1]
xyz = [bohr2ang*a for a in xcart[i]]
material.add_atom(Atom(atno,xyz))
else:
raise "Abinit Input: must specify xred, xangst, or xcart"
material.bonds_from_distance()
return material
def load(fullfilename):
filedir, fileprefix, fileext = path_split(fullfilename)
file = open(fullfilename, 'r')
# Initialize atom data
material = Material(fileprefix)
element = [] # Initialize element variable to be appended
timestamp = 1
nat = None
cell = None
lattice_coords = False
scale = 1.
scalez = 1.
conv_to_ang = True
while 1:
line = file.readline()
if not line: break
if p_atomtype.search(line):
# From the headerfile get the number of atom types
line = file.readline()
numberoftypes = int(line)
elif p_coord_type.search(line):
line = file.readline()
line = line.strip().lower()
if line == 'lattice':
lattice_coords = True
elif p_to_lattice.search(line):
raise "Quest to_lattice flags not currently supported"
elif p_scale.search(line):
line = file.readline()
scale = float(line.strip())
elif p_scalez.search(line):
line = file.readline()
scalez = float(line.strip())
# Using the atom type number, set the atom names
elif p_atomfile.search(line):
line = file.readline()
words = string.split(line)
atomname = cleansym(words[0]).capitalize()
#atomname,atomext = path.splitext(words[0])
#atomname = string.capitalize(atomname) # Captitalize the
element.append(atomname) # first letter
elif p_nat.search(line):
line = file.readline()
words = string.split(line)
nat = int(words[0])
# Read in the initial geometry data
elif p_geometry.search(line):
for i in range(nat):
line = file.readline()
words = string.split(line)
num = int(words[0])
try:
type = element[int(words[1]) - 1] #Set the type
atno = sym2no[type]
except:
# Fallback for when atoms are specified with symbols
atno = sym2no[words[1]]
x, y, z = [float(i) for i in words[2:5]]
#print x,y,z
if lattice_coords:
converter = cell.lat2cart_factory()
x, y, z = converter(x, y, z)
#print x,y,z
elif conv_to_ang:
x, y, z = [bohr2ang * i for i in [x, y, z]]
#print x,y,z
xyz = array((x, y, z))
material.add_atom(Atom(atno, xyz))
if cell: material.set_cell(cell)
elif p_newgeo.search(line):
comment = file.readline()
material.new_geo()
for i in range(nat):
line = file.readline()
words = string.split(line)
num = int(words[0])
try:
type = element[int(words[1]) - 1] #Set the type
atno = sym2no[type]
except:
# Fallback for when atoms are specified with symbols
atno = sym2no[words[1]]
x, y, z = [float(i) for i in words[2:5]]
#print x,y,z
if lattice_coords:
converter = cell.lat2cart_factory()
x, y, z = converter(x, y, z)
#print x,y,z
elif conv_to_ang:
x, y, z = [bohr2ang * i for i in [x, y, z]]
#print x,y,z
xyz = array((x, y, z))
material.add_atom(Atom(atno, xyz))
if cell: material.set_cell(cell)
elif p_cell.search(line):
line = file.readline()
words = string.split(line)
ax, ay, az = [float(i) for i in words[:3]]
if conv_to_ang:
ax, ay, az = [bohr2ang * i for i in [ax, ay, az]]
line = file.readline()
words = string.split(line)
bx, by, bz = [float(i) for i in words[:3]]
if conv_to_ang:
bx, by, bz = [bohr2ang * i for i in [bx, by, bz]]
line = file.readline()
words = string.split(line)
cx, cy, cz = [float(i) for i in words[:3]]
if conv_to_ang:
cx, cy, cz = [bohr2ang * i for i in [cx, cy, cz]]
cell = Cell((ax, ay, az), (bx, by, bz), (cx, cy, cz),
scale=scale,
scalez=scalez)
file.close()
material.bonds_from_distance()
return material
def parse_zmat(lines):
material = Material("vimm")
for line in lines:
words = line.split()
if len(words) == 0:
continue
sym = words[0]
if len(words) == 1:
# Atom at origin
x = y = z = 0
elif len(words) == 3:
# Atom along z-axis
x = y = 0
iat = int(words[1]) - 1
assert iat == 0
r = float(words[2])
z = r
elif len(words) == 4:
# This line contains a simple list of cartesian coordinates
x, y, z = map(float, words[1:])
elif len(words) == 5:
# Atom in xy-plane
y = 0
iat = int(words[1]) - 1
r = float(words[2])
jat = int(words[3]) - 1
theta = float(words[4]) * deg2rad
# Change this to simply use the numpy object:
x0, y0, z0 = material.get_atom(iat).get_xyz()
x = x0 + r * sin(theta)
if iat == 0:
z = z0 + r * cos(theta)
else:
z = z0 - r * cos(theta)
else:
# General case
iat = int(words[1]) - 1
r = float(words[2])
jat = int(words[3]) - 1
theta = float(words[4]) * deg2rad
kat = int(words[5]) - 1
phi = float(words[6]) * deg2rad
# Change these to simply use the numpy object:
xi, yi, zi = material.get_atom(iat).get_xyz()
xj, yj, zj = material.get_atom(jat).get_xyz()
xk, yk, zk = material.get_atom(kat).get_xyz()
# Change these to use numpy math:
# Vector from iat -> jat
xx = xj - xi
yy = yj - yi
zz = zj - zi
rinv = 1 / sqrt(xx * xx + yy * yy + zz * zz)
xa = xx * rinv
ya = yy * rinv
za = zz * rinv
# Vector from iat -> kat
xb = xk - xi
yb = yk - yi
zb = zk - zi
# Unit vector from iat -> kat
xc = ya * zb - za * yb
yc = za * xb - xa * zb
zc = xa * yb - ya * xb
rinv = 1 / sqrt(xc * xc + yc * yc + zc * zc)
xc *= rinv
yc *= rinv
zc *= rinv
xb = yc * za - zc * ya
yb = zc * xa - xc * za
zb = xc * ya - yc * xa
zz = r * cos(theta)
xx = r * sin(theta) * cos(phi)
yy = r * sin(theta) * sin(phi)
x = xi + xa * zz + xb * xx + xc * yy
y = yi + ya * zz + yb * xx + yc * yy
z = zi + za * zz + zb * xx + zc * yy
atno = sym2no[sym]
xyz = array([x, y, z])
material.add_atom(Atom(atno, xyz, sym, sym))
material.bonds_from_distance()
return material
def load(fullfilename):
filedir, fileprefix, fileext = path_split(fullfilename)
file = open(fullfilename, 'r')
# Initialize atom data
material = Material(fileprefix)
opts = {}
material.seqquest_options = opts
line = file.readline() # start reading
# Read in the run options
while 1:
if line[:8] == 'output l':
line = file.readline()
opts['lvlout'] = int(line.strip())
line = file.readline()
elif line[:8] == 'do setup':
opts['dosetup'] = True
line = file.readline()
elif line[:8] == 'no setup':
opts['dosetup'] = False
line = file.readline()
elif line[:8] == 'do iters':
opts['doiters'] = True
line = file.readline()
elif line[:8] == 'no iters':
opts['doiters'] = False
line = file.readline()
elif line[:8] == 'do force':
opts['doforce'] = True
line = file.readline()
elif line[:8] == 'no force':
opts['doforce'] = False
line = file.readline()
elif line[:8] == 'do relax':
opts['dorelax'] = True
line = file.readline()
elif line[:8] == 'no relax':
opts['dorelax'] = False
line = file.readline()
elif line[:7] == 'do cell':
opts['docell'] = True
line = file.readline()
elif line[:7] == 'no cell':
opts['docell'] = False
line = file.readline()
elif line[:6] == 'do neb':
opts['doneb'] = True
line = file.readline()
elif line[:6] == 'no neb':
opts['doneb'] = False
line = file.readline()
elif line[:5] == 'do md':
opts['domd'] = True
line = file.readline()
elif line[:5] == 'no md':
opts['domd'] = False
line = file.readline()
elif line[:7] == 'do post':
opts['dopost'] = True
line = file.readline()
elif line[:7] == 'no post':
opts['dopost'] = False
line = file.readline()
elif line[:7] == 'do blas':
opts['doblas3'] = True
line = file.readline()
elif line[:7] == 'no blas':
opts['doblas3'] = False
line = file.readline()
else:
# Comment this out when debugged:
print "Unknown line from command section"
print line,
print "Assuming end of Input Options Section"
break
# end of run options
# Beginning of setup info
if line[:6] == 'input ':
line = file.readline() # skip line
# Title
if line[:5] == 'title':
opts['title'] = []
try:
ntitl = int(line[5])
except:
ntitl = 1
for i in range(ntitl):
line = file.readline()
opts['title'].append(line.strip())
line = file.readline()
if line[:5] == 'scale':
line = file.readline()
opts['scalep'] = float(line.strip())
line = file.readline()
# DFT fcnal
if line[:6] == 'functi':
line = file.readline()
opts['dft_func'] = line.strip()
line = file.readline()
# Spin polarization
if line[:6] == 'spin p':
line = file.readline()
opts['spinpol'] = int(line.strip())
#should put an error condition here if dft requires
# spin and no spinpol input
line = file.readline()
# External electric field
if line[:6] == 'efield':
line = file.readline()
ex, ey, ez = map(float, line.split())
opts['efield'] = (ex, ey, ez) # in Ry/au
line = file.readline()
# External dielectric constant
if line[:6] == 'dielec':
line = file.readline()
opts['dielec'] = float(line.split())
line = file.readline()
# Problem dimension
if line[:6] == 'dimens' or line[:6] == 'lattic':
line = file.readline()
opts['ndim'] = int(line.strip())
line = file.readline()
else:
print line
raise "Dimension must be specified in Quest input"
# Coordinates (lattice or cartesian)
if line[:6] == 'coordi':
line = file.readline()
opts['coordi'] = line.strip()
line = file.readline()
# Problem scaling
# RPM: Need to do a better job of this:
#if line[:6] == 'scalep' or (line[:5] == 'scale' and len(line) == 5):
if line[:6] == 'scalep' or line[:6] == 'scale\n':
line = file.readline()
opts['scalep'] = float(line.strip())
line = file.readline()
if line[:6] == 'scaleu':
line = file.readline()
opts['scaleu'] = float(line.strip())
line = file.readline()
if line[:6] == 'scalex':
line = file.readline()
opts['scalex'] = float(line.strip())
line = file.readline()
if line[:6] == 'scaley':
line = file.readline()
opts['scaley'] = float(line.strip())
line = file.readline()
if line[:6] == 'scalez':
line = file.readline()
opts['scalez'] = float(line.strip())
line = file.readline()
# Strain
if line[:6] == 'strain':
line = file.readline()
xx, xy, xz = map(float, line.split())
line = file.readline()
yx, yy, yz = map(float, line.split())
line = file.readline()
zx, zy, zz = map(float, line.split())
opts['strain'] = (xx, xy, xz, yx, yy, yz, zx, zy, zz)
line = file.readline()
if line[:6] == 'strfac':
line = file.readline()
opts['strfac'] = float(line.strip())
line = file.readline()
# Lattice vectors:
if line[:6] == 'primit':
line = file.readline()
ax, ay, az = map(float, line.split())
axyz = ax * bohr2ang, ay * bohr2ang, az * bohr2ang
line = file.readline()
bx, by, bz = map(float, line.split())
bxyz = bx * bohr2ang, by * bohr2ang, bz * bohr2ang
line = file.readline()
cx, cy, cz = map(float, line.split())
cxyz = cx * bohr2ang, cy * bohr2ang, cz * bohr2ang
cell = Cell(axyz, bxyz, cxyz)
line = file.readline()
# grid dimensions
if line[:6] == 'grid d' or line[:6] == 'points':
line = file.readline()
opts['griddim'] = map(int, line.split())
line = file.readline()
# nearby function
if line[:6] == 'nearby':
line = file.readline()
opts['nearby'] = int(line.strip())
line = file.readline()
# number of atom types
if line[:6] == 'atom t':
line = file.readline()
opts['ntyp'] = int(line.strip())
opts['types'] = []
line = file.readline()
else:
print line, len(line)
raise "Number of atom types must be specified"
# atom types:
for i in range(opts['ntyp']):
if line[:6] == 'atom f':
line = file.readline()
opts['types'].append(line.strip())
line = file.readline()
else:
raise "Error: expecting another atom file"
# number of atoms
if line[:6] == 'number':
line = file.readline()
opts['nat'] = int(line.strip())
line = file.readline()
if line[:6] == 'atom, ':
for i in range(opts['nat']):
line = file.readline()
words = line.split()
inum = int(words[0])
ityp = int(words[1])
x, y, z = map(float, words[2:5])
xyz = x * bohr2ang, y * bohr2ang, z * bohr2ang
xyz = array(xyz)
sym = cleansym(opts['types'][ityp - 1])
atno = sym2no[sym]
material.add_atom(Atom(atno, xyz))
line = file.readline()
material.set_cell(cell)
material.bonds_from_distance()
else:
raise "Error: expected atom listing here"
# to lattice/to cartesian
if line[:6] == 'to_lat':
opts['to_lat'] = True
line = file.readline()
elif line[:6] == 'to_car':
opts['to_car'] = True
line = file.readline()
# origin offset
if line[:6] == 'origin':
line = file.readline()
opts['dorig'] = map(float, line.split())
line = file.readline()
# wigner-seitz origin
if line[:6] == 'wigner':
line = file.readline()
opts['rchrg'] = map(float, line.split())
line = file.readline()
# center of symmetry
if line[:6] == 'symmet':
line = file.readline()
opts['rsym'] = map(float, line.split())
line = file.readline()
# bloch info
if line[:5] == 'kgrid':
line = file.readline()
opts['kgrid'] = map(int, line.split())
line = file.readline()
elif line[:4] == 'khex':
line = file.readline()
opts['khex'] = map(int, line.split())
line = file.readline()
# skipping more detailed bloch info for now
if line[:6] == 'n bloc':
line = file.readline()
opts['nk'] = int(line.strip())
line = file.readline()
if line[:6] == 'scalin':
line = file.readline()
opts['scalin'] = map(float, line.split())
line = file.readline()
if line[:6] == 'lattic':
line = file.readline()
opts['bloch_lattic'] = map(float, line.split())
line = file.readline()
elif line[:6] == 'cartes':
line = file.readline()
opts['bloch_cartes'] = map(float, line.split())
line = file.readline()
if line[:6] == 'bloch ':
opts['bloch_vecs'] = []
for i in range(opts['nk']):
line = file.readline()
opts['bloch_vecs'].append(map(float, line.split()))
line = file.readline()
# symmetry info
if line[:6] == 'symops':
line = file.readline()
opts['nsymi'] = int(line.strip())
line = file.readline()
if line[:6] == 'defini':
opts['symvecs'] = []
for i in range(opts['nsymi']):
line = file.readline()
words = line.split()
type = int(words[0])
s1, s2, s3, s4, s5, s6 = map(float, words[1:])
opts['symvecs'].append((type, s1, s2, s3, s4, s5, s6))
line = file.readline()
if line[:6] == 'end se':
line = file.readline()
else:
raise "Expected end setup phase tag"
# End of setup info
# Beginning of Run Data
if line[:6] == 'run ph':
while 1:
line = file.readline()
if not line: break
if line[:6] == 'end ru' or line[:6] == 'end of':
break
elif line[:6] == 'do fla':
opts['doflag'] = True
elif line[:6] == 'no fla':
opts['doflag'] = False
elif line[:6] == 'first ':
line = file.readline()
opts['itstart'] = int(line.strip())
elif line[:6] == 'last i':
line = file.readline()
opts['itstop'] = int(line.strip())
elif line[:6] == 'histor':
line = file.readline()
opts['nhiste'] = int(line.strip())
elif line[:6] == 'restar':
line = file.readline()
opts['itrst'] = int(line.strip())
elif line[:6] == 'states':
line = file.readline()
opts['nstate'] = int(line.strip())
elif line[:6] == 'temper':
line = file.readline()
opts['etemp'] = float(line.strip())
elif line[:6] == 'blend ' or line[:6] == 'percen':
line = file.readline()
opts['scfblnd'] = float(line.strip())
elif line[:6] == 'scfbl2':
line = file.readline()
opts['scfbl2'] = float(line.strip())
elif line[:6] == 'conver':
line = file.readline()
opts['scfconv'] = float(line.strip())
elif line[:6] == 'alfast':
line = file.readline()
opts['alfast'] = float(line.strip())
elif line[:6] == 'cutii ':
line = file.readline()
opts['convii'] = float(line.strip())
elif line[:6] == 'cutslo':
line = file.readline()
opts['convsl'] = float(line.strip())
elif line[:6] == 'cut2s ':
line = file.readline()
opts['conv2s'] = float(line.strip())
elif line[:6] == 'cutset':
line = file.readline()
opts['cutset'] = float(line.strip())
elif line[:6] == 'cutfrc':
line = file.readline()
opts['cutfrc'] = float(line.strip())
elif line[:6] == 'cutgrd':
line = file.readline()
opts['convgr'] = float(line.strip())
elif line[:6] == 'cut1c ':
line = file.readline()
opts['conv1c'] = float(line.strip())
elif line[:6] == 'geomet':
# Jump into Geometry Data
opts['write_geo_sect'] = True
while 1:
line = file.readline()
if line[:4] == 'stop' or line[:3] == 'end':
break
elif line[:6] == 'relax ':
opts['dorelax'] = True
opts['geo_dorelax'] = True
elif line[:6] == 'grelax':
line = file.readline()
opts['relax_range'] = map(int, line.split())
elif line[:6] == 'gfixed':
line = file.readline()
opts['fixed_range'] = map(int, line.split())
elif line[:6] == 'only r':
line = file.readline()
opts['only_relax'] = int(line.strip())
elif line[:6] == 'frame ':
line = file.readline()
opts['relax_frame'] = map(int, line.split())
elif line[:6] == 'defect':
line = file.readline()
opts['defect'] = int(line.strip())
elif line[:6] == 'gblend':
line = file.readline()
opts['gblend'] = float(line.strip())
elif line[:5] == 'gconv':
line = file.readline()
opts['gconv'] = float(line.strip())
elif line[:6] == 'gstart':
line = file.readline()
opts['gstart'] = int(line.strip())
elif line[:6] == 'gsteps':
line = file.readline()
opts['gsteps'] = int(line.strip())
elif line[:6] == 'ghisto':
line = file.readline()
opts['nhistg'] = int(line.strip())
elif line[:6] == 'no ges':
opts['igges'] = 0
elif line[:6] == 'guess ':
line = file.readline()
opts['igges'] = int(line.strip())
elif line[:6] == 'gmetho':
line = file.readline()
opts['gmethod'] = line.strip()
elif line[:6] == 'timest':
line = file.readline()
opts['gtstep'] = float(line.strip())
else:
print "Unknown geomdata line:"
print line
# End of Geometry Data
elif line[:5] == 'cell ':
# Jump into Cell Data
opts['write_cell_sect'] = True
while 1:
line = file.readline()
if line[:6] == 'end ce':
break
elif line[:6] == 'ucstep':
line = file.readline()
opts['maxucsteps'] = int(line.strip())
elif line[:6] == 'ucconv':
line = file.readline()
opts['ucconv'] = float(line.strip())
elif line[:6] == 'pressu':
line = file.readline()
opts['pressure'] = float(line.strip())
elif line[:6] == 'uniaxi':
line = file.readline()
opts['uniaxial'] = map(float, line.split())
elif line[:6] == 'stress':
opts['stress'] = []
for i in range(opts['ndim']):
line = file.readline()
opts['stress'].append(map(float, line.split()))
elif line[:6] == 'uchist':
line = file.readline()
opts['nhistuc'] = int(line.strip())
elif line[:6] == 'ucmeth':
line = file.readline()
opts['ucmeth'] = line.strip()
elif line[:6] == 'str_br':
line = file.readline()
opts['strsbroy'] = float(line.strip())
elif line[:6] == 'max_st':
line = file.readline()
opts['strnmax'] = float(line.strip())
elif line[:6] == 'cell_f':
line = file.readline()
opts['cell_f'] = float(line.strip())
elif line[:6] == 'bulk_m':
line = file.readline()
opts['bmod'] = float(line.strip())
elif line[:6] == 'uc_ble':
line = file.readline()
opts['ucblend'] = float(line.strip())
else:
print "Unknown celldata line:"
print line
# End of Cell Data
else:
print "Unknown rundata line:"
print line
# End of Run Data
# Start of MD Data
line = file.readline()
if line[:6] == 'md dat':
while 1:
line = file.readline()
if line[:3] == 'end':
break
elif line[:6] == 'temper':
line = file.readline()
opts['mdtemp'] = float(line.strip())
elif line[:6] == 'time s':
line = file.readline()
opts['ntstep'] = int(line.strip())
elif line[:6] == 'equil ':
line = file.readline()
opts['neqsteps'] = int(line.strip())
elif line[:6] == 'step s':
line = file.readline()
opts['md_dt'] = float(line.strip())
elif line[:6] == 'md typ':
line = file.readline()
opts['mdtype'] = line.strip()
else:
print "Unknown md flag"
print line
return material
def build_the_slab(material, cleave_dir, depth, vacuum):
name = material.get_name()
cell = material.get_cell()
atomlist = material.get_atom_list()
if not cleave_dir: cleave_dir = 'C'
axyz = cell.axyz
bxyz = cell.bxyz
cxyz = cell.cxyz
if depth == 1 and vacuum == 0:
return material # do nothing
newname = "%s_slab" % name
newmaterial = Material(newname)
#
# Replace abc -> uvw (w is the cleave direction) so we can
# cleave in more general ways:
#
if cleave_dir == "C":
uxyz = axyz
vxyz = bxyz
wxyz = cxyz
idir = 2
elif cleave_dir == "B":
uxyz = cxyz
vxyz = axyz
wxyz = bxyz
idir = 1
elif cleave_dir == "A":
uxyz = bxyz
vxyz = cxyz
wxyz = axyz
idir = 0
wlength = sqrt(dot(wxyz, wxyz))
wscale = (wlength * depth + vacuum) / wlength
nwxyz = wxyz * wscale
for atom in atomlist:
atno = atom.get_atno()
xyz = atom.get_position()
for k in range(depth):
xyznew = xyz + k * wxyz
xyznew[idir] += vacuum / 2.
newmaterial.add_atom(Atom(atno, xyznew))
if abs(xyz[idir]) < 1e-2: # Periodic image of bottom:
xyznew = xyz + depth * wxyz
xyznew[idir] += vacuum / 2.
newmaterial.add_atom(Atom(atno, xyznew))
# I can't tell whether I have to do the cyclic permutations here
# i.e. output w,u,v in some cases.
newmaterial.set_cell(Cell(uxyz, vxyz, nwxyz))
opts = getattr(material, "seqquest_options", {})
if opts: newmaterial.seqquest_options = opts.copy()
opts = getattr(material, "socorro_options", {})
if opts: newmaterial.socorro_options = opts.copy()
newmaterial.center()
newmaterial.bonds_from_distance()
return newmaterial
def create_nanotube_material(n, m, ncells):
bondlength = 1.35 # Angstroms
buffer = 2 # Angstroms to pack around nt in uc
np, nq, ndr = gen11(n, m)
rt3 = sqrt(3)
a = rt3 * bondlength
r = a * sqrt(np * np + nq * nq + np * nq)
c = a * sqrt(n * n + m * m + n * m)
t = rt3 * c / ndr
rs = c / 2 / pi
nn = 2 * (n * n + m * m + n * m) / ndr # hexagons in unit cell N
#print 'Nanotube unit cell length ',t
#print 'Nanotube radius ',rs
#print 'Nanotube unit cell atoms ',nn*2
q1 = atan((rt3 * m) / (2 * n + m)) # Chiral angle for C_h
q2 = atan((rt3 * nq) / (2 * np + nq)) # Chiral angle for R
q3 = q1 - q2 # Angle btw C_h and R
q4 = 2 * pi / nn # Period of angle for A atom
q5 = bondlength * cos(pi / 6 - q1) / c * 2 * pi
# diff of the angle btw A and B atoms
h1 = abs(t) / abs(sin(q3))
h2 = bondlength * sin(pi / 6 - q1) # dz btw A and B atoms
xyz = []
for i in range(nn):
# A atom
k = int(i * abs(r) / h1)
x1 = rs * cos(i * q4)
y1 = rs * sin(i * q4)
z1 = (i * abs(r) - k * h1) * sin(q3)
kk2 = abs(int(z1 / t)) + 1
# Insure A in unit cell
if z1 > t - 0.02: z1 -= t * kk2
if z1 < -0.02: z1 += t * kk2
xyz.append((x1, y1, z1))
# B atom
# Insure B in unit cell
z3 = (i * abs(r) - k * h1) * sin(q3) - h2
if z3 > -0.02 and z3 < t - 0.02:
x2 = rs * cos(i * q4 + q5)
y2 = rs * sin(i * q4 + q5)
z2 = (i * abs(r) - k * h1) * sin(q3) - h2
xyz.append((x2, y2, z2))
else:
x2 = rs * cos(i * q4 + q5)
y2 = rs * sin(i * q4 + q5)
z2 = (i * abs(r) - (k + 1) * h1) * sin(q3) - h2
kk = abs(int(z2 / t)) + 1
if z2 > t - 0.01: z2 -= t * kk
if z2 < -0.01: z2 += t * kk
xyz.append((x2, y2, z2))
xyznew = []
ii = 0
dxy = rs + buffer
for j in range(ncells):
dz = j * t
for i in range(2 * nn):
x, y, z = xyz[i]
xyznew.append((x + dxy, y + dxy, z + dz))
#for x,y,z in xyznew: print " C %10.4f %10.4f %10.4f" % (x,y,z)
material = Material('nanotube%d%d%d' % (ncells, n, m))
for xyz in xyznew:
material.add_atom(Atom(6, array(xyz)))
material.bonds_from_distance()
material.set_cell(
Cell((2 * dxy, 0, 0), (0, 2 * dxy, 0), (0, 0, ncells * t)))
return material
def load(fullfilename):
gstep = 0
filedir, fileprefix, fileext = path_split(fullfilename)
file=open(fullfilename, 'r')
# Initialize atom data
material = Material(fileprefix)
opts = {}
material.seqquest_options = opts
dconv = 1. # default to Angstroms, which don't need conversion
cell = None
while 1:
line = file.readline()
if not line: break
line = line.strip()
if line == '@=KEYCHAR':
continue # ignore other keychars for now
elif line == '@DISTANCE UNIT':
line = file.readline().strip()
if line == 'ANGSTROM':
continue
elif line == 'BOHR':
dconv = bohr2ang
else:
print "Warning: unknown distance unit ",line
elif line == '@DIMENSION':
line = file.readline().strip()
opts['ndim'] = int(line)
elif line == '@NUMBER OF ATOMS':
line = file.readline().strip()
opts['nat'] = int(line)
opts['attypes'] = []
nread = int(ceil(opts['nat']/20.))
for i in range(nread):
line = file.readline().strip()
opts['attypes'].extend(map(int,line.split()))
assert len(opts['attypes']) == opts['nat']
elif line == '@TYPES':
line = file.readline().strip()
opts['ntyp'] = int(line)
opts['types'] = []
for i in range(opts['ntyp']):
line = file.readline().strip()
opts['types'].append(cleansym(line))
elif line == '@CELL VECTORS':
line = file.readline()
axyz = map(float,line.split())
line = file.readline()
bxyz = map(float,line.split())
line = file.readline()
cxyz = map(float,line.split())
if abs(dconv-1) > 1e-4: # careful when comparing floats
axyz = axyz[0]*dconv,axyz[1]*dconv,axyz[2]*dconv
bxyz = bxyz[0]*dconv,bxyz[1]*dconv,bxyz[2]*dconv
cxyz = cxyz[0]*dconv,cxyz[1]*dconv,cxyz[2]*dconv
cell = Cell(axyz,bxyz,cxyz)
elif line == '@GSTEP':
line = file.readline().strip()
gstep = int(line)
elif line == '@COORDINATES':
atoms = []
for i in range(opts['nat']):
line = file.readline()
xyz = map(float,line.split())
if abs(dconv-1) > 1e-4: # careful when comparing floats
xyz = xyz[0]*dconv,xyz[1]*dconv,xyz[2]*dconv
isym = opts['attypes'][i]
sym = opts['types'][isym-1]
atoms.append((sym,xyz))
if gstep > 1: material.new_geo()
for i in range(opts['nat']):
sym,xyz = atoms[i]
atno = sym2no[sym]
xyz = array(xyz)
material.add_atom(Atom(atno,xyz))
if cell: material.set_cell(cell)
elif line == '@ESCF':
line = file.readline().strip()
escf = float(line)
# Consider saving these for plotting
elif line == '@FORCES':
forces = []
for i in range(opts['nat']):
line = file.readline()
forces.append(map(float,line.split()))
elif line == '@FMAX':
line = file.readline().strip()
fmax = float(line)
elif line == '@FRMS':
line = file.readline().strip()
frms = float(line)
else:
print "Unknown line ",line
material.bonds_from_distance()
return material