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')
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 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 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):
#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):
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
def load(fullfilename):
filedir, fileprefix, fileext = path_split(fullfilename)
material = Material(fileprefix)
from Scientific.IO.NetCDF import NetCDFFile
file = NetCDFFile(fullfilename, 'r')
allDimNames = file.dimensions.keys()
print 'allDimNames', allDimNames
vars = file.variables.keys()
print 'vars', vars
if file.variables.has_key('dsf'):
sf = file.variables['dsf'].getValue() #numpy array
zLabel = 'S(Q,Omega) (a.u.)'
elif file.variables.has_key('sf'):
sf = file.variables['sf'].getValue() #numpy array
zLabel = 'F(Q,t) (a.u.)'
print sf
q = file.variables['q'].getValue()
print 'q', q
if file.variables.has_key('frequency'):
timeOrFreq = file.variables['frequency'].getValue() #numpy array
yLabel = 'Omega (1/ps)'
elif file.variables.has_key('time'):
timeOrFreq = file.variables['time'].getValue() #numpy array
yLabel = 'Time (ps)'
print 'timeOrFreq', timeOrFreq
material.new_geo()
#triangulate and plot the surface
#from vimm.Shapes import Triangles
triangleCoords = [] #Triangles((1.,0.,1.))
#start across the first axis as x
xLen, yLen = sf.shape
# for i in range(xLen):
# for j in range(yLen):
# triangleCoords.append((q[i],timeOrFreq[j],sf[i,j]))
for i in range(xLen - 1):
for j in [0, 1]: #range(yLen-1):
#use the spacing given in the q and timeOrFrequency
#triangulate each of the squares in the grid
#lower triangle
#3\
#| \
#1--2
triangleCoords.append(((q[i], timeOrFreq[j], sf[i, j]),
(q[i + 1], timeOrFreq[j], sf[i + 1, j]),
(q[i], timeOrFreq[j + 1], sf[i, j + 1])))
#upper triangle
#3--2
# \ |
# \1
triangleCoords.append(
((q[i + 1], timeOrFreq[j], sf[i + 1, j]),
(q[i + 1], timeOrFreq[j + 1],
sf[i + 1, j + 1]), (q[i], timeOrFreq[j + 1], sf[i, j + 1])))
material.geo.surface = triangleCoords
#add the axes to the plot--assume orthogonal for now
aLen = q[-1] - q[0]
bLen = timeOrFreq[-1] - timeOrFreq[0]
cLen = sf.max() - sf.min()
a = (aLen, 0, 0)
b = (0, bLen, 0)
c = (0, 0, cLen)
# scale the axes so they are roughly equal
scaleA = 1 / aLen
scaleB = 1 / bLen
scaleC = 2 / cLen #C axis is half as large
from vimm.Cell import Cell
cell = Cell(a, b, c, scaleA=scaleA, scaleB=scaleB, scaleC=scaleC)
cell.aLabel = 'Q (1/Ang)'
cell.bLabel = yLabel
cell.cLabel = zLabel
# add tick mark labels /data point labels to the plot
cell.tickmarks = {
'A': [(qPoint, 0, 0) for qPoint in q],
'B': [(0, timeOrFreqPoint, 0) for timeOrFreqPoint in timeOrFreq]
}
material.set_cell(cell)
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
