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 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 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 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)
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
