def argumentHandler(self,argv):
#no argument: start GUI
if len(argv) == 1:
self.gui = MainWindow(self)
else:
self.gui = MainWindow(self)
for i in range(1,len(argv)):
#load a single configuration, start GUI
if argv[i] == '-pwi':
self.readFile('PWScf Input',argv[i+1])
self.gui.centralWidget().loadView()
if argv[i] == '-pwo':
self.readFile('PWScf Output',argv[i+1])
self.gui.centralWidget().loadView()
elif argv[i] == '-xyz':
self.readFile('xyz',argv[i+1])
self.gui.centralWidget().loadView()
class TBController(QApplication):
def __init__(self,argv):
super(TBController,self).__init__(argv)
self.mol = []
self.pwdata = []
self.indict = OrderedDict([('xyz',self.parseXyz),
('PWScf Input',self.parsePwi),
('PWScf Output' , self.parsePwo)])
self.outdict= OrderedDict([('PWScf Input',self.writePwi),
('xyz',self.writeXyz)])
self.argumentHandler(argv)
#####################################################################
# Handle command line arguments:
#####################################################################
def argumentHandler(self,argv):
#no argument: start GUI
if len(argv) == 1:
self.gui = MainWindow(self)
else:
self.gui = MainWindow(self)
for i in range(1,len(argv)):
#load a single configuration, start GUI
if argv[i] == '-pwi':
self.readFile('PWScf Input',argv[i+1])
self.gui.centralWidget().loadView()
if argv[i] == '-pwo':
self.readFile('PWScf Output',argv[i+1])
self.gui.centralWidget().loadView()
elif argv[i] == '-xyz':
self.readFile('xyz',argv[i+1])
self.gui.centralWidget().loadView()
#####################################################################
# GET FUNCTIONS
#####################################################################
def get_mol(self,index,step):
return self.mol[index][step]
def get_lmol(self,index):
return len(self.mol[index])
def get_nmol(self):
return len(self.mol)
def get_pw(self,index):
return self.pwdata[index]
def get_npw(self):
return len(self.pwdata)
#####################################################################
# READ FUNCTIONS
#####################################################################
def readFile(self,fmt,filename):
data = open(filename,'r').readlines()
self.indict[fmt](data)
#return data
def parseXyz(self,data):
# create list of mol, trajectory support
tlist = []
# if first line does not contain nat exit
if not data[0].strip().isdigit():
print 'not a xyz file'
return
i=0
while i < len(data):
# handle empty lines at eof or between molecules
if not data[i].strip().isdigit(): i+=1
# create new molecule
tmol = Molecule()
#fixed format nat and comment
nat = int(data[i])
tmol.comment = data[i+1]
#read coordinates and types
for j in range(i+2,i+nat+2):
line = data[j].split()
tmol.create_atom(line[0],float(line[1]),float(line[2]),float(line[3]))
i+=nat+2
tlist.append(tmol)
#append to list of molecules
self.mol.append(tlist)
def parsePwi(self,data):
# no need for list, only one molecule per file
tmol = Molecule()
tparam = PWParam()
tcoord = []
#parse data and create tparam
while data:
header = data.pop(0).strip().split()
# ignore empty lines
if not header:
pass
#debug output. case not really needed.
# parse namelists
elif header[0][0] == '&':
tnl = {}
# parse entries
line = data.pop(0).strip().split(',')
while line[0] != '/':
for j in range(len(line)):
tnl[line[j].split('=')[0].strip()]=line[j].split('=')[1].strip()
line = data.pop(0).strip().split(',')
tparam[header[0]]=tnl
#debug output
# parse card
elif header[0][0].isupper():
# 7 types of cards, need hardcoding
# 4 supported for now
#ATOMIC_SPECIES:
#Name Weight PP-file
if header[0] == 'ATOMIC_SPECIES':
for i in range(int(tparam['&system']['ntyp'])):
line = data.pop(0).strip().split()
tparam['pse'][line[0]][1] = float(line[1])
tparam['pse'][line[0]].append(line[2])
#ATOMIC_POSITIONS fmt
#Name x y z
#Saved in temp list for parsing
elif header[0] == 'ATOMIC_POSITIONS':
fmt = header[1]
for i in range(int(tparam['&system']['nat'])):
#support empty lines
temp = data.pop(0).strip().split()
while not temp:
temp = data.pop(0).strip().split()
tcoord.append(temp)
#K_POINTS fmt
elif header[0] == 'K_POINTS':
#Gamma point only
if header[1] == 'gamma':
tparam['K_POINTS']=['gamma']
#MPGrid:
#x y z offset
#passed as whole string for now
elif header[1] == 'automatic':
#line = data.pop(0).strip().split()
line = data.pop(0)
#tparam['K_POINTS']=['automatic',[line[0:3],line[3:7]]]
tparam['K_POINTS']=['automatic',line]
#else:
#number of kpoints
#x y z weight
#passed as whole string for now
else:
nk = data.pop(0).strip().split()
kpoints = []
for i in range(nk):
#kpoints.append(data.pop(0).strip().split())
kpoints.append(data.pop(0))
taparam['K_POINTS']=[header[1],nk,kpoints]
#TODO: care for different formats
elif header[0] == 'CELL_PARAMETERS':
vec=[[0,0,0],[0,0,0],[0,0,0]]
for i in range(3):
line = data.pop(0).strip().split()
vec[i]=[float(x)for x in line]
tmol.set_vec(vec)
else:
pass
#Create Molecule after getting the cell parameters
#set celldm from input
tmol.set_celldm(tparam['&system']['celldm(1)'])
#create atoms:
for i in range(len(tcoord)):
tmol.create_atom(tcoord[i][0],float(tcoord[i][1]),float(tcoord[i][2]),float(tcoord[i][3]),fmt)
#delete nat and ntype before returning to controller
del tparam['&system']['nat']
del tparam['&system']['ntyp']
#Append to controller
self.mol.append([tmol])
self.pwdata.append(tparam)
#TODO: 2nd routine that only reads final config?
def parsePwo(self,data):
#Multiple configs supported
tlist = []
#no parameters for now
#tparam=PWParam()
#read list of molecules:
i=0
vec=[[0,0,0],[0,0,0],[0,0,0]]
while i<len(data):
line = data[i].split()
#ignore empty lines
if not line:
pass
#read number of atoms
elif line[0:3] == ['number', 'of', 'atoms/cell']:
nat = int(line[4])
#TODO: tweak to recognize celldm(n), save if !0 in param
#read cell dimension
elif line[0] == 'celldm(1)=':
celldm = float(line[1])
#TODO: care for different formats
#read initial cell vectors
elif line[0:2] == ['crystal','axes:']:
for j in range(3):
temp = data[i+1+j].split()
vec[j]=[float(x) for x in temp[3:6]]
# read initial positions:
elif line[0] == 'site':
tmol = Molecule()
tmol.set_celldm(celldm)
tmol.set_vec(vec)
for j in range(i+1,i+nat+1):
atom = data[j].split()
tmol.create_atom(atom[1],float(atom[6]),float(atom[7]),float(atom[8]),'alat')
i+=nat
tlist.append(tmol)
#read step-vectors if cell is variable
elif line[0] == 'CELL_PARAMETERS':
for j in range(3):
temp = data[i+1+j].split()
vec[j]=[float(x) for x in temp[0:3]]
#read step-coordinates
elif line[0] == 'ATOMIC_POSITIONS':
tmol = Molecule()
tmol.set_celldm(celldm)
tmol.set_vec(vec)
for j in range(i+1,i+nat+1):
atom = data[j].split()
tmol.create_atom(atom[0],float(atom[1]),float(atom[2]),float(atom[3]),line[1].strip(')').strip('('))
i+=nat
tlist.append(tmol)
#break on reaching final coordinates (duplicate)
elif line[0] == 'Begin':
break
#ignore everything else
else:
pass
i+=1
self.mol.append(tlist)
#############################################################################
# WRITE FUNCTIONS
#############################################################################
def writeFile(self,ftype,mol,filename,param="",coordfmt=""):
self.outdict[ftype](mol,filename,param,coordfmt)
def writeXyz(self,mol,filename,param,coordfmt):
if filename == "":
f=sys.stdout
else:
f=open(filename,'w')
# fixed format nat and comment
f.write(str(mol.get_nat())+'\n')
f.write(mol.get_comment()+'\n')
# write coordinates
for cntat in range(0,mol.get_nat()):
atom=mol.get_atom(cntat,'angstrom')
f.write('{:4s} {:15.10f} {:15.10f} {:15.10f}'.format(
atom[0],atom[1][0],atom[1][1],atom[1][2])+'\n')
f.close()
def writePwi(self,mol,filename,param,coordfmt):
if filename == "":
f=sys.stdout
else:
f=open(filename,'w')
#&control, &system and &electron namelists are mandatory
for i in ['&control','&system','&electrons']:
f.write(i+'\n')
#write all parameters
if i == '&system':
f.write(' nat='+str(mol.get_nat())+'\n')
f.write(' ntyp='+str(mol.get_ntyp())+'\n')
for j in range(len(param[i])):
f.write(' '+param[i].keys()[j]+'='+param[i].values()[j]+'\n')
f.write('/\n\n')
#&ions only when needed
if param['&control']['calculation'] in ["'relax'","'vc-relax'","'md'","'vc-md'"]:
f.write('&ions'+'\n')
for j in range(len(param['&ions'])):
f.write(' '+param['&ions'].keys()[j]+'='+param['&ions'].values()[j]+'\n')
f.write('/\n\n')
#&cell only when needed
if param['&control']['calculation'] in ["'vc-relax'","'vc-md'"]:
f.write('&cell'+'\n')
for j in range(len(param['&cell'])):
f.write(' '+param['&cell'].keys()[j]+'='+param['&cell'].values()[j]+'\n')
f.write('/\n\n')
#ATOMIC_SPECIES card:
f.write('ATOMIC_SPECIES'+'\n')
types = list(mol.get_types())
for i in range(len(mol.get_types())):
atom = types[i]
f.write(atom+' '+str(param['pse'][atom][1])+' '+str(param['pse'][atom][2])+'\n')
f.write('\n')
#ATOMIC_POSITIONS
f.write('ATOMIC_POSITIONS'+' '+coordfmt+'\n')
for i in range(mol.get_nat()):
atom=mol.get_atom(i)
f.write('{:4s} {:15.10f} {:15.10f} {:15.10f}'.format(
atom[0],atom[1][0],atom[1][1],atom[1][2])+'\n')
f.write('\n')
#K_POINTS
f.write('K_POINTS'+' '+param['K_POINTS'][0]+'\n')
#Gamma point only
if param['K_POINTS'][0] == 'gamma':
pass
#MPGrid:
#x y z offset
#passed as whole string for now
elif param['K_POINTS'][0] == 'automatic':
#f.write('{:4i}{:4i}{:4i}{:4i}{:4i}{:4i}'.format(
# param['K_POINTS'][1][0][0],
# param['K_POINTS'][1][0][1],
# param['K_POINTS'][1][0][2],
# param['K_POINTS'][1][0][0],
# param['K_POINTS'][1][1][1],
# param['K_POINTS'][1][1][2]
# )+'\n\n')
f.write(param['K_POINTS'][1])
#number of kpoints
#x y z weight
#passed as whole string for now
#UNTESTED, beware!
else:
f.write(param['K_POINTS'][1])
for i in range(param['K_POINTS'][1]):
f.write(param['K_POINTS'][2][i])
f.write('\n')
#Cell parameters
f.write('CELL_PARAMETERS'+'\n')
vec = mol.get_vec()
fmt='{0[0][0]:15.10f} {0[0][1]:15.10f} {0[0][2]:15.10f}\n' + \
'{0[1][0]:15.10f} {0[1][1]:15.10f} {0[1][2]:15.10f}\n' + \
'{0[2][0]:15.10f} {0[2][1]:15.10f} {0[2][2]:15.10f}\n'
f.write(fmt.format(mol.get_vec()))
#Close file
f.close()