def write_siesta_struct(atoms, cell1, cell2, cell3, cellparameter):
#---------------STRUCT.fdf----------------
fileS = open('STRUCT.fdf', 'w')
natm = len(atoms)
fileS.write("NumberOfAtoms %d # Number of atoms\n" % natm)
unique_symbs = get_unique_symbs(atoms)
fileS.write("NumberOfSpecies %d # Number of species\n\n" % len(unique_symbs))
fileS.write("%block ChemicalSpeciesLabel\n")
for symb in unique_symbs:
fileS.write(" %d %d %s\n" % (unique_symbs.index(symb)+1,atomic_number(symb),symb) )
fileS.write("%endblock ChemicalSpeciesLabel\n")
#Lattice
fileS.write("\n#(3) Lattice, coordinates, k-sampling\n\n")
fileS.write("LatticeConstant %15.9f Ang\n" % cellparameter)
fileS.write("%block LatticeVectors\n")
#va,vb,vc = atoms.get_cell()
va, vb, vc = cell1, cell2, cell3
fileS.write("%15.9f %15.9f %15.9f\n" % tuple(va))
fileS.write("%15.9f %15.9f %15.9f\n" % tuple(vb))
fileS.write("%15.9f %15.9f %15.9f\n" % tuple(vc))
fileS.write("%endblock LatticeVectors\n\n")
#Coordinates
fileS.write("AtomicCoordinatesFormat Ang\n")
fileS.write("%block AtomicCoordinatesAndAtomicSpecies\n")
for atom in atoms:
x,y,z = atom.get_position(); symb = atom.get_symbol()
fileS.write(" %15.9f %15.9f %15.9f %4d %4d\n" %\
(x,y,z,unique_symbs.index(symb)+1, atom.get_serial()))
fileS.write("%endblock AtomicCoordinatesAndAtomicSpecies\n")
fileS.close()
def write_siesta_basis(atoms, param_scf='LDA'):
#--------------BASIS.fdf---------------
fileB = open('BASIS.fdf', 'w')
unique_symbs = get_unique_symbs(atoms)
print unique_symbs
fileB.write("\n#(1) Basis definition\n\n")
fileB.write("%block PAO.Basis\n")
fileB.write("\n")
for symb in unique_symbs:
if param_scf == 'GGA':
f = open('%s.txt_GGA' % symb)
basis_info = f.readlines()
print basis_info
for info in basis_info:
fileB.write(info)
fileB.write("\n")
elif param_scf =='LDA':
f = open('%s.txt_LDA' % symb)
basis_info = f.readlines()
print basis_info
for info in basis_info:
fileB.write(info)
fileB.write("\n")
else: print "Unknown parameter : %s\n" % param_scf
fileB.write("%endblock PAO.Basis\n\n")
fileB.close()
def make_seqquest_positions(atoms):
# positions
atoms1 = []
atoms1.append("atom types\n")
unique_symbs = get_unique_symbs(atoms)
atoms1.append(" %d \n" % len(unique_symbs))
for symb in unique_symbs:
atoms1.append("atom file\n")
atoms1.append(" %s.atm\n" % symb)
atoms1.append("number of atoms in unit cell\n")
atoms1.append(" %d\n" % len(atoms))
atoms1.append("atom, type, position vector\n")
n = 1
for atom in atoms:
symb = atom.get_symbol(); x,y,z = atom.get_position()
atoms1.append(" %4d %3d %15.9f %15.9f %15.9f\n" % \
(n,unique_symbs.index(symb)+1,
x*ang2bohr,y*ang2bohr,z*ang2bohr))
n = n + 1
return atoms1
def make_seqquest_positions(atoms):
# positions
atoms1 = []
atoms1.append("atom types\n")
unique_symbs = get_unique_symbs(atoms)
atoms1.append(" %d \n" % len(unique_symbs))
for symb in unique_symbs:
atoms1.append("atom file\n")
atoms1.append(" %s.atm\n" % symb)
atoms1.append("number of atoms in unit cell\n")
atoms1.append(" %d\n" % len(atoms))
atoms1.append("atom, type, position vector\n")
n = 1
for atom in atoms:
symb = atom.get_symbol()
x, y, z = atom.get_position()
atoms1.append(" %4d %3d %15.9f %15.9f %15.9f\n" % \
(n,unique_symbs.index(symb)+1,
x*ang2bohr,y*ang2bohr,z*ang2bohr))
n = n + 1
return atoms1
def write_siesta(atoms, params_opt, params_scf, params_post):
print 'Writing SIESTA input ...'
#--------------STRUCT.fdf--------------
write_siesta_struct(atoms, params_scf['CellVector1'], params_scf['CellVector2'], params_scf['CellVector3'],
params_scf['CellParameter'])
#--------------BASIS.fdf---------------
#write_siesta_basis(atoms, params_scf['XCfunc'])
fileB = open('BASIS.fdf', 'w')
unique_symbs = get_unique_symbs(atoms)
fileB.write("\n#(1) Basis definition\n\n")
fileB.write("PAO.BasisSize %s\n" % params_scf['Basis'])
fileB.close()
#--------------KPT.fdf-----------------
fileK = open('KPT.fdf','w')
fileK.write("%block kgrid_Monkhorst_Pack\n")
fileK.write(" %i 0 0 0.5\n" %params_scf['kgrid'][0])
fileK.write(" 0 %i 0 0.5\n" %params_scf['kgrid'][1])
fileK.write(" 0 0 %i 0.5\n" %params_scf['kgrid'][2])
fileK.write("%endblock kgrid_Monkhorst_Pack\n")
fileK.close()
#--------------RUN.fdf-----------------
file = open('RUN.fdf', 'w')
file.write("#(1) General system descriptors\n\n")
file.write("SystemName %s # Descriptive name of the system\n" % params_opt['Name'])
file.write("SystemLabel %s # Short name for naming files\n" % params_opt['Label'])
file.write("%include STRUCT.fdf\n")
file.write("%include KPT.fdf\n")
file.write("%include BASIS.fdf\n")
#if params_scf['Solution'][0] == 't' or params_scf['Solution'][0] == 'T':
# file.write("%include TS.fdf\n")
#if params_post['Denchar']==1:
# file.write("%include DENC.fdf\n")
## XC OPTIONS ##
file.write("\n#(4) DFT, Grid, SCF\n\n")
file.write("XC.functional %s # LDA or GGA (default = LDA)\n" % params_scf['XCfunc'])
file.write("XC.authors %s # CA (Ceperley-Aldr) = PZ\n" % params_scf['XCauthor'])
#file.write(" # (Perdew-Zunger) - LDA - Default\n")
#file.write(" # PW92 (Perdew-Wang-92) - LDA\n")
#file.write(" # PBE (Perdew-Burke-Ernzerhof) - GGA\n")
file.write("MeshCutoff %f Ry # Default: 50.0 Ry ~ 0.444 Bohr\n" % params_scf['MeshCutoff'])
## SCF OPTIONS ##
file.write(" # 100.0 Ry ~ 0.314 Bohr\n")
file.write("MaxSCFIterations %d # Default: 50\n" % params_scf['MaxIt'])
file.write("DM.MixingWeight %3.2f # Default: 0.25\n" % params_scf['MixingWt'])
file.write("DM.NumberPulay %d # Default: 0\n" % params_scf['Npulay'])
file.write("DM.PulayOnFile F # SystemLabel.P1, SystemLabel.P2\n")
file.write("DM.Tolerance 1.d-4 # Default: 1.d-4\n")
file.write("DM.UseSaveDM .true. # because of the bug\n")
file.write("SCFMustConverge .true. \n")
file.write("NeglNonOverlapInt F # Default: F\n")
file.write("\n#(5) Eigenvalue problem: order-N or diagonalization\n\n")
file.write("SolutionMethod %s \n" %params_scf['Solution'])
file.write("ElectronicTemperature %4.1f K # Default: 300.0 K\n" %params_scf['Temp'])
file.write("Diag.ParallelOverK true\n\n")
## Calculation OPTIONS ##
# Now available : CG / MD / LDOS
if params_opt['Optimization'] == 1:
file.write("\n#(6) Molecular dynamics and relaxations\n\n")
file.write("MD.TypeOfRun %s # Type of dynamics:\n" %params_opt['Run'])
#file.write(" # - CG\n")
#file.write(" # - Verlet\n")
#file.write(" # - Nose\n")
#file.write(" # - ParrinelloRahman\n")
#file.write(" # - NoseParrinelloRahman\n")
#file.write(" # - Anneal\n")
#file.write(" # - FC\n")
#file.write(" # - Phonon\n")
#file.write("MD.VariableCell %s\n" %params_opt['cell_opt'])
file.write("MD.NumCGsteps %d # Default: 0\n" % params_opt['CGsteps'])
#file.write("MD.MaxCGDispl 0.1 Ang # Default: 0.2 Bohr\n")
file.write("MD.MaxForceTol %f eV/Ang # Default: 0.04 eV/Ang\n" % params_opt['ForceTol'])
#file.write("MD.MaxStressTol 1.0 GPa # Default: 1.0 GPa\n")
if params_opt['MD'] == 1:
file.write("\n#(6) Molecular dynamics and relaxations\n\n")
file.write("MD.TypeOfRun %s # Type of dynamics:\n" % params_opt['Run'])
#file.write("MD.VariableCell %s\n" %params_opt['cell_opt'])
file.write("MD.NumCGsteps %d # Default: 0\n" % params_opt['CGsteps'])
#file.write("MD.MaxCGDispl 0.1 Ang # Default: 0.2 Bohr\n")
file.write("MD.MaxForceTol %f eV/Ang # Default: 0.04 eV/Ang\n" % params_opt['ForceTol'])
#file.write("MD.MaxStressTol 1.0 GPa # Default: 1.0 GPa\n")
file.write("MD.InitialTimeStep 1\n")
file.write("MD.FinalTimeStep %i\n" % params_opt['MDsteps'])
file.write("MD.LengthTimeStep %f fs # Default : 1.0 fs\n" % params_opt['MDTimeStep'])
file.write("MD.InitialTemperature %f K # Default : 0.0 K\n" % params_opt['MDInitTemp'])
file.write("MD.TargetTemperature %f K # Default : 0.0 K\n" % params_opt['MDTargTemp'])
file.write("WriteCoorStep %s # default : .false.\n"% params_opt['WriteCoorStep'])
if params_post['LDOS'] == 1:
file.write("# LDOS \n\n")
file.write("%block LocalDensityOfStates\n")
file.write(" %f %f eV\n" %(params_post['LDOSE'][0],params_post['LDOSE'][1]))
file.write("%endblock LocalDensityOfStates\n")
if params_post['PDOS'] == 1:
file.write("%block ProjectedDensityOfStates\n")
file.write(" %f %f %f %i eV\n" % tuple(params_post['PDOSE'])) #-20.00 10.00 0.200 500 eV Emin Emax broad Ngrid
file.write("%endblock ProjectedDensityOfStates\n")
#file.write("%block GeometryConstraints\n")
#file.write("#position from 1 to %d\n" % natm)
#file.write("stress 4 5 6\n")
#file.write("%endblock GeometryConstraints\n")
#file.write("kgrid_cutoff 15.0 Ang\n")
#file.write("ProjectedDensityOfStates\n")
## OUT OPTIONS ##
#file.write("\n#(9) Output options\n\n")
#file.write("WriteCoorInitial F # SystemLabel.out\n")
#file.write("WriteKpoints F # SystemLabel.out\n")
#file.write("WriteEigenvalues F # SystemLabel.out [otherwise ~.EIG]\n")
#file.write("WriteKbands T # SystemLabel.out, band structure\n")
#file.write("WriteBands T # SystemLabel.bands, band structure\n")
#file.write("WriteMDXmol F # SystemLabel.ANI\n")
#file.write("WriteCoorXmol .true. \n")
#file.write("WriteDM.NetCDF F \n")
#file.write("WriteDMHS.NetCDF F \n")
#file.write("AllocReportLevel 0 # SystemLabel.alloc, Default: 0\n")
#file.write("%include banddata\n")
#file.write("""%block BandLines
# 1 1.000 1.000 1.000 L # Begin at L
#20 0.000 0.000 0.000 \Gamma # 20 points from L to gamma
#25 2.000 0.000 0.000 X # 25 points from gamma to X
#30 2.000 2.000 2.000 \Gamma # 30 points from X to gamma
#%endblock BandLines""")
#file.write("\n#(10) Options for saving/reading information\n\n")
#file.write("SaveHS F # SystemLabel.HS\n")
#file.write("SaveRho F # SystemLabel.RHO\n")
#file.write("SaveDeltaRho F # SystemLabel.DRHO\n")
#file.write("SaveNeutralAtomPotential F # SystemLabel.VNA\n")
#file.write("SaveIonicCharge F # SystemLabel.IOCH\n")
#file.write("SaveElectrostaticPotential F # SystemLabel.VH\n")
#file.write("SaveTotalPotential F # SystemLabel.VT\n")
#file.write("SaveTotalCharge F # SystemLabel.TOCH\n")
#file.write("SaveInitialChargeDenaisty F # SystemLabel.RHOINIT\n")
file.close()
#---------------TS.fdf-------------------#
## TRANSIESTA OPTIONS ##
if (params_scf['Solution'][0] == 't') or (params_scf['Solution'][0] == 'T'):
fileT = open('TS.fdf', 'w')
fileT.write("TS.WriteHS .true.\n")
fileT.write("TS.SaveHS .true.\n")
fileT.write("TS.NumUsedAtomsLeft %d\n" %Nleft)
fileT.write("TS.NumUsedAtomsRight %d\n" %Nright)
cur_dir = os.getcwd()
os.chdir(L_loc)
L_file = glob.glob('*.TSHS')[0]
os.chdir(R_loc)
R_file = glob.glob('*.TSHS')[0]
os.chdir(cur_dir)
fileT.write("TS.HSFileLeft './%s'\n"%L_file)
fileT.write("TS.HSFileRight './%s'\n"%R_file)
#fileT.write("TS.HSFileLeft '%s'\n" %L_loc)
#fileT.write("TS.HSFileRight '%s'\n" %R_loc)
fileT.write("TS.TBT.HSFile './%s.TSHS'\n" %params_opt['Label'])
fileT.write("TS.TBT.Emin -2.0 eV\n")
fileT.write("TS.TBT.Emax 2.0 eV\n")
fileT.write("TS.TBT.NPoints 201\n")
fileT.close()
#---------------DENC.fdf-------------------#
## DENCHAR OPTIONS ##
if params_post['Denchar']==1:
fileD = open('DENC.fdf', 'w')
fileD.write("COOP.Write T # to get WFS\n")
#fileD.write("WFS.EnergyMin -0.1 eV #Control! \n")
#fileD.write("WFS.EnergyMax 0.1 eV #Control! \n")
fileD.write("WriteDenchar T #SystemLabel.PLD --> .DM & .WFS : run wfsx2wfs (WFSX --> WFS)\n")
fileD.write("Denchar.TypeOfRun 3D\n")
fileD.write("Denchar.PlotCharge T #.DM should exist\n")
fileD.write("Denchar.PlotWaveFunctions T #.WFS should exist\n")
fileD.write("Denchar.CoorUnits Ang #Ang or Bohr\n")
fileD.write("Denchar.DensityUnits Ele/Ang**3 #Ele/Bohr**3, Ele/Ang**3, or Ele/UnitCell\n")
fileD.write("Denchar.NumberPointsX 100 #grid X\n")
fileD.write("Denchar.NumberPointsY 100 #grid Y\n")
fileD.write("Denchar.NumberPointsZ 100 #grid Z, only when Denchar.TypeOfRun=3D\n")
### GRID : Not sure ... Test needed. ###
fileD.write("Denchar.MinX 0.0 bohr\n")
fileD.write("Denchar.MinY 0.0 bohr\n")
fileD.write("Denchar.MinZ 0.0 bohr\n")
fileD.write("Denchar.MaxX %f bohr\n" %(tuple(vc)[2]*ang2bohr))
fileD.write("Denchar.MinY %f bohr\n" %(tuple(vb)[1]*ang2bohr))
fileD.write("Denchar.MinZ %f bohr\n" %(tuple(va)[0]*ang2bohr))
fileD.write("Denchar.PlaneGeneration NormalVector #NormalVector, TwoLines, ThreePoints, or ThreeAtomicIndices \n")
fileD.write("""%block WaveFuncKPoints
0.0 0.0 0.0 from X to Y #at Gamma point, Eigenvalue from X to Y #<-- put the X and Y
%endblock WaveFuncKpoints """)
fileD.write("""%block Denchar.CompNormalVector
0.0 0.00 1.00
%endblock Denchar.CompNormalVector
#only when PlaneGeneration = NormalVector\n""")
fileD.write("""%block Denchar.PlaneOrigin
0.00 0.00 0.00
%endblock Denchar.PlaneOrigin\n""")
#fileD.write("Denchar.X-Axis T\n")
fileD.write("""%block Denchar.AtomsInPlane
1
2
3
%endblock Denchar.AtomsInPlane\n""")
fileD.write("""%block Denchar.X_Axis
1.0000 0.0000 0.0000
%endblock Denchar.X_Axis""")
fileD.close()
return
