def generate(self):
### WRITE the SEEDNAME_FILES file ######
with open(self.SEEDDIR + self.seedname + ".files", 'w',
newline='\n') as file:
file.write(self.seedname + ".in" + "\n")
file.write(self.seedname + ".out" + "\n")
file.write(self.seedname + "_i" + "\n")
file.write(self.seedname + "_o" + "\n")
file.write(self.seedname + "_1" + "\n")
#### WRITE psuedopotentails to PPDIR
PPSAVE = []
znulc = ""
for x in np.unique(self.species)[::-1]:
PP = gb.glob(self.pseudodir + str(x) + ".*")
sendPPdir = self.SEEDDIR + "PP/" + ''.join(map(
str, PP))[len(self.pseudodir):] # get directory to send PP
file.write("PP/" +
''.join(map(str, PP))[len(self.pseudodir):] + " \n")
copyfile(''.join(map(str, PP)), ''.join(map(str, sendPPdir)))
#### GET Z for znucl
PP = gb.glob(self.pseudodir + str(x) + ".*")
readpp = minidom.parse(''.join(map(str, PP)))
items = readpp.getElementsByTagName('atom')
znulc += str(round(float(
items[0].attributes['Z'].value))) + " "
with open(self.SEEDDIR + self.seedname + ".in", 'w',
newline='\n') as file:
file.write("ndtset %i \n" % (2)) # for wanniertools
file.write("enunit 1 #change to EV\n")
file.write("prtvol 2 #print all kpoints\n")
file.write("##### " + self.seedname +
" stucture ######\n") # header
file.write("acell %12.8f %12.8f %12.8f angstrom \n" %
(self.a, self.b, self.c)) # cell parameters
file.write("angdeg %12.8f %12.8f %12.8f \n" %
(self.alpha, self.beta, self.gamma)) #angle param
file.write("natom " + str(self.natom) + "\n") #number of atoms
#### write atom positions ####
file.write("xred\n") # Fractional coordinates
for x in self.cords:
file.write("%12.8f%12.8f%12.8f\n" % (x[0], x[1], x[2]))
##### end write atom positions ####
file.write("ntypat " + repr(self.ntypat) +
" #number of unique atoms\n")
file.write("typat " + self.typat + "#identity of atoms\n")
#### Write Z of atoms ####
file.write("znucl " + znulc)
# for item in np.unique(self.struct.atomic_numbers):
# file.write(str(item) + " ")
file.write(" # atomic mass of atoms\n")
#### END of Z write ###
file.write("optforces 0 \n"
) # enforce calculation of forces at each SCF step
############ Plane wave ########
file.write("########### PLANE WAVE INFO ##########\n")
file.write("ecut 20 ry \n")
file.write("pawecutdg 22 ry\n")
file.write("pawovlp 15\n")
file.write("nstep 100\n")
#### USE DFT+U ####
is_HF = False
csvfile = open('HF.csv', newline='')
HF = csv.reader(csvfile, delimiter=',')
DFTUmat = np.full(len(self.UNIQUE_ATOMS), -1)
Umat = np.zeros(len(self.UNIQUE_ATOMS))
Jmat = np.zeros(len(self.UNIQUE_ATOMS))
for index, atom in enumerate(self.UNIQUE_ATOMS):
for el in HF:
if str(atom) in str(el[0]) and len(str(atom)) == len(
el[0]):
is_HF = True
DFTUmat[index] = 2
Umat[index] = el[1] ### U TERM
Jmat[index] = el[2] ### J0 terM
### reset csv reader
csvfile = open('HF.csv', newline='')
HF = csv.reader(csvfile, delimiter=',')
if is_HF:
file.write("usepawu 1\n")
file.write("lpawu %s\n" % (' '.join(map(str, DFTUmat))))
file.write("upawu %s\n" % (' '.join(map(str, Umat))))
file.write("jpawu %s\n" % (' '.join(map(str, Jmat))))
#### USE SOC ###
if self.SOC:
file.write("pawspnorb 1\n")
file.write("nspinor 2\n")
file.write("nsppol 1\n")
file.write("nspden 1\n")
file.write("######### END plane wave info ############\n\n\n")
######### END plane wave info ############
#############SCF STEP ##########
#
#
#
#
##################################
file.write("########### SCF STEP ##########\n")
file.write("iscf 17\n")
file.write("tolvrs1 1.00d-12 \n")
file.write("ngkpt1 8 8 8\n")
if self.SOC:
file.write("kptopt1 4\n")
else:
file.write("kptopt1 1\n")
file.write("nshiftk 1 #just one shift is supported by wannier90\n")
file.write("shiftk 0.00 0.00 0.00 #no shift \n")
file.write("prtden1 1\n")
file.write(
"istwfk1 512*1 #Controls the form of the wavefunctions\n")
############ End SCF Step ################
############# NSCF STEP #################
#
#
#
#############################################
file.write("########### NSCF STEP ##########\n")
file.write("prtvol2 1\n")
file.write("prtden2 1\n")
file.write("iscf2 -2 \n")
file.write("nstep2 0\n")
file.write("tolwfr2 1.d-12\n")
file.write("getwfk2 -1 # Get from SCF\n")
file.write("getden2 -1 # Get den from SCF\n")
file.write(
"istwfk2 %i*1 #Controls the form of the wavefunctions\n" %
(self.kpts[0] * self.kpts[1] * self.kpts[2]))
file.write("prtwant2 2 # Call to Wannier90\n")
file.write("w90iniprj2 2\n")
file.write(
"w90prtunk2 0 #Prints UNK files (for plotting the Wannier functions) \n"
)
file.write("kptopt2 0\n")
file.write(
kmesh.ABINIT(self.kpts[0], self.kpts[1], self.kpts[2], 2))
#########WANNIER90 FILE####################33
with open(self.SEEDDIR + "w90.win", 'w', newline='\n') as f:
f.write("write_hr = .TRUE.\n")
f.write("write_xyz = .TRUE.\n")
f.write("wannier_plot = .TRUE. \n")
f.write("spinors = %s\n" % (self.SOC))
f.write("num_wann = %i\n" % (self.wan))
f.write("num_iter = 2000\n\n\n\n")
f.write("begin unit_cell_cart\n")
f.write(str(self.lattice) + "\n") ### atomic structure
f.write("end unit_cell_cart\n\n\n")
f.write("begin atoms_frac\n")
for index, x in enumerate(self.cords):
f.write("%s %f %f %f\n" %
(str(self.species[index]), x[0], x[1], x[2]))
f.write("end atoms_frac\n\n\n")
f.write("begin projections \n")
f.write("random \n")
f.write("end projections\n\n\n")
f.write(kmesh.WANNIER(self.kpts[0], self.kpts[1], self.kpts[2]))
#def write_wt(self):
with open(self.SEEDDIR + "WT/wt.in", 'w', newline='\n') as f:
f.write("#### wt file ###########\n")
f.write("&TB_FILE\n")
f.write("Hrfile = 'w90_hr.dat'\n")
f.write("Package = 'ESPRESSO'\n")
f.write("/\n\n\n")
f.write("LATTICE\n")
f.write("Angstrom\n")
f.write(str(self.lattice) + "\n\n\n") ### atomic structure
f.write("ATOM_POSITIONS\n")
f.write("%i !Number of atoms for projectors\n" % (len(self.cords)))
f.write("Direct ! Direct or Cartisen coordinateS\n")
for index, x in enumerate(self.cords):
f.write("%s %f %f %f\n" %
(str(self.species[index]), x[0], x[1], x[2]))
f.write("\n\n\n\n")
f.write("PROJECTORS\n")
#### Places prjectors and stoms into PRJCARD in wannier tools
proj = int(self.WTwan / self.natom)
proj_rem = self.WTwan % self.natom
sumproj = 0
PROJPARAM = ""
projector = ["s", "pz", "px", "py"]
LATPARAM = str(self.lattice) + "\n" ### atomic structur
PROJCARD = ""
ATOMCARD = ""
appen = 0 #### append number
for index, atom in enumerate(self.species):
if proj_rem > 0:
appen = 1
proj_rem = proj_rem - 1
PROJPARAM += str(proj + appen) + " "
PROJCARD += str(atom) + " " + ' '.join(map(str,
projector)) + "\n"
#print(str(atom) + str(proj + appen))
sumproj += proj + appen
#print(sumproj)
appen = 0
f.write(PROJPARAM + "\n")
f.write(PROJCARD)
f.write("\n\n\n")
f.write("&CONTROL\n")
f.write("! BULK BAND CALCULATIONS \n")
f.write("BulkBand_calc = F\n")
f.write("BulkBand_plane_calc = F \n")
f.write("BulkFS_calc = F \n")
f.write("BulkFS_Plane_calc = F\n")
f.write("SlabBand_calc = F\n")
f.write("Dos_calc = F\n")
f.write("! BULK GAP\n")
f.write("BulkGap_cube_calc = F\n")
f.write("BulkGap_plane_calc = F\n")
f.write("! SURFACE STATES\n")
f.write("SlabSS_calc = T\n")
f.write("SlabArc_calc = T\n")
f.write("SlabSpintexture_calc = F\n")
f.write("! TOPO INV\n")
f.write("wanniercenter_calc = F\n")
f.write("BerryPhase_calc = F\n")
f.write("BerryCurvature_calc = F\n")
f.write("BerryCurvature_slab_calc = F\n")
f.write("Z2_3D_calc = F\n")
f.write("WeylChirality_calc = F\n")
f.write("NLChirality_calc = F\n")
f.write("Chern_3D_calc = F\n")
f.write("MirrorChern_calc = F\n")
f.write("!QUASIPARTICLE (STM)\n")
f.write("JDos_calc = F\n")
f.write("FindNodes_calc = F\n")
f.write("EffectiveMass_calc = F\n")
f.write("AHC_calc = F\n")
f.write("Boltz_OHE_calc = F\n")
f.write("LOTO_correction = F\n")
f.write("OrbitalTexture_calc = F\n")
f.write("OrbitalTexture_3D_calc = F\n")
f.write("LandauLevel_k_calc = F\n")
f.write("LandauLevel_B_calc = F\n")
f.write("LandauLevel_wavefunction_calc = F\n")
f.write("Fit_kp_calc = F\n")
f.write("DMFT_MAG_calc = F\n")
f.write("Translate_to_WS_calc= F\n")
f.write("LandauLevel_kplane_calc = F\n")
f.write("LandauLevel_k_dos_calc = F\n")
f.write("LandauLevel_B_dos_calc = F \n/\n\n\n")
f.write("&SYSTEM\n")
f.write("NSLAB = 20 ! for thin film system\n")
f.write("NumOccupied = %i ! NumOccupied\n" %
(self.WTwan / 2))
soc = 0
if self.SOC:
soc = 1
f.write("SOC = %i\n" % (soc))
f.write("E_FERMI = 0.0\n")
f.write("surf_onsite= 0.0\n")
f.write("/\n\n\n")
f.write("&PARAMETERS \n")
f.write(
"Eta_Arc = 0.01 ! infinite small value, like brodening \n")
f.write(
"E_arc = 0.0 ! energy level for contour plot of spectrum\n"
)
f.write("OmegaNum = 401 ! omega number \n")
f.write("OmegaMin = -1.0 ! energy interval\n")
f.write("OmegaMax = 1.0 ! energy interval\n")
f.write(
"Nk1 = 101 ! number k points odd number would be better\n"
)
f.write(
"Nk2 = 101 ! number k points odd number would be better\n"
)
f.write(
"Nk3 = 11 ! number k points odd number would be better\n"
)
f.write("NP = 2 ! number of principle layers\n")
f.write(
"Gap_threshold = 0.01 ! threshold for FindNodes_calc output\n")
f.write("/\n\n\n")
f.write("MILLER_INDEX\n")
f.write("0 0 1\n\n\n")
f.write("KPATH_BULK ! k point path \n")
f.write("4 ! number of k line only for bulk band\n")
f.write("G 0.00000 0.00000 0.0000 Z 0.00000 0.00000 0.5000\n")
f.write("Z 0.00000 0.00000 0.5000 F 0.50000 0.50000 0.0000\n")
f.write("F 0.50000 0.50000 0.0000 G 0.00000 0.00000 0.0000\n ")
f.write(
"G 0.00000 0.00000 0.0000 L 0.50000 0.00000 0.0000 \n\n\n\n")
###
f.write("KPATH_SLAB \n")
f.write("4 ! numker of k line for 2D case \n")
f.write("Y 0.0 0.5 G 0.0 0.0\n")
f.write("G 0.0 0.0 X 0.5 0.0\n")
f.write("X 0.5 0.0 M 0.5 0.5\n ")
f.write("M 0.5 0.5 G 0.0 0.0\n\n\n")
###
f.write("KPLANE_SLAB \n")
f.write("-0.5 -0.5 ! Original point for 2D k plane\n")
f.write("1.0 0.0 ! The first vector to define 2D k plane \n")
f.write(
"0.0 1.0 ! The second vector to define 2D k plane for arc plots\n\n\n"
)
####
f.write("KCUBE_BULK\n")
f.write("0.50 0.50 0.50 ! Original point for 3D k plane \n")
f.write(
"1.00 0.00 0.00 ! The first vector to define 3d k space plane\n"
)
f.write(
"0.00 1.00 0.00 ! The second vector to define 3d k space plane\n "
)
f.write(
"0.00 0.00 1.00 ! The third vector to define 3d k cube\n\n"
)
f.write("KPLANE_BULK\n")
f.write("0.00 0.00 0.00 ! Original point for 3D k plane \n")
f.write(
"1.00 0.00 0.00 ! The first vector to define 3d k space plane\n"
)
f.write(
"0.00 1.00 0.00 ! The second vector to define 3d k space plane\n\n\n"
)
#Write main slurm file
with open(self.SEEDDIR + "abi.slurm", 'w', newline='\n') as f:
f.write("#!/bin/bash\n")
#f.write("#SBATCH --ntasks=%i\n" %(self.NCORE))
f.write("#SBATCH --ntasks=1\n")
f.write("#SBATCH --time=12:00:00\n")
f.write("#SBATCH --error=job.%J.err\n")
f.write("#SBATCH --output=job.%J.out\n")
f.write("#SBATCH --job-name=%s_ABI\n" % (self.seedname))
f.write('#SBATCH --mail-user=%s\n' % (self.EMAIL))
f.write("#SBATCH --mail-type=ALL\n\n\n")
f.write('#Select how logs get stored\n')
f.write("mkdir $SLURM_JOB_ID\n")
f.write(
'export debug_logs="$SLURM_JOB_ID/job_$SLURM_JOB_ID.log"\n')
f.write(
'export benchmark_logs="$SLURM_JOB_ID/job_$SLURM_JOB_ID.log"\n\n\n'
)
f.write('#Load Modules\n')
f.write('ml load abinit\n\n\n')
f.write("cd $SLURM_SUBMIT_DIR\n")
f.write('# Create Log File\n')
f.write('echo $SLURM_SUBMIT_DIR')
f.write('echo "JobID: $SLURM_JOB_ID" >> $debug_logs\n')
f.write('echo "Running on $SLURM_JOB_NODELIST" >> $debug_logs\n')
f.write(
'echo "Running on $SLURM_JOB_NNODES nodes." >> $debug_logs\n')
f.write(
'echo "Running on $SLURM_JOB_NPROCS processors." >> $debug_logs\n'
)
f.write(
'echo "Current working directory is `pwd`" >> $debug_logs\n\n\n'
)
f.write('# Module debugging\n')
f.write('module list >> $debug_logs\n')
f.write('which mpirun >> $debug_logs\n\n\n')
f.write('#Start Timestamp\n')
f.write('date >> $benchmark_logs\n')
f.write('echo "ulimit -l: " >> $benchmark_logs\n')
f.write('ulimit -l >> $benchmark_logs\n\n\n')
f.write('# run file\n')
f.write('abinit <%s.files > log 2> err\n' % (self.seedname))
f.write('sleep 3\n')
f.write('grep CONV w90.wout >> Wconv.txt\n')
f.write(
'echo "Program is finished with exit code $? at: `date`"\n\n\n'
)
f.write('#End Timestamp\n')
f.write('date >> $benchmark_logs\n')
f.write('echo "ulimit -l" >> $benchmark_logs\n')
f.write('ulimit -l >> $benchmark_logs\n\n\n')
f.write('#Cleanup\n')
f.write('mv job.$SLURM_JOB_ID.err $SLURM_JOB_ID/\n')
f.write('mv job.$SLURM_JOB_ID.out $SLURM_JOB_ID/\n')
f.write('rm -rf $SLURM_JOB_ID\n')
######### WRITE WT SLURM #########
with open(self.SEEDDIR + "WT/wt.slurm", 'w', newline='\n') as f:
f.write("#!/bin/bash\n")
f.write("#SBATCH --ntasks=%i\n" % (self.NCORE))
f.write("#SBATCH --time=12:00:00\n")
f.write("#SBATCH --error=job.%J.err\n")
f.write("#SBATCH --output=job.%J.out\n")
f.write("#SBATCH --job-name=%s_WT\n" % (self.seedname))
f.write('#SBATCH --mail-user=%s\n' % (self.EMAIL))
f.write("#SBATCH --mail-type=ALL\n\n\n")
f.write('#Select how logs get stored\n')
f.write("mkdir $SLURM_JOB_ID\n")
f.write(
'export debug_logs="$SLURM_JOB_ID/job_$SLURM_JOB_ID.log"\n')
f.write(
'export benchmark_logs="$SLURM_JOB_ID/job_$SLURM_JOB_ID.log"\n\n\n'
)
f.write('#Load Modules\n')
f.write('ml load wannier_tools\n\n\n')
f.write("cd $SLURM_SUBMIT_DIR\n")
f.write('# Create Log File\n')
f.write('echo $SLURM_SUBMIT_DIR')
f.write('echo "JobID: $SLURM_JOB_ID" >> $debug_logs\n')
f.write('echo "Running on $SLURM_JOB_NODELIST" >> $debug_logs\n')
f.write(
'echo "Running on $SLURM_JOB_NNODES nodes." >> $debug_logs\n')
f.write(
'echo "Running on $SLURM_JOB_NPROCS processors." >> $debug_logs\n'
)
f.write(
'echo "Current working directory is `pwd`" >> $debug_logs\n\n\n'
)
f.write('# Module debugging\n')
f.write('module list >> $debug_logs\n')
f.write('which mpirun >> $debug_logs\n\n\n')
f.write('#Start Timestamp\n')
f.write('date >> $benchmark_logs\n')
f.write('echo "ulimit -l: " >> $benchmark_logs\n')
f.write('ulimit -l >> $benchmark_logs\n\n\n')
f.write('# run file\n')
f.write('mpirun -np %i wt.x\n' % (self.NCORE))
f.write(
'echo "Program is finished with exit code $? at: `date`"\n\n\n'
)
f.write('#End Timestamp\n')
f.write('date >> $benchmark_logs\n')
f.write('echo "ulimit -l" >> $benchmark_logs\n')
f.write('ulimit -l >> $benchmark_logs\n\n\n')
f.write('#Cleanup\n')
f.write('mv job.$SLURM_JOB_ID.err $SLURM_JOB_ID/\n')
f.write('mv job.$SLURM_JOB_ID.out $SLURM_JOB_ID/\n')
f.write('rm -rf $SLURM_JOB_ID\n')
#Write clean file
with open(self.SEEDDIR + "/cleandft.sh", 'w', newline='\n') as file:
file.write("rm job.*\n")
file.write("rm *.1o*\n")
file.write("rm *.out*\n")
file.write("rm log\n")
file.write("rm w90.eig\n")
file.write("rm w90.mmn\n")
file.write("rm w90.werr\n")
file.write("rm err\n")
file.write("rm w90.nnkp\n")
file.write("rm w90.wout\n")
file.write("rm wannier90random.amn\n")
def generate(self):
with open(self.SEEDDIR + self.seedname + ".fdf",'w',newline='\n') as f:
f.write("#FDF for SIESTA\n")
f.write("SystemName%10s\n" %(self.seedname))
f.write("SystemLabel%10s\n" %(self.seedname))
f.write("NumberOfSpecies%10i\n"%(self.UNIQUE_ATOMS.size))
f.write("NumberOfAtoms%10i\n\n\n"%(self.natom))
f.write("#\n")
f.write("User-Basis .false.\n")
f.write("#\n\n\n")
f.write("# Output options\n")
f.write("WriteCoorStep\n")
f.write("WriteMullikenPop 1\n\n\n")
f.write("%"+"block ChemicalSpeciesLabel\n")
# find the number of each unique atoms
typnum = np.zeros(self.UNIQUE_ATOMS.size)
atomlabel = np.zeros(self.UNIQUE_ATOMS.size)
for i in range(0,self.UNIQUE_ATOMS.size):
typnum[i] = np.asarray(np.where(self.struct.atomic_numbers == self.atomnum[i])).size
atomlabel[i] = i+1
for i,x in enumerate(self.UNIQUE_ATOMS):
f.write("%5i%5i%5s\n" %(i+1,x.Z,x.symbol)) # label, atomic number, symbol
f.write("%"+"endblock ChemicalSpeciesLabel\n\n")
f.write("LatticeConstant 1 Ang\n\n")
f.write("%"+ "block LatticeVectors\n")
f.write(str(self.struct.lattice) + "\n")
f.write("%" + "endblock LatticeVectors\n\n\n")
f.write("AtomicCoordinatesFormat ScaledCartesian\n\n")
f.write("%" + "block AtomicCoordinatesAndAtomicSpecies\n")
prtlabel = np.zeros(self.numlist.size)
for index,x in enumerate(self.struct.frac_coords):
for i,Z in enumerate(np.unique(self.numlist)):
if Z == self.numlist[index]:
prtlabel[index] = atomlabel[i]
for index,x in enumerate(self.struct.frac_coords):
f.write("%f %f %f %i\n" %(x[0], x[1], x[2], int(prtlabel[index])))
f.write("%" + "endblock AtomicCoordinatesAndAtomicSpecies\n")
f.write("PAO.SplitNorm 0.20\n")
f.write("PAO.EnergyShift 0.1 eV\n\n\n")
f.write("\n\n\n#SCF INFO\n")
#f.write("kgrid_cutoff %5i Ang\n" %(5))
f.write("MeshCutoff %5i Ry \n" %(self.cutoff))
f.write("MaxSCFIterations %5i \n" %(100))
f.write("DM.MixingWeight %5.1f \n" %(0.7))
f.write("DM.NumberPulay %5i\n" %(3))
f.write("DM.Tolerance %5s\n" %("1.d-9"))
f.write("DM.UseSaveDM %5s .true.\n\n\n")
f.write("xc.functional %5s GGA %5s# Exchange-correlation functional\n")
f.write("xc.authors%5sPBE%5s# Exchange-correlation version\n")
if self.SOC:
f.write("SpinPolarized%5strue%5s# Logical parameters are: yes or no\n")
else:
f.write("SpinPolarized%5sfalse%5s# Logical parameters are: yes or no\n")
f.write("SolutionMethod%5sdiagon%5s # OrderN or Diagon\n")
f.write("ElectronicTemperature%5s25 meV%5s# Temp. for Fermi smearing\n")
f.write("Diag.DivideAndConquer .true.\n")
f.write("Diag.ParallelOverK .true.\n")
f.write("WriteEigenvalues .true.\n")
f.write("WriteKbands .true.\n")
f.write("WriteBands .true.\n")
f.write("%" + "block kgrid_Monkhorst_Pack\n")
f.write("%3i%3i%3i%3i\n" %(self.kpts[0],0,0,0))
f.write("%3i%3i%3i%3i\n" %(0,self.kpts[1],0,0))
f.write("%3i%3i%3i%3i\n" %(0,0,self.kpts[2],0))
f.write("%" + "endblock kgrid_Monkhorst_Pack\n\n\n")
f.write("\n\n\n")
f.write("#\n")
f.write("# Variables related with the Wannierization of the manifolds\n")
f.write("NumberOfBandManifoldsForWannier 1\n")
f.write("%"+"block WannierProjections\n")
f.write("1 # Sequential index of the manifold, from 1 to NumberOfBandManifoldsForWannier\n")
f.write("%i %3i # Indices of the initial and final band of the manifold\n" %(1,self.nbnd))
f.write("%i # Number of bands for Wannier transformation\n" %(self.nbnd))
f.write("num_iter 0 # Number of iterations for the minimization of \Omega\n")
f.write("write_hr # Write the Hamiltonian in the WF basis\n")
f.write("%"+"endblock WannierProjections\n\n")
f.write("%"+"block kMeshforWannier\n")
f.write("%3i%3i%3i\n" %(self.kpts[0],self.kpts[1],self.kpts[2]))
f.write("%"+"endblock kMeshforWannier\n\n\n")
########################
f.write("###Siesta2wannier inputs###\n")
f.write("Siesta2Wannier90.WriteMmn .true.\n")
f.write("Siesta2Wannier90.WriteAmn .true.\n")
f.write("Siesta2Wannier90.WriteEig .true.\n")
f.write("Siesta2Wannier90.NumberOfBands%5i\n" %(self.nbnd))
f.write("\n")
#WRITING SLURM FILE
with open(self.SEEDDIR + "siesta.slurm",'w',newline= '\n') as f:
f.write("#!/bin/bash\n")
#f.write("#SBATCH --ntasks=%i\n" %(self.NCORE))
f.write("#SBATCH --ntasks=%i\n" %(self.NCORE))
f.write("#SBATCH --time=5:00:00\n")
f.write("#SBATCH --error=job.%J.err\n")
f.write("#SBATCH --output=job.%J.out\n")
f.write("#SBATCH --job-name=%s_SIESTA\n" %(self.seedname))
f.write('#SBATCH --mail-user=%s\n' %(self.EMAIL))
f.write("#SBATCH --mail-type=NONE\n\n\n")
f.write('#Select how logs get stored\n')
f.write("mkdir $SLURM_JOB_ID\n")
f.write('export debug_logs="$SLURM_JOB_ID/job_$SLURM_JOB_ID.log"\n')
f.write('export benchmark_logs="$SLURM_JOB_ID/job_$SLURM_JOB_ID.log"\n\n\n')
f.write('#Load Modules\n')
f.write('ml load wannier90\n')
f.write('ml load siesta\n\n\n')
f.write("cd $SLURM_SUBMIT_DIR\n")
f.write('# Create Log File\n')
f.write('echo $SLURM_SUBMIT_DIR')
f.write('echo "JobID: $SLURM_JOB_ID" >> $debug_logs\n')
f.write('echo "Running on $SLURM_JOB_NODELIST" >> $debug_logs\n')
f.write('echo "Running on $SLURM_JOB_NNODES nodes." >> $debug_logs\n')
f.write('echo "Running on $SLURM_JOB_NPROCS processors." >> $debug_logs\n')
f.write('echo "Current working directory is `pwd`" >> $debug_logs\n\n\n')
f.write('# Module debugging\n')
f.write('module list >> $debug_logs\n')
f.write('which mpirun >> $debug_logs\n\n\n')
f.write('#Start Timestamp\n')
f.write('date >> $benchmark_logs\n')
f.write('echo "ulimit -l: " >> $benchmark_logs\n')
f.write('ulimit -l >> $benchmark_logs\n\n\n')
f.write('# run file\n')
f.write('wannier90.x -pp %s' %(self.seedname))
f.write('sleep 3\n')
f.write('mpirun -np %i siesta <%s.fdf> %s.out\n' %(self.NCORE,self.seedname,self.seedname))
f.write('sleep 3\n')
f.write('mv %s.eigW %s.eig\n' %(self.seedname,self.seedname))
f.write('sleep 3\n')
f.write('wannier90.x %s' %(self.seedname))
f.write('grep CONV w90.wout >> Wconv.txt\n')
f.write('echo "Program is finished with exit code $? at: `date`"\n\n\n')
f.write('#End Timestamp\n')
f.write('date >> $benchmark_logs\n')
f.write('echo "ulimit -l" >> $benchmark_logs\n')
f.write('ulimit -l >> $benchmark_logs\n\n\n')
f.write('#Cleanup\n')
f.write('mv job.$SLURM_JOB_ID.err $SLURM_JOB_ID/\n')
f.write('mv job.$SLURM_JOB_ID.out $SLURM_JOB_ID/\n')
f.write('rm -rf $SLURM_JOB_ID\n')
#WRITING CLEAN DFT FILE
with open(self.SEEDDIR + "cleandft.sh",'w',newline='\n') as f:
f.write("rm INPUT_TMP.*\n")
f.write("rm *.ion\n")
f.write("rm *.log\n")
f.write("rm *ion.xml\n")
f.write("rm *.XV\n")
f.write("rm *.FA\n")
f.write("rm *.DM\n")
f.write("rm *.ORB_INDX\n")
f.write("rm OCCS\n")
f.write("rm MESSAGES\n")
f.write("rm *.BONDS\n")
f.write("rm *.BONDS_FINAL\n")
f.write("rm *.KP\n")
f.write("rm *.STRUCT_OUT\n")
f.write("rm *.xml\n")
f.write("rm *.alloc\n")
f.write("rm FORCE_STRESS\n")
f.write("rm NON_TRIMMED_KP_LIST\n")
f.write("rm CLOCK\n")
f.write("rm BASIS_ENTHALPY\n")
f.write("rm BASIS_HARRIS_ENTHALPY\n")
f.write("rm Wconv.txt\n")
f.write("rm *.werr\n")
f.write("rm *.wout\n")
f.write("rm *.nnkp\n")
f.write("rm *.EIG\n")
f.write("rm *.xyz\n")
f.write("rm *_wsvec.dat\n")
f.write("rm *.mmn\n")
f.write("rm *.eig\n")
f.write("rm *.amn\n")
f.write("rm *.err\n")
f.write("rm *_NORMAL_EXIT\n")
f.write("rm *.DOS \n")
f.write("rm *.chk \n")
f.write("rm *.PDOS\n")
f.write("rm *.out\n")
f.write("rm *.dat\n")
#########WANNIER90 FILE####################33
with open(self.SEEDDIR + self.seedname + ".win",'w',newline='\n') as f:
f.write("write_hr = .TRUE.\n")
f.write("write_xyz = .TRUE.\n")
f.write("!wannier_plot = .TRUE. \n")
f.write("spinors = %s\n" %(self.lspinorb))
f.write("num_wann = %i\n" %(self.wan))
f.write("dis_num_iter=1000\n")
f.write("!trial_step=50\n")
f.write("num_iter = 1000\n\n\n\n")
f.write("begin unit_cell_cart\n")
f.write(str(self.struct.lattice) + "\n") ### atomic structure
f.write("end unit_cell_cart\n\n\n")
f.write("begin atoms_frac\n")
for index,x in enumerate(self.struct.frac_coords):
f.write("%s %f %f %f\n" %(str(self.struct.species[index]),x[0], x[1], x[2]))
f.write("end atoms_frac\n\n\n")
f.write("begin projections \n")
f.write("random \n")
f.write("end projections\n\n\n")
f.write(kmesh.WANNIER(self.kpts[0],self.kpts[1],self.kpts[2]))
#WRITE Wanniertools file
with open(self.SEEDDIR + "WT/wt.in",'w',newline='\n') as f:
f.write("#### wt file ###########\n")
f.write("&TB_FILE\n")
f.write("Hrfile = '%s_hr.dat'\n" %(self.seedname))
f.write("Package = 'ESPRESSO'\n")
f.write("/\n\n\n")
f.write("LATTICE\n")
f.write("Angstrom\n")
f.write(str(self.struct.lattice) + "\n\n\n") ### atomic structure
f.write("ATOM_POSITIONS\n")
f.write("%i !Number of atoms for projectors\n" %(len(self.struct.frac_coords)))
f.write("Direct ! Direct or Cartisen coordinateS\n")
for index,x in enumerate(self.struct.frac_coords):
f.write("%s %f %f %f\n" %(str(self.struct.species[index]),x[0], x[1], x[2]))
f.write("\n\n\n\n")
f.write("PROJECTORS\n")
#### Places prjectors and stoms into PRJCARD in wannier tools
proj = int(self.WTwan/self.natom)
proj_rem = self.WTwan % self.natom
sumproj = 0
PROJPARAM = ""
projector = ["s", "pz","px", "py"]
LATPARAM = str(self.struct.lattice) + "\n" ### atomic structur
PROJCARD =""
ATOMCARD = ""
appen = 0 #### append number
for index,atom in enumerate(self.struct.species):
if proj_rem > 0:
appen = 1
proj_rem = proj_rem - 1
PROJPARAM += str(proj + appen) + " "
PROJCARD += str(atom) + " " + ' '.join(map(str,projector)) + "\n"
#print(str(atom) + str(proj + appen))
sumproj += proj + appen
#print(sumproj)
appen = 0
f.write(PROJPARAM + "\n")
f.write(PROJCARD)
f.write("\n\n\n")
f.write("&CONTROL\n")
f.write("! BULK BAND CALCULATIONS \n")
f.write("BulkBand_calc = F\n")
f.write("BulkBand_plane_calc = F \n")
f.write("BulkFS_calc = F \n")
f.write("BulkFS_Plane_calc = F\n")
f.write("SlabBand_calc = F\n")
f.write("Dos_calc = F\n")
f.write("! BULK GAP\n")
f.write("BulkGap_cube_calc = F\n")
f.write("BulkGap_plane_calc = F\n")
f.write("! SURFACE STATES\n")
f.write("SlabSS_calc = T\n")
f.write("SlabArc_calc = T\n")
f.write("SlabSpintexture_calc = F\n")
f.write("! TOPO INV\n")
f.write("wanniercenter_calc = F\n")
f.write("BerryPhase_calc = F\n")
f.write("BerryCurvature_calc = F\n")
f.write("BerryCurvature_slab_calc = F\n")
f.write("Z2_3D_calc = F\n")
f.write("WeylChirality_calc = F\n")
f.write("NLChirality_calc = F\n")
f.write("Chern_3D_calc = F\n")
f.write("MirrorChern_calc = F\n")
f.write("!QUASIPARTICLE (STM)\n")
f.write("JDos_calc = F\n")
f.write("FindNodes_calc = F\n")
f.write("EffectiveMass_calc = F\n")
f.write("AHC_calc = F\n")
f.write("Boltz_OHE_calc = F\n")
f.write("LOTO_correction = F\n")
f.write("OrbitalTexture_calc = F\n")
f.write("OrbitalTexture_3D_calc = F\n")
f.write("LandauLevel_k_calc = F\n")
f.write("LandauLevel_B_calc = F\n")
f.write("LandauLevel_wavefunction_calc = F\n")
f.write("Fit_kp_calc = F\n")
f.write("DMFT_MAG_calc = F\n")
f.write("Translate_to_WS_calc= F\n")
f.write("LandauLevel_kplane_calc = F\n")
f.write("LandauLevel_k_dos_calc = F\n")
f.write("LandauLevel_B_dos_calc = F \n/\n\n\n")
f.write("&SYSTEM\n")
f.write("NSLAB = 20 ! for thin film system\n")
f.write("NumOccupied = %i ! NumOccupied\n" %(self.WTwan/2))
soc = 0
if self.SOC:
soc = 1
f.write("SOC = %i\n" %(soc))
f.write("E_FERMI = 0.0\n")
f.write("surf_onsite= 0.0\n")
f.write("/\n\n\n")
f.write("&PARAMETERS \n")
f.write("Eta_Arc = 0.01 ! infinite small value, like brodening \n")
f.write("E_arc = 0.0 ! energy level for contour plot of spectrum\n")
f.write("OmegaNum = 401 ! omega number \n")
f.write("OmegaMin = -1.0 ! energy interval\n")
f.write("OmegaMax = 1.0 ! energy interval\n")
f.write("Nk1 = 101 ! number k points odd number would be better\n")
f.write("Nk2 = 101 ! number k points odd number would be better\n")
f.write("Nk3 = 11 ! number k points odd number would be better\n")
f.write("NP = 2 ! number of principle layers\n")
f.write("Gap_threshold = 0.01 ! threshold for FindNodes_calc output\n")
f.write("/\n\n\n")
f.write("MILLER_INDEX\n")
f.write("0 0 1\n\n\n")
f.write("KPATH_BULK ! k point path \n")
f.write("4 ! number of k line only for bulk band\n")
f.write("G 0.00000 0.00000 0.0000 Z 0.00000 0.00000 0.5000\n")
f.write("Z 0.00000 0.00000 0.5000 F 0.50000 0.50000 0.0000\n")
f.write("F 0.50000 0.50000 0.0000 G 0.00000 0.00000 0.0000\n ")
f.write("G 0.00000 0.00000 0.0000 L 0.50000 0.00000 0.0000 \n\n\n\n")
###
f.write("KPATH_SLAB \n")
f.write("4 ! numker of k line for 2D case \n")
f.write("Y 0.0 0.5 G 0.0 0.0\n")
f.write("G 0.0 0.0 X 0.5 0.0\n")
f.write("X 0.5 0.0 M 0.5 0.5\n ")
f.write("M 0.5 0.5 G 0.0 0.0\n\n\n")
###
f.write("KPLANE_SLAB \n")
f.write("-0.5 -0.5 ! Original point for 2D k plane\n")
f.write("1.0 0.0 ! The first vector to define 2D k plane \n")
f.write("0.0 1.0 ! The second vector to define 2D k plane for arc plots\n\n\n")
####
f.write("KCUBE_BULK\n")
f.write("0.50 0.50 0.50 ! Original point for 3D k plane \n")
f.write("1.00 0.00 0.00 ! The first vector to define 3d k space plane\n")
f.write("0.00 1.00 0.00 ! The second vector to define 3d k space plane\n ")
f.write("0.00 0.00 1.00 ! The third vector to define 3d k cube\n\n")
f.write("KPLANE_BULK\n")
f.write("0.00 0.00 0.00 ! Original point for 3D k plane \n")
f.write("1.00 0.00 0.00 ! The first vector to define 3d k space plane\n")
f.write("0.00 1.00 0.00 ! The second vector to define 3d k space plane\n\n\n")
with open(self.SEEDDIR + "WT/wt.slurm",'w',newline= '\n') as f:
f.write("#!/bin/bash\n")
f.write("#SBATCH --ntasks=%i\n" %(self.NCORE))
f.write("#SBATCH --time=5-12:00:00\n")
f.write("#SBATCH --error=job.%J.err\n")
f.write("#SBATCH --output=job.%J.out\n")
f.write("#SBATCH --job-name=%s_WT\n" %(self.seedname))
f.write('#SBATCH --mail-user=%s\n' %(self.EMAIL))
f.write("#SBATCH --mail-type=ALL\n\n\n")
f.write('#Select how logs get stored\n')
f.write("mkdir $SLURM_JOB_ID\n")
f.write('export debug_logs="$SLURM_JOB_ID/job_$SLURM_JOB_ID.log"\n')
f.write('export benchmark_logs="$SLURM_JOB_ID/job_$SLURM_JOB_ID.log"\n\n\n')
f.write('#Load Modules\n')
f.write('ml load wannier_tools\n\n\n')
f.write("cd $SLURM_SUBMIT_DIR\n")
f.write('# Create Log File\n')
f.write('echo $SLURM_SUBMIT_DIR')
f.write('echo "JobID: $SLURM_JOB_ID" >> $debug_logs\n')
f.write('echo "Running on $SLURM_JOB_NODELIST" >> $debug_logs\n')
f.write('echo "Running on $SLURM_JOB_NNODES nodes." >> $debug_logs\n')
f.write('echo "Running on $SLURM_JOB_NPROCS processors." >> $debug_logs\n')
f.write('echo "Current working directory is `pwd`" >> $debug_logs\n\n\n')
f.write('# Module debugging\n')
f.write('module list >> $debug_logs\n')
f.write('which mpirun >> $debug_logs\n\n\n')
f.write('#Start Timestamp\n')
f.write('date >> $benchmark_logs\n')
f.write('echo "ulimit -l: " >> $benchmark_logs\n')
f.write('ulimit -l >> $benchmark_logs\n\n\n')
f.write('# run file\n')
f.write('mpirun -np %i wt.x\n' %(self.NCORE))
f.write('echo "Program is finished with exit code $? at: `date`"\n\n\n')
f.write('#End Timestamp\n')
f.write('date >> $benchmark_logs\n')
f.write('echo "ulimit -l" >> $benchmark_logs\n')
f.write('ulimit -l >> $benchmark_logs\n\n\n')
f.write('#Cleanup\n')
f.write('mv job.$SLURM_JOB_ID.err $SLURM_JOB_ID/\n')
f.write('mv job.$SLURM_JOB_ID.out $SLURM_JOB_ID/\n')
f.write('rm -rf $SLURM_JOB_ID\n')
def generate(self):
with open(self.SEEDDIR + 'pbe/' + "INCAR", 'w', newline='\n') as f:
f.write("ALGO = Fast\n")
f.write("EDIFF = 1.0e-8\n")
f.write("ENCUT = 500\n")
f.write("ISIF = 2\n")
f.write("ISMEAR = -5\n")
f.write("KPAR = 2\n")
f.write("LCHARG = .FALSE.\n")
f.write("LREAL = .FALSE.\n")
f.write("NBANDS = %i\n" % (self.NBND))
f.write("NEDOS = 2000\n")
f.write("NPAR = 1\n")
f.write("PREC = Accurate\n")
f.write("SYSTEM = %s\n" % (self.seedname))
with open(self.SEEDDIR + 'pbe/' + "KPOINTS", 'w', newline='\n') as f:
f.write("Automatic %ix%ix%i\n" %
(self.kpts[0], self.kpts[1], self.kpts[2]))
f.write("0\n")
f.write("Gamma\n")
f.write("\t%i %i %i" % (self.kpts[0], self.kpts[1], self.kpts[2]))
with open(self.SEEDDIR + 'pbe/' + "POSCAR", 'w', newline='\n') as f:
f.write("%s\n" % (self.seedname))
f.write("1\n")
f.write(str(self.lattice) + "\n")
f.write("\t" + ' '.join(map(str, self.UNIQUE_ATOMS)) + "\n")
typnum = np.zeros(self.UNIQUE_ATOMS.size)
for i in range(0, self.UNIQUE_ATOMS.size):
typnum[i] = np.asarray(
np.where(self.atomic_numbers == self.atomnum[i])).size
f.write("\t" + ' '.join(map(str, typnum)) + "\n")
f.write("Direct\n")
for index, x in enumerate(self.cord):
f.write("%f %f %f\n" % (x[0], x[1], x[2]))
#def write_hse(self):
with open(self.SEEDDIR + 'HSE06/' + "INCAR", 'w', newline='\n') as f:
f.write("ALGO = Fast\n")
f.write("EDIFF = 1.0e-8\n")
f.write("ENCUT = 500\n")
f.write("ISIF = 2\n")
f.write("ISMEAR = -5\n")
f.write("KPAR = 2\n")
f.write("LCHARG = .FALSE.\n")
f.write("LREAL = .FALSE.\n")
f.write("NBANDS = %i\n" % (self.NBND))
f.write("NEDOS = 2000\n")
f.write("NPAR = 1\n")
f.write("PREC = Accurate\n")
f.write("SYSTEM = %s\n" % (self.seedname))
f.write("LHFCALC = .TRUE.\n")
f.write("HFSCREEN = 0.2\n")
with open(self.SEEDDIR + 'HSE06/' + "KPOINTS", 'w', newline='\n') as f:
f.write("Automatic %ix%ix%i\n" %
(self.kpts[0], self.kpts[1], self.kpts[2]))
f.write("0\n")
f.write("Gamma\n")
f.write("\t%i %i %i" % (self.kpts[0], self.kpts[1], self.kpts[2]))
with open(self.SEEDDIR + 'HSE06/' + "POSCAR", 'w', newline='\n') as f:
f.write("%s\n" % (self.seedname))
f.write("1\n")
f.write(str(self.lattice) + "\n")
f.write("\t" + ' '.join(map(str, self.UNIQUE_ATOMS)) + "\n")
typnum = np.zeros(self.UNIQUE_ATOMS.size)
for i in range(0, self.UNIQUE_ATOMS.size):
typnum[i] = np.asarray(
np.where(self.atomic_numbers == self.atomnum[i])).size
f.write("\t" + ' '.join(map(str, typnum)) + "\n")
f.write("Direct\n")
for index, x in enumerate(self.cord):
f.write("%f %f %f\n" % (x[0], x[1], x[2]))
#def write_w90(self):
with open(self.SEEDDIR + 'W90/' + "INCAR", 'w', newline='\n') as f:
f.write("ALGO = Fast\n")
f.write("EDIFF = 1.0e-8\n")
f.write("ENCUT = 500\n")
f.write("ISIF = 2\n")
f.write("ISMEAR = -5\n")
f.write("KPAR = 2\n")
f.write("LCHARG = .FALSE.\n")
f.write("LREAL = .FALSE.\n")
f.write("NBANDS = %i\n" % (self.NBND))
f.write("NEDOS = 2000\n")
f.write("NPAR = 1\n")
f.write("PREC = Accurate\n")
f.write("SYSTEM = %s\n" % (self.seedname))
f.write("LHFCALC = .TRUE.\n")
f.write("HFSCREEN = 0.2\n")
f.write("LWANNIER90 = .TRUE.\n")
with open(self.SEEDDIR + 'W90/' + "KPOINTS", 'w', newline='\n') as f:
f.write("Automatic %ix%ix%i\n" %
(self.kpts[0], self.kpts[1], self.kpts[2]))
f.write("0\n")
f.write("Gamma\n")
f.write("\t%i %i %i" % (self.kpts[0], self.kpts[1], self.kpts[2]))
with open(self.SEEDDIR + 'W90/' + "POSCAR", 'w', newline='\n') as f:
f.write("%s\n" % (self.seedname))
f.write("1\n")
f.write(str(self.lattice) + "\n")
f.write("\t" + ' '.join(map(str, self.UNIQUE_ATOMS)) + "\n")
typnum = np.zeros(self.UNIQUE_ATOMS.size)
for i in range(0, self.UNIQUE_ATOMS.size):
typnum[i] = np.asarray(
np.where(self.atomic_numbers == self.atomnum[i])).size
f.write("\t" + ' '.join(map(str, typnum)) + "\n")
f.write("Direct\n")
for index, x in enumerate(self.cord):
f.write("%f %f %f\n" % (x[0], x[1], x[2]))
with open(self.SEEDDIR + 'W90/wannier90.win', 'w', newline='\n') as f:
f.write("!write_hr = .TRUE.\n")
f.write("!write_xyz = .TRUE.\n")
f.write("guiding_centres= .TRUE.\n")
f.write("!wannier_plot = .TRUE. \n")
f.write("spinors = %s\n" % (self.lspinorb))
f.write("num_wann = %i\n" % (self.wan))
f.write("dis_num_iter=1000\n")
f.write("num_iter = 2000\n\n\n\n")
f.write("begin unit_cell_cart\n")
f.write(str(self.lattice) + "\n") ### atomic structure
f.write("end unit_cell_cart\n\n\n")
f.write("begin atoms_frac\n")
for index, x in enumerate(self.cord):
f.write("%s %f %f %f\n" %
(str(self.species[index]), x[0], x[1], x[2]))
f.write("end atoms_frac\n\n\n")
f.write("begin projections \n")
f.write("random \n")
f.write("end projections\n\n\n")
f.write(kmesh.WANNIER(self.kpts[0], self.kpts[1], self.kpts[2]))
#def write_wt(self):
with open(self.SEEDDIR + "WT/wt.in", 'w', newline='\n') as f:
f.write("#### wt file ###########\n")
f.write("&TB_FILE\n")
f.write("Hrfile = '%s_hr.dat'\n" % (self.seedname))
f.write("Package = 'ESPRESSO'\n")
f.write("/\n\n\n")
f.write("LATTICE\n")
f.write("Angstrom\n")
f.write(str(self.lattice) + "\n\n\n") ### atomic structure
f.write("ATOM_POSITIONS\n")
f.write("%i !Number of atoms for projectors\n" % (len(self.cord)))
f.write("Direct ! Direct or Cartisen coordinateS\n")
for index, x in enumerate(self.cord):
f.write("%s %f %f %f\n" %
(str(self.species[index]), x[0], x[1], x[2]))
f.write("\n\n\n\n")
f.write("PROJECTORS\n")
#### Places prjectors and stoms into PRJCARD in wannier tools
proj = int(self.WTwan / self.natom)
proj_rem = self.WTwan % self.natom
sumproj = 0
PROJPARAM = ""
projector = ["s", "pz", "px", "py"]
LATPARAM = str(self.lattice) + "\n" ### atomic structur
PROJCARD = ""
ATOMCARD = ""
appen = 0 #### append number
for index, atom in enumerate(self.species):
if proj_rem > 0:
appen = 1
proj_rem = proj_rem - 1
PROJPARAM += str(proj + appen) + " "
PROJCARD += str(atom) + " " + ' '.join(map(str,
projector)) + "\n"
#print(str(atom) + str(proj + appen))
sumproj += proj + appen
#print(sumproj)
appen = 0
f.write(PROJPARAM + "\n")
f.write(PROJCARD)
f.write("\n\n\n")
f.write("&CONTROL\n")
f.write("! BULK BAND CALCULATIONS \n")
f.write("BulkBand_calc = F\n")
f.write("BulkBand_plane_calc = F \n")
f.write("BulkFS_calc = F \n")
f.write("BulkFS_Plane_calc = F\n")
f.write("SlabBand_calc = F\n")
f.write("Dos_calc = F\n")
f.write("! BULK GAP\n")
f.write("BulkGap_cube_calc = F\n")
f.write("BulkGap_plane_calc = F\n")
f.write("! SURFACE STATES\n")
f.write("SlabSS_calc = T\n")
f.write("SlabArc_calc = T\n")
f.write("SlabSpintexture_calc = F\n")
f.write("! TOPO INV\n")
f.write("wanniercenter_calc = F\n")
f.write("BerryPhase_calc = F\n")
f.write("BerryCurvature_calc = F\n")
f.write("BerryCurvature_slab_calc = F\n")
f.write("Z2_3D_calc = F\n")
f.write("WeylChirality_calc = F\n")
f.write("NLChirality_calc = F\n")
f.write("Chern_3D_calc = F\n")
f.write("MirrorChern_calc = F\n")
f.write("!QUASIPARTICLE (STM)\n")
f.write("JDos_calc = F\n")
f.write("FindNodes_calc = F\n")
f.write("EffectiveMass_calc = F\n")
f.write("AHC_calc = F\n")
f.write("Boltz_OHE_calc = F\n")
f.write("LOTO_correction = F\n")
f.write("OrbitalTexture_calc = F\n")
f.write("OrbitalTexture_3D_calc = F\n")
f.write("LandauLevel_k_calc = F\n")
f.write("LandauLevel_B_calc = F\n")
f.write("LandauLevel_wavefunction_calc = F\n")
f.write("Fit_kp_calc = F\n")
f.write("DMFT_MAG_calc = F\n")
f.write("Translate_to_WS_calc= F\n")
f.write("LandauLevel_kplane_calc = F\n")
f.write("LandauLevel_k_dos_calc = F\n")
f.write("LandauLevel_B_dos_calc = F \n/\n\n\n")
f.write("&SYSTEM\n")
f.write("NSLAB = 20 ! for thin film system\n")
f.write("NumOccupied = %i ! NumOccupied\n" %
(self.WTwan / 2))
soc = 0
if self.SOC:
soc = 1
f.write("SOC = %i\n" % (soc))
f.write("E_FERMI = 0.0\n")
f.write("surf_onsite= 0.0\n")
f.write("/\n\n\n")
f.write("&PARAMETERS \n")
f.write(
"Eta_Arc = 0.01 ! infinite small value, like brodening \n")
f.write(
"E_arc = 0.0 ! energy level for contour plot of spectrum\n"
)
f.write("OmegaNum = 401 ! omega number \n")
f.write("OmegaMin = -1.0 ! energy interval\n")
f.write("OmegaMax = 1.0 ! energy interval\n")
f.write(
"Nk1 = 101 ! number k points odd number would be better\n"
)
f.write(
"Nk2 = 101 ! number k points odd number would be better\n"
)
f.write(
"Nk3 = 11 ! number k points odd number would be better\n"
)
f.write("NP = 2 ! number of principle layers\n")
f.write(
"Gap_threshold = 0.01 ! threshold for FindNodes_calc output\n")
f.write("/\n\n\n")
f.write("MILLER_INDEX\n")
f.write("0 0 1\n\n\n")
f.write("KPATH_BULK ! k point path \n")
f.write("4 ! number of k line only for bulk band\n")
f.write("G 0.00000 0.00000 0.0000 Z 0.00000 0.00000 0.5000\n")
f.write("Z 0.00000 0.00000 0.5000 F 0.50000 0.50000 0.0000\n")
f.write("F 0.50000 0.50000 0.0000 G 0.00000 0.00000 0.0000\n ")
f.write(
"G 0.00000 0.00000 0.0000 L 0.50000 0.00000 0.0000 \n\n\n\n")
###
f.write("KPATH_SLAB \n")
f.write("4 ! numker of k line for 2D case \n")
f.write("Y 0.0 0.5 G 0.0 0.0\n")
f.write("G 0.0 0.0 X 0.5 0.0\n")
f.write("X 0.5 0.0 M 0.5 0.5\n ")
f.write("M 0.5 0.5 G 0.0 0.0\n\n\n")
###
f.write("KPLANE_SLAB \n")
f.write("-0.5 -0.5 ! Original point for 2D k plane\n")
f.write("1.0 0.0 ! The first vector to define 2D k plane \n")
f.write(
"0.0 1.0 ! The second vector to define 2D k plane for arc plots\n\n\n"
)
####
f.write("KCUBE_BULK\n")
f.write("0.50 0.50 0.50 ! Original point for 3D k plane \n")
f.write(
"1.00 0.00 0.00 ! The first vector to define 3d k space plane\n"
)
f.write(
"0.00 1.00 0.00 ! The second vector to define 3d k space plane\n "
)
f.write(
"0.00 0.00 1.00 ! The third vector to define 3d k cube\n\n"
)
f.write("KPLANE_BULK\n")
f.write("0.00 0.00 0.00 ! Original point for 3D k plane \n")
f.write(
"1.00 0.00 0.00 ! The first vector to define 3d k space plane\n"
)
f.write(
"0.00 1.00 0.00 ! The second vector to define 3d k space plane\n\n\n"
)
with open(self.SEEDDIR + "WT/wt.slurm", 'w', newline='\n') as f:
f.write("#!/bin/bash\n")
f.write("#SBATCH --ntasks=%i\n" % (self.NCORE))
f.write("#SBATCH --time=5-12:00:00\n")
f.write("#SBATCH --error=job.%J.err\n")
f.write("#SBATCH --output=job.%J.out\n")
f.write("#SBATCH --job-name=%s_WT\n" % (self.seedname))
f.write('#SBATCH --mail-user=%s\n' % (self.EMAIL))
f.write("#SBATCH --mail-type=ALL\n\n\n")
f.write('#Select how logs get stored\n')
f.write("mkdir $SLURM_JOB_ID\n")
f.write(
'export debug_logs="$SLURM_JOB_ID/job_$SLURM_JOB_ID.log"\n')
f.write(
'export benchmark_logs="$SLURM_JOB_ID/job_$SLURM_JOB_ID.log"\n\n\n'
)
f.write('#Load Modules\n')
f.write('ml load wannier_tools\n\n\n')
f.write("cd $SLURM_SUBMIT_DIR\n")
f.write('# Create Log File\n')
f.write('echo $SLURM_SUBMIT_DIR')
f.write('echo "JobID: $SLURM_JOB_ID" >> $debug_logs\n')
f.write('echo "Running on $SLURM_JOB_NODELIST" >> $debug_logs\n')
f.write(
'echo "Running on $SLURM_JOB_NNODES nodes." >> $debug_logs\n')
f.write(
'echo "Running on $SLURM_JOB_NPROCS processors." >> $debug_logs\n'
)
f.write(
'echo "Current working directory is `pwd`" >> $debug_logs\n\n\n'
)
f.write('# Module debugging\n')
f.write('module list >> $debug_logs\n')
f.write('which mpirun >> $debug_logs\n\n\n')
f.write('#Start Timestamp\n')
f.write('date >> $benchmark_logs\n')
f.write('echo "ulimit -l: " >> $benchmark_logs\n')
f.write('ulimit -l >> $benchmark_logs\n\n\n')
f.write('# run file\n')
f.write('mpirun -np %i wt.x\n' % (self.NCORE))
f.write(
'echo "Program is finished with exit code $? at: `date`"\n\n\n'
)
f.write('#End Timestamp\n')
f.write('date >> $benchmark_logs\n')
f.write('echo "ulimit -l" >> $benchmark_logs\n')
f.write('ulimit -l >> $benchmark_logs\n\n\n')
f.write('#Cleanup\n')
f.write('mv job.$SLURM_JOB_ID.err $SLURM_JOB_ID/\n')
f.write('mv job.$SLURM_JOB_ID.out $SLURM_JOB_ID/\n')
f.write('rm -rf $SLURM_JOB_ID\n')
#def write_slurm(self):
with open(self.SEEDDIR + "vsp.slurm", 'w', newline='\n') as f:
f.write("#!/bin/bash\n")
f.write("#SBATCH --ntasks=%i\n" % (self.NCORE))
f.write("#SBATCH --time=10:00:00\n")
f.write("#SBATCH --error=job.%J.err\n")
f.write("#SBATCH --output=job.%J.out\n")
f.write("#SBATCH --job-name=%s_NSCF\n" % (self.seedname))
f.write('#SBATCH --mail-user=%s\n' % (self.EMAIL))
f.write("#SBATCH --mail-type=ALL\n\n\n")
f.write('#Select how logs get stored\n')
f.write("mkdir $SLURM_JOB_ID\n")
f.write(
'export debug_logs="$SLURM_JOB_ID/job_$SLURM_JOB_ID.log"\n')
f.write(
'export benchmark_logs="$SLURM_JOB_ID/job_$SLURM_JOB_ID.log"\n\n\n'
)
f.write('#Load Modules\n')
f.write('ml load espresso\n\n\n')
f.write("cd $SLURM_SUBMIT_DIR\n")
f.write('# Create Log File\n')
f.write('echo $SLURM_SUBMIT_DIR')
f.write('echo "JobID: $SLURM_JOB_ID" >> $debug_logs\n')
f.write('echo "Running on $SLURM_JOB_NODELIST" >> $debug_logs\n')
f.write(
'echo "Running on $SLURM_JOB_NNODES nodes." >> $debug_logs\n')
f.write(
'echo "Running on $SLURM_JOB_NPROCS processors." >> $debug_logs\n'
)
f.write(
'echo "Current working directory is `pwd`" >> $debug_logs\n\n\n'
)
f.write('# Module debugging\n')
f.write('module list >> $debug_logs\n')
f.write('which mpirun >> $debug_logs\n\n\n')
f.write('#Start Timestamp\n')
f.write('date >> $benchmark_logs\n')
f.write('echo "ulimit -l: " >> $benchmark_logs\n')
f.write('ulimit -l >> $benchmark_logs\n\n\n')
f.write('# run file\n')
f.write('mpirun -n %i vasp_std\n' % (self.NCORE))
f.write(
'echo "Program is finished with exit code $? at: `date`"\n\n\n'
)
f.write('#End Timestamp\n')
f.write('date >> $benchmark_logs\n')
f.write('echo "ulimit -l" >> $benchmark_logs\n')
f.write('ulimit -l >> $benchmark_logs\n\n\n')
f.write('#Cleanup\n')
f.write('mv job.$SLURM_JOB_ID.err $SLURM_JOB_ID/\n')
f.write('mv job.$SLURM_JOB_ID.out $SLURM_JOB_ID/\n')
f.write('rm -rf $SLURM_JOB_ID\n')
f.write('#sbatch p2w.slurm\n')