def __init__(self, args):
self.dft = args.dft
self.np = args.np
self.structurename = args.structurename
self.nowin = args.nowin
# Update the total number of bands after DFT calculation.
# If you don't want this set flag nowin.
self.updatewanbands = True
self.wanbands = 0
# import the VASP class. This can be used for other DFT codes as well.
self.create_DFTmu()
self.DFT = VASP.VASP_class(dft=self.dft,
structurename=self.structurename)
# Initial guess for Fermi energy
self.DFT.EFERMI = 7.0
# Wannier parameters
self.kmeshtol = 1e-06
self.dos_kmesh = 64
self.num_iter = 1000
# create bands_plot directory
if not os.path.exists("bands_plot"):
os.makedirs("bands_plot")
# Starting the calculation
if self.dft == "siesta":
self.fdf_to_poscar()
self.dft_run()
self.postw90_run()
self.calculator()
idx[d_orb.index(orb)] = loc_idx
sym_idx.append(idx.tolist())
#print sym_idx
# for at in ats:
# for i,ats in enumerate(cor_at):
# for ii,at in enumerate(ats):
# at_idx=int(at[-1])-1
# d_orb=TB.TB_orbs[at]
# for j,orbs in enumerate(cor_orb[i]):
# if ii==0: loc_idx+=1
# for orb in orbs:
# idx[d_orb.index(orb)]=loc_idx
# sym_idx[at_idx].append(idx)
DMFT = DMFT_MOD.DMFT_class(p, pC, TB)
DFT = VASP.VASP_class()
ETOT_old = 0.0
ETOT2_old = 0.0
ETOT = 0.0
ETOT2 = 0.0
CHGDIFF = 0.
CHGDIFF2 = 0.
shutil.copy2('sig.inp', 'sig.inp.0')
for itt in range(p['Niter']):
main_out.write('--- Starting Charge loop ' + str(itt + 1) + now() +
'---')
main_out.write('\n')
main_out.flush()
[9.77481016, 7.79245421, 7.98959054],
[15.22469429, 7.79201704, 7.98943559],
[8.46632515, 10.17202968, 7.99540983],
[8.53256540, 5.62907836, 7.99458204],
[16.46612157, 5.62801086, 7.99582303],
[16.53337285, 10.17092209, 7.99467923],
[11.13544681, 19.42130452, 7.97773530],
[13.86508896, 19.42136867, 7.97785955],
[5.82074273, 10.21941636, 7.97126648],
[19.17882835, 10.21844766, 7.97010409],
[7.18631774, 7.85639597, 7.96997322],
[17.81284174, 7.85499234, 7.97028496]]
# hlcluster.py inputfile.gjf -n +n n-n
lattice, basis, elements, num_atoms, selectiveflag, coordinate_type, coordinates, selective = VASP.read_poscar(
'POSCAR')
with open(sys.argv[1]) as IN:
input_file = IN.readlines()
space = re.compile(r'\s+')
a = int(sys.argv[2]) - 1
b = int(sys.argv[3]) - 1
temp = sys.argv[4].split('-')
c = int(temp[0]) - 1
d = int(temp[1])
gjfcoord = []
for i in xrange(5, len(input_file)):
if input_file[i].strip() == '':
break
line = space.split(input_file[i].strip())
gjfcoord.append(
# -*- coding=utf-8 -*-
import VASP
import sys
# if len(sys.argv) < 4:
# print "Usage: gvextend.py file1 file2 ... X Y Z"
# print "Try again!"
# exit(0)
elements, num_atoms, coordinates = VASP.read_gjf('temp.gjf')
print elements
print num_atoms
loc_idx = 0
for i, ats in enumerate(cor_at):
d_orb = TB.TB_orbs[ats[0]]
# idx=zeros(len(d_orb),dtype=int)
idx = zeros(len(d_orb) * p["nspin"], dtype=int)
for ispin in range(p["nspin"]):
for j, orbs in enumerate(cor_orb[i]):
loc_idx += 1
for orb in orbs:
# idx[d_orb.index(orb)]=loc_idx
idx[d_orb.index(orb) + ispin * len(d_orb)] = loc_idx
sym_idx.append(idx.tolist())
DMFT = DMFT_MOD.DMFT_class(p, pC, TB)
DFT = VASP.VASP_class(dft=args.dft,
structurename=args.structurename,
aiida=args.aiida)
ETOT_old = 0.0
ETOT2_old = 0.0
ETOT = 0.0
ETOT2 = 0.0
CHGDIFF = 0.0
CHGDIFF2 = 0.0
shutil.copy2("sig.inp", "sig.inp.0")
# ----------------------- Starting DFT+DMFT loop -----------------------------
for itt in range(p["Niter"]):
main_out.write("--- Starting charge loop " + str(itt + 1) + now() +
"---")
#!/home/noische/python
from VASP import *
import numpy as np
from numpy import sqrt
import bgftools
m = VASP()
#h = m._latticeVectors = [[5.0, 0, 0], [5*sqrt(2)/2, 5*sqrt(2)/2, 0], [0, 0, 5.0]]
h = m._latticeVectors = [[5.0, 0, 0], [5, 5, 0], [0, 0, 5.0]]
hinv = m._inv_latticeVectors = np.linalg.inv(m._latticeVectors)
#dim = [1.0, 1.0, 2.0]
#points = [[0, 0, 0], [1, 1, 2], [1, 0, 2], [0.5, 0.5, 1.5]]
points = [[2, 1, 0], [2, 3, 0]]
for i in points:
for j in points:
if i==j: continue;
print("vasp dist: " + str(i) + str(j) + str(m.distance(i, j, h, hinv)))
#print("pbc_dist: " + str(i) + str(j) + str(bgftools.pbc_dist(i, j, dim)))
print("")
print(sqrt(5))
print(sqrt(10))
#!/home/noische/python
import sys
import nutils as nu
from VASP import *
if len(sys.argv) < 2: nu.die(sys.argv[0] + " poscar_file bgf_file")
m = VASP(sys.argv[1])
value = raw_input("Want to create bonds for S? ")
if value: m.find_S_bonds()
m.saveBGF(sys.argv[2])
def __init__(self, args):
"""
Contains common functions for all methods.
This launches the dmft calculation as well.
"""
print("Initializing calculation...\n")
if os.path.exists("para_com.dat"):
fipa = open("para_com.dat", "r")
self.para_com = str(fipa.readline())[:-1]
fipa.close()
else:
self.para_com = "mpirun -np 40"
if os.path.exists("para_com_dft.dat"):
fid = open("para_com_dft.dat")
self.para_com_dft = str(fid.readline())[:-1]
fid.close()
else:
self.para_com_dft = self.para_com
# initial chemical potential
self.create_DFTmu()
# import the VASP class. This can be used for other DFT codes as well.
self.DFT = VASP.VASP_class(dft=args.dft,
aiida=args.aiida,
structurename=args.structurename)
self.dir = os.getcwd() # dft running directory (current directory)
self.structurename = (
args.structurename
) # name of structure. Required for siesta (structurename.fdf).
self.kmeshtol = args.kmeshtol # kmesh tolerence for wannier mesh
self.force = args.force # force dmft calculation True of False
self.v = args.v # Verbosity
self.dft = args.dft # DFT type
self.aiida = args.aiida # Flag for aiida calculation
self.lowdin = args.lowdin # Flag for Siesta Lowdin
self.nowin = args.nowin # Flag for .win generation
####### DFT and wannier90 initialization #######
# wannier90 executable
self.wannier90_exec = "wannier90.x"
self.wanbands = 0
self.updatewanbands = True
# VASP calculation
if self.dft == "vasp":
self.vasp_exec = "vaspDMFT" # vasp executable
# Siesta calculation
elif self.dft == "siesta":
self.siesta_exec = "siesta" # siesta executable
self.fdf_to_poscar()
# QE calculation
elif self.dft == "qe" and self.aiida is False:
# Nothing to do here for now since we only have
# QE aiida calculations.
self.qe_exec = "pw.x"
self.qe_to_poscar()
# aiida calculation
if self.aiida:
self.win_to_poscar(input="aiida.win")
####### DMFT initialization #######
# Generate initial self energy.
self.gen_sig()
# Setting DMFT type
if args.dmft:
self.type = "DMFT"
elif args.hf:
self.type = "HF"
# Launch DMFT calculation
self.run_dmft()
def __init__(self, args):
"""
Contains common functions for all methods.
This launches the dmft calculation as well.
"""
self.kmeshtol = args.kmeshtol # kmesh tolerence for wannier mesh
self.force = args.force # force dmft calculation True of False
self.v = args.v # Verbosity
self.dft = args.dft # DFT type
self.aiida = args.aiida # Flag for aiida calculation
self.lowdin = args.lowdin # Flag for Siesta Lowdin
self.nowin = args.nowin # Flag for .win generation
self.resume = args.resume # Flag to resume existing calculation
####### DFT and wannier90 initialization #######
# wannier90 executable
self.wannier90_exec = "wannier90.x"
self.wanbands = 0
self.updatewanbands = True
# VASP calculation
if self.dft == "vasp":
self.vasp_exec = "vasp_std" # vasp executable
# Siesta calculation
elif self.dft == "siesta":
self.siesta_exec = "siesta" # siesta executable
self.fdf_to_poscar()
# QE calculation
elif self.dft == "qe" and self.aiida is False:
# Nothing to do here for now since we only have
# QE aiida calculations.
self.qe_exec = "pw.x"
self.qe_to_poscar()
# aiida calculation
if self.aiida:
self.win_to_poscar(input="aiida.win")
# setting up parallelization
if os.path.exists("para_com.dat"):
fipa = open("para_com.dat", "r")
self.para_com = str(fipa.readline())[:-1]
fipa.close()
else:
self.para_com = "mpirun -np 40"
if os.path.exists("para_com_dft.dat"):
fid = open("para_com_dft.dat")
self.para_com_dft = str(fid.readline())[:-1]
fid.close()
else:
self.para_com_dft = self.para_com
####### DMFT initialization #######
# Setting DMFT type
if args.dmft:
self.type = "DMFT"
elif args.hf:
self.type = "HF"
if not self.resume:
print("Initializing calculation...\n")
# initial chemical potential
self.create_DFTmu()
# Generate initial self energy.
self.gen_sig()
else:
print("Resuming calculation...\n")
# Checking if previous DMFT calculation exists
pathstr = self.type + os.sep + "INFO_TIME"
if os.path.exists(pathstr):
# cleaning DMFT directory to prepare for resumed calculation
for chgcar in glob.glob("./DMFT/CHGCAR.*"):
os.remove(chgcar)
for gloc in glob.glob("./DMFT/G_loc.out.*"):
os.remove(gloc)
for sig in glob.glob("./DMFT/sig.inp.*"):
os.remove(sig)
else:
print("No previous DMFT calculation has been initialized!")
print("Running from scratch...")
self.resume = False
# initial chemical potential
self.create_DFTmu()
# Generate initial self energy.
self.gen_sig()
# import the VASP class. This can be used for other DFT codes as well.
self.DFT = VASP.VASP_class(dft=args.dft,
aiida=args.aiida,
structurename=args.structurename)
self.dir = os.getcwd() # dft running directory (current directory)
self.structurename = (
args.structurename
) # name of structure. Required for siesta (structurename.fdf).
# Creating seedname.dat for non-VASP calculations
if self.structurename:
fi = open("seedname.dat", "w")
fi.write(str(self.structurename))
fi.close()
# Launch DMFT calculation
self.run_dmft()
while 1:
if content[index].strip() == '':
index += 4
break
index += 1
while 1:
if content[index].strip() == '':
break
lines = space.split(content[index].strip())
elements.append(lines[0])
coordinates.append([float(lines[2]), float(lines[3]), float(lines[4])])
index += 1
total_atoms = len(elements)
content = VASP.grep_outcar("grep 'Standard orientation:' -A %d %s" %
(total_atoms + 5, sys.argv[1][:-4] + '.log'))
with open(sys.argv[1][:-4] + '.xyz', 'w') as xyz_file:
# xyz_file.write(str(total_atoms) + '\n')
# xyz_file.write('Create from *.log file\n')
# for element, coor in zip(elements, coordinates):
# xyz_file.write("%2s %16.10f %16.10f %16.10f\n" % (element, coor[0], coor[1], coor[2]))
pattern = re.compile(r'Standard orientation:')
index = 0
while index < len(content):
while index < len(content):
if pattern.search(content[index]) is not None:
index += 5
break
index += 1