diff --git a/WS2/LDA_SG15/3.0-libxc/comp.py b/WS2/LDA_SG15/3.0-libxc/comp.py
new file mode 100644
index 0000000..9e1d62e
--- /dev/null
+++ b/WS2/LDA_SG15/3.0-libxc/comp.py
@@ -0,0 +1,22 @@
+import numpy as np
+np.set_printoptions(5,suppress=True,linewidth=2000,threshold=2000)
+ha = 27.2116 #eV
+
+matel = np.load('vxc_sub_matel.npy')*ha
+matel_lin = np.load('vxc_sub_linear_matel.npy')*ha
+
+
+print('np.max(np.abs(matel-matel_lin)): ', np.max(np.abs(matel-0.5*matel_lin)), ' eV')
+ik = 0
+print(matel[ik])
+print()
+print(matel_lin[ik])
+print()
+print(matel[ik]-0.5*matel_lin[ik])
+
+mask = (np.abs(matel_lin) < 1e-8)
+ratio = np.abs(matel[~mask] / matel_lin[~mask])
+print(np.max(ratio))
+print(np.average(ratio))
+print(np.min(ratio))
+
diff --git a/WS2/LDA_SG15/3.0-libxc/fft_mod.py b/WS2/LDA_SG15/3.0-libxc/fft_mod.py
index 7e02776..eddf4a1 100644
--- a/WS2/LDA_SG15/3.0-libxc/fft_mod.py
+++ b/WS2/LDA_SG15/3.0-libxc/fft_mod.py
@@ -1,10 +1,88 @@
import os
import time
import numpy as np
-from numpy.fft import fftn, ifftn, ifftshift
+from numpy.fft import fftn, ifftn, fftshift, ifftshift
+
+
+def flat_FFTbox(unkg_FFTbox):
+ """
+ Generate a flattened 1d array 'unkg' and corresponding igvecs from unkg_FFTbox.
+ Assume unkg_FFTbox has its zero-frequency component in unkg_FFTbox[ispin,0,0,0].
+ This functions is a kind of the inverse function of 'put_FFTbox'.
+ Note, because of the zero padding in unkg_FFTbox, unkg may have lots of zeros.
+
+ --Input--
+ unkg_FFTbox : cdouble(nspin,N1,N2,N3)
+ unkg in FFTbox
+ for colinear case, nspin = 1
+ for non-colinear case, nspin = 2
+
+ --Output--
+ unkg : cdouble(nspin*N1*N2*N3)
+ for non-colinear case, the first half is for spin-up,
+ the second half is for spin-dw.
+ gvecs_sym : int(N1*N2*N3,3)
+ array of miller index (h,k,l)
+ """
+ nspin, n1, n2, n3 = unkg_FFTbox.shape
+ ng = n1*n2*n3
+ h_max, k_max, l_max = n1//2, n2//2, n3//2
+
+ hs, ks, ls = np.unravel_index(np.array(range(ng)),(n1,n2,n3))
+
+ #generate zero starting positive index. it is just for reshaping
+ gvecs_pos = np.concatenate([[hs],[ks],[ls]], axis = 0).T
+ hkl2flat = ( n3 * (n2 * gvecs_pos[:, 0] + gvecs_pos[:, 1]) \
+ + gvecs_pos[:, 2])
+ hs[hs>=h_max] -= n1
+ ks[ks>=k_max] -= n2
+ ls[ls>=l_max] -= n3
+
+ #generate zero starting symmetric index. it will be returned
+ gvecs_sym = np.concatenate([[hs],[ks],[ls]], axis = 0).T
+
+ unkg = np.zeros(nspin*ng,dtype=np.cdouble)
+ for ispin in range(nspin):
+ gstart = ispin*ng
+ gend = (ispin + 1)*ng
+ unkg[gstart:gend] = unkg_FFTbox[ispin,:,:,:].flat[hkl2flat]
+
+ return unkg, gvecs_sym
+
+
+def fft_r2g(unkr_FFTbox):
+ """ fft from R space to G space
+
+ ---Input---
+ unkr_FFTbox : cdouble(ispin,N1,N2,N3)
+ unkr in FFTbox
+
+ --Output--
+ unkg_FFTbox : cdouble(ispin,N1,N2,N3)
+ unkg in FFTbox
+ """
+ # FFTgrid
+ nspin, n1, n2, n3 = unkr_FFTbox.shape
+ Nt = n1*n2*n3
+ unkg_FFTbox = np.zeros_like(unkr_FFTbox)
+ start = time.time()
+ for ispin in range(nspin):
+ unkg_FFTbox[ispin,:,:,:] = fftn(unkr_FFTbox[ispin,:,:,:])
+ end = time.time()
+ #print(f'\nFFT time', end-start)
+
+ return unkg_FFTbox
def ifft_g2r(unkg_FFTbox):
- """ ifft from G space to R space
+ """
+ ifft from G space to R space
+
+ with an input array x[l], the output array y[k] satisfy
+ y[k] = np.sum(x * np.exp(2j * np.pi * k * np.arange(n)/n)) / len(x)
+
+ Note unkg_FFTbox have the unk(G=0) component as the first element
+ in the unkg_FFTbox[ispin,0,0,0].
+
---Input---
unkg_FFTbox : cdouble(ispin,N1,N2,N3)
@@ -22,7 +100,7 @@ def ifft_g2r(unkg_FFTbox):
for ispin in range(nspin):
unkr_FFTbox[ispin,:,:,:] = ifftn(unkg_FFTbox[ispin,:,:,:])
end = time.time()
- print(f'\nIFFT time', end-start)
+ #print(f'\nIFFT time', end-start)
return unkr_FFTbox
@@ -48,6 +126,10 @@ def put_FFTbox2(unkg, gvecs, FFTgrid, noncolin, savedir='./', savefn=False):
for colinear case, nspin = 1
for non-colinear case, nspin = 2
+ unkg_FFTbox[ispin,0,0,0] = unk_ispin(G=0),
+ which is a zero frequency start array.
+
+
"""
#fn = savedir+f'./Unkg_FFTbox_k{ik}.npy'
@@ -86,7 +168,7 @@ def put_FFTbox2(unkg, gvecs, FFTgrid, noncolin, savedir='./', savefn=False):
#Save it for later calculation
#np.save(savedir+f'./Unkg_FFTbox_k{ik}.npy',unkg_FFTbox)
- print(f'\nFFTBOX time', end-start)
+ #print(f'\nFFTBOX time', end-start)
return unkg_FFTbox
@@ -139,13 +221,6 @@ def put_FFTbox(ik, FFTgrid, savedir='./'):
# Save it for later calculation
np.save(savedir+f'./Unkg_FFTbox_k{ik}.npy',unkg_FFTbox)
- print(f'\nFFTBOX time', end-start)
+ #print(f'\nFFTBOX time', end-start)
return unkg_FFTbox
-
-if __name__=='__main__':
- ik = 1
- FFTgrid = [495, 495, 83]
- unkg_FFTbox1 = put_FFTbox(ik, FFTgrid, savedir='../../data/')
- unkg_FFTbox2 = put_FFTbox2(ik, FFTgrid, savedir='../../data/')
- print(np.allclose(unkg_FFTbox2,unkg_FFTbox1))
diff --git a/WS2/LDA_SG15/3.0-libxc/libxc_fxc_test.py b/WS2/LDA_SG15/3.0-libxc/libxc_fxc_test.py
index 2789761..d0bcf97 100644
--- a/WS2/LDA_SG15/3.0-libxc/libxc_fxc_test.py
+++ b/WS2/LDA_SG15/3.0-libxc/libxc_fxc_test.py
@@ -26,6 +26,14 @@ def main():
print('max(Error)',np.max(diff))
print('min(Error)',np.min(diff))
print('avg(Error)',np.average(diff))
+
+ fn_vsub = 'vxc_sub'
+ print('Save ',fn_vsub)
+ np.save(fn_vsub, vsub)
+
+ fn_vsub_aprox = 'vxc_sub_linear'
+ print('Save ',fn_vsub_aprox)
+ np.save(fn_vsub_aprox, vsub_aprox)
#diff = np.abs(vsub - vsub_aprox2)
#print()
#print('diff = abs(vsub - vsub_aprox) in Hartree')
diff --git a/WS2/LDA_SG15/3.0-libxc/matel.py b/WS2/LDA_SG15/3.0-libxc/matel.py
new file mode 100644
index 0000000..55fd080
--- /dev/null
+++ b/WS2/LDA_SG15/3.0-libxc/matel.py
@@ -0,0 +1,223 @@
+import numpy as np
+from fft_mod import put_FFTbox2, ifft_g2r, fft_r2g, flat_FFTbox
+from pymatgen.core.structure import Structure
+from pymatgen.io.cube import Cube
+np.set_printoptions(5,suppress=True,linewidth=2000,threshold=2000)
+bohr2ang = 0.529177
+hartree = 27.2116 #eV
+Ha2eV = hartree
+vol = 1449.7341#321798.0168 *((1/bohr2ang)**3)
+
+
+def main():
+ prefix = 'WS2'
+ savedir = '../2.1-wfn/npy.save/'
+ fn_poscar = './struct.POSCAR' # POSCAR file
+ FFTgrid = [ 18, 18, 135] # coarse grid
+ noncolin = False
+ struct = Structure.from_file(fn_poscar)
+ #vol = struct.volume/(bohr2ang**3) # in Bohr^3
+ cell = struct.lattice._matrix*(1/bohr2ang) # in Bohr
+ bcell = 2*np.pi*np.linalg.inv(cell).T # in Bohr^-1
+
+ n1, n2, n3 = FFTgrid
+ nfft = n1*n2*n3
+ nk = 36
+ nbnd = 20
+
+ fn_vh_r_FFTbox = f'./vxc_sub.npy'
+ vh_r_FFTbox = np.load(fn_vh_r_FFTbox)
+
+ #print('sum(rho_r)*(vol/nfft)',np.sum(rho_r_FFTbox)*(vol/nfft))
+ #Eh = np.real(0.5*np.sum(vh_r_FFTbox*rho_r_FFTbox*(vol/nfft)))
+ #print(f'Eh = {2*Eh} in Ry')
+
+ #unkr_FFTbox_set = get_unkr_FFTbox_set(nk, nbnd, FFTgrid,
+ unkr_FFTbox_set = np.load('./unkr_FFTbox_set.npy')
+ vmat = np.zeros((nk,nbnd,nbnd),dtype=np.cdouble)
+ for ik in range(nk):
+ for i in range(nbnd):
+ for j in range(nbnd):
+ print('ik,i,j',f'{ik},{i},{j}')
+ unkr_FFTbox_i = unkr_FFTbox_set[ik,i,0,:,:,:]
+ unkr_FFTbox_j = unkr_FFTbox_set[ik,j,0,:,:,:]
+ matel = np.sum(np.conjugate(unkr_FFTbox_i)*vh_r_FFTbox
+ *unkr_FFTbox_j*(vol/nfft))
+ vmat[ik,i,j] = matel
+
+ print(vmat[ik]*Ha2eV)
+
+ fn_vmat = 'vxc_sub_matel'
+ np.save(fn_vmat, vmat)
+
+
+ return
+
+def get_unkr_FFTbox_set(nk, nbnd, FFTgrid, noncolin, vol, savedir):
+ """
+ get set of unkr in FFTbox
+
+ --output--
+ unkr_FFTbox_set : cdouble(nk, nbnd, nspin, n1, n2, n3)
+
+ """
+ print()
+ print('Start IFFT')
+ if noncolin:
+ nspin = 2
+ else:
+ nspin = 1
+
+ n1,n2,n3 = FFTgrid
+ nfft = np.prod(FFTgrid)
+
+ unkr_FFTbox_set = np.zeros((nk, nbnd, nspin, n1, n2, n3), dtype=np.cdouble)
+
+ for ik in range(nk):
+ gvecs = np.load(savedir+f'Gvecs_k{ik+1}.npy')
+ unkg = np.load(savedir+f'Unkg_k{ik+1}.npy')
+ for ibnd in range(nbnd):
+ print(f'State ibnd = {ibnd}, ik={ik}')
+ unkg_FFTbox = put_FFTbox2(unkg[ibnd], gvecs, \
+ FFTgrid, noncolin, savedir=savedir)
+ unkr_FFTbox = ifft_g2r(unkg_FFTbox)*np.sqrt(nfft)
+ norm_r = np.linalg.norm(unkr_FFTbox)
+ print(f'Norm in R: {norm_r}')
+ print(f'Density in Hartree Atomic Unit')
+ unkr_FFTbox *= np.sqrt(nfft/vol)/norm_r
+ unkr_FFTbox_set[ik,ibnd,:,:,:,:] = unkr_FFTbox
+ #rho_r_FFTbox = get_density(unkr_FFTbox)*(nfft/vol)
+
+ print('End of IFFT')
+ return unkr_FFTbox_set
+
+
+
+
+def get_unkr(ik, ibnd, nfft,vol, savedir):
+ fn_unkr =savedir + f'unkr.K{ik+1}.B{ibnd+1}.npy'
+ unkr_FFTbox = np.load(fn_unkr)*np.sqrt(nfft)
+ norm_r = np.linalg.norm(unkr_FFTbox)
+ unkr_FFTbox /= norm_r
+ unkr_FFTbox *= np.sqrt(nfft/vol)
+ #rho_r_FFTbox = np.abs(unkr_FFTbox)**2
+ #print('sum(rho_r)*(vol/nfft)',np.sum(rho_r_FFTbox)*(vol/nfft))
+ return unkr_FFTbox
+
+
+def get_vh(rho_g, igvec, bcell, FFTgrid, savedir):
+ """
+ --Input--
+ rho_g : complex128(ng)
+ momentum space charge density in Hartree Atomic Unit
+
+ gvec : int(ng,3)
+ momentum space charge density in Hartree Atomic Unit
+
+ bcell_in: float64(3,3)
+ reciprocal lattice vectors (bohr^{-1})
+
+ --Output--
+ vh : float(:,:,:)
+
+ """
+ vh_g = np.zeros_like(rho_g)
+ gvec = igvec.dot(bcell)
+ gvec_sq = np.einsum('ix,ix->i', gvec, gvec) # bohr^{-1} or Ry
+ for ig, g_sq in enumerate(gvec_sq):
+ if g_sq < 1e-12:
+ vh_g[ig] = 0
+ else:
+ vh_g[ig] = 4*np.pi*rho_g[ig]/g_sq
+
+ vh_g_FFTbox = put_FFTbox2(vh_g, igvec, FFTgrid, noncolin=False)
+ vh_r = ifft_g2r(vh_g_FFTbox)
+ return np.real(vh_r[0,:,:,:])
+
+
+
+def get_vxc(rho):
+ """
+ --Input--
+ rho : float(:,:,:)
+ real space charge density in Hartree Atomic Unit
+
+ --Output--
+ vxc : float(:,:,:)
+
+ """
+ inp = {}
+ n1, n2, n3 = rho.shape
+ rho_flatten = rho.flatten()
+ inp["rho"] = rho_flatten
+
+ # Build functional
+ func_c = pylibxc.LibXCFunctional("LDA_C_PZ", "unpolarized")
+ func_x = pylibxc.LibXCFunctional("LDA_X", "unpolarized")
+
+ # Compute exchange part
+ ret_x = func_x.compute(inp, do_fxc=True)
+ v2rho2_x = ret_x['v2rho2'][:,0]
+ vrho_x = ret_x['vrho'][:,0]
+ zk_x = ret_x['zk'][:,0]
+
+ # Compute correlation part
+ ret_c = func_c.compute(inp, do_fxc=True)
+ v2rho2_c = ret_x['v2rho2'][:,0]
+ vrho_c = ret_c['vrho'][:,0]
+ zk_c = ret_c['zk'][:,0]
+
+ vxc = vrho_x + vrho_c
+ fxc = v2rho2_x + v2rho2_c
+
+ vxc_FFTbox = np.reshape(vxc,(n1,n2,n3))
+ fxc_FFTbox = np.reshape(fxc,(n1,n2,n3))
+
+ return vxc_FFTbox, fxc_FFTbox
+
+def vxc_libxc():
+ n1, n2, n3 = [18, 18, 135]
+ #gvec_rho = np.loadtxt('../2.1-wfn/rho_gvec.txt',dtype=np.int32)
+ #rho_pw2bgw = np.load('../2.1-wfn/rho_pw2bgw.npy')
+ #rho_FFTbox = put_FFTbox2(rho_pw2bgw, gvec_rho, [n1,n2,n3], noncolin=False)
+ #rho = ifft_g2r(rho_FFTbox)
+ #rho_pp = Cube("../1.1-pp/Rho.cube")
+ #rho = rho_pp.data
+ rho_pw2bgw = np.load("../2.1-wfn/rhor_pw2bgw.npy")
+ rho = rho_pw2bgw[0,:,:,:]
+ frac = 0.0001
+ rho_f = rho * frac
+ rho_r = rho - rho_f
+
+ # Create input
+ const = 1
+ inp = {}
+ rho_flatten = rho.flatten()
+ rho_r_flatten = rho_r.flatten()
+ rho_f_flatten = rho_f.flatten()
+ inp["rho"] = const*rho_flatten
+
+ # Build functional
+ func_c = pylibxc.LibXCFunctional("LDA_C_PZ", "unpolarized")
+ func_x = pylibxc.LibXCFunctional("LDA_X", "unpolarized")
+
+ # Compute exchange part
+ ret_x = func_x.compute(inp, do_fxc=True)
+ v2rho2_x = ret_x['v2rho2'][:,0]
+ vrho_x = ret_x['vrho'][:,0]
+ zk_x = ret_x['zk'][:,0]
+
+ # Compute correlation part
+ ret_c = func_c.compute(inp, do_fxc=True)
+ v2rho2_c = ret_x['v2rho2'][:,0]
+ vrho_c = ret_c['vrho'][:,0]
+ zk_c = ret_c['zk'][:,0]
+
+ vxc = vrho_x + vrho_c
+ fxc = v2rho2_x + v2rho2_c
+
+ vxc_FFTbox = np.reshape(vxc,(18,18,135))
+ fxc_FFTbox = np.reshape(fxc,(18,18,135))
+ return vxc_FFTbox, fxc_FFTbox
+
+main()
diff --git a/WS2/LDA_SG15/3.0-libxc/struct.POSCAR b/WS2/LDA_SG15/3.0-libxc/struct.POSCAR
new file mode 100644
index 0000000..24ed0aa
--- /dev/null
+++ b/WS2/LDA_SG15/3.0-libxc/struct.POSCAR
@@ -0,0 +1,11 @@
+WS2
+1.0
+3.1500000000000 0.000000000000 0.00
+1.575000000000 2.7279800219 0.00
+0.000000000000 0.000000000000 25.0
+W S
+1 2
+direct
+ 0.33333333333333 0.33333333333333 0.5000000000 W
+ 0.66666666666667 0.66666666666667 0.4360000000 S
+ 0.66666666666667 0.66666666666667 0.5640000000 S
diff --git a/WS2/LDA_SG15/3.0-libxc/total_charge_density.py b/WS2/LDA_SG15/3.0-libxc/total_charge_density.py
new file mode 100644
index 0000000..f571124
--- /dev/null
+++ b/WS2/LDA_SG15/3.0-libxc/total_charge_density.py
@@ -0,0 +1,162 @@
+import os
+import time
+import numpy as np
+from pymatgen.core.structure import Structure
+from fft_mod import put_FFTbox2, ifft_g2r
+np.set_printoptions(5,suppress=True,linewidth=2000,threshold=2000)
+
+bohr2ang = 0.529177
+hartree = 27.2116 #eV
+vol = 1449.7341#321798.0168 *((1/bohr2ang)**3)
+
+def main():
+ prefix = 'WS2'
+ savedir = '../2.1-wfn/npy.save/'
+ fn_poscar = './struct.POSCAR' # POSCAR file
+ #mode = 6 #6 is density
+ ik_lst = np.array(range(1,37)) #Start from 1
+ highest_band = 20
+ lowest_band = 1
+ ibnd_lst = np.array(range(1,21)) #Start from 1 within unkg file
+ FFTgrid = [ 18, 18, 135] # coarse grid
+ noncolin = False
+ save_unkr = True
+
+ #### construct half filling occ ####
+ #### we do not consider spin deg. here ####
+ nk = len(ik_lst)
+ nbnd = len(ibnd_lst)
+ occ = np.zeros((nk,nbnd))
+ occ[:,:] += 1
+ #occ[5,:] = 1/2 # K+
+ #occ[7,:] = 1/2 # K-
+ #### construct half filling occ ####
+
+ struct = Structure.from_file(fn_poscar)
+ total_density(prefix, savedir, struct, ik_lst, highest_band, \
+ lowest_band, ibnd_lst, occ, FFTgrid, noncolin, save_unkr)
+
+def total_density(prefix, savedir, struct, ik_lst, highest_band, \
+ lowest_band, ibnd_lst, occ, FFTgrid, noncolin, save_unkr):
+ """ Plot density
+
+ ---Input---
+ prefix : str
+ system prefix
+
+ savedir : str
+ path to save directory contains Unkg, Gvecs
+
+ struct : Structure
+
+ ik : int
+ k-point id. Start from 1
+
+ highest_band : int
+
+ lowest_band : int
+
+ ibnd_lst: int(:)
+ Band index of the system. Start from 1
+
+ FFTgrid : int(3)
+ 3D FFTgrid N1, N2, N3
+
+ noncolin : bool
+ True for non-colinear calc.
+
+ save_unkr : bool
+
+ """
+ print('\n#############################################')
+ print('#############################################')
+ print('\n')
+ ibnd_lst = np.array(ibnd_lst, dtype=np.int32)
+ nbnd = len(ibnd_lst)
+ ibnd_in_wfsx_lst = ibnd_lst - lowest_band
+ #print(f'Plot charge density ik = {ik}')
+ ##### Normalization
+ n1, n2, n3 = FFTgrid
+ if noncolin:
+ nspin = 2
+ else:
+ nspin = 1
+ rhotot_r_FFTbox = np.zeros((nspin,n1,n2,n3), dtype=np.cdouble)
+
+ nfft = np.prod(FFTgrid)
+ nk = len(ik_lst)
+ nbnd = len(ibnd_lst)
+ wk = 1/nk # we assume a symmetric uniform grid
+ #vol = struct.volume/(bohr2ang**3) # in Bohr**3
+
+ print('FFTgrid: ', FFTgrid)
+ print(' nfft: ', nfft)
+ print(' nk: ', nk)
+ print(' vol: ', vol, ' Bohr^3')
+ #####
+
+ #### construct half filling occ ####
+ occ *= (2/nspin)
+ print('occupation with spin deg.')
+ print(occ)
+ ####
+
+
+ #### save unkr_FFTbox
+ unkr_FFTbox_set = np.zeros((nk, nbnd, nspin, n1, n2, n3), dtype=np.cdouble)
+ #### save unkr_FFTbox
+
+ for ik in ik_lst:
+ gvecs = np.load(savedir+f'Gvecs_k{ik}.npy')
+ unkg = np.load(savedir+f'Unkg_k{ik}.npy')
+ for i in range(nbnd):
+ ibnd = ibnd_lst[i]
+ ibnd_wfsx = ibnd_in_wfsx_lst[i]
+ # We put FFTbox and ifft on-the-fly. We can save it for later.
+ print()
+ print(f'#'*50)
+ print(f'State ibnd = {ibnd}, ik={ik}')
+ unkg_FFTbox = put_FFTbox2(unkg[ibnd_wfsx], gvecs, \
+ FFTgrid, noncolin, savedir=savedir)
+ unkr_FFTbox = ifft_g2r(unkg_FFTbox)*np.sqrt(nfft)
+ norm_r = np.linalg.norm(unkr_FFTbox)
+ print(f'Norm in R: {norm_r}')
+ print(f'Density in Hartree Atomic Unit')
+ unkr_FFTbox *= np.sqrt(nfft/vol)#/norm_r
+ unkr_FFTbox_set[ik-1,i,:,:,:,:] = unkr_FFTbox
+ rho_r_FFTbox = get_density(unkr_FFTbox)
+ print('sum(rho_r)*(vol/nfft)',np.sum(rho_r_FFTbox)*(vol/nfft))
+ rhotot_r_FFTbox[:,:,:,:] += occ[ik-1,i]*wk*rho_r_FFTbox
+
+ print()
+ print()
+ fn_unkr = f'unkr_FFTbox_set'
+ print('Save ',fn_unkr)
+ np.save(fn_unkr, unkr_FFTbox_set)
+ print('sum(rhotot_r)*(vol/nfft)',np.sum(rhotot_r_FFTbox)*(vol/nfft))
+ fn_rhotot_r = f'rhoflat_r_FFTbox'
+ print('Save ',fn_rhotot_r)
+ np.save(fn_rhotot_r,rhotot_r_FFTbox)
+
+ return None
+
+def get_density(wfc):
+ """
+ ---Input---
+ wfc : cdouble(ispin,N1,N2,N3)
+ wfc in FFTbox
+
+ --Output--
+ density : float64(:,:,:)
+ density in FFTbox
+ """
+ nspin, N1, N2, N3 = wfc.shape
+ density = np.zeros((N1,N2,N3), dtype=np.float64)
+ for ispin in range(nspin):
+ density += np.abs(wfc[ispin,:,:,:])**2
+
+ return density
+
+
+if __name__=='__main__':
+ main()
diff --git a/WS2/LDA_SG15/4.0-hartree/compute_hartree.py b/WS2/LDA_SG15/4.0-hartree/compute_hartree.py
index c73e25e..3ed7536 100644
--- a/WS2/LDA_SG15/4.0-hartree/compute_hartree.py
+++ b/WS2/LDA_SG15/4.0-hartree/compute_hartree.py
@@ -28,12 +28,15 @@ def main():
#rho = Cube("../1.1-pp/Rho.cube") #just for struct
#rho_r_FFTbox[0,:,:,:] = rho.data
print('sum(rho_r)*(vol/nfft)',np.sum(rho_r_FFTbox)*(vol/nfft))
+ # print('vol/nfft',vol/nfft)
# debug
- rho_g_FFTbox = fft_r2g(rho_r_FFTbox)
+ rho_g_FFTbox = (vol/nfft)*fft_r2g(rho_r_FFTbox)
rho_g, igvec = flat_FFTbox(rho_g_FFTbox)
- vh_r = get_vh(rho_g, igvec, bcell)
+ print('rho_g[0]',rho_g[0])
+ vh_r = get_vh(rho_g, igvec, bcell, vol, nfft)
rho_r = rho_r_FFTbox
Eh = np.real(0.5*np.sum(vh_r*rho_r*(vol/nfft)))
+ EhG = get_Eh(rho_g, igvec, bcell, vol)
vbh_r = vbh.data/2 # from Ry to Hartree
Eh_ref = np.real(0.5*np.sum(vbh_r*rho_r*(vol/nfft)))
@@ -57,10 +60,46 @@ def main():
#print('min(diff)',np.min(diff))
#print('avg(diff)',np.average(diff))
#print(np.sort(ratio.flat)[-1000:])
+ print("Added part on Oct 20 2024")
+ print("Avg of vh_r: ",np.average(vh_r))
+ print("Avg of vbh_r: ",np.average(vbh_r))
+ print("Eh_ref: ",Eh_ref, " in Hartree")
+ print("Eh: ",Eh, " in Hartree")
+ print("EhG: ",EhG, " in Hartree")
+
return
-def get_vh(rho_g, igvec, bcell):
+def get_Eh(rho_g, igvec, bcell, vol):
+ """
+ --Input--
+ rho_g : complex128(ng)
+ momentum space charge density in Hartree Atomic Unit
+
+ gvec : int(ng,3)
+ momentum space charge density in Hartree Atomic Unit
+
+ bcell_in: float64(3,3)
+ reciprocal lattice vectors (bohr^{-1})
+
+ --Output--
+ Eh : float
+ Hartree energy
+ """
+ gvec = igvec.dot(bcell)
+ gvec_sq = np.einsum('ix,ix->i', gvec, gvec) # bohr^{-1} or Ry
+ Eh = 0.0
+ for ig, g_sq in enumerate(gvec_sq):
+ if g_sq < 1e-6:
+ continue
+ else:
+ Eh += 2*np.pi*(np.abs(rho_g[ig])**2)/g_sq
+ Eh /= vol
+
+ return Eh
+
+
+def get_vh(rho_g, igvec, bcell, vol, nfft):
"""
--Input--
rho_g : complex128(ng)
@@ -87,7 +126,7 @@ def get_vh(rho_g, igvec, bcell):
n1, n2, n3 = [18, 18, 135]
vh_g_FFTbox = put_FFTbox2(vh_g, igvec, [n1, n2, n3], noncolin=False)
- vh_r = ifft_g2r(vh_g_FFTbox)
+ vh_r = (nfft/vol)*ifft_g2r(vh_g_FFTbox)
return np.real(vh_r[0,:,:,:])
diff --git a/WS2/LDA_SG15/4.0-hartree/density2Vh.out b/WS2/LDA_SG15/4.0-hartree/density2Vh.out
new file mode 100644
index 0000000..db8a3dd
--- /dev/null
+++ b/WS2/LDA_SG15/4.0-hartree/density2Vh.out
@@ -0,0 +1,20 @@
+sum(rho_r)*(vol/nfft) (39.999893200894924+0j)
+
+FFT time 0.001336812973022461
+[0. 0.01768816 0.07075265 ... 1.64471906 1.55627824 1.50321375]
+[ True False False ... False False False]
+
+FFTBOX time 0.0008785724639892578
+
+IFFT time 0.0019943714141845703
+Eh_ref = 2020.0347291111416 in Ry
+Eh_ref-Eh = 0.009656602702307282 in Ry
+Eh_ref-Eh/Eh_ref = 4.780414199391707e-06
+Error = abs(vsub - vsub_aprox) in Hartree
+max(Error) 0.002941014702457778
+min(Error) 5.648637113608856e-10
+avg(Error) 0.00019808022879096483
+Ratio = abs(vbh_r/vh_r)
+max(Error) 1.000053763042361
+min(Error) 0.9999419834927064
+avg(Error) 1.0000044062857678
diff --git a/WS2/LDA_SG15/4.0-hartree/density2Vh.py b/WS2/LDA_SG15/4.0-hartree/density2Vh.py
index fe9d877..832e590 100644
--- a/WS2/LDA_SG15/4.0-hartree/density2Vh.py
+++ b/WS2/LDA_SG15/4.0-hartree/density2Vh.py
@@ -72,12 +72,18 @@ def get_vh(rho_g, igvec, bcell):
vh_g = np.zeros_like(rho_g)
gvec = igvec.dot(bcell)
gvec_sq = np.einsum('ix,ix->i', gvec, gvec) # bohr^{-1} or Ry
+ print(gvec_sq)
+ zero_indices = gvec_sq < 1e-12
+ print(zero_indices)
+ vh_g[~zero_indices] = 4*np.pi*rho_g[~zero_indices]/gvec_sq[~zero_indices]
+ vh_g[zero_indices] = 0.0
+ """
for ig, g_sq in enumerate(gvec_sq):
if g_sq < 1e-12:
vh_g[ig] = 0
else:
vh_g[ig] = 4*np.pi*rho_g[ig]/g_sq
-
+ """
n1, n2, n3 = [18, 18, 135]
vh_g_FFTbox = put_FFTbox2(vh_g, igvec, [n1, n2, n3], noncolin=False)
vh_r = ifft_g2r(vh_g_FFTbox)
diff --git a/WS2/LDA_SG15/4.0-hartree/test.py b/WS2/LDA_SG15/4.0-hartree/test.py
new file mode 100644
index 0000000..53c4ee7
--- /dev/null
+++ b/WS2/LDA_SG15/4.0-hartree/test.py
@@ -0,0 +1,18 @@
+import numpy as np
+
+a = np.array([1, 2, 3, 4, 4])
+b = np.array([1, 3, 4, 0, 5])
+
+# Create a copy of array b to avoid modifying the original array
+c = np.copy(b)
+
+# Find indices where b is zero
+zero_indices = np.where(b == 0)
+
+# Perform element-wise division for non-zero elements
+c[~zero_indices] = a[~zero_indices] / b[~zero_indices]
+
+# Set the elements to zero where b is zero
+c[zero_indices] = 0
+
+print(c)
diff --git a/WS2/siesta/LDA/BASIS_ENTHALPY b/WS2/siesta/LDA/BASIS_ENTHALPY
index 6516a9f..8802d02 100644
--- a/WS2/siesta/LDA/BASIS_ENTHALPY
+++ b/WS2/siesta/LDA/BASIS_ENTHALPY
@@ -1,4 +1,4 @@
- -7938.5038606998924
- The above number is the electronic (free)energy: -7939.7643983980397
+ -7938.2607236711965
+ The above number is the electronic (free)energy: -7939.5212613693429
Plus the pressure : 1.3595453680289311E-005 ( 0.20000000000000001 GPa)
times the orbital volume (in Bohr**3): 6814.5636309181073
diff --git a/WS2/siesta/LDA/BASIS_HARRIS_ENTHALPY b/WS2/siesta/LDA/BASIS_HARRIS_ENTHALPY
index dc169a5..ec907f1 100644
--- a/WS2/siesta/LDA/BASIS_HARRIS_ENTHALPY
+++ b/WS2/siesta/LDA/BASIS_HARRIS_ENTHALPY
@@ -1,4 +1,4 @@
- -7938.5038606998933
- The above number is the electronic (free) harris energy: -7939.7643983980406
+ -7938.2607236712020
+ The above number is the electronic (free) harris energy: -7939.5212613693493
Plus the pressure : 1.3595453680289311E-005 ( 0.20000000000000001 GPa)
times the orbital volume (in Bohr**3): 6814.5636309181073
diff --git a/WS2/siesta/LDA/CLOCK b/WS2/siesta/LDA/CLOCK
index 661884e..1063d7b 100644
--- a/WS2/siesta/LDA/CLOCK
+++ b/WS2/siesta/LDA/CLOCK
@@ -1,20 +1,20 @@
Start of run 0.000
--------------- end of scf step 0.713
--------------- end of scf step 0.753
--------------- end of scf step 0.790
--------------- end of scf step 0.834
--------------- end of scf step 0.871
--------------- end of scf step 0.908
--------------- end of scf step 0.953
--------------- end of scf step 0.999
--------------- end of scf step 1.043
--------------- end of scf step 1.080
--------------- end of scf step 1.117
--------------- end of scf step 1.161
--------------- end of scf step 1.204
--------------- end of scf step 1.240
--------------- end of scf step 1.277
--------------- end of scf step 1.318
--------------- end of scf step 1.361
---- end of geometry step 1.416
-End of run 2.187
+-------------- end of scf step 1.533
+-------------- end of scf step 1.655
+-------------- end of scf step 1.769
+-------------- end of scf step 1.892
+-------------- end of scf step 2.006
+-------------- end of scf step 2.117
+-------------- end of scf step 2.229
+-------------- end of scf step 2.343
+-------------- end of scf step 2.461
+-------------- end of scf step 2.578
+-------------- end of scf step 2.696
+-------------- end of scf step 2.814
+-------------- end of scf step 2.928
+-------------- end of scf step 3.050
+-------------- end of scf step 3.168
+-------------- end of scf step 3.285
+-------------- end of scf step 3.404
+--- end of geometry step 3.726
+End of run 4.215
diff --git a/WS2/siesta/LDA/FORCE_STRESS b/WS2/siesta/LDA/FORCE_STRESS
index 26fec07..bb58a68 100644
--- a/WS2/siesta/LDA/FORCE_STRESS
+++ b/WS2/siesta/LDA/FORCE_STRESS
@@ -1,8 +1,8 @@
- -583.5573357243
- 0.000092970 0.000000000 0.000000000
- 0.000000000 0.000092970 0.000000000
- 0.000000000 0.000000000 0.000097602
+ -583.5394656227
+ 0.000109322 0.000000000 -0.000000000
+ 0.000000000 0.000109322 -0.000000000
+ -0.000000000 0.000000000 0.000109205
3
- 1 74 0.000000008 0.000000005 0.000000001 W
- 2 16 -0.000000002 -0.000000003 0.026027818 S
- 2 16 -0.000000004 -0.000000006 -0.026027822 S
+ 1 74 0.000000004 -0.000000000 -0.000000000 W
+ 2 16 -0.000000000 0.000000001 0.025917036 S
+ 2 16 -0.000000000 0.000000001 -0.025917039 S
diff --git a/WS2/siesta/LDA/INPUT_TMP.03114 b/WS2/siesta/LDA/INPUT_TMP.03114
new file mode 100644
index 0000000..0a39246
--- /dev/null
+++ b/WS2/siesta/LDA/INPUT_TMP.03114
@@ -0,0 +1,119 @@
+# SIESTA INPUT #
+SystemLabel WS2
+NumberOfSpecies 2
+%block ChemicalSpeciesLabel
+ 1 74 W
+ 2 16 S
+%endblock ChemicalSpeciesLabel
+LatticeConstant 1.0 Ang
+%block LatticeVectors
+3.1500000000000 0.000000000000 0.00
+1.575000000000 2.7279800219 0.00
+0.000000000000 0.000000000000 25.0
+%endblock LatticeVectors
+NumberOfAtoms 3
+AtomicCoordinatesFormat Fractional
+%block AtomicCoordinatesAndAtomicSpecies
+ 0.33333333333333 0.33333333333333 0.5000000000 1
+ 0.66666666666667 0.66666666666667 0.4360000000 2
+ 0.66666666666667 0.66666666666667 0.5640000000 2
+%endblock AtomicCoordinatesAndAtomicSpecies
+XC.functional LDA
+XC.authors PZ
+PAO.BasisSize DZP
+MeshCutoff 1000 Ry
+OccupationFunction MP
+OccupationMPOrder 1
+ElectronicTemperature 0.000001 eV
+%block kgrid_Monkhorst_Pack
+ 6 0 0 0.0
+ 0 6 0 0.0
+ 0 0 1 0.0
+%endblock kgrid_Monkhorst_Pack
+SolutionMethod diagon
+Diag.ParallelOverK T
+# Diag.Algorithm ELPA
+# NumberOfEigenStates 1300
+DM.UseSaveDM F
+MD.UseSaveXV T
+MD.Steps 0
+MD.TypeOfRun Broyden
+MD.MaxForceTol 0.01 eV/Ang
+MD.VariableCell F
+MaxSCFIterations 1000
+SCF.DM.Converge T
+SCF.DM.Tolerance 1.0d-8
+SCF.MustConverge T
+SCF.Mix Hamiltonian
+SCF.Mixer.Method Pulay
+SCF.Mixer.Variant original
+SCF.Mixer.Weight 0.30
+SCF.Mixer.History 10
+Write.DM T
+Write.H F
+WriteMullikenPop 1
+WriteEigenvalues T
+WriteCoorInitial T
+WriteCoorStep T
+WriteForces T
+XML.Write T
+SaveHS F
+SaveRho T
+SaveDeltaRho F
+SaveRhoXC T
+SaveElectrostaticPotential T
+SaveNeutralAtomPotential F
+SaveTotalPotential T
+SaveIonicCharge F
+SaveBaderCharge F
+SaveTotalCharge F
+CDF.Save T
+CDF.Grid.Precision double
+##################
+# Band Structure #
+##################
+BandLinesScale ReciprocalLatticeVectors
+%block BandLines
+1 0.0000000 0.00000000 0.000 \Gamma
+30 0.3333333 0.66666666 0.000 K
+15 0.5000000 0.50000000 0.000 M
+26 0.0000000 0.00000000 0.000 \Gamma
+%endblock bandlinek
+#WFS.Write.For.Bands T
+#WFS.Band.Min 400
+#WFS.Band.Max 500
+#%block BandLines
+#1 0.0000000 0.00000000 0.000 \Gamma
+#60 7.0000000 -2.33333333 0.000 K
+#60 3.5000000 -3.50000000 0.000 M
+#60 0.0000000 0.00000000 0.000 \Gamma
+#%endblock BandLines
+################
+# Wavefunction #
+#################
+# WriteWaveFunctions F
+# WaveFuncKPointsScale ReciprocalLatticeVectors
+# %block WaveFuncKPoints
+# 0.000 0.000 0.000 from 1 to 10 # Gamma wavefuncs 1 to 10
+# 2.000 0.000 0.000 1 3 5 # X wavefuncs 1,3 and 5
+# 1.500 1.500 1.500 # K wavefuncs, all
+# %endblock WaveFuncKPoints
+########
+# PDOS #
+########
+# %block ProjectedDensityOfStates
+# -10.00 0.00 0.050 500 eV
+# %endblock ProjectedDensityOfStates
+# %block PDOS.kgrid_Monkhorst_Pack
+# 3 0 0 0.0
+# 0 3 0 0.0
+# 0 0 1 0.0
+# %endblock PDOS.kgrid_Monkhorst_Pack
+# %include grimme.fdf
+# Slab.DipoleCorrection vacuum
+# %block Geometry.Charge
+# plane 0
+# delta
+# 0.0 0.0 2.5 Ang # An intersection point, in the plane
+# 0.0 0.0 1.0 # The normal vector to the plane
+# %endblock Geometry.Charge
diff --git a/WS2/siesta/LDA/INPUT_TMP.42946 b/WS2/siesta/LDA/INPUT_TMP.42946
new file mode 100644
index 0000000..d118eb2
--- /dev/null
+++ b/WS2/siesta/LDA/INPUT_TMP.42946
@@ -0,0 +1,119 @@
+# SIESTA INPUT #
+SystemLabel WS2
+NumberOfSpecies 2
+%block ChemicalSpeciesLabel
+ 1 74 W
+ 2 16 S
+%endblock ChemicalSpeciesLabel
+LatticeConstant 1.0 Ang
+%block LatticeVectors
+3.1500000000000 0.000000000000 0.00
+1.575000000000 2.7279800219 0.00
+0.000000000000 0.000000000000 25.0
+%endblock LatticeVectors
+NumberOfAtoms 3
+AtomicCoordinatesFormat Fractional
+%block AtomicCoordinatesAndAtomicSpecies
+ 0.33333333333333 0.33333333333333 0.5000000000 1
+ 0.66666666666667 0.66666666666667 0.4360000000 2
+ 0.66666666666667 0.66666666666667 0.5640000000 2
+%endblock AtomicCoordinatesAndAtomicSpecies
+XC.functional LDA
+XC.authors PW92
+PAO.BasisSize DZP
+MeshCutoff 1000 Ry
+OccupationFunction MP
+OccupationMPOrder 1
+ElectronicTemperature 0.000001 eV
+%block kgrid_Monkhorst_Pack
+ 6 0 0 0.0
+ 0 6 0 0.0
+ 0 0 1 0.0
+%endblock kgrid_Monkhorst_Pack
+SolutionMethod diagon
+Diag.ParallelOverK T
+# Diag.Algorithm ELPA
+# NumberOfEigenStates 1300
+DM.UseSaveDM F
+MD.UseSaveXV T
+MD.Steps 0
+MD.TypeOfRun Broyden
+MD.MaxForceTol 0.01 eV/Ang
+MD.VariableCell F
+MaxSCFIterations 1000
+SCF.DM.Converge T
+SCF.DM.Tolerance 1.0d-8
+SCF.MustConverge T
+SCF.Mix Hamiltonian
+SCF.Mixer.Method Pulay
+SCF.Mixer.Variant original
+SCF.Mixer.Weight 0.30
+SCF.Mixer.History 10
+Write.DM T
+Write.H F
+WriteMullikenPop 1
+WriteEigenvalues T
+WriteCoorInitial T
+WriteCoorStep T
+WriteForces T
+XML.Write T
+SaveHS F
+SaveRho T
+SaveDeltaRho F
+SaveRhoXC T
+SaveElectrostaticPotential T
+SaveNeutralAtomPotential F
+SaveTotalPotential T
+SaveIonicCharge F
+SaveBaderCharge F
+SaveTotalCharge F
+CDF.Save T
+CDF.Grid.Precision double
+##################
+# Band Structure #
+##################
+BandLinesScale ReciprocalLatticeVectors
+%block BandLines
+1 0.0000000 0.00000000 0.000 \Gamma
+30 0.3333333 0.66666666 0.000 K
+15 0.5000000 0.50000000 0.000 M
+26 0.0000000 0.00000000 0.000 \Gamma
+%endblock bandlinek
+#WFS.Write.For.Bands T
+#WFS.Band.Min 400
+#WFS.Band.Max 500
+#%block BandLines
+#1 0.0000000 0.00000000 0.000 \Gamma
+#60 7.0000000 -2.33333333 0.000 K
+#60 3.5000000 -3.50000000 0.000 M
+#60 0.0000000 0.00000000 0.000 \Gamma
+#%endblock BandLines
+################
+# Wavefunction #
+#################
+# WriteWaveFunctions F
+# WaveFuncKPointsScale ReciprocalLatticeVectors
+# %block WaveFuncKPoints
+# 0.000 0.000 0.000 from 1 to 10 # Gamma wavefuncs 1 to 10
+# 2.000 0.000 0.000 1 3 5 # X wavefuncs 1,3 and 5
+# 1.500 1.500 1.500 # K wavefuncs, all
+# %endblock WaveFuncKPoints
+########
+# PDOS #
+########
+# %block ProjectedDensityOfStates
+# -10.00 0.00 0.050 500 eV
+# %endblock ProjectedDensityOfStates
+# %block PDOS.kgrid_Monkhorst_Pack
+# 3 0 0 0.0
+# 0 3 0 0.0
+# 0 0 1 0.0
+# %endblock PDOS.kgrid_Monkhorst_Pack
+# %include grimme.fdf
+# Slab.DipoleCorrection vacuum
+# %block Geometry.Charge
+# plane 0
+# delta
+# 0.0 0.0 2.5 Ang # An intersection point, in the plane
+# 0.0 0.0 1.0 # The normal vector to the plane
+# %endblock Geometry.Charge
diff --git a/WS2/siesta/LDA/PARALLEL_DIST b/WS2/siesta/LDA/PARALLEL_DIST
index 4df0dbb..1e980af 100644
--- a/WS2/siesta/LDA/PARALLEL_DIST
+++ b/WS2/siesta/LDA/PARALLEL_DIST
@@ -1,32 +1,16 @@
- Node 0 handles 2 orbitals.
- Node 1 handles 2 orbitals.
- Node 2 handles 2 orbitals.
- Node 3 handles 2 orbitals.
- Node 4 handles 2 orbitals.
- Node 5 handles 2 orbitals.
- Node 6 handles 2 orbitals.
- Node 7 handles 2 orbitals.
- Node 8 handles 2 orbitals.
- Node 9 handles 2 orbitals.
- Node 10 handles 2 orbitals.
- Node 11 handles 2 orbitals.
- Node 12 handles 2 orbitals.
- Node 13 handles 2 orbitals.
- Node 14 handles 2 orbitals.
- Node 15 handles 2 orbitals.
- Node 16 handles 2 orbitals.
- Node 17 handles 2 orbitals.
- Node 18 handles 2 orbitals.
- Node 19 handles 2 orbitals.
- Node 20 handles 1 orbitals.
- Node 21 handles 1 orbitals.
- Node 22 handles 1 orbitals.
- Node 23 handles 1 orbitals.
- Node 24 handles 1 orbitals.
- Node 25 handles 1 orbitals.
- Node 26 handles 1 orbitals.
- Node 27 handles 1 orbitals.
- Node 28 handles 1 orbitals.
- Node 29 handles 1 orbitals.
- Node 30 handles 1 orbitals.
- Node 31 handles 1 orbitals.
+ Node 0 handles 6 orbitals.
+ Node 1 handles 4 orbitals.
+ Node 2 handles 3 orbitals.
+ Node 3 handles 3 orbitals.
+ Node 4 handles 3 orbitals.
+ Node 5 handles 3 orbitals.
+ Node 6 handles 3 orbitals.
+ Node 7 handles 3 orbitals.
+ Node 8 handles 3 orbitals.
+ Node 9 handles 3 orbitals.
+ Node 10 handles 3 orbitals.
+ Node 11 handles 3 orbitals.
+ Node 12 handles 3 orbitals.
+ Node 13 handles 3 orbitals.
+ Node 14 handles 3 orbitals.
+ Node 15 handles 3 orbitals.
diff --git a/WS2/siesta/LDA/S.ion b/WS2/siesta/LDA/S.ion
index ec1dda9..686ab9e 100644
--- a/WS2/siesta/LDA/S.ion
+++ b/WS2/siesta/LDA/S.ion
@@ -49,2513 +49,2513 @@ S # Label
# PAOs:__________________________
0 3 1 0 2.000000 #orbital l, n, z, is_polarized, population
500 0.8352185907909388E-02 4.167740768046785 # npts, delta, cutoff
- 0.000000000000000 0.1454723861428585
- 0.8352185907909388E-02 0.1455698376797585
- 0.1670437181581878E-01 0.1458629524439588
- 0.2505655772372816E-01 0.1463512121725459
- 0.3340874363163755E-01 0.1470342197680222
- 0.4176092953954694E-01 0.1479114199157746
- 0.5011311544745633E-01 0.1489820996746282
- 0.5846530135536572E-01 0.1502453892472255
- 0.6681748726327510E-01 0.1517002629210438
- 0.7516967317118449E-01 0.1533455401778354
- 0.8352185907909387E-01 0.1551798869697355
- 0.9187404498700327E-01 0.1572018171601542
- 0.1002262308949127 0.1594096941273409
- 0.1085784168028220 0.1618017325282794
- 0.1169306027107314 0.1643760002203409
- 0.1252827886186408 0.1671304203379033
- 0.1336349745265502 0.1700627735209364
- 0.1419871604344596 0.1731707002923473
- 0.1503393463423690 0.1764517035806954
- 0.1586915322502784 0.1799031513846931
- 0.1670437181581877 0.1835222795757353
- 0.1753959040660971 0.1873061948345267
- 0.1837480899740065 0.1912518777177086
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5.090524369549468 0.000000000000000
# Chlocal:__________________________
500 0.1200153541143665E-01 5.988766170306889 # npts, delta, cutoff
diff --git a/WS2/siesta/LDA/S.ion.nc b/WS2/siesta/LDA/S.ion.nc
index e7896a8..e971b0c 100644
Binary files a/WS2/siesta/LDA/S.ion.nc and b/WS2/siesta/LDA/S.ion.nc differ
diff --git a/WS2/siesta/LDA/S.ion.xml b/WS2/siesta/LDA/S.ion.xml
index 7875d3c..194febb 100644
--- a/WS2/siesta/LDA/S.ion.xml
+++ b/WS2/siesta/LDA/S.ion.xml
@@ -63,505 +63,505 @@ L=1 Nkbl=1 erefs: 0.17977+309
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diff --git a/WS2/siesta/LDA/TIMES b/WS2/siesta/LDA/TIMES
index 8e87f42..321bfe6 100644
--- a/WS2/siesta/LDA/TIMES
+++ b/WS2/siesta/LDA/TIMES
@@ -1,77 +1,78 @@
-timer: Number of nodes = 32
-timer: Busiest calculating node was node = 24
-timer: Times refer to node = 24
-timer: Total elapsed wall-clock time (sec) = 2.180
+timer: Number of nodes = 16
+timer: Busiest calculating node was node = 13
+timer: Times refer to node = 13
+timer: Total elapsed wall-clock time (sec) = 4.210
timer: CPU times (sec):
-Calc: Sum, Avge, myNode, Avg/Max = 69.335 2.167 2.170 0.999
+Calc: Sum, Avge, myNode, Avg/Max = 67.107 4.194 4.202 0.998
Comm: Sum, Avge, myNode, Avg/Max = 0.000 0.000 0.000 NaN
-Tot: Sum, Avge, myNode, Avg/Max = 69.335 2.167 2.170 0.999
+Tot: Sum, Avge, myNode, Avg/Max = 67.107 4.194 4.202 0.998
Program times printed if > 0.000E+00 of total
Program Calls Prg.com Prg.com Prg.tot Prg.tot Nod.avg
/Tot.com /Tot.tot/Nod.max
-siesta 1 0.000 0.0000 2.170 1.0000 0.999
-Setup 1 0.000 0.0000 0.133 0.0615 0.996
-bands 3 0.000 0.0000 0.706 0.3255 0.999
-KSV_init 1 0.000 0.0000 0.000 0.0000 0.879
-IterGeom 1 0.000 0.0000 1.276 0.5882 0.999
-geom_init 1 0.000 0.0000 0.539 0.2482 0.999
-state_init 1 0.000 0.0000 0.447 0.2059 0.999
-hsparse 1 0.000 0.0000 0.000 0.0002 0.837
-overlap 1 0.000 0.0000 0.000 0.0001 0.652
-CDF 18 0.000 0.0000 0.003 0.0012 0.057
-Setup_H0 1 0.000 0.0000 0.070 0.0322 0.997
-naefs 2 0.000 0.0000 0.003 0.0015 0.957
-dnaefs 1 0.000 0.0000 0.000 0.0000 0.960
-two-body 1 0.000 0.0000 0.000 0.0000 0.735
-MolMec 2 0.000 0.0000 0.000 0.0000 0.624
-kinefsm 2 0.000 0.0000 0.000 0.0002 0.619
-nlefsm 2 0.000 0.0000 0.040 0.0183 0.750
-DHSCF_Init 1 0.000 0.0000 0.047 0.0217 0.795
-DHSCF1 1 0.000 0.0000 0.009 0.0041 0.700
-InitMesh 1 0.000 0.0000 0.009 0.0041 0.991
-INITMESH 3 0.000 0.0000 0.002 0.0009 0.410
-DHSCF2 1 0.000 0.0000 0.038 0.0175 0.757
-REMESH 1 0.000 0.0000 0.009 0.0040 0.464
-BuildDISTR 2 0.000 0.0000 0.002 0.0009 0.409
-meshCom-Ca 3 0.000 0.0000 0.000 0.0000 0.725
-REORD 5 0.000 0.0000 0.000 0.0000 0.900
-PHION 1 0.000 0.0000 0.014 0.0065 0.741
-dscfComm 1 0.000 0.0000 0.004 0.0018 0.701
-COMM_BSC 82 0.000 0.0000 0.004 0.0017 0.314
-POISON 21 0.000 0.0000 0.024 0.0112 0.982
-fft 42 0.000 0.0000 0.024 0.0110 0.981
-setup_H 18 0.000 0.0000 0.184 0.0848 0.999
-DHSCF 20 0.000 0.0000 0.252 0.1162 0.983
-DHSCF3 20 0.000 0.0000 0.240 0.1107 0.995
-rhoofd 20 0.000 0.0000 0.108 0.0499 0.881
-OtoM 21 0.000 0.0000 0.023 0.0107 0.869
-XC 20 0.000 0.0000 0.017 0.0079 0.932
-GXC-CellXC 20 0.000 0.0000 0.015 0.0071 0.849
-gridxc@cellXC 20 0.000 0.0000 0.015 0.0071 0.849
-vmat 19 0.000 0.0000 0.052 0.0240 0.943
-MtoO 19 0.000 0.0000 0.012 0.0053 0.698
-IterSCF 17 0.000 0.0000 0.689 0.3174 0.999
-compute_dm 17 0.000 0.0000 0.514 0.2369 0.989
-diagon 17 0.000 0.0000 0.380 0.1749 1.000
-MIXER 16 0.000 0.0000 0.004 0.0017 0.950
-PostSCF 1 0.000 0.0000 0.048 0.0223 0.923
-FINAL_HF 1 0.000 0.0000 0.048 0.0223 0.921
-DHSCF4 1 0.000 0.0000 0.012 0.0055 0.721
-dfscf 1 0.000 0.0000 0.010 0.0045 0.672
-overfsm 1 0.000 0.0000 0.000 0.0001 0.605
-state_analysis 1 0.000 0.0000 0.000 0.0000 0.117
-siesta_move 1 0.000 0.0000 0.000 0.0000 0.758
-Analysis 1 0.000 0.0000 0.756 0.3486 0.998
-c-eigval 72 0.000 0.0000 0.697 0.3212 1.000
-c-buildHS 72 0.000 0.0000 0.001 0.0006 0.717
-cdiag 72 0.000 0.0000 0.695 0.3205 0.992
-cdiag1 72 0.000 0.0000 0.059 0.0273 0.983
-cdiag2 72 0.000 0.0000 0.155 0.0715 0.989
-cdiag3 72 0.000 0.0000 0.471 0.2171 0.990
-optical 1 0.000 0.0000 0.000 0.0000 0.832
-CDF-grid 4 0.000 0.0000 0.023 0.0106 0.746
+siesta 1 0.000 0.0000 4.202 1.0000 0.998
+Setup 1 0.000 0.0000 0.143 0.0341 0.988
+bands 3 0.000 0.0000 0.304 0.0725 1.000
+KSV_init 1 0.000 0.0000 0.000 0.0000 0.857
+IterGeom 1 0.000 0.0000 3.583 0.8529 0.999
+geom_init 1 0.000 0.0000 1.278 0.3041 0.998
+state_init 1 0.000 0.0000 0.625 0.1486 0.998
+hsparse 1 0.000 0.0000 0.001 0.0001 0.622
+overlap 1 0.000 0.0000 0.000 0.0001 0.641
+CDF 18 0.000 0.0000 0.089 0.0212 0.939
+Setup_H0 1 0.000 0.0000 0.563 0.1341 0.999
+naefs 2 0.000 0.0000 0.004 0.0010 0.932
+dnaefs 1 0.000 0.0000 0.000 0.0000 0.943
+two-body 1 0.000 0.0000 0.000 0.0000 0.730
+MolMec 2 0.000 0.0000 0.000 0.0000 0.635
+kinefsm 2 0.000 0.0000 0.000 0.0001 0.593
+nlefsm 2 0.000 0.0000 0.032 0.0076 0.706
+DHSCF_Init 1 0.000 0.0000 0.543 0.1292 0.976
+DHSCF1 1 0.000 0.0000 0.093 0.0222 0.933
+InitMesh 1 0.000 0.0000 0.093 0.0222 0.968
+INITMESH 3 0.000 0.0000 0.069 0.0165 0.596
+DHSCF2 1 0.000 0.0000 0.449 0.1069 0.976
+REMESH 1 0.000 0.0000 0.089 0.0212 0.888
+BuildDISTR 2 0.000 0.0000 0.069 0.0165 0.596
+meshCom-Ca 3 0.000 0.0000 0.000 0.0000 0.765
+REORD 5 0.000 0.0000 0.000 0.0001 0.865
+PHION 1 0.000 0.0000 0.188 0.0448 0.709
+dscfComm 1 0.000 0.0000 0.067 0.0160 0.674
+COMM_BSC 82 0.000 0.0000 0.129 0.0306 0.698
+POISON 21 0.000 0.0000 0.300 0.0715 0.981
+fft 42 0.000 0.0000 0.284 0.0675 0.964
+setup_H 18 0.000 0.0000 1.542 0.3670 0.997
+DHSCF 20 0.000 0.0000 1.922 0.4573 0.972
+DHSCF3 20 0.000 0.0000 1.787 0.4252 0.999
+rhoofd 20 0.000 0.0000 0.686 0.1632 0.872
+OtoM 21 0.000 0.0000 0.022 0.0052 0.889
+XC 20 0.000 0.0000 0.170 0.0404 0.921
+GXC-CellXC 20 0.000 0.0000 0.140 0.0334 0.903
+gridxc@cellXC 20 0.000 0.0000 0.140 0.0334 0.903
+vmat 19 0.000 0.0000 0.434 0.1032 0.986
+MtoO 19 0.000 0.0000 0.083 0.0198 0.727
+IterSCF 17 0.000 0.0000 1.980 0.4713 0.998
+compute_dm 17 0.000 0.0000 0.385 0.0917 1.000
+diagon 17 0.000 0.0000 0.384 0.0915 1.000
+cdiag 106 0.000 0.0000 0.314 0.0748 0.974
+cdiag1 106 0.000 0.0000 0.020 0.0047 0.956
+cdiag2 106 0.000 0.0000 0.042 0.0100 0.946
+cdiag3 106 0.000 0.0000 0.243 0.0578 0.977
+cdiag4 17 0.000 0.0000 0.000 0.0001 0.680
+MIXER 16 0.000 0.0000 0.005 0.0011 0.947
+PostSCF 1 0.000 0.0000 0.309 0.0736 0.987
+FINAL_HF 1 0.000 0.0000 0.309 0.0736 0.987
+DHSCF4 1 0.000 0.0000 0.135 0.0321 0.654
+dfscf 1 0.000 0.0000 0.101 0.0240 0.584
+overfsm 1 0.000 0.0000 0.000 0.0001 0.558
+state_analysis 1 0.000 0.0000 0.000 0.0000 0.214
+siesta_move 1 0.000 0.0000 0.000 0.0000 0.554
+Analysis 1 0.000 0.0000 0.471 0.1121 0.996
+c-eigval 72 0.000 0.0000 0.301 0.0717 1.000
+c-buildHS 72 0.000 0.0000 0.003 0.0006 0.524
+optical 1 0.000 0.0000 0.000 0.0000 0.849
+CDF-grid 4 0.000 0.0000 0.055 0.0131 0.611
MPI total 0 0.000 1.0000 0.000 0.0000
Definitions:
diff --git a/WS2/siesta/LDA/W.ion b/WS2/siesta/LDA/W.ion
index 3687424..7311a83 100644
--- a/WS2/siesta/LDA/W.ion
+++ b/WS2/siesta/LDA/W.ion
@@ -80,4019 +80,4019 @@ W # Label
# PAOs:__________________________
0 5 1 0 2.000000 #orbital l, n, z, is_polarized, population
500 0.5291339374976284E-02 2.640378348113166 # npts, delta, cutoff
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- 0.2116535749990514E-01 1.312262854830995
- 0.2645669687488142E-01 1.312422749820505
- 0.3174803624985770E-01 1.312617857718245
- 0.3703937562483399E-01 1.312847987251809
- 0.4233071499981027E-01 1.313112912662889
- 0.4762205437478656E-01 1.313412373851480
- 0.5291339374976285E-01 1.313746076542283
- 0.5820473312473913E-01 1.314113692473059
- 0.6349607249971541E-01 1.314514859604704
- 0.6878741187469170E-01 1.314949182352948
- 0.7407875124966798E-01 1.315416231841415
- 0.7937009062464427E-01 1.315915546175942
- 0.8466142999962055E-01 1.316446630739902
- 0.8995276937459683E-01 1.317008958510349
- 0.9524410874957312E-01 1.317601970394756
- 0.1005354481245494 1.318225075588096
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- 0.1111181268745020 1.319559046401869
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0 1 15.8141575784999997 #kb l, n (sequence number), Reference energy
@@ -8113,505 +8113,505 @@ W # Label
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# Chlocal:__________________________
500 0.1222616832815195E-01 6.100857995747823 # npts, delta, cutoff
diff --git a/WS2/siesta/LDA/W.ion.nc b/WS2/siesta/LDA/W.ion.nc
index 0510825..f896205 100644
Binary files a/WS2/siesta/LDA/W.ion.nc and b/WS2/siesta/LDA/W.ion.nc differ
diff --git a/WS2/siesta/LDA/W.ion.xml b/WS2/siesta/LDA/W.ion.xml
index 7f82c0c..c52327d 100644
--- a/WS2/siesta/LDA/W.ion.xml
+++ b/WS2/siesta/LDA/W.ion.xml
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diff --git a/WS2/siesta/LDA/WS2.DM b/WS2/siesta/LDA/WS2.DM
index 98c7a78..810be5c 100644
Binary files a/WS2/siesta/LDA/WS2.DM and b/WS2/siesta/LDA/WS2.DM differ
diff --git a/WS2/siesta/LDA/WS2.EIG b/WS2/siesta/LDA/WS2.EIG
index 9adbc69..a3225f2 100644
--- a/WS2/siesta/LDA/WS2.EIG
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+ -0.154214099E+01 -0.111870853E+01 -0.148519724E+00 0.222317545E+00 0.157812276E+01 0.377777658E+01 0.479618046E+01 0.686487299E+01 0.709229924E+01 0.771711146E+01
+ 0.113815484E+02 0.123756130E+02 0.126621233E+02 0.139478114E+02 0.150130666E+02 0.153659606E+02 0.156605303E+02 0.187152682E+02 0.210671781E+02 0.213766789E+02
+ 0.245246470E+02 0.253215150E+02 0.277219507E+02 0.287318521E+02 0.350282835E+02 0.372052447E+02 0.400203572E+02 0.409897793E+02 0.483806309E+02 0.495016606E+02
+ 0.570641219E+02 0.930454109E+02
diff --git a/WS2/siesta/LDA/WS2.FA b/WS2/siesta/LDA/WS2.FA
index 868a3d4..c3ecd9f 100644
--- a/WS2/siesta/LDA/WS2.FA
+++ b/WS2/siesta/LDA/WS2.FA
@@ -1,4 +1,4 @@
3
- 1 0.202564912E-06 0.132802924E-06 0.326055146E-07
- 2 -0.449595830E-07 -0.749038266E-07 0.669207641E+00
- 3 -0.114886384E-06 -0.149816666E-06 -0.669207721E+00
+ 1 0.902205531E-07 -0.644655338E-08 -0.835545912E-08
+ 2 -0.680974297E-08 0.328910543E-07 0.666359296E+00
+ 3 -0.884148113E-08 0.291132701E-07 -0.666359371E+00
diff --git a/WS2/siesta/LDA/WS2.alloc b/WS2/siesta/LDA/WS2.alloc
index 56fdbed..265de0e 100644
--- a/WS2/siesta/LDA/WS2.alloc
+++ b/WS2/siesta/LDA/WS2.alloc
@@ -1,6 +1,6 @@
-Allocation summary at 2023/06/29 12:55:12.002 -07:00
+Allocation summary at 2023/07/23 15:05:25.617 -07:00
Present memory all nodes : 0.000000 MB
Added peak mem all nodes : 0.000000 MB
@@ -14,70 +14,42 @@ Maximum memory allocation: 0.000000 MB
Occurred after allocating:
In routine:
-Allocation summary at 2023/06/29 12:55:12.002 -07:00
+Allocation summary at 2023/07/23 15:05:25.617 -07:00
Present memory all nodes : 0.000000 MB
Added peak mem all nodes : 0.000000 MB
Min peak memory in a node: 0.000000 MB
Max peak memory in a node: 0.000000 MB
-Maximum peak of memory occurred in node: 19
+Maximum peak of memory occurred in node: 5
Present memory allocation: 0.000000 MB
Maximum memory allocation: 0.000000 MB
Occurred after allocating:
In routine:
-Allocation summary at 2023/06/29 12:55:12.003 -07:00
+Allocation summary at 2023/07/23 15:05:25.617 -07:00
Present memory all nodes : 0.000000 MB
Added peak mem all nodes : 0.000000 MB
Min peak memory in a node: 0.000000 MB
Max peak memory in a node: 0.000000 MB
-Maximum peak of memory occurred in node: 15
+Maximum peak of memory occurred in node: 12
Present memory allocation: 0.000000 MB
Maximum memory allocation: 0.000000 MB
Occurred after allocating:
In routine:
-Allocation summary at 2023/06/29 12:55:12.003 -07:00
+Allocation summary at 2023/07/23 15:05:25.617 -07:00
Present memory all nodes : 0.000000 MB
Added peak mem all nodes : 0.000000 MB
Min peak memory in a node: 0.000000 MB
Max peak memory in a node: 0.000000 MB
-Maximum peak of memory occurred in node: 31
-
-Present memory allocation: 0.000000 MB
-Maximum memory allocation: 0.000000 MB
-Occurred after allocating:
-In routine:
-
-Allocation summary at 2023/06/29 12:55:12.003 -07:00
-
-Present memory all nodes : 0.000000 MB
-Added peak mem all nodes : 0.000000 MB
-Min peak memory in a node: 0.000000 MB
-Max peak memory in a node: 0.000000 MB
-
-Maximum peak of memory occurred in node: 8
-
-Present memory allocation: 0.000000 MB
-Maximum memory allocation: 0.000000 MB
-Occurred after allocating:
-In routine:
-
-Allocation summary at 2023/06/29 12:55:12.003 -07:00
-
-Present memory all nodes : 0.000000 MB
-Added peak mem all nodes : 0.000000 MB
-Min peak memory in a node: 0.000000 MB
-Max peak memory in a node: 0.000000 MB
-
-Maximum peak of memory occurred in node: 28
+Maximum peak of memory occurred in node: 1
Present memory allocation: 0.000000 MB
Maximum memory allocation: 0.000000 MB
diff --git a/WS2/siesta/LDA/WS2.bands b/WS2/siesta/LDA/WS2.bands
index 0e942c8..7a46473 100644
--- a/WS2/siesta/LDA/WS2.bands
+++ b/WS2/siesta/LDA/WS2.bands
@@ -1,439 +1,439 @@
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+ 1.289918 -78.4234 -42.7407 -42.6646 -42.5628 -32.6827 -32.6761 -32.6206 -32.6205 -32.6140 -32.6091
+ -32.5674 -17.8678 -17.1377 -10.1241 -9.0025 -8.8796 -7.3688 -6.3940 -6.0188 -5.7209
+ -1.9390 -1.8990 -0.7784 -0.0519 3.5424 4.8063 5.6501 8.0624 8.1330 9.0996
+ 9.8810 10.0214 10.9901 11.8824 13.2338 13.9630 14.9607 21.0959 21.2891 21.9862
+ 26.6114 27.9775 29.7640 31.2118 31.8357 35.6019 37.1770 38.6452 42.4070 48.9786
+ 52.8331 67.5740
+ 1.313357 -78.4252 -42.7217 -42.6672 -42.5580 -32.6829 -32.6774 -32.6218 -32.6200 -32.6140 -32.6090
+ -32.5681 -17.9981 -17.1870 -10.0382 -9.0041 -8.7204 -7.2743 -6.3203 -6.1159 -5.6514
+ -2.0061 -1.9102 -0.8927 -0.1202 3.7542 5.0317 5.8354 8.2137 8.2437 9.2415
+ 9.6343 9.7303 10.7660 11.6009 13.0323 13.9767 14.8473 21.1033 21.1864 22.3258
+ 26.7344 28.4954 30.0686 31.1733 31.4032 35.5576 36.7964 39.1038 41.6372 48.8538
+ 52.0075 66.2011
+ 1.336795 -78.4272 -42.7019 -42.6699 -42.5530 -32.6831 -32.6786 -32.6231 -32.6193 -32.6137 -32.6088
+ -32.5687 -18.1276 -17.2362 -9.9989 -8.9675 -8.5561 -7.1733 -6.2415 -6.2187 -5.5601
+ -2.0589 -1.9090 -1.0073 -0.1976 3.9525 5.2720 6.0021 8.2507 8.3788 9.3046
+ 9.4379 9.5043 10.5546 11.4206 12.8453 13.9944 14.7291 21.0487 21.1301 22.6515
+ 26.8364 29.0033 30.3464 30.9904 31.0120 35.5674 36.4604 39.6483 40.9248 48.7249
+ 51.2272 65.1367
+ 1.360234 -78.4292 -42.6816 -42.6727 -42.5478 -32.6834 -32.6799 -32.6245 -32.6183 -32.6133 -32.6087
+ -32.5693 -18.2547 -17.2846 -10.0129 -8.8832 -8.3887 -7.0667 -6.3252 -6.1593 -5.4533
+ -2.0953 -1.8958 -1.1185 -0.2841 4.1359 5.5213 6.1243 8.2409 8.3973 9.2600
+ 9.3679 9.3717 10.3591 11.3686 12.6743 14.0149 14.6070 20.8774 21.1797 22.9633
+ 26.9149 29.4921 30.5818 30.6555 30.7015 35.5772 36.1909 40.2649 40.2819 48.5955
+ 50.5490 64.3144
+ 1.383673 -78.4313 -42.6754 -42.6609 -42.5427 -32.6838 -32.6811 -32.6259 -32.6172 -32.6128 -32.6085
+ -32.5700 -18.3778 -17.3314 -10.0711 -8.7576 -8.2196 -6.9553 -6.4335 -6.0762 -5.3382
+ -2.1129 -1.8714 -1.2227 -0.3789 4.3000 5.7708 6.1774 8.2084 8.2715 9.1124
+ 9.3372 9.4595 10.1819 11.4386 12.5214 14.0357 14.4818 20.6744 21.2560 23.2610
+ 26.9673 29.9538 30.3280 30.3515 30.7615 35.5337 36.0090 39.7170 40.9395 48.4681
+ 50.0184 63.6779
+ 1.407112 -78.4334 -42.6781 -42.6404 -42.5375 -32.6842 -32.6823 -32.6273 -32.6160 -32.6122 -32.6084
+ -32.5706 -18.4955 -17.3760 -10.1579 -8.6042 -8.0504 -6.8405 -6.5414 -5.9955 -5.2215
+ -2.1099 -1.8373 -1.3161 -0.4813 4.4343 6.0056 6.1548 8.0779 8.1894 8.8960
+ 9.3829 9.6472 10.0243 11.5942 12.3899 14.0532 14.3549 20.4420 21.3633 23.5433
+ 26.9901 29.9792 30.0251 30.3813 30.8806 35.4043 35.9295 39.2342 41.6573 48.3435
+ 49.6584 63.1848
+ 1.430551 -78.4356 -42.6807 -42.6202 -42.5325 -32.6847 -32.6835 -32.6287 -32.6147 -32.6116 -32.6082
+ -32.5712 -18.6065 -17.4180 -10.2594 -8.4352 -7.8822 -6.7235 -6.6468 -5.9210 -5.1097
+ -2.0852 -1.7952 -1.3953 -0.5897 4.5188 6.0854 6.1994 7.8977 8.1943 8.6466
+ 9.4916 9.8687 9.8872 11.7982 12.2855 14.0634 14.2279 20.1828 21.5061 23.8085
+ 26.9785 29.6150 29.7447 30.7694 30.9480 35.1867 35.9544 38.8341 42.4022 48.2204
+ 49.4632 62.8052
+ 1.453990 -78.4377 -42.6832 -42.6008 -42.5277 -32.6852 -32.6846 -32.6300 -32.6134 -32.6109 -32.6080
+ -32.5718 -18.7098 -17.4568 -10.3661 -8.2595 -7.7160 -6.7478 -6.6061 -5.8567 -5.0076
+ -2.0388 -1.7470 -1.4571 -0.7022 4.5256 6.0264 6.3106 7.7962 8.2068 8.3882
+ 9.6544 9.7703 10.0884 12.0245 12.2176 14.0619 14.1024 19.8995 21.6885 24.0540
+ 26.9265 29.2829 29.4864 30.9874 31.1147 34.9070 36.0721 38.5131 43.1574 48.0960
+ 49.3974 62.5203
+ 1.477429 -78.4397 -42.6855 -42.5824 -42.5232 -32.6858 -32.6856 -32.6311 -32.6121 -32.6103 -32.6078
+ -32.5724 -18.8043 -17.4921 -10.4715 -8.0837 -7.5528 -6.8428 -6.4902 -5.8065 -4.9186
+ -1.9727 -1.6950 -1.4993 -0.8166 4.4362 6.0268 6.3024 7.8197 8.1356 8.2074
+ 9.6730 9.8649 10.2782 12.2010 12.2562 13.9807 14.0445 19.5951 21.9138 24.2771
+ 26.8282 29.0004 29.2513 31.0310 31.4161 34.6117 36.2603 38.2647 43.9050 47.9657
+ 49.4045 62.3193
+ 1.500867 -78.4416 -42.6876 -42.5653 -42.5190 -32.6865 -32.6865 -32.6322 -32.6109 -32.6097 -32.6076
+ -32.5728 -18.8892 -17.5237 -10.5711 -7.9132 -7.3936 -6.9300 -6.3779 -5.7739 -4.8442
+ -1.8905 -1.6415 -1.5214 -0.9299 4.2648 6.0968 6.1895 7.8982 7.9588 8.1856
+ 9.5939 10.1150 10.4116 12.2519 12.4823 13.8650 14.0075 19.2734 22.1829 24.4747
+ 26.6809 28.7776 29.0412 31.1100 31.6746 34.3574 36.4938 38.0794 44.6264 47.8248
+ 49.4175 62.1956
+ 1.524306 -78.4434 -42.6895 -42.5499 -42.5153 -32.6873 -32.6871 -32.6331 -32.6098 -32.6091 -32.6074
+ -32.5733 -18.9637 -17.5511 -10.6619 -7.7530 -7.2394 -7.0083 -6.2718 -5.7608 -4.7844
+ -1.7978 -1.5887 -1.5243 -1.0390 4.0475 6.0220 6.2177 7.6821 8.1390 8.1668
+ 9.5314 10.3951 10.4713 12.3781 12.6942 13.7578 13.9484 18.9398 22.4934 24.6446
+ 26.4877 28.6153 28.8583 31.2467 31.8923 34.2015 36.7479 37.9461 45.3027 47.6696
+ 49.3710 62.1430
+ 1.547745 -78.4450 -42.6912 -42.5364 -42.5120 -32.6880 -32.6878 -32.6338 -32.6088 -32.6086 -32.6072
+ -32.5737 -19.0272 -17.5745 -10.7417 -7.6074 -7.0920 -7.0764 -6.1746 -5.7674 -4.7379
+ -1.7012 -1.5390 -1.5114 -1.1402 3.8187 5.8407 6.3681 7.4921 8.0690 8.4058
+ 9.4835 10.4583 10.6948 12.5681 12.8854 13.6615 13.8658 18.6026 22.8377 24.7850
+ 26.2573 28.5061 28.7044 31.4479 32.0724 34.1935 37.0009 37.8536 45.9152 47.4999
+ 49.2122 62.1518
+ 1.571184 -78.4463 -42.6925 -42.5251 -42.5092 -32.6886 -32.6884 -32.6344 -32.6081 -32.6081 -32.6069
+ -32.5740 -19.0794 -17.5935 -10.8087 -7.4809 -7.1334 -6.9539 -6.0893 -5.7919 -4.7031
+ -1.6081 -1.4947 -1.4876 -1.2301 3.6032 5.6700 6.5324 7.3318 7.9788 8.6537
+ 9.4481 10.3870 11.0022 12.7951 13.0501 13.5786 13.7607 18.2743 23.2025 24.8957
+ 26.0005 28.4385 28.5805 31.7019 32.2175 34.3631 37.2343 37.7916 46.4457 47.3209
+ 48.9140 62.2058
+ 1.594623 -78.4474 -42.6936 -42.5160 -42.5070 -32.6891 -32.6889 -32.6348 -32.6078 -32.6077 -32.6065
+ -32.5742 -19.1199 -17.6083 -10.8618 -7.3775 -7.1785 -6.8293 -6.0189 -5.8295 -4.6781
+ -1.5262 -1.4592 -1.4578 -1.3047 3.4185 5.5245 6.6994 7.2040 7.8735 8.8971
+ 9.4231 10.2746 11.3008 13.0268 13.1836 13.5114 13.6381 17.9733 23.5700 24.9779
+ 25.7281 28.4004 28.4866 31.9779 32.3295 34.7006 37.4325 37.7514 46.8780 47.1453
+ 48.4904 62.2832
+ 1.618062 -78.4482 -42.6944 -42.5095 -42.5055 -32.6895 -32.6894 -32.6351 -32.6075 -32.6074 -32.6062
+ -32.5744 -19.1487 -17.6189 -10.9003 -7.3007 -7.2111 -6.7255 -5.9663 -5.8724 -4.6613
+ -1.4620 -1.4328 -1.4301 -1.3609 3.2775 5.4140 6.8566 7.1111 7.7620 9.1236
+ 9.4068 10.1385 11.5658 13.2297 13.2820 13.4618 13.5107 17.7243 23.9189 25.0337
+ 25.4528 28.3812 28.4214 32.2302 32.4093 35.1323 37.5833 37.7268 46.9932 47.1977
+ 48.0130 62.3601
+ 1.641501 -78.4487 -42.6949 -42.5055 -42.5045 -32.6897 -32.6896 -32.6352 -32.6074 -32.6073 -32.6059
+ -32.5745 -19.1659 -17.6252 -10.9236 -7.2534 -7.2309 -6.6537 -5.9336 -5.9082 -4.6516
+ -1.4211 -1.4143 -1.4128 -1.3958 3.1891 5.3451 6.9828 7.0546 7.6638 9.3104
+ 9.3976 10.0048 11.7591 13.3423 13.3705 13.4054 13.4314 17.5569 24.2153 25.0658
+ 25.2022 28.3730 28.3833 32.4087 32.4573 35.5114 37.6775 37.7136 46.8883 47.3941
+ 47.6173 62.4157
+ 1.664939 -78.4489 -42.6950 -42.5042 -42.5042 -32.6897 -32.6897 -32.6353 -32.6073 -32.6073 -32.6058
+ -32.5745 -19.1716 -17.6273 -10.9314 -7.2375 -7.2375 -6.6274 -5.9226 -5.9226 -4.6485
+ -1.4077 -1.4077 -1.4070 -1.4070 3.1590 5.3217 7.0357 7.0357 7.6203 9.3946
+ 9.3946 9.9380 11.8324 13.3626 13.3626 13.4212 13.4212 17.4973 24.3568 25.0762
+ 25.0762 28.3707 28.3707 32.4734 32.4734 35.6652 37.7095 37.7095 46.8507 47.4604
+ 47.4604 62.4358
4
0.000000 'Gamma'
0.703686 'K'
diff --git a/WS2/siesta/LDA/WS2.nc b/WS2/siesta/LDA/WS2.nc
index bd3528c..28d3c25 100644
Binary files a/WS2/siesta/LDA/WS2.nc and b/WS2/siesta/LDA/WS2.nc differ
diff --git a/WS2/siesta/LDA/WS2.times b/WS2/siesta/LDA/WS2.times
index 389e0d0..1ca3953 100644
--- a/WS2/siesta/LDA/WS2.times
+++ b/WS2/siesta/LDA/WS2.times
@@ -1,77 +1,78 @@
-timer: Number of nodes = 32
-timer: Busiest calculating node was node = 24
-timer: Times refer to node = 24
-timer: Total elapsed wall-clock time (sec) = 2.180
+timer: Number of nodes = 16
+timer: Busiest calculating node was node = 13
+timer: Times refer to node = 13
+timer: Total elapsed wall-clock time (sec) = 4.210
timer: CPU times (sec):
-Calc: Sum, Avge, myNode, Avg/Max = 69.335 2.167 2.170 0.999
+Calc: Sum, Avge, myNode, Avg/Max = 67.107 4.194 4.202 0.998
Comm: Sum, Avge, myNode, Avg/Max = 0.000 0.000 0.000 NaN
-Tot: Sum, Avge, myNode, Avg/Max = 69.335 2.167 2.170 0.999
+Tot: Sum, Avge, myNode, Avg/Max = 67.107 4.194 4.202 0.998
Program times printed if > 0.000E+00 of total
Program Calls Prg.com Prg.com Prg.tot Prg.tot Nod.avg
/Tot.com /Tot.tot/Nod.max
-siesta 1 0.000 0.0000 2.170 1.0000 0.999
-Setup 1 0.000 0.0000 0.133 0.0615 0.996
-bands 3 0.000 0.0000 0.706 0.3255 0.999
-KSV_init 1 0.000 0.0000 0.000 0.0000 0.879
-IterGeom 1 0.000 0.0000 1.276 0.5882 0.999
-geom_init 1 0.000 0.0000 0.539 0.2482 0.999
-state_init 1 0.000 0.0000 0.447 0.2059 0.999
-hsparse 1 0.000 0.0000 0.000 0.0002 0.837
-overlap 1 0.000 0.0000 0.000 0.0001 0.652
-CDF 18 0.000 0.0000 0.003 0.0012 0.057
-Setup_H0 1 0.000 0.0000 0.070 0.0322 0.997
-naefs 2 0.000 0.0000 0.003 0.0015 0.957
-dnaefs 1 0.000 0.0000 0.000 0.0000 0.960
-two-body 1 0.000 0.0000 0.000 0.0000 0.735
-MolMec 2 0.000 0.0000 0.000 0.0000 0.624
-kinefsm 2 0.000 0.0000 0.000 0.0002 0.619
-nlefsm 2 0.000 0.0000 0.040 0.0183 0.750
-DHSCF_Init 1 0.000 0.0000 0.047 0.0217 0.795
-DHSCF1 1 0.000 0.0000 0.009 0.0041 0.700
-InitMesh 1 0.000 0.0000 0.009 0.0041 0.991
-INITMESH 3 0.000 0.0000 0.002 0.0009 0.410
-DHSCF2 1 0.000 0.0000 0.038 0.0175 0.757
-REMESH 1 0.000 0.0000 0.009 0.0040 0.464
-BuildDISTR 2 0.000 0.0000 0.002 0.0009 0.409
-meshCom-Ca 3 0.000 0.0000 0.000 0.0000 0.725
-REORD 5 0.000 0.0000 0.000 0.0000 0.900
-PHION 1 0.000 0.0000 0.014 0.0065 0.741
-dscfComm 1 0.000 0.0000 0.004 0.0018 0.701
-COMM_BSC 82 0.000 0.0000 0.004 0.0017 0.314
-POISON 21 0.000 0.0000 0.024 0.0112 0.982
-fft 42 0.000 0.0000 0.024 0.0110 0.981
-setup_H 18 0.000 0.0000 0.184 0.0848 0.999
-DHSCF 20 0.000 0.0000 0.252 0.1162 0.983
-DHSCF3 20 0.000 0.0000 0.240 0.1107 0.995
-rhoofd 20 0.000 0.0000 0.108 0.0499 0.881
-OtoM 21 0.000 0.0000 0.023 0.0107 0.869
-XC 20 0.000 0.0000 0.017 0.0079 0.932
-GXC-CellXC 20 0.000 0.0000 0.015 0.0071 0.849
-gridxc@cellXC 20 0.000 0.0000 0.015 0.0071 0.849
-vmat 19 0.000 0.0000 0.052 0.0240 0.943
-MtoO 19 0.000 0.0000 0.012 0.0053 0.698
-IterSCF 17 0.000 0.0000 0.689 0.3174 0.999
-compute_dm 17 0.000 0.0000 0.514 0.2369 0.989
-diagon 17 0.000 0.0000 0.380 0.1749 1.000
-MIXER 16 0.000 0.0000 0.004 0.0017 0.950
-PostSCF 1 0.000 0.0000 0.048 0.0223 0.923
-FINAL_HF 1 0.000 0.0000 0.048 0.0223 0.921
-DHSCF4 1 0.000 0.0000 0.012 0.0055 0.721
-dfscf 1 0.000 0.0000 0.010 0.0045 0.672
-overfsm 1 0.000 0.0000 0.000 0.0001 0.605
-state_analysis 1 0.000 0.0000 0.000 0.0000 0.117
-siesta_move 1 0.000 0.0000 0.000 0.0000 0.758
-Analysis 1 0.000 0.0000 0.756 0.3486 0.998
-c-eigval 72 0.000 0.0000 0.697 0.3212 1.000
-c-buildHS 72 0.000 0.0000 0.001 0.0006 0.717
-cdiag 72 0.000 0.0000 0.695 0.3205 0.992
-cdiag1 72 0.000 0.0000 0.059 0.0273 0.983
-cdiag2 72 0.000 0.0000 0.155 0.0715 0.989
-cdiag3 72 0.000 0.0000 0.471 0.2171 0.990
-optical 1 0.000 0.0000 0.000 0.0000 0.832
-CDF-grid 4 0.000 0.0000 0.023 0.0106 0.746
+siesta 1 0.000 0.0000 4.202 1.0000 0.998
+Setup 1 0.000 0.0000 0.143 0.0341 0.988
+bands 3 0.000 0.0000 0.304 0.0725 1.000
+KSV_init 1 0.000 0.0000 0.000 0.0000 0.857
+IterGeom 1 0.000 0.0000 3.583 0.8529 0.999
+geom_init 1 0.000 0.0000 1.278 0.3041 0.998
+state_init 1 0.000 0.0000 0.625 0.1486 0.998
+hsparse 1 0.000 0.0000 0.001 0.0001 0.622
+overlap 1 0.000 0.0000 0.000 0.0001 0.641
+CDF 18 0.000 0.0000 0.089 0.0212 0.939
+Setup_H0 1 0.000 0.0000 0.563 0.1341 0.999
+naefs 2 0.000 0.0000 0.004 0.0010 0.932
+dnaefs 1 0.000 0.0000 0.000 0.0000 0.943
+two-body 1 0.000 0.0000 0.000 0.0000 0.730
+MolMec 2 0.000 0.0000 0.000 0.0000 0.635
+kinefsm 2 0.000 0.0000 0.000 0.0001 0.593
+nlefsm 2 0.000 0.0000 0.032 0.0076 0.706
+DHSCF_Init 1 0.000 0.0000 0.543 0.1292 0.976
+DHSCF1 1 0.000 0.0000 0.093 0.0222 0.933
+InitMesh 1 0.000 0.0000 0.093 0.0222 0.968
+INITMESH 3 0.000 0.0000 0.069 0.0165 0.596
+DHSCF2 1 0.000 0.0000 0.449 0.1069 0.976
+REMESH 1 0.000 0.0000 0.089 0.0212 0.888
+BuildDISTR 2 0.000 0.0000 0.069 0.0165 0.596
+meshCom-Ca 3 0.000 0.0000 0.000 0.0000 0.765
+REORD 5 0.000 0.0000 0.000 0.0001 0.865
+PHION 1 0.000 0.0000 0.188 0.0448 0.709
+dscfComm 1 0.000 0.0000 0.067 0.0160 0.674
+COMM_BSC 82 0.000 0.0000 0.129 0.0306 0.698
+POISON 21 0.000 0.0000 0.300 0.0715 0.981
+fft 42 0.000 0.0000 0.284 0.0675 0.964
+setup_H 18 0.000 0.0000 1.542 0.3670 0.997
+DHSCF 20 0.000 0.0000 1.922 0.4573 0.972
+DHSCF3 20 0.000 0.0000 1.787 0.4252 0.999
+rhoofd 20 0.000 0.0000 0.686 0.1632 0.872
+OtoM 21 0.000 0.0000 0.022 0.0052 0.889
+XC 20 0.000 0.0000 0.170 0.0404 0.921
+GXC-CellXC 20 0.000 0.0000 0.140 0.0334 0.903
+gridxc@cellXC 20 0.000 0.0000 0.140 0.0334 0.903
+vmat 19 0.000 0.0000 0.434 0.1032 0.986
+MtoO 19 0.000 0.0000 0.083 0.0198 0.727
+IterSCF 17 0.000 0.0000 1.980 0.4713 0.998
+compute_dm 17 0.000 0.0000 0.385 0.0917 1.000
+diagon 17 0.000 0.0000 0.384 0.0915 1.000
+cdiag 106 0.000 0.0000 0.314 0.0748 0.974
+cdiag1 106 0.000 0.0000 0.020 0.0047 0.956
+cdiag2 106 0.000 0.0000 0.042 0.0100 0.946
+cdiag3 106 0.000 0.0000 0.243 0.0578 0.977
+cdiag4 17 0.000 0.0000 0.000 0.0001 0.680
+MIXER 16 0.000 0.0000 0.005 0.0011 0.947
+PostSCF 1 0.000 0.0000 0.309 0.0736 0.987
+FINAL_HF 1 0.000 0.0000 0.309 0.0736 0.987
+DHSCF4 1 0.000 0.0000 0.135 0.0321 0.654
+dfscf 1 0.000 0.0000 0.101 0.0240 0.584
+overfsm 1 0.000 0.0000 0.000 0.0001 0.558
+state_analysis 1 0.000 0.0000 0.000 0.0000 0.214
+siesta_move 1 0.000 0.0000 0.000 0.0000 0.554
+Analysis 1 0.000 0.0000 0.471 0.1121 0.996
+c-eigval 72 0.000 0.0000 0.301 0.0717 1.000
+c-buildHS 72 0.000 0.0000 0.003 0.0006 0.524
+optical 1 0.000 0.0000 0.000 0.0000 0.849
+CDF-grid 4 0.000 0.0000 0.055 0.0131 0.611
MPI total 0 0.000 1.0000 0.000 0.0000
Definitions:
diff --git a/WS2/siesta/LDA/WS2.xml b/WS2/siesta/LDA/WS2.xml
index 4b86ec2..6ec4e29 100644
--- a/WS2/siesta/LDA/WS2.xml
+++ b/WS2/siesta/LDA/WS2.xml
@@ -16,11 +16,11 @@
-
+
+ content="b94da7e0-292f-11ee-53d9-fb039b9fb9d4" />
-
+
@@ -30,7 +30,7 @@
- PW92
+ PZ
@@ -106,7 +106,7 @@
- 160
+ 1000
@@ -336,22 +336,22 @@
- 24 24 192
+ 54 54 480
- 160
+ 1000
- 163.013700096
+ 1018.83562565
- -1775.612391
+ -1775.255690
@@ -359,15 +359,15 @@
- 1699.344058
+ 1699.580665
- 2891.317012
+ 2891.262600
- -1188.597975
+ -1188.675958
@@ -379,7 +379,7 @@
- 80.813700
+ 80.730930
@@ -387,7 +387,7 @@
- 33.956928
+ 33.898767
@@ -395,15 +395,15 @@
- -607.129352
+ -607.114022
- -67.845766
+ -67.619067
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diff --git a/WS2/siesta/LDA/density2Vh.py b/WS2/siesta/LDA/density2Vh.py
new file mode 100644
index 0000000..210abb7
--- /dev/null
+++ b/WS2/siesta/LDA/density2Vh.py
@@ -0,0 +1,175 @@
+import numpy as np
+from fft_mod import put_FFTbox2, ifft_g2r, fft_r2g, flat_FFTbox
+from netCDF4 import Dataset
+from pymatgen.core.structure import Structure
+#from pymatgen.io.cube import Cube
+bohr2ang = 0.529177
+hartree = 27.2116 #eV
+vol = 214.828427 *((1/bohr2ang)**3)
+
+
+def main():
+ prefix = 'WS2'
+ #savedir = '../wfs/highcutoff/'
+ fn_poscar = './struct.POSCAR' # POSCAR file
+ #FFTgrid = [864, 864, 180] # coarse grid
+ noncolin = False
+ struct = Structure.from_file(fn_poscar)
+
+ ## Reading the total charge density ##
+ print(' Reading total charge density from SIESTA')
+ rootgrp = Dataset("./WS2.nc", "r", format="NETCDF4")
+ Rho = rootgrp['GRID']['Rho'][:].data
+ nspin, n3, n2, n1 = Rho.shape
+ print(' nspin, n1, n2, n3:', nspin, n1, n2, n3)
+ FFTgrid = np.array([n1,n2,n3], dtype=np.int32)
+ nfft = n1*n2*n3
+ print('nfft: ', nfft)
+ print(' vol: ', vol, ' Bohr^3')
+ print(' np.sum(Rho)*vol/nfft = ', np.sum(Rho[0,:,:,:])*vol/nfft)
+ rho_r_FFTbox = np.array([(Rho[0,:,:,:].T)])
+
+ #n1, n2, n3 = FFTgrid
+ #nfft = n1*n2*n3
+ # vh
+ #vol = struct.volume/(bohr2ang**3) # in Bohr^3
+ cell = struct.lattice._matrix*(1/bohr2ang) # in Bohr
+ bcell = 2*np.pi*np.linalg.inv(cell).T # in Bohr^-1
+
+ # debug
+ rho_g_FFTbox = fft_r2g(rho_r_FFTbox)
+ rho_g, igvec = flat_FFTbox(rho_g_FFTbox)
+ fn_vh_r_FFTbox= f'vh_r_FFTbox'
+ vh_r_FFTbox = get_vh(rho_g, igvec, bcell, FFTgrid)
+ np.save(fn_vh_r_FFTbox, vh_r_FFTbox)
+ Eh = np.real(0.5*np.sum(vh_r_FFTbox*rho_r_FFTbox*(vol/nfft)))
+
+
+ #diff = np.abs(vbh_r-vh_r)
+ print(f'Eh = {2*Eh} in Ry')
+ print(f'Eh = {2*Eh*hartree/2} in eV')
+ #print()
+ #print('diff = abs(vsub - vsub_aprox) in Hartree')
+ #print('max(diff)',np.max(diff))
+ #print('min(diff)',np.min(diff))
+ #print('avg(diff)',np.average(diff))
+ #print(np.sort(ratio.flat)[-1000:])
+ return
+
+
+def get_vh(rho_g, igvec, bcell, FFTgrid):
+ """
+ --Input--
+ rho_g : complex128(ng)
+ momentum space charge density in Hartree Atomic Unit
+
+ gvec : int(ng,3)
+ momentum space charge density in Hartree Atomic Unit
+
+ bcell_in: float64(3,3)
+ reciprocal lattice vectors (bohr^{-1})
+
+ --Output--
+ vh : float(:,:,:)
+
+ """
+ vh_g = np.zeros_like(rho_g)
+ gvec = igvec.dot(bcell)
+ gvec_sq = np.einsum('ix,ix->i', gvec, gvec) # bohr^{-1} or Ry
+ for ig, g_sq in enumerate(gvec_sq):
+ if g_sq < 1e-12:
+ vh_g[ig] = 0
+ else:
+ vh_g[ig] = 4*np.pi*rho_g[ig]/g_sq
+
+ vh_g_FFTbox = put_FFTbox2(vh_g, igvec, FFTgrid, noncolin=False)
+ vh_r = ifft_g2r(vh_g_FFTbox)
+ return np.real(vh_r)
+
+
+
+def get_vxc(rho):
+ """
+ --Input--
+ rho : float(:,:,:)
+ real space charge density in Hartree Atomic Unit
+
+ --Output--
+ vxc : float(:,:,:)
+
+ """
+ inp = {}
+ n1, n2, n3 = rho.shape
+ rho_flatten = rho.flatten()
+ inp["rho"] = rho_flatten
+
+ # Build functional
+ func_c = pylibxc.LibXCFunctional("LDA_C_PZ", "unpolarized")
+ func_x = pylibxc.LibXCFunctional("LDA_X", "unpolarized")
+
+ # Compute exchange part
+ ret_x = func_x.compute(inp, do_fxc=True)
+ v2rho2_x = ret_x['v2rho2'][:,0]
+ vrho_x = ret_x['vrho'][:,0]
+ zk_x = ret_x['zk'][:,0]
+
+ # Compute correlation part
+ ret_c = func_c.compute(inp, do_fxc=True)
+ v2rho2_c = ret_x['v2rho2'][:,0]
+ vrho_c = ret_c['vrho'][:,0]
+ zk_c = ret_c['zk'][:,0]
+
+ vxc = vrho_x + vrho_c
+ fxc = v2rho2_x + v2rho2_c
+
+ vxc_FFTbox = np.reshape(vxc,(n1,n2,n3))
+ fxc_FFTbox = np.reshape(fxc,(n1,n2,n3))
+
+ return vxc_FFTbox, fxc_FFTbox
+
+def vxc_libxc():
+ n1, n2, n3 = [18, 18, 135]
+ #gvec_rho = np.loadtxt('../2.1-wfn/rho_gvec.txt',dtype=np.int32)
+ #rho_pw2bgw = np.load('../2.1-wfn/rho_pw2bgw.npy')
+ #rho_FFTbox = put_FFTbox2(rho_pw2bgw, gvec_rho, [n1,n2,n3], noncolin=False)
+ #rho = ifft_g2r(rho_FFTbox)
+ #rho_pp = Cube("../1.1-pp/Rho.cube")
+ #rho = rho_pp.data
+ rho_pw2bgw = np.load("../2.1-wfn/rhor_pw2bgw.npy")
+ rho = rho_pw2bgw[0,:,:,:]
+ frac = 0.0001
+ rho_f = rho * frac
+ rho_r = rho - rho_f
+
+ # Create input
+ const = 1
+ inp = {}
+ rho_flatten = rho.flatten()
+ rho_r_flatten = rho_r.flatten()
+ rho_f_flatten = rho_f.flatten()
+ inp["rho"] = const*rho_flatten
+
+ # Build functional
+ func_c = pylibxc.LibXCFunctional("LDA_C_PZ", "unpolarized")
+ func_x = pylibxc.LibXCFunctional("LDA_X", "unpolarized")
+
+ # Compute exchange part
+ ret_x = func_x.compute(inp, do_fxc=True)
+ v2rho2_x = ret_x['v2rho2'][:,0]
+ vrho_x = ret_x['vrho'][:,0]
+ zk_x = ret_x['zk'][:,0]
+
+ # Compute correlation part
+ ret_c = func_c.compute(inp, do_fxc=True)
+ v2rho2_c = ret_x['v2rho2'][:,0]
+ vrho_c = ret_c['vrho'][:,0]
+ zk_c = ret_c['zk'][:,0]
+
+ vxc = vrho_x + vrho_c
+ fxc = v2rho2_x + v2rho2_c
+
+ vxc_FFTbox = np.reshape(vxc,(18,18,135))
+ fxc_FFTbox = np.reshape(fxc,(18,18,135))
+ return vxc_FFTbox, fxc_FFTbox
+
+main()
diff --git a/WS2/siesta/LDA/fdf.20230723T145601.236.log b/WS2/siesta/LDA/fdf.20230723T145601.236.log
new file mode 100644
index 0000000..aed0b5f
--- /dev/null
+++ b/WS2/siesta/LDA/fdf.20230723T145601.236.log
@@ -0,0 +1,537 @@
+SystemName # default value
+SystemLabel WS2
+SpinPolarized F # default value
+NonCollinearSpin F # default value
+SpinOrbit F # default value
+#:block? SpinPolarized F
+#:defined? SpinPolarized F
+#:block? NonCollinearSpin F
+#:defined? NonCollinearSpin F
+#:block? SpinOrbit F
+#:defined? SpinOrbit F
+Spin none # default value
+TimeReversalSymmetry T # default value
+DebugObjects.Node 0 # default value
+DebugObjects F # default value
+XML.Write T
+timer_report_threshold 0.000000000 # default value
+UseParallelTimer T # default value
+UseTreeTimer F # default value
+timing-split-scf-steps F # default value
+use-walltime F # default value
+alloc_report_level 0 # default value
+alloc_report_threshold 0.000000000 # default value
+xc.functional LDA
+xc.authors PW92
+#:block? XC.hybrid F
+#:defined? XC.hybrid F
+#:block? XC.cocktail F
+#:defined? XC.cocktail F
+MM.Cutoff 30.00000000 Bohr # default value
+MM.UnitsEnergy eV # default value
+MM.UnitsDistance Ang # default value
+Atom.Debug F # default value
+WriteIonPlotFiles F # default value
+Atom.Debug.KB.Generation F # default value
+KB.New.Reference.Orbitals F # default value
+user-basis F # default value
+user-basis-netcdf F # default value
+#:block? DFTU.proj F
+#:defined? DFTU.proj F
+#:block? LDAU.proj F
+#:defined? LDAU.proj F
+Number_of_species 2
+%block Chemical_species_label
+ 1 74 W
+ 2 16 S
+%endblock Chemical_species_label
+ReparametrizePseudos F # default value
+Restricted.Radial.Grid T # default value
+Rmax.Radial.Grid 0.000000000 # default value
+PAO.BasisSize DZP
+PAO.BasisType split # default value
+PAO.SoftDefault F # default value
+PAO.SoftInnerRadius 0.9000000000 # default value
+PAO.SoftPotential 40.00000000 # default value
+PAO.SplitNorm 0.1500000000 # default value
+PAO.SplitNormH -1.000000000 # default value
+PAO.Polarization.NonPerturbative F # default value
+PAO.NonPerturbative.Polarization.Orbitals F # default value
+PAO.Polarization.NonPerturbative.Fallback F # default value
+LDAU.ProjectorGenerationMethod 2 # default value
+DFTU.ProjectorGenerationMethod 2 # default value
+LDAU.EnergyShift 0.5000000000E-01 Ry # default value
+DFTU.EnergyShift 0.5000000000E-01 Ry # default value
+LDAU.CutoffNorm 0.9000000000 # default value
+DFTU.CutoffNorm 0.9000000000 # default value
+PAO.SoftDefault F # default value
+PAO.SoftInnerRadius 0.9000000000 # default value
+PAO.SoftPotential 40.00000000 # default value
+LDAU.ThresholdTol 0.1000000000E-01 # default value
+DFTU.ThresholdTol 0.1000000000E-01 # default value
+LDAU.PopTol 0.1000000000E-02 # default value
+DFTU.PopTol 0.1000000000E-02 # default value
+LDAU.PotentialShift F # default value
+DFTU.PotentialShift F # default value
+LDAU.FirstIteration F # default value
+DFTU.FirstIteration F # default value
+FilterCutoff 0.000000000 Ry # default value
+FilterTol 0.000000000 Ry # default value
+spin-orbit-strength 1.000000000 # default value
+Use.PSML.KB.Projectors T # default value
+Use.PSML.Vlocal T # default value
+PSML.KB.Projectors T # default value
+PSML.Vlocal T # default value
+psml.chlocal.build.r0 0.4000000000E-02 # default value
+psml.chlocal.build.delta 0.5000000000E-02 # default value
+psml.chlocal.build.poly_order_rlin 4 # default value
+chlocal-use-charge-cutoff-for-vlocal-fit F # default value
+psml.chlocal.build.rr1 0.1000000000E-02 # default value
+psml.chlocal.build.exp_al 1.012000000 # default value
+psml.chlocal.build.poly_order_rofi 7 # default value
+PAO.EnergyShift 0.2000000000E-01 Ry # default value
+PAO.SplitTailNorm F # default value
+PAO.FixSplitTable F # default value
+PAO.NewSplitCode F # default value
+PAO.Filter F # default value
+PAO.Filter F # default value
+PAO.Filter F # default value
+PAO.Filter F # default value
+PAO.Filter F # default value
+PAO.Filter F # default value
+PAO.Filter F # default value
+PAO.OldStylePolorbs T # default value
+PAO.SplitTailNorm F # default value
+PAO.FixSplitTable F # default value
+PAO.NewSplitCode F # default value
+PAO.Filter F # default value
+Vna.Filter F # default value
+FilterCutoff 0.000000000 Ry # default value
+FilterTol 0.000000000 Ry # default value
+spin-orbit-strength 1.000000000 # default value
+Use.PSML.KB.Projectors T # default value
+Use.PSML.Vlocal T # default value
+PSML.KB.Projectors T # default value
+PSML.Vlocal T # default value
+psml.chlocal.build.r0 0.4000000000E-02 # default value
+psml.chlocal.build.delta 0.5000000000E-02 # default value
+psml.chlocal.build.poly_order_rlin 4 # default value
+chlocal-use-charge-cutoff-for-vlocal-fit F # default value
+psml.chlocal.build.rr1 0.1000000000E-02 # default value
+psml.chlocal.build.exp_al 1.012000000 # default value
+psml.chlocal.build.poly_order_rofi 7 # default value
+PAO.EnergyShift 0.2000000000E-01 Ry # default value
+PAO.SplitTailNorm F # default value
+PAO.FixSplitTable F # default value
+PAO.NewSplitCode F # default value
+PAO.Filter F # default value
+PAO.Filter F # default value
+PAO.Filter F # default value
+PAO.Filter F # default value
+PAO.OldStylePolorbs T # default value
+PAO.SplitTailNorm F # default value
+PAO.FixSplitTable F # default value
+PAO.NewSplitCode F # default value
+PAO.Filter F # default value
+Vna.Filter F # default value
+PAO.BasisType split # default value
+Debug.Elec.Corr F # default value
+Atom-Setup-Only F # default value
+UseStructFile F # default value
+MD.UseStructFile F # default value
+#:block? LatticeParameters F
+%block LatticeVectors
+LatticeConstant 1.889726878 Bohr
+# above item originally: LatticeConstant 1.000000000 Ang
+ 3.1500000000000 0.000000000000 0.00
+ 1.575000000000 2.7279800219 0.00
+ 0.000000000000 0.000000000000 25.0
+%endblock LatticeVectors
+AtomicCoordinatesFormat Fractional
+NumberOfAtoms 3
+#:block? AtomicCoordinatesOrigin F
+#:defined? AtomicCoordinatesOrigin F
+ZM.UnitsLength Bohr # default value
+ZM.UnitsAngle rad # default value
+ZM.ForceTolLength 0.1555740000E-02 Ry/Bohr # default value
+ZM.ForceTolAngle 0.3565490000E-02 Ry/rad # default value
+ZM.MaxDisplLength 0.2000000000 Bohr # default value
+ZM.MaxDisplAngle 0.3000000000E-02 rad # default value
+ZM.CalcAllForces F # default value
+%block AtomicCoordinatesAndAtomicSpecies
+ 0.33333333333333 0.33333333333333 0.5000000000 1
+ 0.66666666666667 0.66666666666667 0.4360000000 2
+ 0.66666666666667 0.66666666666667 0.5640000000 2
+%endblock AtomicCoordinatesAndAtomicSpecies
+MD.UseSaveXV T
+MD.UseSaveZM F # default value
+WriteCoorInitial T
+MD.TypeOfRun Broyden
+MD.TypeOfRun Broyden
+MD.InitialTimeStep 1 # default value
+MD.FinalTimeStep 1 # default value
+MD.TypeOfRun Broyden
+MaxBondDistance 6.000000000 Bohr # default value
+Output-Structure-Only F # default value
+WriteCoorXmol F # default value
+#:physical? MaxWalltime F
+MaxWalltime 0.1797693135+309 # default value
+#:physical? MaxWalltime.Slack F
+MaxWalltime.Slack 5.000000000 # default value
+HSetupOnly F # default value
+LongOutput F # default value
+WriteDenchar F # default value
+WriteMullikenPop 1
+WriteOrbMom F # default value
+WriteHirshfeldPop F # default value
+WriteVoronoiPop F # default value
+PartialChargesAtEveryGeometry F # default value
+PartialChargesAtEveryScfStep F # default value
+MeshCutoff 1000.000000 Ry
+# above item originally: MeshCutoff 1000.000000 Ry
+NetCharge 0.000000000 # default value
+MinSCFIterations 0 # default value
+MaxSCFIterations 1000
+SCF.MustConverge T
+#:block? TS.MixH F
+#:defined? TS.MixH F
+#:block? MixHamiltonian F
+#:defined? MixHamiltonian F
+#:block? MixCharge F
+#:defined? MixCharge F
+TS.MixH T # default value
+MixHamiltonian T # default value
+MixCharge F # default value
+SCF.Mix Hamiltonian
+Compat-pre-v4-DM-H F # default value
+SCF.MixAfterConvergence F # default value
+SCF.Recompute-H-After-Scf F # default value
+DM.NumberPulay 0 # default value
+DM.NumberBroyden 0 # default value
+DM.FIRE.Mixing F # default value
+DM.MixSCF1 T # default value
+SCF.Mix.First T # default value
+SCF.Mix.First.Force F # default value
+DM.PulayOnFile F # default value
+DM.MixingWeight 0.2500000000 # default value
+DM.OccupancyTolerance 0.1000000000E-11 # default value
+DM.NumberKick 0 # default value
+DM.KickMixingWeight 0.5000000000 # default value
+DM.RequireHarrisConvergence F # default value
+SCF.Harris.Converge F # default value
+DM.HarrisTolerance 0.7349806700E-05 Ry # default value
+SCF.Harris.Tolerance 0.7349806700E-05 Ry # default value
+SCF.DM.Converge T
+DM.Tolerance 0.1000000000E-03 # default value
+SCF.DM.Tolerance 0.1000000000E-07
+SCF.EDM.Converge F # default value
+SCF.EDM.Tolerance 0.7349806700E-04 Ry # default value
+SCF.H.Converge T # default value
+SCF.H.Tolerance 0.7349806700E-04 Ry # default value
+DM.RequireEnergyConvergence F # default value
+SCF.FreeE.Converge F # default value
+DM.EnergyTolerance 0.7349806700E-05 Ry # default value
+SCF.FreeE.Tolerance 0.7349806700E-05 Ry # default value
+MonitorForcesInSCF F # default value
+SCF.MonitorForces F # default value
+DFTD3 F # default value
+UseSaveData F # default value
+DM.UseSaveDM F
+NeglNonOverlapInt F # default value
+SolutionMethod diagon
+ElectronicTemperature 0.7349798845E-07 Ry
+# above item originally: ElectronicTemperature 0.1000000000E-05 eV
+FixSpin F # default value
+Spin.Fix F # default value
+ON.MaxNumIter 1000 # default value
+ON.etol 0.1000000000E-07 # default value
+ON.eta 0.000000000 Ry # default value
+ON.eta_alpha 0.000000000 Ry # default value
+ON.eta_beta 0.000000000 Ry # default value
+On.RcLWF 9.500000000 Bohr # default value
+ON.UseSaveLWF F # default value
+ON.functional kim # default value
+ON.ChemicalPotentialUse F # default value
+ON.ChemicalPotential F # default value
+ON.ChemicalPotentialRc 9.500000000 Bohr # default value
+ON.ChemicalPotentialTemperature 0.5000000000E-01 Ry # default value
+ON.ChemicalPotentialOrder 100 # default value
+TDED.WF.Initialize F # default value
+TDED.Saverho F # default value
+TDED.Nsaverho 100 # default value
+TDED.Write.Etot T # default value
+TDED.Write.Eig F # default value
+TDED.Write.Dipole F # default value
+TDED.Extrapolate F # default value
+TDED.TimeStep 0.1000000000E-02 fs # default value
+TDED.Nsteps 1 # default value
+TDED.Extrapolate.Substeps 3 # default value
+TDED.Inverse.Linear T # default value
+TDED.WF.Save F # default value
+MD.VariableCell F
+compat-pre-v4-dynamics F # default value
+MD.TypeOfRun Broyden
+MD.NumCGsteps 0 # default value
+MD.Steps 0
+MD.MaxCGDispl 0.2000000000 Bohr # default value
+MD.MaxDispl 0.2000000000 Bohr # default value
+MD.MaxForceTol 0.3889348769E-03 Ry/Bohr
+# above item originally: MD.MaxForceTol 0.1000000000E-01 eV/Ang
+MD.MaxStressTol 0.6797730000E-04 Ry/Bohr**3 # default value
+GeometryMustConverge F # default value
+MD.InitialTimeStep 1 # default value
+#:defined? MD.Steps T
+MD.FinalTimeStep 1 # default value
+MD.LengthTimeStep 1.000000000 fs # default value
+MD.Quench F # default value
+MD.FireQuench F # default value
+MD.InitialTemperature 0.000000000 K # default value
+MD.TargetTemperature 0.000000000 K # default value
+#:block? MD.TargetPressure F
+#:defined? MD.TargetPressure F
+MD.TargetPressure 0.000000000 Ry/Bohr**3 # default value
+Target.Pressure 0.000000000 Ry/Bohr**3 # default value
+MD.NoseMass 100.0000000 Ry*fs**2 # default value
+MD.ParrinelloRahmanMass 100.0000000 Ry*fs**2 # default value
+MD.AnnealOption TemperatureAndPressure # default value
+MD.TauRelax 100.0000000 fs # default value
+MD.BulkModulus 0.6797730000E-02 Ry/Bohr**3 # default value
+MD.FCDispl 0.4000000000E-01 Bohr # default value
+MD.FCfirst 1 # default value
+MD.FClast 3 # default value
+UseSpatialDecomposition F # default value
+UseDomainDecomposition F # default value
+SCF.Mix.Spin all # default value
+Mixer.Debug F # default value
+Mixer.Debug.MPI F # default value
+DM.NumberPulay 2 # default value
+DM.NumberBroyden 0 # default value
+DM.MixingWeight 0.2500000000 # default value
+DM.NumberKick 0 # default value
+DM.KickMixingWeight 0.5000000000 # default value
+SCF.LinearMixingAfterPulay F # default value
+SCF.MixingWeightAfterPulay 0.2500000000 # default value
+SCF.Mixer.History 10
+SCF.Mixer.Weight 0.3000000000
+SCF.Mixer.Kick 0 # default value
+SCF.Mixer.Kick.Weight 0.5000000000 # default value
+SCF.Mixer.Restart 0 # default value
+SCF.Mixer.Restart.Save 1 # default value
+SCF.Mixer.Method Pulay
+SCF.Mixer.Variant original
+SCF.Mixer.Linear.After -1 # default value
+SCF.Mixer.Linear.After.Weight 0.2500000000 # default value
+#:block? ChargeGeometries F
+#:defined? ChargeGeometries F
+#:block? ChargeGeometries F
+#:defined? ChargeGeometries F
+BulkBias.V 0.000000000 Ry # default value
+BulkBias.Voltage 0.000000000 Ry # default value
+BulkBias.Tolerance 0.1000000000E-14 # default value
+BulkBias.Current T # default value
+Harris_functional F # default value
+ForceAuxCell F # default value
+#:block? Optim.Broyden.History.Steps F
+#:defined? Optim.Broyden.History.Steps F
+#:block? Optim.Broyden.Cycle.On.Maxit F
+#:defined? Optim.Broyden.Cycle.On.Maxit F
+#:block? Optim.Broyden.Variable.Weight F
+#:defined? Optim.Broyden.Variable.Weight F
+#:block? Optim.Broyden.Debug F
+#:defined? Optim.Broyden.Debug F
+#:block? Optim.Broyden.Initial.Inverse.Jacobian F
+#:defined? Optim.Broyden.Initial.Inverse.Jacobian F
+Write.Kpoints F # default value
+Write.Forces T
+Write.DM T
+Write.DM.End.Of.Cycle T # default value
+Write.H F
+Write.H.End.Of.Cycle F # default value
+Write.DM.NetCDF F # default value
+WriteDM.History.NetCDF F # default value
+WriteDMHS.NetCDF F # default value
+WriteDMHS.History.NetCDF F # default value
+SCF.Read.Charge.NetCDF F # default value
+SCF.Read.Deformation.Charge.NetCDF F # default value
+Write.TSHS.History F # default value
+SaveInitialChargeDensity F # default value
+AnalyzeChargeDensityOnly F # default value
+UseNewDiagk F # default value
+Diag.WFS.Cache none # default value
+WriteBands F # default value
+WriteKbands F # default value
+WriteEigenvalues T
+WriteCoorStep T
+WriteMDhistory F # default value
+WriteMDXmol F # default value
+WriteOrbitalIndex T # default value
+Write.Graphviz none # default value
+WriteCoorStep T
+SaveHS F
+ReInitialiseDM T # default value
+DM.AllowReuse T # default value
+DM.AllowExtrapolation T # default value
+DM.History.Depth 1 # default value
+DM.NormalizationTolerance 0.1000000000E-04 # default value
+DM.NormalizeDuringSCF T # default value
+MullikenInSCF F # default value
+SpinInSCF F # default value
+WarningMinimumAtomicDistance 1.000000000 Bohr # default value
+BornCharge F # default value
+ChangeKgridInMD F # default value
+MD.RelaxCellOnly F # default value
+MD.RemoveIntraMolecularPressure F # default value
+COOP.Write F # default value
+SaveRho T
+SaveDeltaRho F
+SaveRhoXC T
+SaveElectrostaticPotential T
+SaveNeutralAtomPotential F
+SaveTotalPotential T
+SaveIonicCharge F
+SaveBaderCharge F
+SaveTotalCharge F
+Siesta2Wannier90.WriteMmn F # default value
+Siesta2Wannier90.WriteUnk F # default value
+Siesta2Wannier90.WriteAmn F # default value
+Siesta2Wannier90.WriteEig F # default value
+#:block? Siesta2Wannier90.NumberOfBandsUp F
+#:defined? Siesta2Wannier90.NumberOfBandsUp F
+#:block? Siesta2Wannier90.NumberOfBandsDown F
+#:defined? Siesta2Wannier90.NumberOfBandsDown F
+#:block? Siesta2Wannier90.NumberOfBands F
+#:defined? Siesta2Wannier90.NumberOfBands F
+Siesta2Wannier90.NumberOfBandsUp 0 # default value
+Siesta2Wannier90.NumberOfBandsDown 0 # default value
+Siesta2Wannier90.NumberOfBands 0 # default value
+CDF.Save T
+CDF.Compress 0 # default value
+CDF.MPI F # default value
+CDF.Read.Parallel F # default value
+CDF.Grid.Precision double
+DM.AllowReuse T # default value
+DM.AllowExtrapolation T # default value
+DM.AllowExtrapolation F # default value
+NumberOfEigenStates 52 # default value
+RcSpatial 0.000000000 Bohr # default value
+ProcessorGridX 1 # default value
+ProcessorGridY 1 # default value
+ProcessorGridZ 1 # default value
+FFT.ProcessorY.traditional F # default value
+processorY 2 # default value
+blocksize 3 # default value
+Spin.Spiral F # default value
+TimeReversalSymmetryForKpoints T # default value
+%block kgrid.MonkhorstPack
+ 6 0 0 0.0
+ 0 6 0 0.0
+ 0 0 1 0.0
+%endblock kgrid.MonkhorstPack
+#:block? ProjectedDensityOfStates F
+#:block? LocalDensityOfStates F
+Diag.ParallelOverK T
+Diag.ProcessorY 4 # default value
+Diag.BlockSize 3 # default value
+Diag.Use2D T # default value
+Diag.UpperLower lower # default value
+Diag.DivideAndConquer T # default value
+Diag.MRRR F # default value
+Diag.NoExpert F # default value
+Diag.Algorithm Divide-and-Conquer # default value
+Diag.AbsTol 0.1000000000E-15 # default value
+Diag.OrFac 0.1000000000E-05 # default value
+Diag.Memory 1.000000000 # default value
+#:block? BandLines T
+#:defined? BandLines T
+#:block? BandPoints F
+#:defined? BandPoints F
+BandLinesScale ReciprocalLatticeVectors
+%block BandLines
+ 1 0.0000000 0.00000000 0.000 \Gamma
+ 30 0.3333333 0.66666666 0.000 K
+ 15 0.5000000 0.50000000 0.000 M
+ 26 0.0000000 0.00000000 0.000 \Gamma
+%endblock BandLines
+#:block? BandLines T
+#:defined? BandLines T
+#:block? BandPoints F
+#:defined? BandPoints F
+BandLinesScale ReciprocalLatticeVectors
+%block BandLines
+ 1 0.0000000 0.00000000 0.000 \Gamma
+ 30 0.3333333 0.66666666 0.000 K
+ 15 0.5000000 0.50000000 0.000 M
+ 26 0.0000000 0.00000000 0.000 \Gamma
+%endblock BandLines
+LongOutput F # default value
+WriteWaveFunctions F # default value
+#:block-line-count? MetaForce (iirrr) 0
+#:block? TS.BufferAtomsLeft F
+#:defined? TS.BufferAtomsLeft F
+#:block? TS.BufferAtomsRight F
+#:defined? TS.BufferAtomsRight F
+#:list? TS.Atoms.Buffer F
+TS.HS.Save F # default value
+TS.DE.Save F # default value
+TS.onlyS F # default value
+TS.S.Save F # default value
+Spin.Spiral F # default value
+TimeReversalSymmetryForKpoints T # default value
+#:list? TS.kgrid.MonkhorstPack F
+#:block? TS.kgrid.Cutoff F
+#:defined? TS.kgrid.Cutoff F
+#:block? TS.kgrid.File F
+#:defined? TS.kgrid.File F
+AtomicCoordinatesFormat Fractional
+AtomCoorFormatOut Fractional # default value
+LatticeConstant 1.889726878 Bohr
+# above item originally: LatticeConstant 1.000000000 Ang
+debug-folding F # default value
+Save.Overlap.Gradient F # default value
+Sonly F # default value
+DM.Init atomic # default value
+DM.Init.RandomStates 0 # default value
+Sonly F # default value
+Debug.DHSCF F # default value
+MeshSubDivisions 2 # default value
+#:list? Mesh.Sizes F
+#:block? MeshSizes F
+#:defined? MeshSizes F
+CDF.Grid.Precision double
+#:block? LocalDensityOfStates F
+#:defined? LocalDensityOfStates F
+XC.Use.BSC.CellXC F # default value
+DirectPhi F # default value
+SimulateDoping F # default value
+Slab.DipoleCorrection none # default value
+Read-H-from-file F # default value
+timing-split-scf-steps F # default value
+SingleExcitation F # default value
+OccupationFunction MP
+OccupationMPOrder 1
+OccupationFunction MP
+OccupationMPOrder 1
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+compute-forces T # default value
+#:list? Grid.CellSampling F
+Read-H-from-file F # default value
+WriteCoorXmol F # default value
+WriteCoorCerius F # default value
+WFS.Write.For.Bands F # default value
+BasisPressure 0.2000000000 GPa # default value
+OpticalCalculation F # default value
diff --git a/WS2/siesta/LDA/fdf.20230723T150521.405.log b/WS2/siesta/LDA/fdf.20230723T150521.405.log
new file mode 100644
index 0000000..9af5c59
--- /dev/null
+++ b/WS2/siesta/LDA/fdf.20230723T150521.405.log
@@ -0,0 +1,537 @@
+SystemName # default value
+SystemLabel WS2
+SpinPolarized F # default value
+NonCollinearSpin F # default value
+SpinOrbit F # default value
+#:block? SpinPolarized F
+#:defined? SpinPolarized F
+#:block? NonCollinearSpin F
+#:defined? NonCollinearSpin F
+#:block? SpinOrbit F
+#:defined? SpinOrbit F
+Spin none # default value
+TimeReversalSymmetry T # default value
+DebugObjects.Node 0 # default value
+DebugObjects F # default value
+XML.Write T
+timer_report_threshold 0.000000000 # default value
+UseParallelTimer T # default value
+UseTreeTimer F # default value
+timing-split-scf-steps F # default value
+use-walltime F # default value
+alloc_report_level 0 # default value
+alloc_report_threshold 0.000000000 # default value
+xc.functional LDA
+xc.authors PZ
+#:block? XC.hybrid F
+#:defined? XC.hybrid F
+#:block? XC.cocktail F
+#:defined? XC.cocktail F
+MM.Cutoff 30.00000000 Bohr # default value
+MM.UnitsEnergy eV # default value
+MM.UnitsDistance Ang # default value
+Atom.Debug F # default value
+WriteIonPlotFiles F # default value
+Atom.Debug.KB.Generation F # default value
+KB.New.Reference.Orbitals F # default value
+user-basis F # default value
+user-basis-netcdf F # default value
+#:block? DFTU.proj F
+#:defined? DFTU.proj F
+#:block? LDAU.proj F
+#:defined? LDAU.proj F
+Number_of_species 2
+%block Chemical_species_label
+ 1 74 W
+ 2 16 S
+%endblock Chemical_species_label
+ReparametrizePseudos F # default value
+Restricted.Radial.Grid T # default value
+Rmax.Radial.Grid 0.000000000 # default value
+PAO.BasisSize DZP
+PAO.BasisType split # default value
+PAO.SoftDefault F # default value
+PAO.SoftInnerRadius 0.9000000000 # default value
+PAO.SoftPotential 40.00000000 # default value
+PAO.SplitNorm 0.1500000000 # default value
+PAO.SplitNormH -1.000000000 # default value
+PAO.Polarization.NonPerturbative F # default value
+PAO.NonPerturbative.Polarization.Orbitals F # default value
+PAO.Polarization.NonPerturbative.Fallback F # default value
+LDAU.ProjectorGenerationMethod 2 # default value
+DFTU.ProjectorGenerationMethod 2 # default value
+LDAU.EnergyShift 0.5000000000E-01 Ry # default value
+DFTU.EnergyShift 0.5000000000E-01 Ry # default value
+LDAU.CutoffNorm 0.9000000000 # default value
+DFTU.CutoffNorm 0.9000000000 # default value
+PAO.SoftDefault F # default value
+PAO.SoftInnerRadius 0.9000000000 # default value
+PAO.SoftPotential 40.00000000 # default value
+LDAU.ThresholdTol 0.1000000000E-01 # default value
+DFTU.ThresholdTol 0.1000000000E-01 # default value
+LDAU.PopTol 0.1000000000E-02 # default value
+DFTU.PopTol 0.1000000000E-02 # default value
+LDAU.PotentialShift F # default value
+DFTU.PotentialShift F # default value
+LDAU.FirstIteration F # default value
+DFTU.FirstIteration F # default value
+FilterCutoff 0.000000000 Ry # default value
+FilterTol 0.000000000 Ry # default value
+spin-orbit-strength 1.000000000 # default value
+Use.PSML.KB.Projectors T # default value
+Use.PSML.Vlocal T # default value
+PSML.KB.Projectors T # default value
+PSML.Vlocal T # default value
+psml.chlocal.build.r0 0.4000000000E-02 # default value
+psml.chlocal.build.delta 0.5000000000E-02 # default value
+psml.chlocal.build.poly_order_rlin 4 # default value
+chlocal-use-charge-cutoff-for-vlocal-fit F # default value
+psml.chlocal.build.rr1 0.1000000000E-02 # default value
+psml.chlocal.build.exp_al 1.012000000 # default value
+psml.chlocal.build.poly_order_rofi 7 # default value
+PAO.EnergyShift 0.2000000000E-01 Ry # default value
+PAO.SplitTailNorm F # default value
+PAO.FixSplitTable F # default value
+PAO.NewSplitCode F # default value
+PAO.Filter F # default value
+PAO.Filter F # default value
+PAO.Filter F # default value
+PAO.Filter F # default value
+PAO.Filter F # default value
+PAO.Filter F # default value
+PAO.Filter F # default value
+PAO.OldStylePolorbs T # default value
+PAO.SplitTailNorm F # default value
+PAO.FixSplitTable F # default value
+PAO.NewSplitCode F # default value
+PAO.Filter F # default value
+Vna.Filter F # default value
+FilterCutoff 0.000000000 Ry # default value
+FilterTol 0.000000000 Ry # default value
+spin-orbit-strength 1.000000000 # default value
+Use.PSML.KB.Projectors T # default value
+Use.PSML.Vlocal T # default value
+PSML.KB.Projectors T # default value
+PSML.Vlocal T # default value
+psml.chlocal.build.r0 0.4000000000E-02 # default value
+psml.chlocal.build.delta 0.5000000000E-02 # default value
+psml.chlocal.build.poly_order_rlin 4 # default value
+chlocal-use-charge-cutoff-for-vlocal-fit F # default value
+psml.chlocal.build.rr1 0.1000000000E-02 # default value
+psml.chlocal.build.exp_al 1.012000000 # default value
+psml.chlocal.build.poly_order_rofi 7 # default value
+PAO.EnergyShift 0.2000000000E-01 Ry # default value
+PAO.SplitTailNorm F # default value
+PAO.FixSplitTable F # default value
+PAO.NewSplitCode F # default value
+PAO.Filter F # default value
+PAO.Filter F # default value
+PAO.Filter F # default value
+PAO.Filter F # default value
+PAO.OldStylePolorbs T # default value
+PAO.SplitTailNorm F # default value
+PAO.FixSplitTable F # default value
+PAO.NewSplitCode F # default value
+PAO.Filter F # default value
+Vna.Filter F # default value
+PAO.BasisType split # default value
+Debug.Elec.Corr F # default value
+Atom-Setup-Only F # default value
+UseStructFile F # default value
+MD.UseStructFile F # default value
+#:block? LatticeParameters F
+%block LatticeVectors
+LatticeConstant 1.889726878 Bohr
+# above item originally: LatticeConstant 1.000000000 Ang
+ 3.1500000000000 0.000000000000 0.00
+ 1.575000000000 2.7279800219 0.00
+ 0.000000000000 0.000000000000 25.0
+%endblock LatticeVectors
+AtomicCoordinatesFormat Fractional
+NumberOfAtoms 3
+#:block? AtomicCoordinatesOrigin F
+#:defined? AtomicCoordinatesOrigin F
+ZM.UnitsLength Bohr # default value
+ZM.UnitsAngle rad # default value
+ZM.ForceTolLength 0.1555740000E-02 Ry/Bohr # default value
+ZM.ForceTolAngle 0.3565490000E-02 Ry/rad # default value
+ZM.MaxDisplLength 0.2000000000 Bohr # default value
+ZM.MaxDisplAngle 0.3000000000E-02 rad # default value
+ZM.CalcAllForces F # default value
+%block AtomicCoordinatesAndAtomicSpecies
+ 0.33333333333333 0.33333333333333 0.5000000000 1
+ 0.66666666666667 0.66666666666667 0.4360000000 2
+ 0.66666666666667 0.66666666666667 0.5640000000 2
+%endblock AtomicCoordinatesAndAtomicSpecies
+MD.UseSaveXV T
+MD.UseSaveZM F # default value
+WriteCoorInitial T
+MD.TypeOfRun Broyden
+MD.TypeOfRun Broyden
+MD.InitialTimeStep 1 # default value
+MD.FinalTimeStep 1 # default value
+MD.TypeOfRun Broyden
+MaxBondDistance 6.000000000 Bohr # default value
+Output-Structure-Only F # default value
+WriteCoorXmol F # default value
+#:physical? MaxWalltime F
+MaxWalltime 0.1797693135+309 # default value
+#:physical? MaxWalltime.Slack F
+MaxWalltime.Slack 5.000000000 # default value
+HSetupOnly F # default value
+LongOutput F # default value
+WriteDenchar F # default value
+WriteMullikenPop 1
+WriteOrbMom F # default value
+WriteHirshfeldPop F # default value
+WriteVoronoiPop F # default value
+PartialChargesAtEveryGeometry F # default value
+PartialChargesAtEveryScfStep F # default value
+MeshCutoff 1000.000000 Ry
+# above item originally: MeshCutoff 1000.000000 Ry
+NetCharge 0.000000000 # default value
+MinSCFIterations 0 # default value
+MaxSCFIterations 1000
+SCF.MustConverge T
+#:block? TS.MixH F
+#:defined? TS.MixH F
+#:block? MixHamiltonian F
+#:defined? MixHamiltonian F
+#:block? MixCharge F
+#:defined? MixCharge F
+TS.MixH T # default value
+MixHamiltonian T # default value
+MixCharge F # default value
+SCF.Mix Hamiltonian
+Compat-pre-v4-DM-H F # default value
+SCF.MixAfterConvergence F # default value
+SCF.Recompute-H-After-Scf F # default value
+DM.NumberPulay 0 # default value
+DM.NumberBroyden 0 # default value
+DM.FIRE.Mixing F # default value
+DM.MixSCF1 T # default value
+SCF.Mix.First T # default value
+SCF.Mix.First.Force F # default value
+DM.PulayOnFile F # default value
+DM.MixingWeight 0.2500000000 # default value
+DM.OccupancyTolerance 0.1000000000E-11 # default value
+DM.NumberKick 0 # default value
+DM.KickMixingWeight 0.5000000000 # default value
+DM.RequireHarrisConvergence F # default value
+SCF.Harris.Converge F # default value
+DM.HarrisTolerance 0.7349806700E-05 Ry # default value
+SCF.Harris.Tolerance 0.7349806700E-05 Ry # default value
+SCF.DM.Converge T
+DM.Tolerance 0.1000000000E-03 # default value
+SCF.DM.Tolerance 0.1000000000E-07
+SCF.EDM.Converge F # default value
+SCF.EDM.Tolerance 0.7349806700E-04 Ry # default value
+SCF.H.Converge T # default value
+SCF.H.Tolerance 0.7349806700E-04 Ry # default value
+DM.RequireEnergyConvergence F # default value
+SCF.FreeE.Converge F # default value
+DM.EnergyTolerance 0.7349806700E-05 Ry # default value
+SCF.FreeE.Tolerance 0.7349806700E-05 Ry # default value
+MonitorForcesInSCF F # default value
+SCF.MonitorForces F # default value
+DFTD3 F # default value
+UseSaveData F # default value
+DM.UseSaveDM F
+NeglNonOverlapInt F # default value
+SolutionMethod diagon
+ElectronicTemperature 0.7349798845E-07 Ry
+# above item originally: ElectronicTemperature 0.1000000000E-05 eV
+FixSpin F # default value
+Spin.Fix F # default value
+ON.MaxNumIter 1000 # default value
+ON.etol 0.1000000000E-07 # default value
+ON.eta 0.000000000 Ry # default value
+ON.eta_alpha 0.000000000 Ry # default value
+ON.eta_beta 0.000000000 Ry # default value
+On.RcLWF 9.500000000 Bohr # default value
+ON.UseSaveLWF F # default value
+ON.functional kim # default value
+ON.ChemicalPotentialUse F # default value
+ON.ChemicalPotential F # default value
+ON.ChemicalPotentialRc 9.500000000 Bohr # default value
+ON.ChemicalPotentialTemperature 0.5000000000E-01 Ry # default value
+ON.ChemicalPotentialOrder 100 # default value
+TDED.WF.Initialize F # default value
+TDED.Saverho F # default value
+TDED.Nsaverho 100 # default value
+TDED.Write.Etot T # default value
+TDED.Write.Eig F # default value
+TDED.Write.Dipole F # default value
+TDED.Extrapolate F # default value
+TDED.TimeStep 0.1000000000E-02 fs # default value
+TDED.Nsteps 1 # default value
+TDED.Extrapolate.Substeps 3 # default value
+TDED.Inverse.Linear T # default value
+TDED.WF.Save F # default value
+MD.VariableCell F
+compat-pre-v4-dynamics F # default value
+MD.TypeOfRun Broyden
+MD.NumCGsteps 0 # default value
+MD.Steps 0
+MD.MaxCGDispl 0.2000000000 Bohr # default value
+MD.MaxDispl 0.2000000000 Bohr # default value
+MD.MaxForceTol 0.3889348769E-03 Ry/Bohr
+# above item originally: MD.MaxForceTol 0.1000000000E-01 eV/Ang
+MD.MaxStressTol 0.6797730000E-04 Ry/Bohr**3 # default value
+GeometryMustConverge F # default value
+MD.InitialTimeStep 1 # default value
+#:defined? MD.Steps T
+MD.FinalTimeStep 1 # default value
+MD.LengthTimeStep 1.000000000 fs # default value
+MD.Quench F # default value
+MD.FireQuench F # default value
+MD.InitialTemperature 0.000000000 K # default value
+MD.TargetTemperature 0.000000000 K # default value
+#:block? MD.TargetPressure F
+#:defined? MD.TargetPressure F
+MD.TargetPressure 0.000000000 Ry/Bohr**3 # default value
+Target.Pressure 0.000000000 Ry/Bohr**3 # default value
+MD.NoseMass 100.0000000 Ry*fs**2 # default value
+MD.ParrinelloRahmanMass 100.0000000 Ry*fs**2 # default value
+MD.AnnealOption TemperatureAndPressure # default value
+MD.TauRelax 100.0000000 fs # default value
+MD.BulkModulus 0.6797730000E-02 Ry/Bohr**3 # default value
+MD.FCDispl 0.4000000000E-01 Bohr # default value
+MD.FCfirst 1 # default value
+MD.FClast 3 # default value
+UseSpatialDecomposition F # default value
+UseDomainDecomposition F # default value
+SCF.Mix.Spin all # default value
+Mixer.Debug F # default value
+Mixer.Debug.MPI F # default value
+DM.NumberPulay 2 # default value
+DM.NumberBroyden 0 # default value
+DM.MixingWeight 0.2500000000 # default value
+DM.NumberKick 0 # default value
+DM.KickMixingWeight 0.5000000000 # default value
+SCF.LinearMixingAfterPulay F # default value
+SCF.MixingWeightAfterPulay 0.2500000000 # default value
+SCF.Mixer.History 10
+SCF.Mixer.Weight 0.3000000000
+SCF.Mixer.Kick 0 # default value
+SCF.Mixer.Kick.Weight 0.5000000000 # default value
+SCF.Mixer.Restart 0 # default value
+SCF.Mixer.Restart.Save 1 # default value
+SCF.Mixer.Method Pulay
+SCF.Mixer.Variant original
+SCF.Mixer.Linear.After -1 # default value
+SCF.Mixer.Linear.After.Weight 0.2500000000 # default value
+#:block? ChargeGeometries F
+#:defined? ChargeGeometries F
+#:block? ChargeGeometries F
+#:defined? ChargeGeometries F
+BulkBias.V 0.000000000 Ry # default value
+BulkBias.Voltage 0.000000000 Ry # default value
+BulkBias.Tolerance 0.1000000000E-14 # default value
+BulkBias.Current T # default value
+Harris_functional F # default value
+ForceAuxCell F # default value
+#:block? Optim.Broyden.History.Steps F
+#:defined? Optim.Broyden.History.Steps F
+#:block? Optim.Broyden.Cycle.On.Maxit F
+#:defined? Optim.Broyden.Cycle.On.Maxit F
+#:block? Optim.Broyden.Variable.Weight F
+#:defined? Optim.Broyden.Variable.Weight F
+#:block? Optim.Broyden.Debug F
+#:defined? Optim.Broyden.Debug F
+#:block? Optim.Broyden.Initial.Inverse.Jacobian F
+#:defined? Optim.Broyden.Initial.Inverse.Jacobian F
+Write.Kpoints F # default value
+Write.Forces T
+Write.DM T
+Write.DM.End.Of.Cycle T # default value
+Write.H F
+Write.H.End.Of.Cycle F # default value
+Write.DM.NetCDF F # default value
+WriteDM.History.NetCDF F # default value
+WriteDMHS.NetCDF F # default value
+WriteDMHS.History.NetCDF F # default value
+SCF.Read.Charge.NetCDF F # default value
+SCF.Read.Deformation.Charge.NetCDF F # default value
+Write.TSHS.History F # default value
+SaveInitialChargeDensity F # default value
+AnalyzeChargeDensityOnly F # default value
+UseNewDiagk F # default value
+Diag.WFS.Cache none # default value
+WriteBands F # default value
+WriteKbands F # default value
+WriteEigenvalues T
+WriteCoorStep T
+WriteMDhistory F # default value
+WriteMDXmol F # default value
+WriteOrbitalIndex T # default value
+Write.Graphviz none # default value
+WriteCoorStep T
+SaveHS F
+ReInitialiseDM T # default value
+DM.AllowReuse T # default value
+DM.AllowExtrapolation T # default value
+DM.History.Depth 1 # default value
+DM.NormalizationTolerance 0.1000000000E-04 # default value
+DM.NormalizeDuringSCF T # default value
+MullikenInSCF F # default value
+SpinInSCF F # default value
+WarningMinimumAtomicDistance 1.000000000 Bohr # default value
+BornCharge F # default value
+ChangeKgridInMD F # default value
+MD.RelaxCellOnly F # default value
+MD.RemoveIntraMolecularPressure F # default value
+COOP.Write F # default value
+SaveRho T
+SaveDeltaRho F
+SaveRhoXC T
+SaveElectrostaticPotential T
+SaveNeutralAtomPotential F
+SaveTotalPotential T
+SaveIonicCharge F
+SaveBaderCharge F
+SaveTotalCharge F
+Siesta2Wannier90.WriteMmn F # default value
+Siesta2Wannier90.WriteUnk F # default value
+Siesta2Wannier90.WriteAmn F # default value
+Siesta2Wannier90.WriteEig F # default value
+#:block? Siesta2Wannier90.NumberOfBandsUp F
+#:defined? Siesta2Wannier90.NumberOfBandsUp F
+#:block? Siesta2Wannier90.NumberOfBandsDown F
+#:defined? Siesta2Wannier90.NumberOfBandsDown F
+#:block? Siesta2Wannier90.NumberOfBands F
+#:defined? Siesta2Wannier90.NumberOfBands F
+Siesta2Wannier90.NumberOfBandsUp 0 # default value
+Siesta2Wannier90.NumberOfBandsDown 0 # default value
+Siesta2Wannier90.NumberOfBands 0 # default value
+CDF.Save T
+CDF.Compress 0 # default value
+CDF.MPI F # default value
+CDF.Read.Parallel F # default value
+CDF.Grid.Precision double
+DM.AllowReuse T # default value
+DM.AllowExtrapolation T # default value
+DM.AllowExtrapolation F # default value
+NumberOfEigenStates 52 # default value
+RcSpatial 0.000000000 Bohr # default value
+ProcessorGridX 1 # default value
+ProcessorGridY 1 # default value
+ProcessorGridZ 1 # default value
+FFT.ProcessorY.traditional F # default value
+processorY 2 # default value
+blocksize 3 # default value
+Spin.Spiral F # default value
+TimeReversalSymmetryForKpoints T # default value
+%block kgrid.MonkhorstPack
+ 6 0 0 0.0
+ 0 6 0 0.0
+ 0 0 1 0.0
+%endblock kgrid.MonkhorstPack
+#:block? ProjectedDensityOfStates F
+#:block? LocalDensityOfStates F
+Diag.ParallelOverK T
+Diag.ProcessorY 4 # default value
+Diag.BlockSize 3 # default value
+Diag.Use2D T # default value
+Diag.UpperLower lower # default value
+Diag.DivideAndConquer T # default value
+Diag.MRRR F # default value
+Diag.NoExpert F # default value
+Diag.Algorithm Divide-and-Conquer # default value
+Diag.AbsTol 0.1000000000E-15 # default value
+Diag.OrFac 0.1000000000E-05 # default value
+Diag.Memory 1.000000000 # default value
+#:block? BandLines T
+#:defined? BandLines T
+#:block? BandPoints F
+#:defined? BandPoints F
+BandLinesScale ReciprocalLatticeVectors
+%block BandLines
+ 1 0.0000000 0.00000000 0.000 \Gamma
+ 30 0.3333333 0.66666666 0.000 K
+ 15 0.5000000 0.50000000 0.000 M
+ 26 0.0000000 0.00000000 0.000 \Gamma
+%endblock BandLines
+#:block? BandLines T
+#:defined? BandLines T
+#:block? BandPoints F
+#:defined? BandPoints F
+BandLinesScale ReciprocalLatticeVectors
+%block BandLines
+ 1 0.0000000 0.00000000 0.000 \Gamma
+ 30 0.3333333 0.66666666 0.000 K
+ 15 0.5000000 0.50000000 0.000 M
+ 26 0.0000000 0.00000000 0.000 \Gamma
+%endblock BandLines
+LongOutput F # default value
+WriteWaveFunctions F # default value
+#:block-line-count? MetaForce (iirrr) 0
+#:block? TS.BufferAtomsLeft F
+#:defined? TS.BufferAtomsLeft F
+#:block? TS.BufferAtomsRight F
+#:defined? TS.BufferAtomsRight F
+#:list? TS.Atoms.Buffer F
+TS.HS.Save F # default value
+TS.DE.Save F # default value
+TS.onlyS F # default value
+TS.S.Save F # default value
+Spin.Spiral F # default value
+TimeReversalSymmetryForKpoints T # default value
+#:list? TS.kgrid.MonkhorstPack F
+#:block? TS.kgrid.Cutoff F
+#:defined? TS.kgrid.Cutoff F
+#:block? TS.kgrid.File F
+#:defined? TS.kgrid.File F
+AtomicCoordinatesFormat Fractional
+AtomCoorFormatOut Fractional # default value
+LatticeConstant 1.889726878 Bohr
+# above item originally: LatticeConstant 1.000000000 Ang
+debug-folding F # default value
+Save.Overlap.Gradient F # default value
+Sonly F # default value
+DM.Init atomic # default value
+DM.Init.RandomStates 0 # default value
+Sonly F # default value
+Debug.DHSCF F # default value
+MeshSubDivisions 2 # default value
+#:list? Mesh.Sizes F
+#:block? MeshSizes F
+#:defined? MeshSizes F
+CDF.Grid.Precision double
+#:block? LocalDensityOfStates F
+#:defined? LocalDensityOfStates F
+XC.Use.BSC.CellXC F # default value
+DirectPhi F # default value
+SimulateDoping F # default value
+Slab.DipoleCorrection none # default value
+Read-H-from-file F # default value
+timing-split-scf-steps F # default value
+SingleExcitation F # default value
+OccupationFunction MP
+OccupationMPOrder 1
+OccupationFunction MP
+OccupationMPOrder 1
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+compute-forces T # default value
+#:list? Grid.CellSampling F
+Read-H-from-file F # default value
+WriteCoorXmol F # default value
+WriteCoorCerius F # default value
+WFS.Write.For.Bands F # default value
+BasisPressure 0.2000000000 GPa # default value
+OpticalCalculation F # default value
diff --git a/WS2/siesta/LDA/fft_mod.py b/WS2/siesta/LDA/fft_mod.py
index 7e02776..eddf4a1 100644
--- a/WS2/siesta/LDA/fft_mod.py
+++ b/WS2/siesta/LDA/fft_mod.py
@@ -1,10 +1,88 @@
import os
import time
import numpy as np
-from numpy.fft import fftn, ifftn, ifftshift
+from numpy.fft import fftn, ifftn, fftshift, ifftshift
+
+
+def flat_FFTbox(unkg_FFTbox):
+ """
+ Generate a flattened 1d array 'unkg' and corresponding igvecs from unkg_FFTbox.
+ Assume unkg_FFTbox has its zero-frequency component in unkg_FFTbox[ispin,0,0,0].
+ This functions is a kind of the inverse function of 'put_FFTbox'.
+ Note, because of the zero padding in unkg_FFTbox, unkg may have lots of zeros.
+
+ --Input--
+ unkg_FFTbox : cdouble(nspin,N1,N2,N3)
+ unkg in FFTbox
+ for colinear case, nspin = 1
+ for non-colinear case, nspin = 2
+
+ --Output--
+ unkg : cdouble(nspin*N1*N2*N3)
+ for non-colinear case, the first half is for spin-up,
+ the second half is for spin-dw.
+ gvecs_sym : int(N1*N2*N3,3)
+ array of miller index (h,k,l)
+ """
+ nspin, n1, n2, n3 = unkg_FFTbox.shape
+ ng = n1*n2*n3
+ h_max, k_max, l_max = n1//2, n2//2, n3//2
+
+ hs, ks, ls = np.unravel_index(np.array(range(ng)),(n1,n2,n3))
+
+ #generate zero starting positive index. it is just for reshaping
+ gvecs_pos = np.concatenate([[hs],[ks],[ls]], axis = 0).T
+ hkl2flat = ( n3 * (n2 * gvecs_pos[:, 0] + gvecs_pos[:, 1]) \
+ + gvecs_pos[:, 2])
+ hs[hs>=h_max] -= n1
+ ks[ks>=k_max] -= n2
+ ls[ls>=l_max] -= n3
+
+ #generate zero starting symmetric index. it will be returned
+ gvecs_sym = np.concatenate([[hs],[ks],[ls]], axis = 0).T
+
+ unkg = np.zeros(nspin*ng,dtype=np.cdouble)
+ for ispin in range(nspin):
+ gstart = ispin*ng
+ gend = (ispin + 1)*ng
+ unkg[gstart:gend] = unkg_FFTbox[ispin,:,:,:].flat[hkl2flat]
+
+ return unkg, gvecs_sym
+
+
+def fft_r2g(unkr_FFTbox):
+ """ fft from R space to G space
+
+ ---Input---
+ unkr_FFTbox : cdouble(ispin,N1,N2,N3)
+ unkr in FFTbox
+
+ --Output--
+ unkg_FFTbox : cdouble(ispin,N1,N2,N3)
+ unkg in FFTbox
+ """
+ # FFTgrid
+ nspin, n1, n2, n3 = unkr_FFTbox.shape
+ Nt = n1*n2*n3
+ unkg_FFTbox = np.zeros_like(unkr_FFTbox)
+ start = time.time()
+ for ispin in range(nspin):
+ unkg_FFTbox[ispin,:,:,:] = fftn(unkr_FFTbox[ispin,:,:,:])
+ end = time.time()
+ #print(f'\nFFT time', end-start)
+
+ return unkg_FFTbox
def ifft_g2r(unkg_FFTbox):
- """ ifft from G space to R space
+ """
+ ifft from G space to R space
+
+ with an input array x[l], the output array y[k] satisfy
+ y[k] = np.sum(x * np.exp(2j * np.pi * k * np.arange(n)/n)) / len(x)
+
+ Note unkg_FFTbox have the unk(G=0) component as the first element
+ in the unkg_FFTbox[ispin,0,0,0].
+
---Input---
unkg_FFTbox : cdouble(ispin,N1,N2,N3)
@@ -22,7 +100,7 @@ def ifft_g2r(unkg_FFTbox):
for ispin in range(nspin):
unkr_FFTbox[ispin,:,:,:] = ifftn(unkg_FFTbox[ispin,:,:,:])
end = time.time()
- print(f'\nIFFT time', end-start)
+ #print(f'\nIFFT time', end-start)
return unkr_FFTbox
@@ -48,6 +126,10 @@ def put_FFTbox2(unkg, gvecs, FFTgrid, noncolin, savedir='./', savefn=False):
for colinear case, nspin = 1
for non-colinear case, nspin = 2
+ unkg_FFTbox[ispin,0,0,0] = unk_ispin(G=0),
+ which is a zero frequency start array.
+
+
"""
#fn = savedir+f'./Unkg_FFTbox_k{ik}.npy'
@@ -86,7 +168,7 @@ def put_FFTbox2(unkg, gvecs, FFTgrid, noncolin, savedir='./', savefn=False):
#Save it for later calculation
#np.save(savedir+f'./Unkg_FFTbox_k{ik}.npy',unkg_FFTbox)
- print(f'\nFFTBOX time', end-start)
+ #print(f'\nFFTBOX time', end-start)
return unkg_FFTbox
@@ -139,13 +221,6 @@ def put_FFTbox(ik, FFTgrid, savedir='./'):
# Save it for later calculation
np.save(savedir+f'./Unkg_FFTbox_k{ik}.npy',unkg_FFTbox)
- print(f'\nFFTBOX time', end-start)
+ #print(f'\nFFTBOX time', end-start)
return unkg_FFTbox
-
-if __name__=='__main__':
- ik = 1
- FFTgrid = [495, 495, 83]
- unkg_FFTbox1 = put_FFTbox(ik, FFTgrid, savedir='../../data/')
- unkg_FFTbox2 = put_FFTbox2(ik, FFTgrid, savedir='../../data/')
- print(np.allclose(unkg_FFTbox2,unkg_FFTbox1))
diff --git a/WS2/siesta/LDA/fort.14 b/WS2/siesta/LDA/fort.14
index f368c91..61e4b50 100644
--- a/WS2/siesta/LDA/fort.14
+++ b/WS2/siesta/LDA/fort.14
@@ -16,29 +16,29 @@ siesta:
netcdf4_mpi: "no"
metis: "no"
chess: "no"
- elpa: "yes"
+ elpa: "no"
flook: "no"
pexsi: "no"
energies:
- Ebs: -0.76939813E+02
+ Ebs: -0.76954969E+02
Eions: 0.79069175E+03
- Ena: 0.12489850E+03
- Ekin: 0.21692091E+03
- Enl: -0.87935973E+02
+ Ena: 0.12491589E+03
+ Ekin: 0.21691121E+03
+ Enl: -0.87941601E+02
Eso: 0.00000000E+00
Edftu: 0.00000000E+00
- DEna: 0.39296272E+01
- DUscf: 0.22013667E+00
+ DEna: 0.39254911E+01
+ DUscf: 0.21969294E+00
DUext: 0.00000000E+00
- Exc: -0.50898787E+02
+ Exc: -0.50878399E+02
Ecorrec: 0.00000000E+00
Emadel: 0.00000000E+00
Emeta: 0.00000000E+00
Emolmec: 0.00000000E+00
Ekinion: 0.00000000E+00
- Eharris: -0.58355734E+03
- Etot: -0.58355734E+03
- FreeEng: -0.58355734E+03
+ Eharris: -0.58353947E+03
+ Etot: -0.58353947E+03
+ FreeEng: -0.58353947E+03
...
diff --git a/WS2/siesta/LDA/input.fdf b/WS2/siesta/LDA/input.fdf
index add605c..e27fc4b 100644
--- a/WS2/siesta/LDA/input.fdf
+++ b/WS2/siesta/LDA/input.fdf
@@ -23,11 +23,11 @@ AtomicCoordinatesFormat Fractional
%endblock AtomicCoordinatesAndAtomicSpecies
XC.functional LDA
-XC.authors PW92
+XC.authors PZ
PAO.BasisSize DZP
-MeshCutoff 160.0 Ry
+MeshCutoff 1000 Ry
OccupationFunction MP
OccupationMPOrder 1
ElectronicTemperature 0.000001 eV
diff --git a/WS2/siesta/LDA/libxc_test.py b/WS2/siesta/LDA/libxc_test.py
index 684c14f..bed5e73 100644
--- a/WS2/siesta/LDA/libxc_test.py
+++ b/WS2/siesta/LDA/libxc_test.py
@@ -35,7 +35,7 @@ def vxc_libxc():
inp["rho"] = const*rho_flatten
# Build functional
- func_c_name = "LDA_C_PW"
+ func_c_name = "LDA_C_PZ"
print(' Functional name of correlation part: ',func_c_name)
func_c = pylibxc.LibXCFunctional(func_c_name, "unpolarized")
func_x = pylibxc.LibXCFunctional("LDA_X", "unpolarized")
diff --git a/WS2/siesta/LDA/siesta.stdout b/WS2/siesta/LDA/siesta.stdout
index ada0c46..3584a68 100644
--- a/WS2/siesta/LDA/siesta.stdout
+++ b/WS2/siesta/LDA/siesta.stdout
@@ -10,15 +10,15 @@ NetCDF-4 support
Runtime information:
* Directory : /pscratch/sd/w/wkim94/Libxc_tutorial/WS2/siesta/LDA
-* Running on 32 nodes in parallel.
->> Start of run: 29-JUN-2023 12:55:09
+* Running on 16 nodes in parallel.
+>> Start of run: 23-JUL-2023 15:05:21
***********************
* WELCOME TO SIESTA *
***********************
reinit: Reading from standard input
-reinit: Dumping input in INPUT_TMP.19145
+reinit: Dumping input in INPUT_TMP.03114
************************** Dump of input data file ****************************
# SIESTA INPUT #
SystemLabel WS2
@@ -41,9 +41,9 @@ AtomicCoordinatesFormat Fractional
0.66666666666667 0.66666666666667 0.5640000000 2
%endblock AtomicCoordinatesAndAtomicSpecies
XC.functional LDA
-XC.authors PW92
+XC.authors PZ
PAO.BasisSize DZP
-MeshCutoff 160.0 Ry
+MeshCutoff 1000 Ry
OccupationFunction MP
OccupationMPOrder 1
ElectronicTemperature 0.000001 eV
@@ -269,8 +269,7 @@ read_vps: ONCVPSP-3.Hamann's oncvpsp
Valence charge in pseudo generation: 28.00000
xc_check: Exchange-correlation functional:
-xc_check: Perdew-Wang 1992
-xc_check: WARNING: Pseudopotential generated with LDA CA functional
+xc_check: Ceperley-Alder
Got Vlocal (oncv-fit) from psml data
Choosing vlocal chloc cutoff: 6.100858
qtot up to nchloc: 28.00010580
@@ -305,10 +304,10 @@ SPLIT: energy shift= 0.020000 Ry
izeta = 1
lambda = 1.000000
rc = 2.640378
- energy = -5.811455
- kinetic = 2.053518
- potential(screened) = -7.864973
- potential(ionic) = -45.765980
+ energy = -5.810277
+ kinetic = 2.053493
+ potential(screened) = -7.863770
+ potential(ionic) = -45.765872
SPLIT: Basis orbitals for state 6s
@@ -318,18 +317,18 @@ SPLIT: energy shift= 0.020000 Ry
izeta = 1
lambda = 1.000000
rc = 5.731224
- energy = -0.617345
- kinetic = 1.704284
- potential(screened) = -2.321630
- potential(ionic) = -26.070414
+ energy = -0.617407
+ kinetic = 1.702840
+ potential(screened) = -2.320246
+ potential(ionic) = -26.063109
izeta = 2
rmatch = 5.251052
splitnorm = 0.150000
- energy = -0.542237
- kinetic = 2.428223
- potential(screened) = -2.970460
- potential(ionic) = -29.480975
+ energy = -0.542233
+ kinetic = 2.426719
+ potential(screened) = -2.968952
+ potential(ionic) = -29.474817
SPLIT: Orbitals with angular momentum L= 1
@@ -341,10 +340,10 @@ SPLIT: energy shift= 0.020000 Ry
izeta = 1
lambda = 1.000000
rc = 3.067687
- energy = -3.168894
- kinetic = 3.812607
- potential(screened) = -6.981501
- potential(ionic) = -42.608942
+ energy = -3.167786
+ kinetic = 3.812400
+ potential(screened) = -6.980186
+ potential(ionic) = -42.608302
SPLIT: Orbitals with angular momentum L= 2
@@ -356,18 +355,18 @@ SPLIT: energy shift= 0.020000 Ry
izeta = 1
lambda = 1.000000
rc = 5.057783
- energy = -0.324156
- kinetic = 3.386937
- potential(screened) = -3.711094
- potential(ionic) = -31.834212
+ energy = -0.323676
+ kinetic = 3.384783
+ potential(screened) = -3.708459
+ potential(ionic) = -31.825385
izeta = 2
rmatch = 3.519875
splitnorm = 0.150000
- energy = -0.127043
- kinetic = 4.745519
- potential(screened) = -4.872561
- potential(ionic) = -36.493873
+ energy = -0.126259
+ kinetic = 4.744757
+ potential(screened) = -4.871017
+ potential(ionic) = -36.491601
SPLIT: Orbitals with angular momentum L= 3
@@ -379,10 +378,10 @@ SPLIT: energy shift= 0.020000 Ry
izeta = 1
lambda = 1.000000
rc = 2.511604
- energy = -2.446547
- kinetic = 11.495783
- potential(screened) = -13.942330
- potential(ionic) = -48.735306
+ energy = -2.445362
+ kinetic = 11.495762
+ potential(screened) = -13.941125
+ potential(ionic) = -48.735282
POLgen: Perturbative polarization orbital with L= 1
@@ -390,10 +389,10 @@ POLgen: Polarization orbital for state 6s
izeta = 1
rc = 5.731224
- energy = 0.125558
- kinetic = 2.090213
- potential(screened) = -1.964655
- potential(ionic) = -23.008569
+ energy = 0.124955
+ kinetic = 2.088992
+ potential(screened) = -1.964037
+ potential(ionic) = -23.003641
atom: Total number of Sankey-type orbitals: 26
atm_pop: Valence configuration (for local Pseudopot. screening):
@@ -448,8 +447,7 @@ read_vps: ONCVPSP-3.Hamann's oncvpsp
Valence charge in pseudo generation: 6.00000
xc_check: Exchange-correlation functional:
-xc_check: Perdew-Wang 1992
-xc_check: WARNING: Pseudopotential generated with LDA CA functional
+xc_check: Ceperley-Alder
Got Vlocal (oncv-fit) from psml data
Choosing vlocal chloc cutoff: 5.988766
qtot up to nchloc: 6.00041856
@@ -480,18 +478,18 @@ SPLIT: energy shift= 0.020000 Ry
izeta = 1
lambda = 1.000000
rc = 4.167741
- energy = -1.252365
- kinetic = 0.959115
- potential(screened) = -2.211480
- potential(ionic) = -7.250483
+ energy = -1.252260
+ kinetic = 0.958827
+ potential(screened) = -2.211087
+ potential(ionic) = -7.249940
izeta = 2
rmatch = 3.498614
splitnorm = 0.150000
- energy = -1.071675
- kinetic = 1.523266
- potential(screened) = -2.594941
- potential(ionic) = -7.866378
+ energy = -1.071418
+ kinetic = 1.523173
+ potential(screened) = -2.594591
+ potential(ionic) = -7.866180
SPLIT: Orbitals with angular momentum L= 1
@@ -503,18 +501,18 @@ SPLIT: energy shift= 0.020000 Ry
izeta = 1
lambda = 1.000000
rc = 5.090524
- energy = -0.504939
- kinetic = 1.511387
- potential(screened) = -2.016326
- potential(ionic) = -6.697066
+ energy = -0.505027
+ kinetic = 1.510775
+ potential(screened) = -2.015802
+ potential(ionic) = -6.695996
izeta = 2
rmatch = 3.818550
splitnorm = 0.150000
- energy = -0.354690
- kinetic = 2.187127
- potential(screened) = -2.541817
- potential(ionic) = -7.626502
+ energy = -0.354657
+ kinetic = 2.186722
+ potential(screened) = -2.541379
+ potential(ionic) = -7.625989
*Note: V_local used for l= 2
** Using vlocal for PAOs with L= 2
@@ -525,10 +523,10 @@ POLgen: Polarization orbital for state 3p
izeta = 1
rc = 5.090524
- energy = 0.728568
- kinetic = 2.183809
- potential(screened) = -1.455241
- potential(ionic) = -5.701294
+ energy = 0.727988
+ kinetic = 2.182980
+ potential(screened) = -1.454992
+ potential(ionic) = -5.700287
atom: Total number of Sankey-type orbitals: 13
atm_pop: Valence configuration (for local Pseudopot. screening):
@@ -610,7 +608,7 @@ redata: Number of Atomic Species = 2
redata: Charge density info will appear in .RHO file
redata: Write Mulliken Pop. = Atomic and Orbital charges
redata: Matel table size (NRTAB) = 1024
-redata: Mesh Cutoff = 160.0000 Ry
+redata: Mesh Cutoff = 1000.0000 Ry
redata: Net charge of the system = 0.0000 |e|
redata: Min. number of SCF Iter = 0
redata: Max. number of SCF Iter = 1000
@@ -672,10 +670,10 @@ Size of DM history Fstack: 1
Total number of electrons: 40.000000
Total ionic charge: 40.000000
-* ProcessorY, Blocksize: 2 1
+* ProcessorY, Blocksize: 2 3
-* Orbital distribution balance (max,min): 2 1
+* Orbital distribution balance (max,min): 6 3
k-point displ. along 1 input, could be: 0.00 0.50
k-point displ. along 2 input, could be: 0.00 0.50
@@ -692,8 +690,8 @@ siesta: k-grid: 0 0 1 0.000
diag: Algorithm = D&C
diag: Parallel over k = T
diag: Use parallel 2D distribution = T
-diag: Parallel block-size = 1
-diag: Parallel distribution = 4 x 8
+diag: Parallel block-size = 3
+diag: Parallel distribution = 4 x 4
diag: Used triangular part = Lower
diag: Absolute tolerance = 0.100E-15
diag: Orthogonalization factor = 0.100E-05
@@ -739,202 +737,156 @@ outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 60.0000
outcell: Cell volume (Ang**3) : 214.8284
-
+ nrows_g=52 nrows=6 sparsity=1.7574 nnzs=4752, refcount: 7>
+
refcount: 1>
new_DM -- step: 1
Initializing Density Matrix...
DM filled with atomic data:
-
+ nrows_g=52 nrows=6 sparsity=1.7574 nnzs=4752, refcount: 8>
+
refcount: 1>
-No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 13 260
+No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 22 260
-InitMesh: MESH = 24 x 24 x 192 = 110592
-InitMesh: Mesh cutoff (required, used) = 160.000 163.014 Ry
+InitMesh: MESH = 54 x 54 x 480 = 1399680
+InitMesh: Mesh cutoff (required, used) = 1000.000 1018.836 Ry
New grid distribution: 1
- 1 1: 12 1: 6 1: 6
- 2 1: 12 1: 6 7: 12
- 3 1: 12 1: 6 13: 18
- 4 1: 12 1: 6 19: 24
- 5 1: 12 1: 6 25: 30
- 6 1: 12 1: 6 31: 36
- 7 1: 12 1: 6 37: 42
- 8 1: 12 1: 6 43: 48
- 9 1: 12 1: 6 49: 54
- 10 1: 12 1: 6 55: 60
- 11 1: 12 1: 6 61: 66
- 12 1: 12 1: 6 67: 72
- 13 1: 12 1: 6 73: 78
- 14 1: 12 1: 6 79: 84
- 15 1: 12 1: 6 85: 90
- 16 1: 12 1: 6 91: 96
- 17 1: 12 7: 12 1: 6
- 18 1: 12 7: 12 7: 12
- 19 1: 12 7: 12 13: 18
- 20 1: 12 7: 12 19: 24
- 21 1: 12 7: 12 25: 30
- 22 1: 12 7: 12 31: 36
- 23 1: 12 7: 12 37: 42
- 24 1: 12 7: 12 43: 48
- 25 1: 12 7: 12 49: 54
- 26 1: 12 7: 12 55: 60
- 27 1: 12 7: 12 61: 66
- 28 1: 12 7: 12 67: 72
- 29 1: 12 7: 12 73: 78
- 30 1: 12 7: 12 79: 84
- 31 1: 12 7: 12 85: 90
- 32 1: 12 7: 12 91: 96
-timer(meshCom-Ca) : 3.9935E-06 4.4685E-06 6.0201E-06
-timer(BuildDISTR) : 4.4501E-04 8.7864E-03 2.2027E-02
+ 1 1: 27 1: 14 1: 30
+ 2 1: 27 1: 14 31: 60
+ 3 1: 27 1: 14 61: 90
+ 4 1: 27 1: 14 91: 120
+ 5 1: 27 1: 14 121: 150
+ 6 1: 27 1: 14 151: 180
+ 7 1: 27 1: 14 181: 210
+ 8 1: 27 1: 14 211: 240
+ 9 1: 27 15: 27 1: 30
+ 10 1: 27 15: 27 31: 60
+ 11 1: 27 15: 27 61: 90
+ 12 1: 27 15: 27 91: 120
+ 13 1: 27 15: 27 121: 150
+ 14 1: 27 15: 27 151: 180
+ 15 1: 27 15: 27 181: 210
+ 16 1: 27 15: 27 211: 240
+timer(meshCom-Ca) : 4.0531E-06 6.1318E-06 9.0599E-06
+timer(BuildDISTR) : 7.6294E-04 5.5838E-02 9.4224E-02
New grid distribution: 2
- 1 1: 12 1: 12 1: 38
- 2 1: 12 1: 12 39: 40
- 3 1: 12 1: 6 41: 42
- 4 1: 12 7: 12 41: 42
- 5 1: 6 1: 6 43: 45
- 6 7: 12 1: 6 43: 45
- 7 1: 5 7: 12 43: 45
- 8 6: 12 7: 12 43: 45
- 9 1: 6 1: 3 46: 48
- 10 1: 6 4: 6 46: 48
- 11 7: 12 1: 3 46: 48
- 12 7: 12 4: 6 46: 48
- 13 1: 5 7: 9 46: 48
- 14 1: 5 10: 12 46: 48
- 15 6: 9 7: 12 46: 48
- 16 10: 12 7: 12 46: 48
- 17 1: 6 1: 3 49: 51
- 18 1: 6 4: 6 49: 51
- 19 7: 12 1: 3 49: 51
- 20 7: 12 4: 6 49: 51
- 21 1: 5 7: 9 49: 51
- 22 1: 5 10: 12 49: 51
- 23 6: 9 7: 12 49: 51
- 24 10: 12 7: 12 49: 51
- 25 1: 6 1: 6 52: 54
- 26 7: 12 1: 6 52: 54
- 27 1: 5 7: 12 52: 54
- 28 6: 12 7: 12 52: 54
- 29 1: 12 1: 6 55: 56
- 30 1: 12 7: 12 55: 56
- 31 1: 12 1: 12 57: 58
- 32 1: 12 1: 12 59: 96
-timer(meshCom-Ca) : 2.9802E-06 3.6843E-06 6.0201E-06
-timer(meshCom-Ca) : 2.9802E-06 3.4701E-06 6.0201E-06
-timer(BuildDISTR) : 3.3802E-04 3.7713E-04 4.0495E-04
+ 1 1: 27 1: 27 1: 101
+ 2 1: 27 1: 27 102: 106
+ 3 1: 27 1: 13 107: 112
+ 4 1: 27 14: 27 107: 112
+ 5 1: 14 1: 13 113: 120
+ 6 15: 27 1: 13 113: 120
+ 7 1: 12 14: 27 113: 120
+ 8 13: 27 14: 27 113: 120
+ 9 1: 14 1: 13 121: 128
+ 10 15: 27 1: 13 121: 128
+ 11 1: 12 14: 27 121: 128
+ 12 13: 27 14: 27 121: 128
+ 13 1: 27 1: 13 129: 135
+ 14 1: 27 14: 27 129: 135
+ 15 1: 27 1: 27 136: 140
+ 16 1: 27 1: 27 141: 240
+timer(meshCom-Ca) : 1.9073E-06 2.1942E-06 2.9802E-06
+timer(meshCom-Ca) : 1.9073E-06 2.4289E-06 3.0994E-06
+timer(BuildDISTR) : 7.8595E-04 8.1039E-04 8.6999E-04
New grid distribution: 3
- 1 1: 12 1: 12 1: 33
- 2 1: 12 1: 12 34: 34
- 3 1: 12 1: 6 35: 36
- 4 1: 12 7: 12 35: 36
- 5 1: 6 1: 6 37: 40
- 6 7: 12 1: 6 37: 40
- 7 1: 6 7: 12 37: 40
- 8 7: 12 7: 12 37: 40
- 9 1: 6 1: 6 41: 44
- 10 1: 6 1: 6 45: 48
- 11 7: 12 1: 6 41: 44
- 12 7: 12 1: 6 45: 48
- 13 1: 6 7: 12 41: 44
- 14 1: 6 7: 12 45: 48
- 15 7: 12 7: 12 41: 44
- 16 7: 12 7: 12 45: 48
- 17 1: 6 1: 6 49: 52
- 18 1: 6 1: 6 53: 56
- 19 7: 12 1: 6 49: 52
- 20 7: 12 1: 6 53: 56
- 21 1: 6 7: 12 49: 52
- 22 1: 6 7: 12 53: 56
- 23 7: 12 7: 12 49: 52
- 24 7: 12 7: 12 53: 56
- 25 1: 6 1: 6 57: 60
- 26 7: 12 1: 6 57: 60
- 27 1: 6 7: 12 57: 60
- 28 7: 12 7: 12 57: 60
- 29 1: 12 1: 6 61: 62
- 30 1: 12 7: 12 61: 62
- 31 1: 12 1: 12 63: 63
- 32 1: 12 1: 12 64: 96
+ 1 1: 27 1: 27 1: 86
+ 2 1: 27 1: 27 87: 91
+ 3 1: 27 1: 13 92: 101
+ 4 1: 27 14: 27 92: 101
+ 5 1: 13 1: 13 102: 120
+ 6 14: 27 1: 13 102: 120
+ 7 1: 13 14: 27 102: 120
+ 8 14: 27 14: 27 102: 120
+ 9 1: 13 1: 13 121: 140
+ 10 14: 27 1: 13 121: 140
+ 11 1: 13 14: 27 121: 140
+ 12 14: 27 14: 27 121: 140
+ 13 1: 27 1: 13 141: 150
+ 14 1: 27 14: 27 141: 150
+ 15 1: 27 1: 27 151: 155
+ 16 1: 27 1: 27 156: 240
Setting up quadratic distribution...
stepf: Methfessel-Paxton step function
Using Hermite-Gauss polynomials of order 1
siesta: Program's energy decomposition (eV):
-siesta: Ebs = -1775.612391
+siesta: Ebs = -1775.255690
siesta: Eions = 10757.993862
-siesta: Ena = 1699.344058
-siesta: Ekin = 2891.317012
-siesta: Enl = -1188.597975
+siesta: Ena = 1699.580665
+siesta: Ekin = 2891.262600
+siesta: Enl = -1188.675958
siesta: Eso = 0.000000
siesta: Edftu = 0.000000
-siesta: DEna = 80.813700
-siesta: DUscf = 33.956928
+siesta: DEna = 80.730930
+siesta: DUscf = 33.898767
siesta: DUext = 0.000000
-siesta: Ex = -607.129352
-siesta: Ec = -67.845766
-siesta: Exc = -674.975119
+siesta: Ex = -607.114022
+siesta: Ec = -67.619067
+siesta: Exc = -674.733088
siesta: EbV = 0.000000
siesta: eta*DQ = 0.000000
siesta: Emadel = 0.000000
siesta: Emeta = 0.000000
siesta: Emolmec = 0.000000
siesta: Ekinion = 0.000000
-siesta: Eharris = -7876.948217
-siesta: Etot = -7916.135257
-siesta: FreeEng = -7916.135257
+siesta: Eharris = -7876.778542
+siesta: Etot = -7915.929946
+siesta: FreeEng = -7915.929946
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
- scf: 1 -7876.948217 -7916.135257 -7916.135257 1.115926 0.707918 38.817660
-timer(IterSCF ) : 4.1270E-02 4.1607E-02 4.8971E-02
- scf: 2 -7901.823962 -7931.960055 -7931.960055 0.562804 -5.669338 18.287970
- scf: 3 -7939.354865 -7939.449650 -7939.449650 0.235558 -2.527705 3.620456
- scf: 4 -7938.410306 -7939.369129 -7939.369129 0.119522 -3.877475 4.170330
- scf: 5 -7939.576286 -7939.476141 -7939.476141 0.007737 -3.796210 3.517353
- scf: 6 -7939.833338 -7939.764022 -7939.764022 0.035775 -3.462084 0.137851
- scf: 7 -7939.747308 -7939.759074 -7939.759074 0.008388 -3.375785 0.535059
- scf: 8 -7939.764966 -7939.764386 -7939.764386 0.005691 -3.446766 0.016172
- scf: 9 -7939.764397 -7939.764398 -7939.764398 0.000311 -3.446339 0.002462
- scf: 10 -7939.764399 -7939.764398 -7939.764398 0.000083 -3.445713 0.002461
- scf: 11 -7939.764398 -7939.764398 -7939.764398 0.000006 -3.445753 0.001929
- scf: 12 -7939.764398 -7939.764398 -7939.764398 0.000026 -3.445964 0.000272
- scf: 13 -7939.764398 -7939.764398 -7939.764398 0.000003 -3.445933 0.000031
- scf: 14 -7939.764398 -7939.764398 -7939.764398 0.000000 -3.445933 0.000011
- scf: 15 -7939.764398 -7939.764398 -7939.764398 0.000000 -3.445932 0.000002
- scf: 16 -7939.764398 -7939.764398 -7939.764398 0.000000 -3.445932 0.000000
- scf: 17 -7939.764398 -7939.764398 -7939.764398 0.000000 -3.445932 0.000000
+ scf: 1 -7876.778542 -7915.929946 -7915.929946 1.115855 0.726121 38.785310
+timer(IterSCF ) : 1.2010E-01 1.2377E-01 1.2418E-01
+ scf: 2 -7901.664920 -7931.734515 -7931.734515 0.561723 -5.641452 18.265063
+ scf: 3 -7939.117251 -7939.207618 -7939.207618 0.234527 -2.502916 3.613030
+ scf: 4 -7938.177840 -7939.129005 -7939.129005 0.119206 -3.849556 4.152652
+ scf: 5 -7939.331558 -7939.233579 -7939.233579 0.007578 -3.769928 3.512997
+ scf: 6 -7939.590012 -7939.520889 -7939.520889 0.035726 -3.436126 0.136988
+ scf: 7 -7939.504224 -7939.515952 -7939.515952 0.008375 -3.350051 0.534488
+ scf: 8 -7939.521823 -7939.521249 -7939.521249 0.005684 -3.420997 0.016395
+ scf: 9 -7939.521260 -7939.521261 -7939.521261 0.000309 -3.420555 0.002308
+ scf: 10 -7939.521261 -7939.521261 -7939.521261 0.000071 -3.420016 0.002499
+ scf: 11 -7939.521261 -7939.521261 -7939.521261 0.000016 -3.419942 0.002069
+ scf: 12 -7939.521261 -7939.521261 -7939.521261 0.000028 -3.420166 0.000275
+mix: Pulay -- inversion failed, > SVD [rank/size] 5 / 9
+ scf: 13 -7939.521261 -7939.521261 -7939.521261 0.000003 -3.420131 0.000007
+ scf: 14 -7939.521261 -7939.521261 -7939.521261 0.000000 -3.420135 0.000010
+mix: Pulay -- inversion failed, > SVD [rank/size] 5 / 9
+ scf: 15 -7939.521261 -7939.521261 -7939.521261 0.000000 -3.420134 0.000000
+ scf: 16 -7939.521261 -7939.521261 -7939.521261 0.000000 -3.420134 0.000000
+ scf: 17 -7939.521261 -7939.521261 -7939.521261 0.000000 -3.420134 0.000000
SCF Convergence by DM+H criterion
-max |DM_out - DM_in| : 0.0000000009
-max |H_out - H_in| (eV) : 0.0000000065
+max |DM_out - DM_in| : 0.0000000006
+max |H_out - H_in| (eV) : 0.0000000051
SCF cycle converged after 17 iterations
Using DM_out to compute the final energy and forces
- E_bs from EDM: -1046.8277091552172
-No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 13 260
+ E_bs from EDM: -1047.0339158795994
+No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 22 260
-siesta: E_KS(eV) = -7939.7644
+siesta: E_KS(eV) = -7939.5213
-siesta: E_KS - E_eggbox = -7939.7644
+siesta: E_KS - E_eggbox = -7939.5213
siesta: Atomic forces (eV/Ang):
- 1 0.000000 0.000000 0.000000
- 2 -0.000000 -0.000000 0.669208
- 3 -0.000000 -0.000000 -0.669208
+ 1 0.000000 -0.000000 -0.000000
+ 2 -0.000000 0.000000 0.666359
+ 3 -0.000000 0.000000 -0.666359
----------------------------------------
- Tot 0.000000 -0.000000 -0.000000
+ Tot 0.000000 0.000000 -0.000000
----------------------------------------
- Max 0.669208
- Res 0.315468 sqrt( Sum f_i^2 / 3N )
+ Max 0.666359
+ Res 0.314125 sqrt( Sum f_i^2 / 3N )
----------------------------------------
- Max 0.669208 constrained
+ Max 0.666359 constrained
-Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 13.68 13.68 14.36 0.00 0.00 0.00
-(Free)E + p*V (eV/cell) -7941.6287
-Target enthalpy (eV/cell) -7939.7644
+Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 16.08 16.08 16.06 0.00 -0.00 0.00
+(Free)E + p*V (eV/cell) -7941.6768
+Target enthalpy (eV/cell) -7939.5213
mulliken: Atomic and Orbital Populations:
@@ -944,8 +896,8 @@ Atom Qatom Qorb
5dz2 5dxz 5dx2-y2 5dxy 5dyz 5dz2 5dxz 5dx2-y2
4fy(3x2-4fxyz 4fz2y 4fz3 4fz2x 4fz(x2-y4fx(x2-36Ppy
6Ppz 6Ppx
- 1 27.395 1.988 0.974 -0.425 1.972 1.964 1.972 0.917 0.699
- 0.921 0.699 0.917 -0.019 0.088 0.008 0.088 -0.019
+ 1 27.394 1.986 0.975 -0.426 1.973 1.965 1.973 0.915 0.696
+ 0.920 0.696 0.915 -0.018 0.089 0.008 0.089 -0.018
1.998 1.996 1.997 1.998 1.997 1.996 1.997 0.223
@@ -955,9 +907,9 @@ Species: S
Atom Qatom Qorb
3s 3s 3py 3pz 3px 3py 3pz 3px
3Pdxy 3Pdyz 3Pdz2 3Pdxz 3Pdx2-y2
- 2 6.303 1.465 0.272 1.381 1.602 1.381 0.007 -0.080 0.007
+ 2 6.303 1.463 0.273 1.381 1.603 1.381 0.007 -0.080 0.007
0.053 0.054 0.053 0.054 0.053
- 3 6.303 1.465 0.272 1.381 1.602 1.381 0.007 -0.080 0.007
+ 3 6.303 1.463 0.273 1.381 1.603 1.381 0.007 -0.080 0.007
0.053 0.054 0.053 0.054 0.053
mulliken: Qtot = 40.000
@@ -967,8 +919,8 @@ Computing bands...
diag: Algorithm = D&C
diag: Parallel over k = F
diag: Use parallel 2D distribution = T
-diag: Parallel block-size = 1
-diag: Parallel distribution = 4 x 8
+diag: Parallel block-size = 3
+diag: Parallel distribution = 4 x 4
diag: Used triangular part = Lower
diag: Absolute tolerance = 0.100E-15
diag: Orthogonalization factor = 0.100E-05
@@ -976,208 +928,208 @@ diag: Memory factor = 1.0000
siesta: Eigenvalues (eV):
ik is eps
- 1 1 -78.4160 -42.7604 -42.6582 -42.5657 -32.6805 -32.6724 -32.6187 -32.6169 -32.6116 -32.6068
- -32.5642 -17.6888 -17.0654 -10.2732 -9.0718 -8.9649 -7.4762 -6.4739 -5.8927 -5.7645
- -1.8589 -1.8250 -0.6256 0.0308 3.2482 4.5485 5.4150 7.8171 7.9894 8.8609
- 10.2301 10.4670 11.3108 12.3676 13.5290 13.9627 15.1092 21.1174 21.3810 21.5260
- 26.4252 27.2952 29.3509 31.0352 32.4964 35.8203 37.7094 38.1870 43.5013 49.1271
- 53.9057 69.9618
- 2 1 -78.4331 -42.6807 -42.5911 -42.5231 -32.6833 -32.6828 -32.6283 -32.6108 -32.6084 -32.6056
- -32.5696 -18.7345 -17.4612 -10.3936 -8.1930 -7.6536 -6.7729 -6.5606 -5.8294 -4.9702
- -2.0130 -1.7239 -1.4674 -0.7345 4.5117 6.0286 6.3324 7.7993 8.2182 8.3170
- 9.7290 9.7470 10.1656 12.1117 12.2126 14.0671 14.0701 19.8143 21.7718 24.1463
- 26.9127 29.1985 29.4306 30.9947 31.2286 34.8168 36.1440 38.4406 43.3934 48.0435
- 49.4075 62.4537
- 3 1 -78.4434 -42.6915 -42.5011 -42.5011 -32.6877 -32.6876 -32.6332 -32.6050 -32.6050 -32.6036
- -32.5721 -19.1636 -17.6196 -10.9239 -7.2307 -7.2307 -6.6178 -5.9165 -5.9165 -4.6426
- -1.4014 -1.4014 -1.4014 -1.4014 3.1635 5.3320 7.0506 7.0506 7.6286 9.4062
- 9.4062 9.9430 11.8400 13.3718 13.3718 13.4274 13.4274 17.5137 24.3696 25.0954
- 25.0954 28.3967 28.3967 32.4857 32.4857 35.6611 37.7292 37.7292 46.8317 47.4436
- 47.4436 62.5076
- 4 1 -78.4088 -42.8346 -42.6469 -42.5843 -32.6803 -32.6665 -32.6139 -32.6121 -32.6073 -32.6041
- -32.5613 -17.0163 -16.8214 -11.0310 -9.7711 -8.9673 -7.8372 -6.7318 -5.5455 -5.4516
- -1.5356 -1.1124 -0.1416 0.2282 1.5871 3.7899 4.8034 6.8745 7.1031 7.7309
- 11.3897 12.3846 12.6698 13.9546 15.0230 15.3722 15.6661 18.7325 21.0732 21.3802
- 24.5331 25.3294 27.7316 28.7354 35.0216 37.2410 40.0038 40.9925 48.3774 49.5014
- 57.0468 92.9794
- 5 1 -78.4094 -42.7944 -42.6468 -42.6263 -32.6792 -32.6687 -32.6211 -32.6126 -32.6083 -32.6072
- -32.5615 -17.0408 -16.8009 -10.4734 -9.8029 -8.7536 -8.0363 -7.2254 -6.5555 -5.0742
- -1.8763 -1.0493 -0.7905 0.5468 2.6886 5.2241 5.5530 6.8523 7.1828 8.1746
- 10.0557 10.4972 11.8862 12.2648 14.4872 15.6450 18.4764 19.0251 20.5469 21.6218
- 24.1928 26.3902 29.1937 30.0618 33.2359 37.0622 37.6318 40.9746 41.4674 56.5119
- 57.0300 78.6297
- 6 1 -78.4205 -42.7048 -42.6641 -42.5698 -32.6809 -32.6750 -32.6197 -32.6170 -32.6108 -32.6082
- -32.5656 -17.9808 -17.1715 -9.8296 -8.9998 -8.4453 -7.9524 -6.6514 -5.8420 -5.3920
- -2.4327 -1.5825 -1.3415 0.1820 4.3476 6.2945 6.6680 7.2340 7.6569 8.0955
- 8.9987 9.3511 11.4062 12.0470 12.2324 14.8664 15.3176 20.2267 21.3119 23.1833
- 25.7661 29.7113 30.6651 30.7028 31.8610 33.7279 36.3159 40.8807 41.9327 51.6187
- 51.9334 66.2110
- 7 1 -78.4331 -42.6807 -42.5911 -42.5231 -32.6833 -32.6828 -32.6283 -32.6108 -32.6084 -32.6056
- -32.5696 -18.7345 -17.4612 -10.3936 -8.1930 -7.6536 -6.7729 -6.5606 -5.8294 -4.9702
- -2.0130 -1.7239 -1.4674 -0.7345 4.5117 6.0286 6.3324 7.7993 8.2182 8.3170
- 9.7290 9.7470 10.1656 12.1117 12.2126 14.0671 14.0701 19.8143 21.7718 24.1463
- 26.9127 29.1985 29.4306 30.9947 31.2286 34.8168 36.1440 38.4406 43.3934 48.0435
- 49.4075 62.4537
- 8 1 -78.4331 -42.6807 -42.5911 -42.5231 -32.6833 -32.6828 -32.6283 -32.6108 -32.6084 -32.6056
- -32.5696 -18.7345 -17.4612 -10.3936 -8.1930 -7.6536 -6.7729 -6.5606 -5.8294 -4.9702
- -2.0130 -1.7239 -1.4674 -0.7345 4.5117 6.0286 6.3324 7.7993 8.2182 8.3170
- 9.7290 9.7470 10.1656 12.1117 12.2126 14.0671 14.0701 19.8143 21.7718 24.1463
- 26.9127 29.1985 29.4306 30.9947 31.2286 34.8168 36.1440 38.4406 43.3934 48.0435
- 49.4075 62.4537
- 9 1 -78.4205 -42.7048 -42.6641 -42.5698 -32.6809 -32.6750 -32.6197 -32.6170 -32.6108 -32.6082
- -32.5656 -17.9808 -17.1715 -9.8296 -8.9998 -8.4453 -7.9524 -6.6514 -5.8420 -5.3920
- -2.4327 -1.5825 -1.3415 0.1820 4.3476 6.2945 6.6680 7.2340 7.6569 8.0955
- 8.9987 9.3511 11.4062 12.0470 12.2324 14.8664 15.3176 20.2267 21.3119 23.1833
- 25.7661 29.7113 30.6651 30.7028 31.8610 33.7279 36.3159 40.8807 41.9327 51.6187
- 51.9334 66.2110
- 10 1 -78.4094 -42.7944 -42.6468 -42.6263 -32.6792 -32.6687 -32.6211 -32.6126 -32.6083 -32.6072
- -32.5615 -17.0408 -16.8009 -10.4734 -9.8029 -8.7536 -8.0363 -7.2254 -6.5555 -5.0742
- -1.8763 -1.0493 -0.7905 0.5468 2.6886 5.2241 5.5530 6.8523 7.1828 8.1746
- 10.0557 10.4972 11.8862 12.2648 14.4872 15.6450 18.4764 19.0251 20.5469 21.6218
- 24.1928 26.3902 29.1937 30.0618 33.2359 37.0622 37.6318 40.9746 41.4674 56.5119
- 57.0300 78.6297
- 11 1 -78.4056 -42.7495 -42.7202 -42.6407 -32.6778 -32.6689 -32.6289 -32.6120 -32.6109 -32.6082
- -32.5603 -16.6843 -16.6304 -10.3519 -9.8574 -9.0220 -8.3665 -7.8155 -6.9820 -4.4883
- -2.4072 -1.2101 -0.4698 1.1918 3.2550 3.3208 6.7748 7.8119 8.1827 9.1039
- 9.1452 9.4481 11.1164 11.1200 15.6396 15.8431 18.0932 19.0724 20.5227 22.4830
- 24.3614 24.8106 28.8436 31.2275 35.1431 37.3973 37.9249 38.2572 39.2524 57.2097
- 58.7976 65.9759
- 12 1 -78.4094 -42.7944 -42.6468 -42.6263 -32.6792 -32.6687 -32.6211 -32.6126 -32.6083 -32.6072
- -32.5615 -17.0408 -16.8009 -10.4734 -9.8029 -8.7536 -8.0363 -7.2254 -6.5555 -5.0742
- -1.8763 -1.0493 -0.7905 0.5468 2.6886 5.2241 5.5530 6.8523 7.1828 8.1746
- 10.0557 10.4972 11.8862 12.2648 14.4872 15.6450 18.4764 19.0251 20.5469 21.6218
- 24.1928 26.3902 29.1937 30.0618 33.2359 37.0623 37.6318 40.9746 41.4674 56.5119
- 57.0300 78.6297
- 13 1 -78.4160 -42.7604 -42.6582 -42.5657 -32.6805 -32.6724 -32.6187 -32.6169 -32.6116 -32.6068
- -32.5642 -17.6888 -17.0654 -10.2732 -9.0718 -8.9649 -7.4762 -6.4739 -5.8927 -5.7645
- -1.8589 -1.8250 -0.6256 0.0308 3.2482 4.5485 5.4150 7.8171 7.9894 8.8609
- 10.2301 10.4670 11.3108 12.3676 13.5290 13.9627 15.1092 21.1174 21.3810 21.5260
- 26.4252 27.2952 29.3509 31.0352 32.4964 35.8203 37.7094 38.1870 43.5013 49.1271
- 53.9057 69.9618
- 14 1 -78.4205 -42.7048 -42.6641 -42.5698 -32.6809 -32.6750 -32.6197 -32.6170 -32.6108 -32.6082
- -32.5656 -17.9808 -17.1715 -9.8296 -8.9998 -8.4453 -7.9524 -6.6514 -5.8420 -5.3920
- -2.4327 -1.5825 -1.3415 0.1820 4.3476 6.2945 6.6680 7.2340 7.6569 8.0955
- 8.9987 9.3511 11.4062 12.0470 12.2324 14.8664 15.3176 20.2267 21.3119 23.1833
- 25.7661 29.7113 30.6651 30.7028 31.8610 33.7279 36.3159 40.8807 41.9327 51.6187
- 51.9334 66.2110
- 15 1 -78.4160 -42.7604 -42.6582 -42.5657 -32.6805 -32.6724 -32.6187 -32.6169 -32.6116 -32.6068
- -32.5642 -17.6888 -17.0654 -10.2732 -9.0718 -8.9649 -7.4762 -6.4739 -5.8927 -5.7645
- -1.8589 -1.8250 -0.6256 0.0308 3.2482 4.5485 5.4150 7.8171 7.9894 8.8609
- 10.2301 10.4670 11.3108 12.3676 13.5290 13.9627 15.1092 21.1174 21.3810 21.5260
- 26.4252 27.2952 29.3509 31.0352 32.4964 35.8203 37.7094 38.1870 43.5013 49.1271
- 53.9057 69.9618
- 16 1 -78.4094 -42.7944 -42.6468 -42.6263 -32.6792 -32.6687 -32.6211 -32.6126 -32.6083 -32.6072
- -32.5615 -17.0408 -16.8009 -10.4734 -9.8029 -8.7536 -8.0363 -7.2254 -6.5555 -5.0742
- -1.8763 -1.0493 -0.7905 0.5468 2.6886 5.2241 5.5530 6.8523 7.1828 8.1746
- 10.0557 10.4972 11.8862 12.2648 14.4872 15.6450 18.4764 19.0251 20.5469 21.6218
- 24.1928 26.3902 29.1937 30.0618 33.2359 37.0622 37.6318 40.9746 41.4674 56.5119
- 57.0300 78.6297
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-siesta: Fermi energy = -3.445932 eV
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+ -1.8828 -1.0553 -0.7975 0.5413 2.6796 5.2140 5.5422 6.8424 7.1721 8.1647
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+ -32.5640 -17.0480 -16.8084 -10.4827 -9.8120 -8.7620 -8.0447 -7.2352 -6.5634 -5.0819
+ -1.8828 -1.0553 -0.7975 0.5413 2.6796 5.2140 5.5422 6.8424 7.1721 8.1647
+ 10.0460 10.4903 11.8785 12.2575 14.4762 15.6348 18.4696 19.0160 20.5401 21.6182
+ 24.1852 26.3844 29.1841 30.0536 33.2221 37.0689 37.6372 40.9461 41.4732 56.5158
+ 57.0500 78.6925
+ 22 1 -78.4142 -42.8380 -42.6498 -42.5873 -32.6823 -32.6687 -32.6162 -32.6144 -32.6095 -32.6064
+ -32.5638 -17.0235 -16.8289 -11.0402 -9.7810 -8.9756 -7.8445 -6.7394 -5.5542 -5.4605
+ -1.5421 -1.1187 -0.1485 0.2223 1.5781 3.7778 4.7962 6.8649 7.0923 7.7171
+ 11.3815 12.3756 12.6621 13.9478 15.0131 15.3660 15.6605 18.7153 21.0672 21.3767
+ 24.5246 25.3215 27.7220 28.7319 35.0283 37.2052 40.0204 40.9898 48.3806 49.5017
+ 57.0641 93.0454
+siesta: Fermi energy = -3.420134 eV
siesta: Program's energy decomposition (eV):
-siesta: Ebs = -1046.827709
+siesta: Ebs = -1047.033916
siesta: Eions = 10757.993862
-siesta: Ena = 1699.344058
-siesta: Ekin = 2951.382529
-siesta: Enl = -1196.439257
+siesta: Ena = 1699.580665
+siesta: Ekin = 2951.250551
+siesta: Enl = -1196.515834
siesta: Eso = 0.000000
siesta: Edftu = 0.000000
-siesta: DEna = 53.465721
-siesta: DUscf = 2.995136
+siesta: DEna = 53.409446
+siesta: DUscf = 2.989098
siesta: DUext = 0.000000
-siesta: Ex = -624.023690
-siesta: Ec = -68.495033
-siesta: Exc = -692.518723
+siesta: Ex = -623.989715
+siesta: Ec = -68.251610
+siesta: Exc = -692.241325
siesta: EbV = 0.000000
siesta: eta*DQ = 0.000000
siesta: Emadel = 0.000000
siesta: Emeta = 0.000000
siesta: Emolmec = 0.000000
siesta: Ekinion = 0.000000
-siesta: Eharris = -7939.764398
-siesta: Etot = -7939.764398
-siesta: FreeEng = -7939.764398
+siesta: Eharris = -7939.521261
+siesta: Etot = -7939.521261
+siesta: FreeEng = -7939.521261
siesta: Final energy (eV):
-siesta: Band Struct. = -1046.827709
-siesta: Kinetic = 2951.382529
-siesta: Hartree = 27679.643713
+siesta: Band Struct. = -1047.033916
+siesta: Kinetic = 2951.250551
+siesta: Hartree = 27679.117259
siesta: Edftu = 0.000000
siesta: Eso = 0.000000
siesta: Ext. field = 0.000000
-siesta: Exch. = -624.023690
-siesta: Corr. = -68.495033
+siesta: Exch. = -623.989715
+siesta: Corr. = -68.251610
siesta: Bulk bias = 0.000000
-siesta: Exch.-corr. = -692.518723
-siesta: Ion-electron = -58448.488320
-siesta: Ion-ion = 20570.216402
+siesta: Exch.-corr. = -692.241325
+siesta: Ion-electron = -58447.941988
+siesta: Ion-ion = 20570.294242
siesta: Ekinion = 0.000000
siesta: D3 dispersion = 0.000000
-siesta: Total = -7939.764398
-siesta: Fermi = -3.445932
+siesta: Total = -7939.521261
+siesta: Fermi = -3.420134
siesta: Atomic forces (eV/Ang):
-siesta: 1 0.000000 0.000000 0.000000
-siesta: 2 -0.000000 -0.000000 0.669208
-siesta: 3 -0.000000 -0.000000 -0.669208
+siesta: 1 0.000000 -0.000000 -0.000000
+siesta: 2 -0.000000 0.000000 0.666359
+siesta: 3 -0.000000 0.000000 -0.666359
siesta: ----------------------------------------
-siesta: Tot 0.000000 -0.000000 -0.000000
+siesta: Tot 0.000000 0.000000 -0.000000
siesta: Stress tensor (static) (eV/Ang**3):
-siesta: 0.008536 0.000000 0.000000
-siesta: 0.000000 0.008536 0.000000
-siesta: 0.000000 0.000000 0.008961
+siesta: 0.010038 0.000000 -0.000000
+siesta: 0.000000 0.010038 -0.000000
+siesta: -0.000000 0.000000 0.010027
siesta: Cell volume = 214.828427 Ang**3
siesta: Pressure (static):
siesta: Solid Molecule Units
-siesta: -0.00009451 -0.00005832 Ry/Bohr**3
-siesta: -0.00867794 -0.00535519 eV/Ang**3
-siesta: -13.90374202 -8.58004819 kBar
-(Free)E+ p_basis*V_orbitals = -7938.503861
-(Free)Eharris+ p_basis*V_orbitals = -7938.503861
+siesta: -0.00010928 -0.00007325 Ry/Bohr**3
+siesta: -0.01003400 -0.00672539 eV/Ang**3
+siesta: -16.07641456 -10.77538086 kBar
+(Free)E+ p_basis*V_orbitals = -7938.260724
+(Free)Eharris+ p_basis*V_orbitals = -7938.260724
-siesta: Electric dipole (a.u.) = -0.000000 -0.000000 -0.000000
-siesta: Electric dipole (Debye) = -0.000000 -0.000000 -0.000000
+siesta: Electric dipole (a.u.) = 0.000000 0.000000 0.000000
+siesta: Electric dipole (Debye) = 0.000000 0.000000 0.000000
-dhscf: Vacuum level (max, mean) = 0.404996 0.393255 eV
+dhscf: Vacuum level (max, mean) = 0.404318 0.393552 eV
cite: Please see "WS2.bib" for an exhaustive BiBTeX file.
cite: Please clearly indicate Siesta version in published work: MaX-1.0-55-g0612142bc
@@ -1187,5 +1139,5 @@ cite: which are encouraged to be cited in a published work.
DOI: www.doi.org/10.1088/0953-8984/14/11/302
->> End of run: 29-JUN-2023 12:55:12
+>> End of run: 23-JUL-2023 15:05:25
Job completed
diff --git a/WS2/siesta/LDA/struct.POSCAR b/WS2/siesta/LDA/struct.POSCAR
new file mode 100644
index 0000000..8621a34
--- /dev/null
+++ b/WS2/siesta/LDA/struct.POSCAR
@@ -0,0 +1,12 @@
+WS2
+1.0
+3.1500000000000 0.000000000000 0.00
+1.575000000000 2.7279800219 0.00
+0.000000000000 0.000000000000 25.0
+W S
+1 2
+direct
+ 0.33333333333333 0.33333333333333 0.5000000000 W
+ 0.66666666666667 0.66666666666667 0.4360000000 S
+ 0.66666666666667 0.66666666666667 0.5640000000 S
+
diff --git a/WS2/siesta/LDA_NLCC/density2Vh.py b/WS2/siesta/LDA_NLCC/density2Vh.py
new file mode 100644
index 0000000..210abb7
--- /dev/null
+++ b/WS2/siesta/LDA_NLCC/density2Vh.py
@@ -0,0 +1,175 @@
+import numpy as np
+from fft_mod import put_FFTbox2, ifft_g2r, fft_r2g, flat_FFTbox
+from netCDF4 import Dataset
+from pymatgen.core.structure import Structure
+#from pymatgen.io.cube import Cube
+bohr2ang = 0.529177
+hartree = 27.2116 #eV
+vol = 214.828427 *((1/bohr2ang)**3)
+
+
+def main():
+ prefix = 'WS2'
+ #savedir = '../wfs/highcutoff/'
+ fn_poscar = './struct.POSCAR' # POSCAR file
+ #FFTgrid = [864, 864, 180] # coarse grid
+ noncolin = False
+ struct = Structure.from_file(fn_poscar)
+
+ ## Reading the total charge density ##
+ print(' Reading total charge density from SIESTA')
+ rootgrp = Dataset("./WS2.nc", "r", format="NETCDF4")
+ Rho = rootgrp['GRID']['Rho'][:].data
+ nspin, n3, n2, n1 = Rho.shape
+ print(' nspin, n1, n2, n3:', nspin, n1, n2, n3)
+ FFTgrid = np.array([n1,n2,n3], dtype=np.int32)
+ nfft = n1*n2*n3
+ print('nfft: ', nfft)
+ print(' vol: ', vol, ' Bohr^3')
+ print(' np.sum(Rho)*vol/nfft = ', np.sum(Rho[0,:,:,:])*vol/nfft)
+ rho_r_FFTbox = np.array([(Rho[0,:,:,:].T)])
+
+ #n1, n2, n3 = FFTgrid
+ #nfft = n1*n2*n3
+ # vh
+ #vol = struct.volume/(bohr2ang**3) # in Bohr^3
+ cell = struct.lattice._matrix*(1/bohr2ang) # in Bohr
+ bcell = 2*np.pi*np.linalg.inv(cell).T # in Bohr^-1
+
+ # debug
+ rho_g_FFTbox = fft_r2g(rho_r_FFTbox)
+ rho_g, igvec = flat_FFTbox(rho_g_FFTbox)
+ fn_vh_r_FFTbox= f'vh_r_FFTbox'
+ vh_r_FFTbox = get_vh(rho_g, igvec, bcell, FFTgrid)
+ np.save(fn_vh_r_FFTbox, vh_r_FFTbox)
+ Eh = np.real(0.5*np.sum(vh_r_FFTbox*rho_r_FFTbox*(vol/nfft)))
+
+
+ #diff = np.abs(vbh_r-vh_r)
+ print(f'Eh = {2*Eh} in Ry')
+ print(f'Eh = {2*Eh*hartree/2} in eV')
+ #print()
+ #print('diff = abs(vsub - vsub_aprox) in Hartree')
+ #print('max(diff)',np.max(diff))
+ #print('min(diff)',np.min(diff))
+ #print('avg(diff)',np.average(diff))
+ #print(np.sort(ratio.flat)[-1000:])
+ return
+
+
+def get_vh(rho_g, igvec, bcell, FFTgrid):
+ """
+ --Input--
+ rho_g : complex128(ng)
+ momentum space charge density in Hartree Atomic Unit
+
+ gvec : int(ng,3)
+ momentum space charge density in Hartree Atomic Unit
+
+ bcell_in: float64(3,3)
+ reciprocal lattice vectors (bohr^{-1})
+
+ --Output--
+ vh : float(:,:,:)
+
+ """
+ vh_g = np.zeros_like(rho_g)
+ gvec = igvec.dot(bcell)
+ gvec_sq = np.einsum('ix,ix->i', gvec, gvec) # bohr^{-1} or Ry
+ for ig, g_sq in enumerate(gvec_sq):
+ if g_sq < 1e-12:
+ vh_g[ig] = 0
+ else:
+ vh_g[ig] = 4*np.pi*rho_g[ig]/g_sq
+
+ vh_g_FFTbox = put_FFTbox2(vh_g, igvec, FFTgrid, noncolin=False)
+ vh_r = ifft_g2r(vh_g_FFTbox)
+ return np.real(vh_r)
+
+
+
+def get_vxc(rho):
+ """
+ --Input--
+ rho : float(:,:,:)
+ real space charge density in Hartree Atomic Unit
+
+ --Output--
+ vxc : float(:,:,:)
+
+ """
+ inp = {}
+ n1, n2, n3 = rho.shape
+ rho_flatten = rho.flatten()
+ inp["rho"] = rho_flatten
+
+ # Build functional
+ func_c = pylibxc.LibXCFunctional("LDA_C_PZ", "unpolarized")
+ func_x = pylibxc.LibXCFunctional("LDA_X", "unpolarized")
+
+ # Compute exchange part
+ ret_x = func_x.compute(inp, do_fxc=True)
+ v2rho2_x = ret_x['v2rho2'][:,0]
+ vrho_x = ret_x['vrho'][:,0]
+ zk_x = ret_x['zk'][:,0]
+
+ # Compute correlation part
+ ret_c = func_c.compute(inp, do_fxc=True)
+ v2rho2_c = ret_x['v2rho2'][:,0]
+ vrho_c = ret_c['vrho'][:,0]
+ zk_c = ret_c['zk'][:,0]
+
+ vxc = vrho_x + vrho_c
+ fxc = v2rho2_x + v2rho2_c
+
+ vxc_FFTbox = np.reshape(vxc,(n1,n2,n3))
+ fxc_FFTbox = np.reshape(fxc,(n1,n2,n3))
+
+ return vxc_FFTbox, fxc_FFTbox
+
+def vxc_libxc():
+ n1, n2, n3 = [18, 18, 135]
+ #gvec_rho = np.loadtxt('../2.1-wfn/rho_gvec.txt',dtype=np.int32)
+ #rho_pw2bgw = np.load('../2.1-wfn/rho_pw2bgw.npy')
+ #rho_FFTbox = put_FFTbox2(rho_pw2bgw, gvec_rho, [n1,n2,n3], noncolin=False)
+ #rho = ifft_g2r(rho_FFTbox)
+ #rho_pp = Cube("../1.1-pp/Rho.cube")
+ #rho = rho_pp.data
+ rho_pw2bgw = np.load("../2.1-wfn/rhor_pw2bgw.npy")
+ rho = rho_pw2bgw[0,:,:,:]
+ frac = 0.0001
+ rho_f = rho * frac
+ rho_r = rho - rho_f
+
+ # Create input
+ const = 1
+ inp = {}
+ rho_flatten = rho.flatten()
+ rho_r_flatten = rho_r.flatten()
+ rho_f_flatten = rho_f.flatten()
+ inp["rho"] = const*rho_flatten
+
+ # Build functional
+ func_c = pylibxc.LibXCFunctional("LDA_C_PZ", "unpolarized")
+ func_x = pylibxc.LibXCFunctional("LDA_X", "unpolarized")
+
+ # Compute exchange part
+ ret_x = func_x.compute(inp, do_fxc=True)
+ v2rho2_x = ret_x['v2rho2'][:,0]
+ vrho_x = ret_x['vrho'][:,0]
+ zk_x = ret_x['zk'][:,0]
+
+ # Compute correlation part
+ ret_c = func_c.compute(inp, do_fxc=True)
+ v2rho2_c = ret_x['v2rho2'][:,0]
+ vrho_c = ret_c['vrho'][:,0]
+ zk_c = ret_c['zk'][:,0]
+
+ vxc = vrho_x + vrho_c
+ fxc = v2rho2_x + v2rho2_c
+
+ vxc_FFTbox = np.reshape(vxc,(18,18,135))
+ fxc_FFTbox = np.reshape(fxc,(18,18,135))
+ return vxc_FFTbox, fxc_FFTbox
+
+main()
diff --git a/WS2/siesta/LDA_NLCC/fft_mod.py b/WS2/siesta/LDA_NLCC/fft_mod.py
index 7e02776..eddf4a1 100644
--- a/WS2/siesta/LDA_NLCC/fft_mod.py
+++ b/WS2/siesta/LDA_NLCC/fft_mod.py
@@ -1,10 +1,88 @@
import os
import time
import numpy as np
-from numpy.fft import fftn, ifftn, ifftshift
+from numpy.fft import fftn, ifftn, fftshift, ifftshift
+
+
+def flat_FFTbox(unkg_FFTbox):
+ """
+ Generate a flattened 1d array 'unkg' and corresponding igvecs from unkg_FFTbox.
+ Assume unkg_FFTbox has its zero-frequency component in unkg_FFTbox[ispin,0,0,0].
+ This functions is a kind of the inverse function of 'put_FFTbox'.
+ Note, because of the zero padding in unkg_FFTbox, unkg may have lots of zeros.
+
+ --Input--
+ unkg_FFTbox : cdouble(nspin,N1,N2,N3)
+ unkg in FFTbox
+ for colinear case, nspin = 1
+ for non-colinear case, nspin = 2
+
+ --Output--
+ unkg : cdouble(nspin*N1*N2*N3)
+ for non-colinear case, the first half is for spin-up,
+ the second half is for spin-dw.
+ gvecs_sym : int(N1*N2*N3,3)
+ array of miller index (h,k,l)
+ """
+ nspin, n1, n2, n3 = unkg_FFTbox.shape
+ ng = n1*n2*n3
+ h_max, k_max, l_max = n1//2, n2//2, n3//2
+
+ hs, ks, ls = np.unravel_index(np.array(range(ng)),(n1,n2,n3))
+
+ #generate zero starting positive index. it is just for reshaping
+ gvecs_pos = np.concatenate([[hs],[ks],[ls]], axis = 0).T
+ hkl2flat = ( n3 * (n2 * gvecs_pos[:, 0] + gvecs_pos[:, 1]) \
+ + gvecs_pos[:, 2])
+ hs[hs>=h_max] -= n1
+ ks[ks>=k_max] -= n2
+ ls[ls>=l_max] -= n3
+
+ #generate zero starting symmetric index. it will be returned
+ gvecs_sym = np.concatenate([[hs],[ks],[ls]], axis = 0).T
+
+ unkg = np.zeros(nspin*ng,dtype=np.cdouble)
+ for ispin in range(nspin):
+ gstart = ispin*ng
+ gend = (ispin + 1)*ng
+ unkg[gstart:gend] = unkg_FFTbox[ispin,:,:,:].flat[hkl2flat]
+
+ return unkg, gvecs_sym
+
+
+def fft_r2g(unkr_FFTbox):
+ """ fft from R space to G space
+
+ ---Input---
+ unkr_FFTbox : cdouble(ispin,N1,N2,N3)
+ unkr in FFTbox
+
+ --Output--
+ unkg_FFTbox : cdouble(ispin,N1,N2,N3)
+ unkg in FFTbox
+ """
+ # FFTgrid
+ nspin, n1, n2, n3 = unkr_FFTbox.shape
+ Nt = n1*n2*n3
+ unkg_FFTbox = np.zeros_like(unkr_FFTbox)
+ start = time.time()
+ for ispin in range(nspin):
+ unkg_FFTbox[ispin,:,:,:] = fftn(unkr_FFTbox[ispin,:,:,:])
+ end = time.time()
+ #print(f'\nFFT time', end-start)
+
+ return unkg_FFTbox
def ifft_g2r(unkg_FFTbox):
- """ ifft from G space to R space
+ """
+ ifft from G space to R space
+
+ with an input array x[l], the output array y[k] satisfy
+ y[k] = np.sum(x * np.exp(2j * np.pi * k * np.arange(n)/n)) / len(x)
+
+ Note unkg_FFTbox have the unk(G=0) component as the first element
+ in the unkg_FFTbox[ispin,0,0,0].
+
---Input---
unkg_FFTbox : cdouble(ispin,N1,N2,N3)
@@ -22,7 +100,7 @@ def ifft_g2r(unkg_FFTbox):
for ispin in range(nspin):
unkr_FFTbox[ispin,:,:,:] = ifftn(unkg_FFTbox[ispin,:,:,:])
end = time.time()
- print(f'\nIFFT time', end-start)
+ #print(f'\nIFFT time', end-start)
return unkr_FFTbox
@@ -48,6 +126,10 @@ def put_FFTbox2(unkg, gvecs, FFTgrid, noncolin, savedir='./', savefn=False):
for colinear case, nspin = 1
for non-colinear case, nspin = 2
+ unkg_FFTbox[ispin,0,0,0] = unk_ispin(G=0),
+ which is a zero frequency start array.
+
+
"""
#fn = savedir+f'./Unkg_FFTbox_k{ik}.npy'
@@ -86,7 +168,7 @@ def put_FFTbox2(unkg, gvecs, FFTgrid, noncolin, savedir='./', savefn=False):
#Save it for later calculation
#np.save(savedir+f'./Unkg_FFTbox_k{ik}.npy',unkg_FFTbox)
- print(f'\nFFTBOX time', end-start)
+ #print(f'\nFFTBOX time', end-start)
return unkg_FFTbox
@@ -139,13 +221,6 @@ def put_FFTbox(ik, FFTgrid, savedir='./'):
# Save it for later calculation
np.save(savedir+f'./Unkg_FFTbox_k{ik}.npy',unkg_FFTbox)
- print(f'\nFFTBOX time', end-start)
+ #print(f'\nFFTBOX time', end-start)
return unkg_FFTbox
-
-if __name__=='__main__':
- ik = 1
- FFTgrid = [495, 495, 83]
- unkg_FFTbox1 = put_FFTbox(ik, FFTgrid, savedir='../../data/')
- unkg_FFTbox2 = put_FFTbox2(ik, FFTgrid, savedir='../../data/')
- print(np.allclose(unkg_FFTbox2,unkg_FFTbox1))
diff --git a/WS2/siesta/LDA_NLCC/struct.POSCAR b/WS2/siesta/LDA_NLCC/struct.POSCAR
new file mode 100644
index 0000000..8621a34
--- /dev/null
+++ b/WS2/siesta/LDA_NLCC/struct.POSCAR
@@ -0,0 +1,12 @@
+WS2
+1.0
+3.1500000000000 0.000000000000 0.00
+1.575000000000 2.7279800219 0.00
+0.000000000000 0.000000000000 25.0
+W S
+1 2
+direct
+ 0.33333333333333 0.33333333333333 0.5000000000 W
+ 0.66666666666667 0.66666666666667 0.4360000000 S
+ 0.66666666666667 0.66666666666667 0.5640000000 S
+
diff --git a/graphene/siesta/SG15v1.2/ref/0_NORMAL_EXIT b/graphene/siesta/SG15v1.2/ref/0_NORMAL_EXIT
new file mode 100644
index 0000000..26810cc
--- /dev/null
+++ b/graphene/siesta/SG15v1.2/ref/0_NORMAL_EXIT
@@ -0,0 +1 @@
+SIESTA completed, MPI exit: 0
diff --git a/graphene/siesta/SG15v1.2/ref/BASIS_ENTHALPY b/graphene/siesta/SG15v1.2/ref/BASIS_ENTHALPY
new file mode 100644
index 0000000..4425b85
--- /dev/null
+++ b/graphene/siesta/SG15v1.2/ref/BASIS_ENTHALPY
@@ -0,0 +1,4 @@
+ -309.80938620194246
+ The above number is the electronic (free)energy: -310.40924494825106
+ Plus the pressure : 1.3595453680289311E-005 ( 0.20000000000000001 GPa)
+ times the orbital volume (in Bohr**3): 3242.8824638012043
diff --git a/graphene/siesta/SG15v1.2/ref/BASIS_HARRIS_ENTHALPY b/graphene/siesta/SG15v1.2/ref/BASIS_HARRIS_ENTHALPY
new file mode 100644
index 0000000..4c55f3b
--- /dev/null
+++ b/graphene/siesta/SG15v1.2/ref/BASIS_HARRIS_ENTHALPY
@@ -0,0 +1,4 @@
+ -309.80938620225356
+ The above number is the electronic (free) harris energy: -310.40924494856222
+ Plus the pressure : 1.3595453680289311E-005 ( 0.20000000000000001 GPa)
+ times the orbital volume (in Bohr**3): 3242.8824638012043
diff --git a/graphene/siesta/SG15v1.2/ref/C.ion b/graphene/siesta/SG15v1.2/ref/C.ion
new file mode 100644
index 0000000..c3a03f1
--- /dev/null
+++ b/graphene/siesta/SG15v1.2/ref/C.ion
@@ -0,0 +1,5572 @@
+
+
+
+===============================================================================
+C Z= 6 Mass= 12.010 Charge= 0.17977+309
+Lmxo=2 Lmxkb= 1 BasisType=split Semic=F
+L=0 Nsemic=0 Cnfigmx=2
+ i=1 nzeta=2 polorb=0 (2s)
+ splnorm: 0.15000
+ vcte: 0.0000
+ rinn: 0.0000
+ qcoe: 0.0000
+ qyuk: 0.0000
+ qwid: 0.10000E-01
+ rcs: 4.1918 3.4319
+ lambdas: 1.0000 1.0000
+L=1 Nsemic=0 Cnfigmx=2
+ i=1 nzeta=2 polorb=1 (2p) (to be polarized perturbatively)
+ splnorm: 0.15000
+ vcte: 0.0000
+ rinn: 0.0000
+ qcoe: 0.0000
+ qyuk: 0.0000
+ qwid: 0.10000E-01
+ rcs: 4.8703 3.4751
+ lambdas: 1.0000 1.0000
+L=2 Nsemic=0 Cnfigmx=3
+ i=1 nzeta=0 polorb=0 (3d) (perturbative polarization orbital) (from 2p)
+-------------------------------------------------------------------------------
+L=0 Nkbl=1 erefs: 0.17977+309
+L=1 Nkbl=1 erefs: 0.17977+309
+===============================================================================
+
+
+
+ C ca nrl nc
+ ONCVPSP-3.2023-07-03Hamann's oncvpsp
+ 2s 2.00 r= 1.42/2p 2.00 r= 1.41/ 2s:2p:
+
+
+C # Symbol
+C # Label
+ 6 # Atomic number
+ 4.00000000000 # Valence charge
+ 12.0100000000 # Mass
+ 33.5129345078 # Self energy
+ 2 5 # Lmax for basis, no. of nl orbitals
+ 1 4 # Lmax for projectors, no. of nl KB projectors
+# PAOs:__________________________
+ 0 2 1 0 2.000000 #orbital l, n, z, is_polarized, population
+ 500 0.8400499466814190E-02 4.191849233940281 # npts, delta, cutoff
+ 0.000000000000000 0.5030996704898009
+ 0.8400499466814190E-02 0.5032035438299329
+ 0.1680099893362838E-01 0.5035201279435505
+ 0.2520149840044257E-01 0.5040471161325382
+ 0.3360199786725676E-01 0.5047835318189627
+ 0.4200249733407095E-01 0.5057280135978148
+ 0.5040299680088514E-01 0.5068788204993798
+ 0.5880349626769933E-01 0.5082338388940990
+ 0.6720399573451352E-01 0.5097905908596948
+ 0.7560449520132771E-01 0.5115462439389552
+ 0.8400499466814190E-01 0.5134976222191769
+ 0.9240549413495609E-01 0.5156412186577363
+ 0.1008059936017703 0.5179732085707444
+ 0.1092064930685845 0.5204894641944886
+ 0.1176069925353987 0.5231855702228073
+ 0.1260074920022128 0.5260568402176513
+ 0.1344079914690270 0.5290983337851000
+ 0.1428084909358412 0.5323048744049079
+ 0.1512089904026554 0.5356710677984193
+ 0.1596094898694696 0.5391913207173288
+ 0.1680099893362838 0.5428598600343768
+ 0.1764104888030980 0.5466707520166190
+ 0.1848109882699122 0.5506179216623853
+ 0.1932114877367264 0.5546951719844904
+ 0.2016119872035406 0.5588962031245820
+ 0.2100124866703548 0.5632146311867742
+ 0.2184129861371689 0.5676440066828053
+ 0.2268134856039831 0.5721778324858638
+ 0.2352139850707973 0.5768095811959524
+ 0.2436144845376115 0.5815327118260537
+ 0.2520149840044257 0.5863406857254347
+ 0.2604154834712399 0.5912269816641289
+ 0.2688159829380541 0.5961851100107823
+ 0.2772164824048683 0.6012086259447721
+ 0.2856169818716825 0.6062911416524660
+ 0.2940174813384966 0.6114263374668633
+ 0.3024179808053108 0.6166079719193706
+ 0.3108184802721251 0.6218298906821486
+ 0.3192189797389392 0.6270860343891542
+ 0.3276194792057534 0.6323704453337115
+ 0.3360199786725676 0.6376772730499556
+ 0.3444204781393818 0.6430007787948724
+ 0.3528209776061960 0.6483353389567068
+ 0.3612214770730102 0.6536754474242040
+ 0.3696219765398244 0.6590157169594550
+ 0.3780224760066386 0.6643508796248360
+ 0.3864229754734527 0.6696757863217793
+ 0.3948234749402669 0.6749854055056804
+ 0.4032239744070811 0.6802748211471330
+ 0.4116244738738953 0.6855392300149010
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+# Vna:__________________________
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diff --git a/graphene/siesta/SG15v1.2/ref/C.ion.nc b/graphene/siesta/SG15v1.2/ref/C.ion.nc
new file mode 100644
index 0000000..27d33f5
Binary files /dev/null and b/graphene/siesta/SG15v1.2/ref/C.ion.nc differ
diff --git a/graphene/siesta/SG15v1.2/ref/C.ion.xml b/graphene/siesta/SG15v1.2/ref/C.ion.xml
new file mode 100644
index 0000000..5fa3b21
--- /dev/null
+++ b/graphene/siesta/SG15v1.2/ref/C.ion.xml
@@ -0,0 +1,6211 @@
+
+ C
+
+ 6
+ 4.00000000000
+ 12.0100000000
+ 33.5129345078
+ 2
+ 5
+ 1
+ 4
+ false
+
+
+
+===============================================================================
+C Z= 6 Mass= 12.010 Charge= 0.17977+309
+Lmxo=2 Lmxkb= 1 BasisType=split Semic=F
+L=0 Nsemic=0 Cnfigmx=2
+ i=1 nzeta=2 polorb=0 (2s)
+ splnorm: 0.15000
+ vcte: 0.0000
+ rinn: 0.0000
+ qcoe: 0.0000
+ qyuk: 0.0000
+ qwid: 0.10000E-01
+ rcs: 4.1918 3.4319
+ lambdas: 1.0000 1.0000
+L=1 Nsemic=0 Cnfigmx=2
+ i=1 nzeta=2 polorb=1 (2p) (to be polarized perturbatively)
+ splnorm: 0.15000
+ vcte: 0.0000
+ rinn: 0.0000
+ qcoe: 0.0000
+ qyuk: 0.0000
+ qwid: 0.10000E-01
+ rcs: 4.8703 3.4751
+ lambdas: 1.0000 1.0000
+L=2 Nsemic=0 Cnfigmx=3
+ i=1 nzeta=0 polorb=0 (3d) (perturbative polarization orbital) (from 2p)
+-------------------------------------------------------------------------------
+L=0 Nkbl=1 erefs: 0.17977+309
+L=1 Nkbl=1 erefs: 0.17977+309
+===============================================================================
+
+
+
+ C ca nrl nc
+ ONCVPSP-3.2023-07-03Hamann's oncvpsp
+ 2s 2.00 r= 1.42/2p 2.00 r= 1.41/ 2s:2p:
+
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diff --git a/graphene/siesta/SG15v1.2/ref/C_LDA_SR.psml b/graphene/siesta/SG15v1.2/ref/C_LDA_SR.psml
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diff --git a/graphene/siesta/SG15v1.2/ref/FORCE_STRESS b/graphene/siesta/SG15v1.2/ref/FORCE_STRESS
new file mode 100644
index 0000000..db49871
--- /dev/null
+++ b/graphene/siesta/SG15v1.2/ref/FORCE_STRESS
@@ -0,0 +1,7 @@
+ -22.8144794829
+ -0.000015330 -0.000000000 0.000000000
+ -0.000000000 -0.000015330 -0.000000000
+ 0.000000000 -0.000000000 0.000000390
+ 2
+ 1 6 -0.000000019 -0.000000003 0.000007146 C
+ 1 6 0.000000020 -0.000000003 0.000007148 C
diff --git a/graphene/siesta/SG15v1.2/ref/INPUT_TMP.00246 b/graphene/siesta/SG15v1.2/ref/INPUT_TMP.00246
new file mode 100644
index 0000000..d8f095c
--- /dev/null
+++ b/graphene/siesta/SG15v1.2/ref/INPUT_TMP.00246
@@ -0,0 +1,104 @@
+# SIESTA INPUT #
+SystemLabel graphene
+%include ./struct.fdf
+%include ./block-PAO.basis
+XC.functional LDA
+XC.authors PZ
+MeshCutoff 160.0 Ry
+OccupationFunction MP
+OccupationMPOrder 1
+ElectronicTemperature 0.001 eV
+%block kgrid_Monkhorst_Pack
+ 6 0 0 0.0
+ 0 6 0 0.0
+ 0 0 1 0.0
+%endblock kgrid_Monkhorst_Pack
+SolutionMethod diagon
+Diag.ParallelOverK T
+# Diag.Algorithm ELPA
+SolutionMethod ELSI
+ELSI.Solver ELPA
+#NumberOfEigenStates 4200
+DM.UseSaveDM F
+MD.UseSaveXV T
+MD.Steps 0
+MD.TypeOfRun Broyden
+MD.MaxForceTol 0.01 eV/Ang
+MD.VariableCell F
+MaxSCFIterations 1000
+SCF.DM.Converge T
+SCF.DM.Tolerance 1.0d-8
+SCF.MustConverge T
+SCF.Mix Hamiltonian
+SCF.Mixer.Method Pulay
+SCF.Mixer.Variant original
+SCF.Mixer.Weight 0.30
+SCF.Mixer.History 10
+Write.DM T
+Write.H F
+WriteMullikenPop 1
+WriteEigenvalues T
+WriteCoorInitial T
+WriteCoorStep T
+WriteForces T
+XML.Write T
+SaveHS F
+SaveRho T
+SaveDeltaRho F
+SaveRhoXC T
+SaveElectrostaticPotential T
+SaveNeutralAtomPotential F
+SaveTotalPotential T
+SaveIonicCharge F
+SaveBaderCharge F
+SaveTotalCharge F
+CDF.Save T
+CDF.Grid.Precision double
+##################
+# Band Structure #
+##################
+BandLinesScale ReciprocalLatticeVectors
+%block BandLines
+1 0.0000000 0.00000000 0.000 \Gamma
+30 0.3333333 0.66666666 0.000 K
+15 0.5000000 0.50000000 0.000 M
+26 0.0000000 0.00000000 0.000 \Gamma
+%endblock bandlinek
+#WFS.Write.For.Bands T
+#WFS.Band.Min 400
+#WFS.Band.Max 500
+#%block BandLines
+#1 0.0000000 0.00000000 0.000 \Gamma
+#60 7.0000000 -2.33333333 0.000 K
+#60 3.5000000 -3.50000000 0.000 M
+#60 0.0000000 0.00000000 0.000 \Gamma
+#%endblock BandLines
+################
+# Wavefunction #
+#################
+# WriteWaveFunctions F
+# WaveFuncKPointsScale ReciprocalLatticeVectors
+# %block WaveFuncKPoints
+# 0.000 0.000 0.000 from 1 to 10 # Gamma wavefuncs 1 to 10
+# 2.000 0.000 0.000 1 3 5 # X wavefuncs 1,3 and 5
+# 1.500 1.500 1.500 # K wavefuncs, all
+# %endblock WaveFuncKPoints
+########
+# PDOS #
+########
+# %block ProjectedDensityOfStates
+# -10.00 0.00 0.050 500 eV
+# %endblock ProjectedDensityOfStates
+# %block PDOS.kgrid_Monkhorst_Pack
+# 3 0 0 0.0
+# 0 3 0 0.0
+# 0 0 1 0.0
+# %endblock PDOS.kgrid_Monkhorst_Pack
+# %include grimme.fdf
+# Slab.DipoleCorrection vacuum
+# %block Geometry.Charge
+# plane 0
+# delta
+# 0.0 0.0 2.5 Ang # An intersection point, in the plane
+# 0.0 0.0 1.0 # The normal vector to the plane
+# %endblock Geometry.Charge
diff --git a/graphene/siesta/SG15v1.2/ref/INPUT_TMP.36686 b/graphene/siesta/SG15v1.2/ref/INPUT_TMP.36686
new file mode 100644
index 0000000..f6cb9cd
--- /dev/null
+++ b/graphene/siesta/SG15v1.2/ref/INPUT_TMP.36686
@@ -0,0 +1,105 @@
+# SIESTA INPUT #
+SystemLabel graphene
+%include ./struct.fdf
+%include ./block-PAO.basis
+XC.functional LDA
+XC.authors PZ
+PAO.BasisSize DZP
+MeshCutoff 160.0 Ry
+OccupationFunction MP
+OccupationMPOrder 1
+ElectronicTemperature 0.001 eV
+%block kgrid_Monkhorst_Pack
+ 6 0 0 0.0
+ 0 6 0 0.0
+ 0 0 1 0.0
+%endblock kgrid_Monkhorst_Pack
+SolutionMethod diagon
+Diag.ParallelOverK T
+# Diag.Algorithm ELPA
+SolutionMethod ELSI
+ELSI.Solver ELPA
+#NumberOfEigenStates 4200
+DM.UseSaveDM F
+MD.UseSaveXV T
+MD.Steps 0
+MD.TypeOfRun Broyden
+MD.MaxForceTol 0.01 eV/Ang
+MD.VariableCell F
+MaxSCFIterations 1000
+SCF.DM.Converge T
+SCF.DM.Tolerance 1.0d-8
+SCF.MustConverge T
+SCF.Mix Hamiltonian
+SCF.Mixer.Method Pulay
+SCF.Mixer.Variant original
+SCF.Mixer.Weight 0.30
+SCF.Mixer.History 10
+Write.DM T
+Write.H F
+WriteMullikenPop 1
+WriteEigenvalues T
+WriteCoorInitial T
+WriteCoorStep T
+WriteForces T
+XML.Write T
+SaveHS F
+SaveRho T
+SaveDeltaRho F
+SaveRhoXC T
+SaveElectrostaticPotential T
+SaveNeutralAtomPotential F
+SaveTotalPotential T
+SaveIonicCharge F
+SaveBaderCharge F
+SaveTotalCharge F
+CDF.Save T
+CDF.Grid.Precision double
+##################
+# Band Structure #
+##################
+BandLinesScale ReciprocalLatticeVectors
+%block BandLines
+1 0.0000000 0.00000000 0.000 \Gamma
+30 0.3333333 0.66666666 0.000 K
+15 0.5000000 0.50000000 0.000 M
+26 0.0000000 0.00000000 0.000 \Gamma
+%endblock bandlinek
+#WFS.Write.For.Bands T
+#WFS.Band.Min 400
+#WFS.Band.Max 500
+#%block BandLines
+#1 0.0000000 0.00000000 0.000 \Gamma
+#60 7.0000000 -2.33333333 0.000 K
+#60 3.5000000 -3.50000000 0.000 M
+#60 0.0000000 0.00000000 0.000 \Gamma
+#%endblock BandLines
+################
+# Wavefunction #
+#################
+# WriteWaveFunctions F
+# WaveFuncKPointsScale ReciprocalLatticeVectors
+# %block WaveFuncKPoints
+# 0.000 0.000 0.000 from 1 to 10 # Gamma wavefuncs 1 to 10
+# 2.000 0.000 0.000 1 3 5 # X wavefuncs 1,3 and 5
+# 1.500 1.500 1.500 # K wavefuncs, all
+# %endblock WaveFuncKPoints
+########
+# PDOS #
+########
+# %block ProjectedDensityOfStates
+# -10.00 0.00 0.050 500 eV
+# %endblock ProjectedDensityOfStates
+# %block PDOS.kgrid_Monkhorst_Pack
+# 3 0 0 0.0
+# 0 3 0 0.0
+# 0 0 1 0.0
+# %endblock PDOS.kgrid_Monkhorst_Pack
+# %include grimme.fdf
+# Slab.DipoleCorrection vacuum
+# %block Geometry.Charge
+# plane 0
+# delta
+# 0.0 0.0 2.5 Ang # An intersection point, in the plane
+# 0.0 0.0 1.0 # The normal vector to the plane
+# %endblock Geometry.Charge
diff --git a/graphene/siesta/SG15v1.2/ref/INPUT_TMP.67819 b/graphene/siesta/SG15v1.2/ref/INPUT_TMP.67819
new file mode 100644
index 0000000..f6cb9cd
--- /dev/null
+++ b/graphene/siesta/SG15v1.2/ref/INPUT_TMP.67819
@@ -0,0 +1,105 @@
+# SIESTA INPUT #
+SystemLabel graphene
+%include ./struct.fdf
+%include ./block-PAO.basis
+XC.functional LDA
+XC.authors PZ
+PAO.BasisSize DZP
+MeshCutoff 160.0 Ry
+OccupationFunction MP
+OccupationMPOrder 1
+ElectronicTemperature 0.001 eV
+%block kgrid_Monkhorst_Pack
+ 6 0 0 0.0
+ 0 6 0 0.0
+ 0 0 1 0.0
+%endblock kgrid_Monkhorst_Pack
+SolutionMethod diagon
+Diag.ParallelOverK T
+# Diag.Algorithm ELPA
+SolutionMethod ELSI
+ELSI.Solver ELPA
+#NumberOfEigenStates 4200
+DM.UseSaveDM F
+MD.UseSaveXV T
+MD.Steps 0
+MD.TypeOfRun Broyden
+MD.MaxForceTol 0.01 eV/Ang
+MD.VariableCell F
+MaxSCFIterations 1000
+SCF.DM.Converge T
+SCF.DM.Tolerance 1.0d-8
+SCF.MustConverge T
+SCF.Mix Hamiltonian
+SCF.Mixer.Method Pulay
+SCF.Mixer.Variant original
+SCF.Mixer.Weight 0.30
+SCF.Mixer.History 10
+Write.DM T
+Write.H F
+WriteMullikenPop 1
+WriteEigenvalues T
+WriteCoorInitial T
+WriteCoorStep T
+WriteForces T
+XML.Write T
+SaveHS F
+SaveRho T
+SaveDeltaRho F
+SaveRhoXC T
+SaveElectrostaticPotential T
+SaveNeutralAtomPotential F
+SaveTotalPotential T
+SaveIonicCharge F
+SaveBaderCharge F
+SaveTotalCharge F
+CDF.Save T
+CDF.Grid.Precision double
+##################
+# Band Structure #
+##################
+BandLinesScale ReciprocalLatticeVectors
+%block BandLines
+1 0.0000000 0.00000000 0.000 \Gamma
+30 0.3333333 0.66666666 0.000 K
+15 0.5000000 0.50000000 0.000 M
+26 0.0000000 0.00000000 0.000 \Gamma
+%endblock bandlinek
+#WFS.Write.For.Bands T
+#WFS.Band.Min 400
+#WFS.Band.Max 500
+#%block BandLines
+#1 0.0000000 0.00000000 0.000 \Gamma
+#60 7.0000000 -2.33333333 0.000 K
+#60 3.5000000 -3.50000000 0.000 M
+#60 0.0000000 0.00000000 0.000 \Gamma
+#%endblock BandLines
+################
+# Wavefunction #
+#################
+# WriteWaveFunctions F
+# WaveFuncKPointsScale ReciprocalLatticeVectors
+# %block WaveFuncKPoints
+# 0.000 0.000 0.000 from 1 to 10 # Gamma wavefuncs 1 to 10
+# 2.000 0.000 0.000 1 3 5 # X wavefuncs 1,3 and 5
+# 1.500 1.500 1.500 # K wavefuncs, all
+# %endblock WaveFuncKPoints
+########
+# PDOS #
+########
+# %block ProjectedDensityOfStates
+# -10.00 0.00 0.050 500 eV
+# %endblock ProjectedDensityOfStates
+# %block PDOS.kgrid_Monkhorst_Pack
+# 3 0 0 0.0
+# 0 3 0 0.0
+# 0 0 1 0.0
+# %endblock PDOS.kgrid_Monkhorst_Pack
+# %include grimme.fdf
+# Slab.DipoleCorrection vacuum
+# %block Geometry.Charge
+# plane 0
+# delta
+# 0.0 0.0 2.5 Ang # An intersection point, in the plane
+# 0.0 0.0 1.0 # The normal vector to the plane
+# %endblock Geometry.Charge
diff --git a/graphene/siesta/SG15v1.2/ref/INPUT_TMP.74396 b/graphene/siesta/SG15v1.2/ref/INPUT_TMP.74396
new file mode 100644
index 0000000..f6cb9cd
--- /dev/null
+++ b/graphene/siesta/SG15v1.2/ref/INPUT_TMP.74396
@@ -0,0 +1,105 @@
+# SIESTA INPUT #
+SystemLabel graphene
+%include ./struct.fdf
+%include ./block-PAO.basis
+XC.functional LDA
+XC.authors PZ
+PAO.BasisSize DZP
+MeshCutoff 160.0 Ry
+OccupationFunction MP
+OccupationMPOrder 1
+ElectronicTemperature 0.001 eV
+%block kgrid_Monkhorst_Pack
+ 6 0 0 0.0
+ 0 6 0 0.0
+ 0 0 1 0.0
+%endblock kgrid_Monkhorst_Pack
+SolutionMethod diagon
+Diag.ParallelOverK T
+# Diag.Algorithm ELPA
+SolutionMethod ELSI
+ELSI.Solver ELPA
+#NumberOfEigenStates 4200
+DM.UseSaveDM F
+MD.UseSaveXV T
+MD.Steps 0
+MD.TypeOfRun Broyden
+MD.MaxForceTol 0.01 eV/Ang
+MD.VariableCell F
+MaxSCFIterations 1000
+SCF.DM.Converge T
+SCF.DM.Tolerance 1.0d-8
+SCF.MustConverge T
+SCF.Mix Hamiltonian
+SCF.Mixer.Method Pulay
+SCF.Mixer.Variant original
+SCF.Mixer.Weight 0.30
+SCF.Mixer.History 10
+Write.DM T
+Write.H F
+WriteMullikenPop 1
+WriteEigenvalues T
+WriteCoorInitial T
+WriteCoorStep T
+WriteForces T
+XML.Write T
+SaveHS F
+SaveRho T
+SaveDeltaRho F
+SaveRhoXC T
+SaveElectrostaticPotential T
+SaveNeutralAtomPotential F
+SaveTotalPotential T
+SaveIonicCharge F
+SaveBaderCharge F
+SaveTotalCharge F
+CDF.Save T
+CDF.Grid.Precision double
+##################
+# Band Structure #
+##################
+BandLinesScale ReciprocalLatticeVectors
+%block BandLines
+1 0.0000000 0.00000000 0.000 \Gamma
+30 0.3333333 0.66666666 0.000 K
+15 0.5000000 0.50000000 0.000 M
+26 0.0000000 0.00000000 0.000 \Gamma
+%endblock bandlinek
+#WFS.Write.For.Bands T
+#WFS.Band.Min 400
+#WFS.Band.Max 500
+#%block BandLines
+#1 0.0000000 0.00000000 0.000 \Gamma
+#60 7.0000000 -2.33333333 0.000 K
+#60 3.5000000 -3.50000000 0.000 M
+#60 0.0000000 0.00000000 0.000 \Gamma
+#%endblock BandLines
+################
+# Wavefunction #
+#################
+# WriteWaveFunctions F
+# WaveFuncKPointsScale ReciprocalLatticeVectors
+# %block WaveFuncKPoints
+# 0.000 0.000 0.000 from 1 to 10 # Gamma wavefuncs 1 to 10
+# 2.000 0.000 0.000 1 3 5 # X wavefuncs 1,3 and 5
+# 1.500 1.500 1.500 # K wavefuncs, all
+# %endblock WaveFuncKPoints
+########
+# PDOS #
+########
+# %block ProjectedDensityOfStates
+# -10.00 0.00 0.050 500 eV
+# %endblock ProjectedDensityOfStates
+# %block PDOS.kgrid_Monkhorst_Pack
+# 3 0 0 0.0
+# 0 3 0 0.0
+# 0 0 1 0.0
+# %endblock PDOS.kgrid_Monkhorst_Pack
+# %include grimme.fdf
+# Slab.DipoleCorrection vacuum
+# %block Geometry.Charge
+# plane 0
+# delta
+# 0.0 0.0 2.5 Ang # An intersection point, in the plane
+# 0.0 0.0 1.0 # The normal vector to the plane
+# %endblock Geometry.Charge
diff --git a/graphene/siesta/SG15v1.2/ref/INPUT_TMP.84495 b/graphene/siesta/SG15v1.2/ref/INPUT_TMP.84495
new file mode 100644
index 0000000..d8f095c
--- /dev/null
+++ b/graphene/siesta/SG15v1.2/ref/INPUT_TMP.84495
@@ -0,0 +1,104 @@
+# SIESTA INPUT #
+SystemLabel graphene
+%include ./struct.fdf
+%include ./block-PAO.basis
+XC.functional LDA
+XC.authors PZ
+MeshCutoff 160.0 Ry
+OccupationFunction MP
+OccupationMPOrder 1
+ElectronicTemperature 0.001 eV
+%block kgrid_Monkhorst_Pack
+ 6 0 0 0.0
+ 0 6 0 0.0
+ 0 0 1 0.0
+%endblock kgrid_Monkhorst_Pack
+SolutionMethod diagon
+Diag.ParallelOverK T
+# Diag.Algorithm ELPA
+SolutionMethod ELSI
+ELSI.Solver ELPA
+#NumberOfEigenStates 4200
+DM.UseSaveDM F
+MD.UseSaveXV T
+MD.Steps 0
+MD.TypeOfRun Broyden
+MD.MaxForceTol 0.01 eV/Ang
+MD.VariableCell F
+MaxSCFIterations 1000
+SCF.DM.Converge T
+SCF.DM.Tolerance 1.0d-8
+SCF.MustConverge T
+SCF.Mix Hamiltonian
+SCF.Mixer.Method Pulay
+SCF.Mixer.Variant original
+SCF.Mixer.Weight 0.30
+SCF.Mixer.History 10
+Write.DM T
+Write.H F
+WriteMullikenPop 1
+WriteEigenvalues T
+WriteCoorInitial T
+WriteCoorStep T
+WriteForces T
+XML.Write T
+SaveHS F
+SaveRho T
+SaveDeltaRho F
+SaveRhoXC T
+SaveElectrostaticPotential T
+SaveNeutralAtomPotential F
+SaveTotalPotential T
+SaveIonicCharge F
+SaveBaderCharge F
+SaveTotalCharge F
+CDF.Save T
+CDF.Grid.Precision double
+##################
+# Band Structure #
+##################
+BandLinesScale ReciprocalLatticeVectors
+%block BandLines
+1 0.0000000 0.00000000 0.000 \Gamma
+30 0.3333333 0.66666666 0.000 K
+15 0.5000000 0.50000000 0.000 M
+26 0.0000000 0.00000000 0.000 \Gamma
+%endblock bandlinek
+#WFS.Write.For.Bands T
+#WFS.Band.Min 400
+#WFS.Band.Max 500
+#%block BandLines
+#1 0.0000000 0.00000000 0.000 \Gamma
+#60 7.0000000 -2.33333333 0.000 K
+#60 3.5000000 -3.50000000 0.000 M
+#60 0.0000000 0.00000000 0.000 \Gamma
+#%endblock BandLines
+################
+# Wavefunction #
+#################
+# WriteWaveFunctions F
+# WaveFuncKPointsScale ReciprocalLatticeVectors
+# %block WaveFuncKPoints
+# 0.000 0.000 0.000 from 1 to 10 # Gamma wavefuncs 1 to 10
+# 2.000 0.000 0.000 1 3 5 # X wavefuncs 1,3 and 5
+# 1.500 1.500 1.500 # K wavefuncs, all
+# %endblock WaveFuncKPoints
+########
+# PDOS #
+########
+# %block ProjectedDensityOfStates
+# -10.00 0.00 0.050 500 eV
+# %endblock ProjectedDensityOfStates
+# %block PDOS.kgrid_Monkhorst_Pack
+# 3 0 0 0.0
+# 0 3 0 0.0
+# 0 0 1 0.0
+# %endblock PDOS.kgrid_Monkhorst_Pack
+# %include grimme.fdf
+# Slab.DipoleCorrection vacuum
+# %block Geometry.Charge
+# plane 0
+# delta
+# 0.0 0.0 2.5 Ang # An intersection point, in the plane
+# 0.0 0.0 1.0 # The normal vector to the plane
+# %endblock Geometry.Charge
diff --git a/graphene/siesta/SG15v1.2/ref/MESSAGES b/graphene/siesta/SG15v1.2/ref/MESSAGES
new file mode 100644
index 0000000..24f2571
--- /dev/null
+++ b/graphene/siesta/SG15v1.2/ref/MESSAGES
@@ -0,0 +1 @@
+INFO: Job completed
diff --git a/graphene/siesta/SG15v1.2/ref/NON_TRIMMED_KP_LIST b/graphene/siesta/SG15v1.2/ref/NON_TRIMMED_KP_LIST
new file mode 100644
index 0000000..c15e75b
--- /dev/null
+++ b/graphene/siesta/SG15v1.2/ref/NON_TRIMMED_KP_LIST
@@ -0,0 +1,25 @@
+ 24
+ 1 -0.450531 0.260114 0.000000 0.027778
+ 2 -0.225265 0.130057 0.000000 0.027778
+ 3 0.000000 0.000000 0.000000 0.027778
+ 4 0.225265 -0.130057 0.000000 0.027778
+ 5 0.450531 -0.260114 0.000000 0.027778
+ 6 0.675796 -0.390171 0.000000 0.027778
+ 7 -0.450531 0.520228 0.000000 0.055556
+ 8 -0.225265 0.390171 0.000000 0.055556
+ 9 0.000000 0.260114 0.000000 0.055556
+ 10 0.225265 0.130057 0.000000 0.055556
+ 11 0.450531 -0.000000 0.000000 0.055556
+ 12 0.675796 -0.130057 0.000000 0.055556
+ 13 -0.450531 0.780342 0.000000 0.055556
+ 14 -0.225265 0.650285 0.000000 0.055556
+ 15 0.000000 0.520228 0.000000 0.055556
+ 16 0.225265 0.390171 0.000000 0.055556
+ 17 0.450531 0.260114 0.000000 0.055556
+ 18 0.675796 0.130057 0.000000 0.055556
+ 19 -0.450531 1.040456 0.000000 0.027778
+ 20 -0.225265 0.910399 0.000000 0.027778
+ 21 0.000000 0.780342 0.000000 0.027778
+ 22 0.225265 0.650285 0.000000 0.027778
+ 23 0.450531 0.520228 0.000000 0.027778
+ 24 0.675796 0.390171 0.000000 0.027778
diff --git a/graphene/siesta/SG15v1.2/ref/OUTVARS.yml b/graphene/siesta/SG15v1.2/ref/OUTVARS.yml
new file mode 100644
index 0000000..1fcecd7
--- /dev/null
+++ b/graphene/siesta/SG15v1.2/ref/OUTVARS.yml
@@ -0,0 +1,44 @@
+%YAML 1.2
+---
+
+siesta:
+ version: "MaX-1.0-55-g0612142bc"
+ arch: "----"
+ compiler: "GNU-10.3.0"
+ fflags: "-O3 -funroll-loops -funsafe-math-optimizations -fallow-argument-mismatch -fallow-argument-mismatch;"
+ fppflags: "----"
+ libs: "----"
+ build: "mpi"
+ openmp: "no"
+ gemm3m: "no"
+ netcdf: "yes"
+ netcdf4: "yes"
+ netcdf4_mpi: "no"
+ metis: "no"
+ chess: "no"
+ elpa: "no"
+ flook: "no"
+ pexsi: "no"
+
+energies:
+ Ebs: -0.78014485E+01
+ Eions: 0.67025869E+02
+ Ena: 0.33885912E+02
+ Ekin: 0.16601925E+02
+ Enl: 0.11435583E+01
+ Eso: 0.00000000E+00
+ Edftu: 0.00000000E+00
+ DEna: -0.51057615E+00
+ DUscf: 0.34481362E-01
+ DUext: 0.00000000E+00
+ Exc: -0.69504459E+01
+ Ecorrec: 0.00000000E+00
+ Emadel: 0.00000000E+00
+ Emeta: 0.00000000E+00
+ Emolmec: 0.00000000E+00
+ Ekinion: 0.00000000E+00
+ Eharris: -0.22821014E+02
+ Etot: -0.22821014E+02
+ FreeEng: -0.22821016E+02
+
+...
diff --git a/graphene/siesta/SG15v1.2/ref/PARALLEL_DIST b/graphene/siesta/SG15v1.2/ref/PARALLEL_DIST
new file mode 100644
index 0000000..705f5e8
--- /dev/null
+++ b/graphene/siesta/SG15v1.2/ref/PARALLEL_DIST
@@ -0,0 +1,16 @@
+ Node 0 handles 2 orbitals.
+ Node 1 handles 2 orbitals.
+ Node 2 handles 2 orbitals.
+ Node 3 handles 2 orbitals.
+ Node 4 handles 2 orbitals.
+ Node 5 handles 2 orbitals.
+ Node 6 handles 2 orbitals.
+ Node 7 handles 2 orbitals.
+ Node 8 handles 2 orbitals.
+ Node 9 handles 2 orbitals.
+ Node 10 handles 1 orbitals.
+ Node 11 handles 1 orbitals.
+ Node 12 handles 1 orbitals.
+ Node 13 handles 1 orbitals.
+ Node 14 handles 1 orbitals.
+ Node 15 handles 1 orbitals.
diff --git a/graphene/siesta/SG15v1.2/ref/TIMES b/graphene/siesta/SG15v1.2/ref/TIMES
new file mode 100644
index 0000000..bf62099
--- /dev/null
+++ b/graphene/siesta/SG15v1.2/ref/TIMES
@@ -0,0 +1,88 @@
+
+timer: Number of nodes = 16
+timer: Busiest calculating node was node = 7
+timer: Times refer to node = 7
+timer: Total elapsed wall-clock time (sec) = 1.805
+timer: CPU times (sec):
+Calc: Sum, Avge, myNode, Avg/Max = 28.678 1.792 1.800 0.996
+Comm: Sum, Avge, myNode, Avg/Max = 0.000 0.000 0.000 NaN
+Tot: Sum, Avge, myNode, Avg/Max = 28.678 1.792 1.800 0.996
+Program times printed if > 0.000E+00 of total
+
+Program Calls Prg.com Prg.com Prg.tot Prg.tot Nod.avg
+ /Tot.com /Tot.tot/Nod.max
+siesta 1 0.000 0.0000 1.800 1.0000 0.996
+Setup 1 0.000 0.0000 0.063 0.0348 0.987
+bands 3 0.000 0.0000 0.258 0.1431 1.000
+KSV_init 1 0.000 0.0000 0.000 0.0000 0.866
+IterGeom 1 0.000 0.0000 1.446 0.8032 0.995
+geom_init 1 0.000 0.0000 0.132 0.0735 0.995
+state_init 1 0.000 0.0000 0.081 0.0451 0.996
+hsparse 1 0.000 0.0000 0.000 0.0001 0.885
+overlap 1 0.000 0.0000 0.000 0.0002 0.640
+CDF 60 0.000 0.0000 0.009 0.0049 0.091
+Setup_H0 1 0.000 0.0000 0.038 0.0211 0.994
+naefs 2 0.000 0.0000 0.002 0.0013 0.930
+dnaefs 1 0.000 0.0000 0.000 0.0000 0.983
+two-body 1 0.000 0.0000 0.000 0.0000 0.751
+MolMec 2 0.000 0.0000 0.000 0.0000 0.865
+kinefsm 2 0.000 0.0000 0.000 0.0003 0.602
+nlefsm 2 0.000 0.0000 0.007 0.0039 0.834
+DHSCF_Init 1 0.000 0.0000 0.032 0.0177 0.965
+DHSCF1 1 0.000 0.0000 0.005 0.0030 0.616
+InitMesh 1 0.000 0.0000 0.005 0.0029 0.955
+INITMESH 3 0.000 0.0000 0.006 0.0034 0.763
+DHSCF2 1 0.000 0.0000 0.026 0.0146 0.949
+REMESH 1 0.000 0.0000 0.008 0.0047 0.856
+BuildDISTR 2 0.000 0.0000 0.006 0.0034 0.762
+meshCom-Ca 3 0.000 0.0000 0.000 0.0000 0.709
+REORD 5 0.000 0.0000 0.000 0.0000 0.852
+PHION 1 0.000 0.0000 0.006 0.0034 0.648
+dscfComm 1 0.000 0.0000 0.005 0.0029 0.739
+COMM_BSC 250 0.000 0.0000 0.103 0.0573 0.670
+POISON 63 0.000 0.0000 0.073 0.0406 0.946
+fft 126 0.000 0.0000 0.070 0.0390 0.946
+setup_H 60 0.000 0.0000 0.496 0.2754 1.000
+DHSCF 62 0.000 0.0000 0.542 0.3008 0.991
+DHSCF3 62 0.000 0.0000 0.533 0.2962 0.999
+rhoofd 62 0.000 0.0000 0.188 0.1042 0.772
+OtoM 63 0.000 0.0000 0.022 0.0121 0.865
+XC 62 0.000 0.0000 0.041 0.0226 0.793
+GXC-CellXC 62 0.000 0.0000 0.022 0.0123 0.868
+gridxc@cellXC 62 0.000 0.0000 0.022 0.0122 0.867
+vmat 61 0.000 0.0000 0.125 0.0694 0.906
+MtoO 61 0.000 0.0000 0.038 0.0211 0.583
+IterSCF 59 0.000 0.0000 0.960 0.5331 0.807
+compute_dm 59 0.000 0.0000 0.451 0.2507 1.000
+diagon 59 0.000 0.0000 0.449 0.2495 0.999
+cdiag 190 0.000 0.0000 0.268 0.1491 0.966
+cdiag1 190 0.000 0.0000 0.025 0.0139 0.955
+cdiag2 190 0.000 0.0000 0.054 0.0301 0.967
+cdiag3 190 0.000 0.0000 0.182 0.1012 0.966
+cdiag4 59 0.000 0.0000 0.000 0.0001 0.662
+MIXER 58 0.000 0.0000 0.010 0.0054 0.958
+PostSCF 1 0.000 0.0000 0.026 0.0144 0.901
+FINAL_HF 1 0.000 0.0000 0.026 0.0144 0.902
+DHSCF4 1 0.000 0.0000 0.008 0.0046 0.678
+dfscf 1 0.000 0.0000 0.006 0.0034 0.619
+overfsm 1 0.000 0.0000 0.000 0.0001 0.592
+state_analysis 1 0.000 0.0000 0.000 0.0001 0.173
+siesta_move 1 0.000 0.0000 0.000 0.0000 0.612
+Analysis 1 0.000 0.0000 0.289 0.1606 0.997
+c-eigval 72 0.000 0.0000 0.255 0.1417 1.000
+c-buildHS 72 0.000 0.0000 0.001 0.0008 0.767
+optical 1 0.000 0.0000 0.000 0.0000 0.873
+CDF-grid 4 0.000 0.0000 0.014 0.0079 0.745
+MPI total 0 0.000 1.0000 0.000 0.0000
+
+Definitions:
+Program: Name of a time-profiled routine (or code section)
+Calls: Number of profiled calls to a program
+Prg.com: CPU time in communications in one program in one node
+Tot.com: CPU time in communications in all progs. in one node
+Prg.tot: total CPU time in one program in one node
+Tot.tot: total CPU time in all programs in one node
+Nod.avg: average calculation time in one program across nodes
+Nod.max: maximum calculation time in one program across nodes
+Calculation time: CPU time excluding communications
+
diff --git a/graphene/siesta/SG15v1.2/ref/bands.png b/graphene/siesta/SG15v1.2/ref/bands.png
new file mode 100644
index 0000000..65e5ad2
Binary files /dev/null and b/graphene/siesta/SG15v1.2/ref/bands.png differ
diff --git a/graphene/siesta/SG15v1.2/ref/block-PAO.basis b/graphene/siesta/SG15v1.2/ref/block-PAO.basis
new file mode 100644
index 0000000..19a3448
--- /dev/null
+++ b/graphene/siesta/SG15v1.2/ref/block-PAO.basis
@@ -0,0 +1,17 @@
+PAO.BasisSize DZP
+
+#%block PAO.basis # define basis set
+#C 4 # We include 3 shells
+# n=2 0 2 # 2s orbitals (double zeta)
+# 0.000 0.000
+# 1.000 1.000
+# n=2 1 2 P # 2p orbitals (double zeta) + polarization (single zeta)
+# 0.000 0.000
+# 1.000 1.000
+# n=3 0 1 # 3s diffuse orbitals (single zeta)
+# 10.000
+# 1.000
+# n=3 1 1 # 3s diffuse orbitals (single zeta)
+# 12.000
+# 1.000
+#%endblock PAO.Basis
diff --git a/graphene/siesta/SG15v1.2/ref/fdf.20230703T191159.308.log b/graphene/siesta/SG15v1.2/ref/fdf.20230703T191159.308.log
new file mode 100644
index 0000000..95d885f
--- /dev/null
+++ b/graphene/siesta/SG15v1.2/ref/fdf.20230703T191159.308.log
@@ -0,0 +1,56 @@
+SystemName # default value
+SystemLabel graphene
+SpinPolarized F # default value
+NonCollinearSpin F # default value
+SpinOrbit F # default value
+#:block? SpinPolarized F
+#:defined? SpinPolarized F
+#:block? NonCollinearSpin F
+#:defined? NonCollinearSpin F
+#:block? SpinOrbit F
+#:defined? SpinOrbit F
+Spin none # default value
+TimeReversalSymmetry T # default value
+DebugObjects.Node 0 # default value
+DebugObjects F # default value
+XML.Write T
+timer_report_threshold 0.000000000 # default value
+UseParallelTimer T # default value
+UseTreeTimer F # default value
+timing-split-scf-steps F # default value
+use-walltime F # default value
+alloc_report_level 0 # default value
+alloc_report_threshold 0.000000000 # default value
+xc.functional LDA
+xc.authors PZ
+#:block? XC.hybrid F
+#:defined? XC.hybrid F
+#:block? XC.cocktail F
+#:defined? XC.cocktail F
+MM.Cutoff 30.00000000 Bohr # default value
+MM.UnitsEnergy eV # default value
+MM.UnitsDistance Ang # default value
+Atom.Debug F # default value
+WriteIonPlotFiles F # default value
+Atom.Debug.KB.Generation F # default value
+KB.New.Reference.Orbitals F # default value
+user-basis F # default value
+user-basis-netcdf F # default value
+#:block? DFTU.proj F
+#:defined? DFTU.proj F
+#:block? LDAU.proj F
+#:defined? LDAU.proj F
+Number_of_species 1
+%block Chemical_species_label
+ 1 6 C
+%endblock Chemical_species_label
+ReparametrizePseudos F # default value
+Restricted.Radial.Grid T # default value
+Rmax.Radial.Grid 0.000000000 # default value
+PAO.BasisSize DZP
+PAO.BasisType split # default value
+PAO.SoftDefault F # default value
+PAO.SoftInnerRadius 0.9000000000 # default value
+PAO.SoftPotential 40.00000000 # default value
+PAO.SplitNorm 0.1500000000 # default value
+PAO.SplitNormH -1.000000000 # default value
diff --git a/graphene/siesta/SG15v1.2/ref/fdf.20230703T191308.175.log b/graphene/siesta/SG15v1.2/ref/fdf.20230703T191308.175.log
new file mode 100644
index 0000000..cf0b5fb
--- /dev/null
+++ b/graphene/siesta/SG15v1.2/ref/fdf.20230703T191308.175.log
@@ -0,0 +1,149 @@
+SystemName # default value
+SystemLabel graphene
+SpinPolarized F # default value
+NonCollinearSpin F # default value
+SpinOrbit F # default value
+#:block? SpinPolarized F
+#:defined? SpinPolarized F
+#:block? NonCollinearSpin F
+#:defined? NonCollinearSpin F
+#:block? SpinOrbit F
+#:defined? SpinOrbit F
+Spin none # default value
+TimeReversalSymmetry T # default value
+DebugObjects.Node 0 # default value
+DebugObjects F # default value
+XML.Write T
+timer_report_threshold 0.000000000 # default value
+UseParallelTimer T # default value
+UseTreeTimer F # default value
+timing-split-scf-steps F # default value
+use-walltime F # default value
+alloc_report_level 0 # default value
+alloc_report_threshold 0.000000000 # default value
+xc.functional LDA
+xc.authors PZ
+#:block? XC.hybrid F
+#:defined? XC.hybrid F
+#:block? XC.cocktail F
+#:defined? XC.cocktail F
+MM.Cutoff 30.00000000 Bohr # default value
+MM.UnitsEnergy eV # default value
+MM.UnitsDistance Ang # default value
+Atom.Debug F # default value
+WriteIonPlotFiles F # default value
+Atom.Debug.KB.Generation F # default value
+KB.New.Reference.Orbitals F # default value
+user-basis F # default value
+user-basis-netcdf F # default value
+#:block? DFTU.proj F
+#:defined? DFTU.proj F
+#:block? LDAU.proj F
+#:defined? LDAU.proj F
+Number_of_species 1
+%block Chemical_species_label
+ 1 6 C
+%endblock Chemical_species_label
+ReparametrizePseudos F # default value
+Restricted.Radial.Grid T # default value
+Rmax.Radial.Grid 0.000000000 # default value
+PAO.BasisSize DZP
+PAO.BasisType split # default value
+PAO.SoftDefault F # default value
+PAO.SoftInnerRadius 0.9000000000 # default value
+PAO.SoftPotential 40.00000000 # default value
+PAO.SplitNorm 0.1500000000 # default value
+PAO.SplitNormH -1.000000000 # default value
+PAO.Polarization.NonPerturbative F # default value
+PAO.NonPerturbative.Polarization.Orbitals F # default value
+PAO.Polarization.NonPerturbative.Fallback F # default value
+%block PAO.Basis
+ C 4 # We include 3 shells
+ n=2 0 2 # 2s orbitals (double zeta)
+ 0.000 0.000
+ 1.000 1.000
+ n=2 1 2 P # 2p orbitals (double zeta) + polarization (single zeta)
+ 0.000 0.000
+ 1.000 1.000
+ n=3 0 1 # 3s diffuse orbitals (single zeta)
+ 10.000
+ 1.000
+ n=3 1 1 # 3s diffuse orbitals (single zeta)
+ 12.000
+ 1.000
+%endblock PAO.Basis
+LDAU.ProjectorGenerationMethod 2 # default value
+DFTU.ProjectorGenerationMethod 2 # default value
+LDAU.EnergyShift 0.5000000000E-01 Ry # default value
+DFTU.EnergyShift 0.5000000000E-01 Ry # default value
+LDAU.CutoffNorm 0.9000000000 # default value
+DFTU.CutoffNorm 0.9000000000 # default value
+PAO.SoftDefault F # default value
+PAO.SoftInnerRadius 0.9000000000 # default value
+PAO.SoftPotential 40.00000000 # default value
+LDAU.ThresholdTol 0.1000000000E-01 # default value
+DFTU.ThresholdTol 0.1000000000E-01 # default value
+LDAU.PopTol 0.1000000000E-02 # default value
+DFTU.PopTol 0.1000000000E-02 # default value
+LDAU.PotentialShift F # default value
+DFTU.PotentialShift F # default value
+LDAU.FirstIteration F # default value
+DFTU.FirstIteration F # default value
+FilterCutoff 0.000000000 Ry # default value
+FilterTol 0.000000000 Ry # default value
+spin-orbit-strength 1.000000000 # default value
+Use.PSML.KB.Projectors T # default value
+Use.PSML.Vlocal T # default value
+PSML.KB.Projectors T # default value
+PSML.Vlocal T # default value
+psml.chlocal.build.r0 0.4000000000E-02 # default value
+psml.chlocal.build.delta 0.5000000000E-02 # default value
+psml.chlocal.build.poly_order_rlin 4 # default value
+chlocal-use-charge-cutoff-for-vlocal-fit F # default value
+psml.chlocal.build.rr1 0.1000000000E-02 # default value
+psml.chlocal.build.exp_al 1.012000000 # default value
+psml.chlocal.build.poly_order_rofi 7 # default value
+PAO.EnergyShift 0.2000000000E-01 Ry # default value
+PAO.SplitTailNorm F # default value
+PAO.FixSplitTable F # default value
+PAO.NewSplitCode F # default value
+PAO.Filter F # default value
+PAO.Filter F # default value
+PAO.Filter F # default value
+PAO.Filter F # default value
+PAO.Filter F # default value
+PAO.Filter F # default value
+PAO.OldStylePolorbs T # default value
+PAO.SplitTailNorm F # default value
+PAO.FixSplitTable F # default value
+PAO.NewSplitCode F # default value
+PAO.Filter F # default value
+Vna.Filter F # default value
+PAO.BasisType split # default value
+Debug.Elec.Corr F # default value
+Atom-Setup-Only F # default value
+UseStructFile F # default value
+MD.UseStructFile F # default value
+#:block? LatticeParameters F
+%block LatticeVectors
+LatticeConstant 4.648728119 Bohr
+# above item originally: LatticeConstant 2.460000000 Ang
+ 1.0000000000 0.0000000000 0.0000000000
+ 0.5000000000 0.8660254038 0.0000000000
+ 0.0000000000 0.0000000000 8.9430894309
+%endblock LatticeVectors
+AtomicCoordinatesFormat Fractional
+NumberOfAtoms 3
+#:block? AtomicCoordinatesOrigin F
+#:defined? AtomicCoordinatesOrigin F
+ZM.UnitsLength Bohr # default value
+ZM.UnitsAngle rad # default value
+ZM.ForceTolLength 0.1555740000E-02 Ry/Bohr # default value
+ZM.ForceTolAngle 0.3565490000E-02 Ry/rad # default value
+ZM.MaxDisplLength 0.2000000000 Bohr # default value
+ZM.MaxDisplAngle 0.3000000000E-02 rad # default value
+ZM.CalcAllForces F # default value
+%block AtomicCoordinatesAndAtomicSpecies
+ 0.3333333333 0.3333333333 0.1020678295 1
+ 0.6666666667 0.6666666667 0.1020678295 1
+%endblock AtomicCoordinatesAndAtomicSpecies
diff --git a/graphene/siesta/SG15v1.2/ref/fdf.20230703T191345.885.log b/graphene/siesta/SG15v1.2/ref/fdf.20230703T191345.885.log
new file mode 100644
index 0000000..d11852e
--- /dev/null
+++ b/graphene/siesta/SG15v1.2/ref/fdf.20230703T191345.885.log
@@ -0,0 +1,520 @@
+SystemName # default value
+SystemLabel graphene
+SpinPolarized F # default value
+NonCollinearSpin F # default value
+SpinOrbit F # default value
+#:block? SpinPolarized F
+#:defined? SpinPolarized F
+#:block? NonCollinearSpin F
+#:defined? NonCollinearSpin F
+#:block? SpinOrbit F
+#:defined? SpinOrbit F
+Spin none # default value
+TimeReversalSymmetry T # default value
+DebugObjects.Node 0 # default value
+DebugObjects F # default value
+XML.Write T
+timer_report_threshold 0.000000000 # default value
+UseParallelTimer T # default value
+UseTreeTimer F # default value
+timing-split-scf-steps F # default value
+use-walltime F # default value
+alloc_report_level 0 # default value
+alloc_report_threshold 0.000000000 # default value
+xc.functional LDA
+xc.authors PZ
+#:block? XC.hybrid F
+#:defined? XC.hybrid F
+#:block? XC.cocktail F
+#:defined? XC.cocktail F
+MM.Cutoff 30.00000000 Bohr # default value
+MM.UnitsEnergy eV # default value
+MM.UnitsDistance Ang # default value
+Atom.Debug F # default value
+WriteIonPlotFiles F # default value
+Atom.Debug.KB.Generation F # default value
+KB.New.Reference.Orbitals F # default value
+user-basis F # default value
+user-basis-netcdf F # default value
+#:block? DFTU.proj F
+#:defined? DFTU.proj F
+#:block? LDAU.proj F
+#:defined? LDAU.proj F
+Number_of_species 1
+%block Chemical_species_label
+ 1 6 C
+%endblock Chemical_species_label
+ReparametrizePseudos F # default value
+Restricted.Radial.Grid T # default value
+Rmax.Radial.Grid 0.000000000 # default value
+PAO.BasisSize DZP
+PAO.BasisType split # default value
+PAO.SoftDefault F # default value
+PAO.SoftInnerRadius 0.9000000000 # default value
+PAO.SoftPotential 40.00000000 # default value
+PAO.SplitNorm 0.1500000000 # default value
+PAO.SplitNormH -1.000000000 # default value
+PAO.Polarization.NonPerturbative F # default value
+PAO.NonPerturbative.Polarization.Orbitals F # default value
+PAO.Polarization.NonPerturbative.Fallback F # default value
+%block PAO.Basis
+ C 4 # We include 3 shells
+ n=2 0 2 # 2s orbitals (double zeta)
+ 0.000 0.000
+ 1.000 1.000
+ n=2 1 2 P # 2p orbitals (double zeta) + polarization (single zeta)
+ 0.000 0.000
+ 1.000 1.000
+ n=3 0 1 # 3s diffuse orbitals (single zeta)
+ 10.000
+ 1.000
+ n=3 1 1 # 3s diffuse orbitals (single zeta)
+ 12.000
+ 1.000
+%endblock PAO.Basis
+LDAU.ProjectorGenerationMethod 2 # default value
+DFTU.ProjectorGenerationMethod 2 # default value
+LDAU.EnergyShift 0.5000000000E-01 Ry # default value
+DFTU.EnergyShift 0.5000000000E-01 Ry # default value
+LDAU.CutoffNorm 0.9000000000 # default value
+DFTU.CutoffNorm 0.9000000000 # default value
+PAO.SoftDefault F # default value
+PAO.SoftInnerRadius 0.9000000000 # default value
+PAO.SoftPotential 40.00000000 # default value
+LDAU.ThresholdTol 0.1000000000E-01 # default value
+DFTU.ThresholdTol 0.1000000000E-01 # default value
+LDAU.PopTol 0.1000000000E-02 # default value
+DFTU.PopTol 0.1000000000E-02 # default value
+LDAU.PotentialShift F # default value
+DFTU.PotentialShift F # default value
+LDAU.FirstIteration F # default value
+DFTU.FirstIteration F # default value
+FilterCutoff 0.000000000 Ry # default value
+FilterTol 0.000000000 Ry # default value
+spin-orbit-strength 1.000000000 # default value
+Use.PSML.KB.Projectors T # default value
+Use.PSML.Vlocal T # default value
+PSML.KB.Projectors T # default value
+PSML.Vlocal T # default value
+psml.chlocal.build.r0 0.4000000000E-02 # default value
+psml.chlocal.build.delta 0.5000000000E-02 # default value
+psml.chlocal.build.poly_order_rlin 4 # default value
+chlocal-use-charge-cutoff-for-vlocal-fit F # default value
+psml.chlocal.build.rr1 0.1000000000E-02 # default value
+psml.chlocal.build.exp_al 1.012000000 # default value
+psml.chlocal.build.poly_order_rofi 7 # default value
+PAO.EnergyShift 0.2000000000E-01 Ry # default value
+PAO.SplitTailNorm F # default value
+PAO.FixSplitTable F # default value
+PAO.NewSplitCode F # default value
+PAO.Filter F # default value
+PAO.Filter F # default value
+PAO.Filter F # default value
+PAO.Filter F # default value
+PAO.Filter F # default value
+PAO.Filter F # default value
+PAO.OldStylePolorbs T # default value
+PAO.SplitTailNorm F # default value
+PAO.FixSplitTable F # default value
+PAO.NewSplitCode F # default value
+PAO.Filter F # default value
+Vna.Filter F # default value
+PAO.BasisType split # default value
+Debug.Elec.Corr F # default value
+Atom-Setup-Only F # default value
+UseStructFile F # default value
+MD.UseStructFile F # default value
+#:block? LatticeParameters F
+%block LatticeVectors
+LatticeConstant 4.648728119 Bohr
+# above item originally: LatticeConstant 2.460000000 Ang
+ 1.0000000000 0.0000000000 0.0000000000
+ 0.5000000000 0.8660254038 0.0000000000
+ 0.0000000000 0.0000000000 8.9430894309
+%endblock LatticeVectors
+AtomicCoordinatesFormat Fractional
+NumberOfAtoms 2
+#:block? AtomicCoordinatesOrigin F
+#:defined? AtomicCoordinatesOrigin F
+ZM.UnitsLength Bohr # default value
+ZM.UnitsAngle rad # default value
+ZM.ForceTolLength 0.1555740000E-02 Ry/Bohr # default value
+ZM.ForceTolAngle 0.3565490000E-02 Ry/rad # default value
+ZM.MaxDisplLength 0.2000000000 Bohr # default value
+ZM.MaxDisplAngle 0.3000000000E-02 rad # default value
+ZM.CalcAllForces F # default value
+%block AtomicCoordinatesAndAtomicSpecies
+ 0.3333333333 0.3333333333 0.1020678295 1
+ 0.6666666667 0.6666666667 0.1020678295 1
+%endblock AtomicCoordinatesAndAtomicSpecies
+MD.UseSaveXV T
+MD.UseSaveZM F # default value
+WriteCoorInitial T
+MD.TypeOfRun Broyden
+MD.TypeOfRun Broyden
+MD.InitialTimeStep 1 # default value
+MD.FinalTimeStep 1 # default value
+MD.TypeOfRun Broyden
+MaxBondDistance 6.000000000 Bohr # default value
+Output-Structure-Only F # default value
+WriteCoorXmol F # default value
+#:physical? MaxWalltime F
+MaxWalltime 0.1797693135+309 # default value
+#:physical? MaxWalltime.Slack F
+MaxWalltime.Slack 5.000000000 # default value
+HSetupOnly F # default value
+LongOutput F # default value
+WriteDenchar F # default value
+WriteMullikenPop 1
+WriteOrbMom F # default value
+WriteHirshfeldPop F # default value
+WriteVoronoiPop F # default value
+PartialChargesAtEveryGeometry F # default value
+PartialChargesAtEveryScfStep F # default value
+MeshCutoff 160.0000000 Ry
+# above item originally: MeshCutoff 160.0000000 Ry
+NetCharge 0.000000000 # default value
+MinSCFIterations 0 # default value
+MaxSCFIterations 1000
+SCF.MustConverge T
+#:block? TS.MixH F
+#:defined? TS.MixH F
+#:block? MixHamiltonian F
+#:defined? MixHamiltonian F
+#:block? MixCharge F
+#:defined? MixCharge F
+TS.MixH T # default value
+MixHamiltonian T # default value
+MixCharge F # default value
+SCF.Mix Hamiltonian
+Compat-pre-v4-DM-H F # default value
+SCF.MixAfterConvergence F # default value
+SCF.Recompute-H-After-Scf F # default value
+DM.NumberPulay 0 # default value
+DM.NumberBroyden 0 # default value
+DM.FIRE.Mixing F # default value
+DM.MixSCF1 T # default value
+SCF.Mix.First T # default value
+SCF.Mix.First.Force F # default value
+DM.PulayOnFile F # default value
+DM.MixingWeight 0.2500000000 # default value
+DM.OccupancyTolerance 0.1000000000E-11 # default value
+DM.NumberKick 0 # default value
+DM.KickMixingWeight 0.5000000000 # default value
+DM.RequireHarrisConvergence F # default value
+SCF.Harris.Converge F # default value
+DM.HarrisTolerance 0.7349806700E-05 Ry # default value
+SCF.Harris.Tolerance 0.7349806700E-05 Ry # default value
+SCF.DM.Converge T
+DM.Tolerance 0.1000000000E-03 # default value
+SCF.DM.Tolerance 0.1000000000E-07
+SCF.EDM.Converge F # default value
+SCF.EDM.Tolerance 0.7349806700E-04 Ry # default value
+SCF.H.Converge T # default value
+SCF.H.Tolerance 0.7349806700E-04 Ry # default value
+DM.RequireEnergyConvergence F # default value
+SCF.FreeE.Converge F # default value
+DM.EnergyTolerance 0.7349806700E-05 Ry # default value
+SCF.FreeE.Tolerance 0.7349806700E-05 Ry # default value
+MonitorForcesInSCF F # default value
+SCF.MonitorForces F # default value
+DFTD3 F # default value
+UseSaveData F # default value
+DM.UseSaveDM F
+NeglNonOverlapInt F # default value
+SolutionMethod diagon
+ElectronicTemperature 0.7349798845E-04 Ry
+# above item originally: ElectronicTemperature 0.1000000000E-02 eV
+FixSpin F # default value
+Spin.Fix F # default value
+ON.MaxNumIter 1000 # default value
+ON.etol 0.1000000000E-07 # default value
+ON.eta 0.000000000 Ry # default value
+ON.eta_alpha 0.000000000 Ry # default value
+ON.eta_beta 0.000000000 Ry # default value
+On.RcLWF 9.500000000 Bohr # default value
+ON.UseSaveLWF F # default value
+ON.functional kim # default value
+ON.ChemicalPotentialUse F # default value
+ON.ChemicalPotential F # default value
+ON.ChemicalPotentialRc 9.500000000 Bohr # default value
+ON.ChemicalPotentialTemperature 0.5000000000E-01 Ry # default value
+ON.ChemicalPotentialOrder 100 # default value
+TDED.WF.Initialize F # default value
+TDED.Saverho F # default value
+TDED.Nsaverho 100 # default value
+TDED.Write.Etot T # default value
+TDED.Write.Eig F # default value
+TDED.Write.Dipole F # default value
+TDED.Extrapolate F # default value
+TDED.TimeStep 0.1000000000E-02 fs # default value
+TDED.Nsteps 1 # default value
+TDED.Extrapolate.Substeps 3 # default value
+TDED.Inverse.Linear T # default value
+TDED.WF.Save F # default value
+MD.VariableCell F
+compat-pre-v4-dynamics F # default value
+MD.TypeOfRun Broyden
+MD.NumCGsteps 0 # default value
+MD.Steps 0
+MD.MaxCGDispl 0.2000000000 Bohr # default value
+MD.MaxDispl 0.2000000000 Bohr # default value
+MD.MaxForceTol 0.3889348769E-03 Ry/Bohr
+# above item originally: MD.MaxForceTol 0.1000000000E-01 eV/Ang
+MD.MaxStressTol 0.6797730000E-04 Ry/Bohr**3 # default value
+GeometryMustConverge F # default value
+MD.InitialTimeStep 1 # default value
+#:defined? MD.Steps T
+MD.FinalTimeStep 1 # default value
+MD.LengthTimeStep 1.000000000 fs # default value
+MD.Quench F # default value
+MD.FireQuench F # default value
+MD.InitialTemperature 0.000000000 K # default value
+MD.TargetTemperature 0.000000000 K # default value
+#:block? MD.TargetPressure F
+#:defined? MD.TargetPressure F
+MD.TargetPressure 0.000000000 Ry/Bohr**3 # default value
+Target.Pressure 0.000000000 Ry/Bohr**3 # default value
+MD.NoseMass 100.0000000 Ry*fs**2 # default value
+MD.ParrinelloRahmanMass 100.0000000 Ry*fs**2 # default value
+MD.AnnealOption TemperatureAndPressure # default value
+MD.TauRelax 100.0000000 fs # default value
+MD.BulkModulus 0.6797730000E-02 Ry/Bohr**3 # default value
+MD.FCDispl 0.4000000000E-01 Bohr # default value
+MD.FCfirst 1 # default value
+MD.FClast 2 # default value
+UseSpatialDecomposition F # default value
+UseDomainDecomposition F # default value
+SCF.Mix.Spin all # default value
+Mixer.Debug F # default value
+Mixer.Debug.MPI F # default value
+DM.NumberPulay 2 # default value
+DM.NumberBroyden 0 # default value
+DM.MixingWeight 0.2500000000 # default value
+DM.NumberKick 0 # default value
+DM.KickMixingWeight 0.5000000000 # default value
+SCF.LinearMixingAfterPulay F # default value
+SCF.MixingWeightAfterPulay 0.2500000000 # default value
+SCF.Mixer.History 10
+SCF.Mixer.Weight 0.3000000000
+SCF.Mixer.Kick 0 # default value
+SCF.Mixer.Kick.Weight 0.5000000000 # default value
+SCF.Mixer.Restart 0 # default value
+SCF.Mixer.Restart.Save 1 # default value
+SCF.Mixer.Method Pulay
+SCF.Mixer.Variant original
+SCF.Mixer.Linear.After -1 # default value
+SCF.Mixer.Linear.After.Weight 0.2500000000 # default value
+#:block? ChargeGeometries F
+#:defined? ChargeGeometries F
+#:block? ChargeGeometries F
+#:defined? ChargeGeometries F
+BulkBias.V 0.000000000 Ry # default value
+BulkBias.Voltage 0.000000000 Ry # default value
+BulkBias.Tolerance 0.1000000000E-14 # default value
+BulkBias.Current T # default value
+Harris_functional F # default value
+ForceAuxCell F # default value
+#:block? Optim.Broyden.History.Steps F
+#:defined? Optim.Broyden.History.Steps F
+#:block? Optim.Broyden.Cycle.On.Maxit F
+#:defined? Optim.Broyden.Cycle.On.Maxit F
+#:block? Optim.Broyden.Variable.Weight F
+#:defined? Optim.Broyden.Variable.Weight F
+#:block? Optim.Broyden.Debug F
+#:defined? Optim.Broyden.Debug F
+#:block? Optim.Broyden.Initial.Inverse.Jacobian F
+#:defined? Optim.Broyden.Initial.Inverse.Jacobian F
+Write.Kpoints F # default value
+Write.Forces T
+Write.DM T
+Write.DM.End.Of.Cycle T # default value
+Write.H F
+Write.H.End.Of.Cycle F # default value
+Write.DM.NetCDF F # default value
+WriteDM.History.NetCDF F # default value
+WriteDMHS.NetCDF F # default value
+WriteDMHS.History.NetCDF F # default value
+SCF.Read.Charge.NetCDF F # default value
+SCF.Read.Deformation.Charge.NetCDF F # default value
+Write.TSHS.History F # default value
+SaveInitialChargeDensity F # default value
+AnalyzeChargeDensityOnly F # default value
+UseNewDiagk F # default value
+Diag.WFS.Cache none # default value
+WriteBands F # default value
+WriteKbands F # default value
+WriteEigenvalues T
+WriteCoorStep T
+WriteMDhistory F # default value
+WriteMDXmol F # default value
+WriteOrbitalIndex T # default value
+Write.Graphviz none # default value
+WriteCoorStep T
+SaveHS F
+ReInitialiseDM T # default value
+DM.AllowReuse T # default value
+DM.AllowExtrapolation T # default value
+DM.History.Depth 1 # default value
+DM.NormalizationTolerance 0.1000000000E-04 # default value
+DM.NormalizeDuringSCF T # default value
+MullikenInSCF F # default value
+SpinInSCF F # default value
+WarningMinimumAtomicDistance 1.000000000 Bohr # default value
+BornCharge F # default value
+ChangeKgridInMD F # default value
+MD.RelaxCellOnly F # default value
+MD.RemoveIntraMolecularPressure F # default value
+COOP.Write F # default value
+SaveRho T
+SaveDeltaRho F
+SaveRhoXC T
+SaveElectrostaticPotential T
+SaveNeutralAtomPotential F
+SaveTotalPotential T
+SaveIonicCharge F
+SaveBaderCharge F
+SaveTotalCharge F
+Siesta2Wannier90.WriteMmn F # default value
+Siesta2Wannier90.WriteUnk F # default value
+Siesta2Wannier90.WriteAmn F # default value
+Siesta2Wannier90.WriteEig F # default value
+#:block? Siesta2Wannier90.NumberOfBandsUp F
+#:defined? Siesta2Wannier90.NumberOfBandsUp F
+#:block? Siesta2Wannier90.NumberOfBandsDown F
+#:defined? Siesta2Wannier90.NumberOfBandsDown F
+#:block? Siesta2Wannier90.NumberOfBands F
+#:defined? Siesta2Wannier90.NumberOfBands F
+Siesta2Wannier90.NumberOfBandsUp 0 # default value
+Siesta2Wannier90.NumberOfBandsDown 0 # default value
+Siesta2Wannier90.NumberOfBands 0 # default value
+CDF.Save T
+CDF.Compress 0 # default value
+CDF.MPI F # default value
+CDF.Read.Parallel F # default value
+CDF.Grid.Precision double
+DM.AllowReuse T # default value
+DM.AllowExtrapolation T # default value
+DM.AllowExtrapolation F # default value
+NumberOfEigenStates 34 # default value
+RcSpatial 0.000000000 Bohr # default value
+ProcessorGridX 1 # default value
+ProcessorGridY 1 # default value
+ProcessorGridZ 1 # default value
+FFT.ProcessorY.traditional F # default value
+processorY 2 # default value
+blocksize 1 # default value
+Spin.Spiral F # default value
+TimeReversalSymmetryForKpoints T # default value
+%block kgrid.MonkhorstPack
+ 6 0 0 0.0
+ 0 6 0 0.0
+ 0 0 1 0.0
+%endblock kgrid.MonkhorstPack
+#:block? ProjectedDensityOfStates F
+#:block? LocalDensityOfStates F
+Diag.ParallelOverK T
+Diag.ProcessorY 4 # default value
+Diag.BlockSize 1 # default value
+Diag.Use2D T # default value
+Diag.UpperLower lower # default value
+Diag.DivideAndConquer T # default value
+Diag.MRRR F # default value
+Diag.NoExpert F # default value
+Diag.Algorithm Divide-and-Conquer # default value
+Diag.AbsTol 0.1000000000E-15 # default value
+Diag.OrFac 0.1000000000E-05 # default value
+Diag.Memory 1.000000000 # default value
+#:block? BandLines T
+#:defined? BandLines T
+#:block? BandPoints F
+#:defined? BandPoints F
+BandLinesScale ReciprocalLatticeVectors
+%block BandLines
+ 1 0.0000000 0.00000000 0.000 \Gamma
+ 30 0.3333333 0.66666666 0.000 K
+ 15 0.5000000 0.50000000 0.000 M
+ 26 0.0000000 0.00000000 0.000 \Gamma
+%endblock BandLines
+#:block? BandLines T
+#:defined? BandLines T
+#:block? BandPoints F
+#:defined? BandPoints F
+BandLinesScale ReciprocalLatticeVectors
+%block BandLines
+ 1 0.0000000 0.00000000 0.000 \Gamma
+ 30 0.3333333 0.66666666 0.000 K
+ 15 0.5000000 0.50000000 0.000 M
+ 26 0.0000000 0.00000000 0.000 \Gamma
+%endblock BandLines
+LongOutput F # default value
+WriteWaveFunctions F # default value
+#:block-line-count? MetaForce (iirrr) 0
+#:block? TS.BufferAtomsLeft F
+#:defined? TS.BufferAtomsLeft F
+#:block? TS.BufferAtomsRight F
+#:defined? TS.BufferAtomsRight F
+#:list? TS.Atoms.Buffer F
+TS.HS.Save F # default value
+TS.DE.Save F # default value
+TS.onlyS F # default value
+TS.S.Save F # default value
+Spin.Spiral F # default value
+TimeReversalSymmetryForKpoints T # default value
+#:list? TS.kgrid.MonkhorstPack F
+#:block? TS.kgrid.Cutoff F
+#:defined? TS.kgrid.Cutoff F
+#:block? TS.kgrid.File F
+#:defined? TS.kgrid.File F
+AtomicCoordinatesFormat Fractional
+AtomCoorFormatOut Fractional # default value
+LatticeConstant 4.648728119 Bohr
+# above item originally: LatticeConstant 2.460000000 Ang
+debug-folding F # default value
+Save.Overlap.Gradient F # default value
+Sonly F # default value
+DM.Init atomic # default value
+DM.Init.RandomStates 0 # default value
+Sonly F # default value
+Debug.DHSCF F # default value
+MeshSubDivisions 2 # default value
+#:list? Mesh.Sizes F
+#:block? MeshSizes F
+#:defined? MeshSizes F
+CDF.Grid.Precision double
+#:block? LocalDensityOfStates F
+#:defined? LocalDensityOfStates F
+XC.Use.BSC.CellXC F # default value
+DirectPhi F # default value
+SimulateDoping F # default value
+Slab.DipoleCorrection none # default value
+Read-H-from-file F # default value
+timing-split-scf-steps F # default value
+SingleExcitation F # default value
+OccupationFunction MP
+OccupationMPOrder 1
+OccupationFunction MP
+OccupationMPOrder 1
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+compute-forces T # default value
+#:list? Grid.CellSampling F
+Read-H-from-file F # default value
+WriteCoorXmol F # default value
+WriteCoorCerius F # default value
+WFS.Write.For.Bands F # default value
+BasisPressure 0.2000000000 GPa # default value
+OpticalCalculation F # default value
diff --git a/graphene/siesta/SG15v1.2/ref/fdf.20230703T191715.984.log b/graphene/siesta/SG15v1.2/ref/fdf.20230703T191715.984.log
new file mode 100644
index 0000000..a16e8f8
--- /dev/null
+++ b/graphene/siesta/SG15v1.2/ref/fdf.20230703T191715.984.log
@@ -0,0 +1,389 @@
+SystemName # default value
+SystemLabel graphene
+SpinPolarized F # default value
+NonCollinearSpin F # default value
+SpinOrbit F # default value
+#:block? SpinPolarized F
+#:defined? SpinPolarized F
+#:block? NonCollinearSpin F
+#:defined? NonCollinearSpin F
+#:block? SpinOrbit F
+#:defined? SpinOrbit F
+Spin none # default value
+TimeReversalSymmetry T # default value
+DebugObjects.Node 0 # default value
+DebugObjects F # default value
+XML.Write T
+timer_report_threshold 0.000000000 # default value
+UseParallelTimer T # default value
+UseTreeTimer F # default value
+timing-split-scf-steps F # default value
+use-walltime F # default value
+alloc_report_level 0 # default value
+alloc_report_threshold 0.000000000 # default value
+xc.functional LDA
+xc.authors PZ
+#:block? XC.hybrid F
+#:defined? XC.hybrid F
+#:block? XC.cocktail F
+#:defined? XC.cocktail F
+MM.Cutoff 30.00000000 Bohr # default value
+MM.UnitsEnergy eV # default value
+MM.UnitsDistance Ang # default value
+Atom.Debug F # default value
+WriteIonPlotFiles F # default value
+Atom.Debug.KB.Generation F # default value
+KB.New.Reference.Orbitals F # default value
+user-basis F # default value
+user-basis-netcdf F # default value
+#:block? DFTU.proj F
+#:defined? DFTU.proj F
+#:block? LDAU.proj F
+#:defined? LDAU.proj F
+Number_of_species 1
+%block Chemical_species_label
+ 1 6 C
+%endblock Chemical_species_label
+ReparametrizePseudos F # default value
+Restricted.Radial.Grid T # default value
+Rmax.Radial.Grid 0.000000000 # default value
+PAO.BasisSize DZP
+PAO.BasisType split # default value
+PAO.SoftDefault F # default value
+PAO.SoftInnerRadius 0.9000000000 # default value
+PAO.SoftPotential 40.00000000 # default value
+PAO.SplitNorm 0.1500000000 # default value
+PAO.SplitNormH -1.000000000 # default value
+PAO.Polarization.NonPerturbative F # default value
+PAO.NonPerturbative.Polarization.Orbitals F # default value
+PAO.Polarization.NonPerturbative.Fallback F # default value
+LDAU.ProjectorGenerationMethod 2 # default value
+DFTU.ProjectorGenerationMethod 2 # default value
+LDAU.EnergyShift 0.5000000000E-01 Ry # default value
+DFTU.EnergyShift 0.5000000000E-01 Ry # default value
+LDAU.CutoffNorm 0.9000000000 # default value
+DFTU.CutoffNorm 0.9000000000 # default value
+PAO.SoftDefault F # default value
+PAO.SoftInnerRadius 0.9000000000 # default value
+PAO.SoftPotential 40.00000000 # default value
+LDAU.ThresholdTol 0.1000000000E-01 # default value
+DFTU.ThresholdTol 0.1000000000E-01 # default value
+LDAU.PopTol 0.1000000000E-02 # default value
+DFTU.PopTol 0.1000000000E-02 # default value
+LDAU.PotentialShift F # default value
+DFTU.PotentialShift F # default value
+LDAU.FirstIteration F # default value
+DFTU.FirstIteration F # default value
+FilterCutoff 0.000000000 Ry # default value
+FilterTol 0.000000000 Ry # default value
+spin-orbit-strength 1.000000000 # default value
+Use.PSML.KB.Projectors T # default value
+Use.PSML.Vlocal T # default value
+PSML.KB.Projectors T # default value
+PSML.Vlocal T # default value
+psml.chlocal.build.r0 0.4000000000E-02 # default value
+psml.chlocal.build.delta 0.5000000000E-02 # default value
+psml.chlocal.build.poly_order_rlin 4 # default value
+chlocal-use-charge-cutoff-for-vlocal-fit F # default value
+psml.chlocal.build.rr1 0.1000000000E-02 # default value
+psml.chlocal.build.exp_al 1.012000000 # default value
+psml.chlocal.build.poly_order_rofi 7 # default value
+PAO.EnergyShift 0.2000000000E-01 Ry # default value
+PAO.SplitTailNorm F # default value
+PAO.FixSplitTable F # default value
+PAO.NewSplitCode F # default value
+PAO.Filter F # default value
+PAO.Filter F # default value
+PAO.Filter F # default value
+PAO.Filter F # default value
+PAO.OldStylePolorbs T # default value
+PAO.SplitTailNorm F # default value
+PAO.FixSplitTable F # default value
+PAO.NewSplitCode F # default value
+PAO.Filter F # default value
+Vna.Filter F # default value
+PAO.BasisType split # default value
+Debug.Elec.Corr F # default value
+Atom-Setup-Only F # default value
+UseStructFile F # default value
+MD.UseStructFile F # default value
+#:block? LatticeParameters F
+%block LatticeVectors
+LatticeConstant 4.648728119 Bohr
+# above item originally: LatticeConstant 2.460000000 Ang
+ 1.0000000000 0.0000000000 0.0000000000
+ 0.5000000000 0.8660254038 0.0000000000
+ 0.0000000000 0.0000000000 8.9430894309
+%endblock LatticeVectors
+AtomicCoordinatesFormat Fractional
+NumberOfAtoms 2
+#:block? AtomicCoordinatesOrigin F
+#:defined? AtomicCoordinatesOrigin F
+ZM.UnitsLength Bohr # default value
+ZM.UnitsAngle rad # default value
+ZM.ForceTolLength 0.1555740000E-02 Ry/Bohr # default value
+ZM.ForceTolAngle 0.3565490000E-02 Ry/rad # default value
+ZM.MaxDisplLength 0.2000000000 Bohr # default value
+ZM.MaxDisplAngle 0.3000000000E-02 rad # default value
+ZM.CalcAllForces F # default value
+%block AtomicCoordinatesAndAtomicSpecies
+ 0.3333333333 0.3333333333 0.1020678295 1
+ 0.6666666667 0.6666666667 0.1020678295 1
+%endblock AtomicCoordinatesAndAtomicSpecies
+MD.UseSaveXV T
+MD.UseSaveZM F # default value
+WriteCoorInitial T
+MD.TypeOfRun Broyden
+MD.TypeOfRun Broyden
+MD.InitialTimeStep 1 # default value
+MD.FinalTimeStep 1 # default value
+MD.TypeOfRun Broyden
+MaxBondDistance 6.000000000 Bohr # default value
+Output-Structure-Only F # default value
+WriteCoorXmol F # default value
+#:physical? MaxWalltime F
+MaxWalltime 0.1797693135+309 # default value
+#:physical? MaxWalltime.Slack F
+MaxWalltime.Slack 5.000000000 # default value
+HSetupOnly F # default value
+LongOutput F # default value
+WriteDenchar F # default value
+WriteMullikenPop 1
+WriteOrbMom F # default value
+WriteHirshfeldPop F # default value
+WriteVoronoiPop F # default value
+PartialChargesAtEveryGeometry F # default value
+PartialChargesAtEveryScfStep F # default value
+MeshCutoff 160.0000000 Ry
+# above item originally: MeshCutoff 160.0000000 Ry
+NetCharge 0.000000000 # default value
+MinSCFIterations 0 # default value
+MaxSCFIterations 1000
+SCF.MustConverge T
+#:block? TS.MixH F
+#:defined? TS.MixH F
+#:block? MixHamiltonian F
+#:defined? MixHamiltonian F
+#:block? MixCharge F
+#:defined? MixCharge F
+TS.MixH T # default value
+MixHamiltonian T # default value
+MixCharge F # default value
+SCF.Mix Hamiltonian
+Compat-pre-v4-DM-H F # default value
+SCF.MixAfterConvergence F # default value
+SCF.Recompute-H-After-Scf F # default value
+DM.NumberPulay 0 # default value
+DM.NumberBroyden 0 # default value
+DM.FIRE.Mixing F # default value
+DM.MixSCF1 T # default value
+SCF.Mix.First T # default value
+SCF.Mix.First.Force F # default value
+DM.PulayOnFile F # default value
+DM.MixingWeight 0.2500000000 # default value
+DM.OccupancyTolerance 0.1000000000E-11 # default value
+DM.NumberKick 0 # default value
+DM.KickMixingWeight 0.5000000000 # default value
+DM.RequireHarrisConvergence F # default value
+SCF.Harris.Converge F # default value
+DM.HarrisTolerance 0.7349806700E-05 Ry # default value
+SCF.Harris.Tolerance 0.7349806700E-05 Ry # default value
+SCF.DM.Converge T
+DM.Tolerance 0.1000000000E-03 # default value
+SCF.DM.Tolerance 0.1000000000E-07
+SCF.EDM.Converge F # default value
+SCF.EDM.Tolerance 0.7349806700E-04 Ry # default value
+SCF.H.Converge T # default value
+SCF.H.Tolerance 0.7349806700E-04 Ry # default value
+DM.RequireEnergyConvergence F # default value
+SCF.FreeE.Converge F # default value
+DM.EnergyTolerance 0.7349806700E-05 Ry # default value
+SCF.FreeE.Tolerance 0.7349806700E-05 Ry # default value
+MonitorForcesInSCF F # default value
+SCF.MonitorForces F # default value
+DFTD3 F # default value
+UseSaveData F # default value
+DM.UseSaveDM F
+NeglNonOverlapInt F # default value
+SolutionMethod diagon
+ElectronicTemperature 0.7349798845E-04 Ry
+# above item originally: ElectronicTemperature 0.1000000000E-02 eV
+FixSpin F # default value
+Spin.Fix F # default value
+ON.MaxNumIter 1000 # default value
+ON.etol 0.1000000000E-07 # default value
+ON.eta 0.000000000 Ry # default value
+ON.eta_alpha 0.000000000 Ry # default value
+ON.eta_beta 0.000000000 Ry # default value
+On.RcLWF 9.500000000 Bohr # default value
+ON.UseSaveLWF F # default value
+ON.functional kim # default value
+ON.ChemicalPotentialUse F # default value
+ON.ChemicalPotential F # default value
+ON.ChemicalPotentialRc 9.500000000 Bohr # default value
+ON.ChemicalPotentialTemperature 0.5000000000E-01 Ry # default value
+ON.ChemicalPotentialOrder 100 # default value
+TDED.WF.Initialize F # default value
+TDED.Saverho F # default value
+TDED.Nsaverho 100 # default value
+TDED.Write.Etot T # default value
+TDED.Write.Eig F # default value
+TDED.Write.Dipole F # default value
+TDED.Extrapolate F # default value
+TDED.TimeStep 0.1000000000E-02 fs # default value
+TDED.Nsteps 1 # default value
+TDED.Extrapolate.Substeps 3 # default value
+TDED.Inverse.Linear T # default value
+TDED.WF.Save F # default value
+MD.VariableCell F
+compat-pre-v4-dynamics F # default value
+MD.TypeOfRun Broyden
+MD.NumCGsteps 0 # default value
+MD.Steps 0
+MD.MaxCGDispl 0.2000000000 Bohr # default value
+MD.MaxDispl 0.2000000000 Bohr # default value
+MD.MaxForceTol 0.3889348769E-03 Ry/Bohr
+# above item originally: MD.MaxForceTol 0.1000000000E-01 eV/Ang
+MD.MaxStressTol 0.6797730000E-04 Ry/Bohr**3 # default value
+GeometryMustConverge F # default value
+MD.InitialTimeStep 1 # default value
+#:defined? MD.Steps T
+MD.FinalTimeStep 1 # default value
+MD.LengthTimeStep 1.000000000 fs # default value
+MD.Quench F # default value
+MD.FireQuench F # default value
+MD.InitialTemperature 0.000000000 K # default value
+MD.TargetTemperature 0.000000000 K # default value
+#:block? MD.TargetPressure F
+#:defined? MD.TargetPressure F
+MD.TargetPressure 0.000000000 Ry/Bohr**3 # default value
+Target.Pressure 0.000000000 Ry/Bohr**3 # default value
+MD.NoseMass 100.0000000 Ry*fs**2 # default value
+MD.ParrinelloRahmanMass 100.0000000 Ry*fs**2 # default value
+MD.AnnealOption TemperatureAndPressure # default value
+MD.TauRelax 100.0000000 fs # default value
+MD.BulkModulus 0.6797730000E-02 Ry/Bohr**3 # default value
+MD.FCDispl 0.4000000000E-01 Bohr # default value
+MD.FCfirst 1 # default value
+MD.FClast 2 # default value
+UseSpatialDecomposition F # default value
+UseDomainDecomposition F # default value
+SCF.Mix.Spin all # default value
+Mixer.Debug F # default value
+Mixer.Debug.MPI F # default value
+DM.NumberPulay 2 # default value
+DM.NumberBroyden 0 # default value
+DM.MixingWeight 0.2500000000 # default value
+DM.NumberKick 0 # default value
+DM.KickMixingWeight 0.5000000000 # default value
+SCF.LinearMixingAfterPulay F # default value
+SCF.MixingWeightAfterPulay 0.2500000000 # default value
+SCF.Mixer.History 10
+SCF.Mixer.Weight 0.3000000000
+SCF.Mixer.Kick 0 # default value
+SCF.Mixer.Kick.Weight 0.5000000000 # default value
+SCF.Mixer.Restart 0 # default value
+SCF.Mixer.Restart.Save 1 # default value
+SCF.Mixer.Method Pulay
+SCF.Mixer.Variant original
+SCF.Mixer.Linear.After -1 # default value
+SCF.Mixer.Linear.After.Weight 0.2500000000 # default value
+#:block? ChargeGeometries F
+#:defined? ChargeGeometries F
+#:block? ChargeGeometries F
+#:defined? ChargeGeometries F
+BulkBias.V 0.000000000 Ry # default value
+BulkBias.Voltage 0.000000000 Ry # default value
+BulkBias.Tolerance 0.1000000000E-14 # default value
+BulkBias.Current T # default value
+Harris_functional F # default value
+ForceAuxCell F # default value
+#:block? Optim.Broyden.History.Steps F
+#:defined? Optim.Broyden.History.Steps F
+#:block? Optim.Broyden.Cycle.On.Maxit F
+#:defined? Optim.Broyden.Cycle.On.Maxit F
+#:block? Optim.Broyden.Variable.Weight F
+#:defined? Optim.Broyden.Variable.Weight F
+#:block? Optim.Broyden.Debug F
+#:defined? Optim.Broyden.Debug F
+#:block? Optim.Broyden.Initial.Inverse.Jacobian F
+#:defined? Optim.Broyden.Initial.Inverse.Jacobian F
+Write.Kpoints F # default value
+Write.Forces T
+Write.DM T
+Write.DM.End.Of.Cycle T # default value
+Write.H F
+Write.H.End.Of.Cycle F # default value
+Write.DM.NetCDF F # default value
+WriteDM.History.NetCDF F # default value
+WriteDMHS.NetCDF F # default value
+WriteDMHS.History.NetCDF F # default value
+SCF.Read.Charge.NetCDF F # default value
+SCF.Read.Deformation.Charge.NetCDF F # default value
+Write.TSHS.History F # default value
+SaveInitialChargeDensity F # default value
+AnalyzeChargeDensityOnly F # default value
+UseNewDiagk F # default value
+Diag.WFS.Cache none # default value
+WriteBands F # default value
+WriteKbands F # default value
+WriteEigenvalues T
+WriteCoorStep T
+WriteMDhistory F # default value
+WriteMDXmol F # default value
+WriteOrbitalIndex T # default value
+Write.Graphviz none # default value
+WriteCoorStep T
+SaveHS F
+ReInitialiseDM T # default value
+DM.AllowReuse T # default value
+DM.AllowExtrapolation T # default value
+DM.History.Depth 1 # default value
+DM.NormalizationTolerance 0.1000000000E-04 # default value
+DM.NormalizeDuringSCF T # default value
+MullikenInSCF F # default value
+SpinInSCF F # default value
+WarningMinimumAtomicDistance 1.000000000 Bohr # default value
+BornCharge F # default value
+ChangeKgridInMD F # default value
+MD.RelaxCellOnly F # default value
+MD.RemoveIntraMolecularPressure F # default value
+COOP.Write F # default value
+SaveRho T
+SaveDeltaRho F
+SaveRhoXC T
+SaveElectrostaticPotential T
+SaveNeutralAtomPotential F
+SaveTotalPotential T
+SaveIonicCharge F
+SaveBaderCharge F
+SaveTotalCharge F
+Siesta2Wannier90.WriteMmn F # default value
+Siesta2Wannier90.WriteUnk F # default value
+Siesta2Wannier90.WriteAmn F # default value
+Siesta2Wannier90.WriteEig F # default value
+#:block? Siesta2Wannier90.NumberOfBandsUp F
+#:defined? Siesta2Wannier90.NumberOfBandsUp F
+#:block? Siesta2Wannier90.NumberOfBandsDown F
+#:defined? Siesta2Wannier90.NumberOfBandsDown F
+#:block? Siesta2Wannier90.NumberOfBands F
+#:defined? Siesta2Wannier90.NumberOfBands F
+Siesta2Wannier90.NumberOfBandsUp 0 # default value
+Siesta2Wannier90.NumberOfBandsDown 0 # default value
+Siesta2Wannier90.NumberOfBands 0 # default value
+CDF.Save T
+CDF.Compress 0 # default value
+CDF.MPI F # default value
+CDF.Read.Parallel F # default value
+CDF.Grid.Precision double
+DM.AllowReuse T # default value
+DM.AllowExtrapolation T # default value
+DM.AllowExtrapolation F # default value
+NumberOfEigenStates 26 # default value
+RcSpatial 0.000000000 Bohr # default value
+ProcessorGridX 1 # default value
+ProcessorGridY 1 # default value
+ProcessorGridZ 1 # default value
+FFT.ProcessorY.traditional F # default value
+processorY 2 # default value
+blocksize 1 # default value
diff --git a/graphene/siesta/SG15v1.2/ref/fdf.20230703T191731.735.log b/graphene/siesta/SG15v1.2/ref/fdf.20230703T191731.735.log
new file mode 100644
index 0000000..2597caf
--- /dev/null
+++ b/graphene/siesta/SG15v1.2/ref/fdf.20230703T191731.735.log
@@ -0,0 +1,546 @@
+SystemName # default value
+SystemLabel graphene
+SpinPolarized F # default value
+NonCollinearSpin F # default value
+SpinOrbit F # default value
+#:block? SpinPolarized F
+#:defined? SpinPolarized F
+#:block? NonCollinearSpin F
+#:defined? NonCollinearSpin F
+#:block? SpinOrbit F
+#:defined? SpinOrbit F
+Spin none # default value
+TimeReversalSymmetry T # default value
+DebugObjects.Node 0 # default value
+DebugObjects F # default value
+XML.Write T
+timer_report_threshold 0.000000000 # default value
+UseParallelTimer T # default value
+UseTreeTimer F # default value
+timing-split-scf-steps F # default value
+use-walltime F # default value
+alloc_report_level 0 # default value
+alloc_report_threshold 0.000000000 # default value
+xc.functional LDA
+xc.authors PZ
+#:block? XC.hybrid F
+#:defined? XC.hybrid F
+#:block? XC.cocktail F
+#:defined? XC.cocktail F
+MM.Cutoff 30.00000000 Bohr # default value
+MM.UnitsEnergy eV # default value
+MM.UnitsDistance Ang # default value
+Atom.Debug F # default value
+WriteIonPlotFiles F # default value
+Atom.Debug.KB.Generation F # default value
+KB.New.Reference.Orbitals F # default value
+user-basis F # default value
+user-basis-netcdf F # default value
+#:block? DFTU.proj F
+#:defined? DFTU.proj F
+#:block? LDAU.proj F
+#:defined? LDAU.proj F
+Number_of_species 1
+%block Chemical_species_label
+ 1 6 C
+%endblock Chemical_species_label
+ReparametrizePseudos F # default value
+Restricted.Radial.Grid T # default value
+Rmax.Radial.Grid 0.000000000 # default value
+PAO.BasisSize DZP
+PAO.BasisType split # default value
+PAO.SoftDefault F # default value
+PAO.SoftInnerRadius 0.9000000000 # default value
+PAO.SoftPotential 40.00000000 # default value
+PAO.SplitNorm 0.1500000000 # default value
+PAO.SplitNormH -1.000000000 # default value
+PAO.Polarization.NonPerturbative F # default value
+PAO.NonPerturbative.Polarization.Orbitals F # default value
+PAO.Polarization.NonPerturbative.Fallback F # default value
+LDAU.ProjectorGenerationMethod 2 # default value
+DFTU.ProjectorGenerationMethod 2 # default value
+LDAU.EnergyShift 0.5000000000E-01 Ry # default value
+DFTU.EnergyShift 0.5000000000E-01 Ry # default value
+LDAU.CutoffNorm 0.9000000000 # default value
+DFTU.CutoffNorm 0.9000000000 # default value
+PAO.SoftDefault F # default value
+PAO.SoftInnerRadius 0.9000000000 # default value
+PAO.SoftPotential 40.00000000 # default value
+LDAU.ThresholdTol 0.1000000000E-01 # default value
+DFTU.ThresholdTol 0.1000000000E-01 # default value
+LDAU.PopTol 0.1000000000E-02 # default value
+DFTU.PopTol 0.1000000000E-02 # default value
+LDAU.PotentialShift F # default value
+DFTU.PotentialShift F # default value
+LDAU.FirstIteration F # default value
+DFTU.FirstIteration F # default value
+FilterCutoff 0.000000000 Ry # default value
+FilterTol 0.000000000 Ry # default value
+spin-orbit-strength 1.000000000 # default value
+Use.PSML.KB.Projectors T # default value
+Use.PSML.Vlocal T # default value
+PSML.KB.Projectors T # default value
+PSML.Vlocal T # default value
+psml.chlocal.build.r0 0.4000000000E-02 # default value
+psml.chlocal.build.delta 0.5000000000E-02 # default value
+psml.chlocal.build.poly_order_rlin 4 # default value
+chlocal-use-charge-cutoff-for-vlocal-fit F # default value
+psml.chlocal.build.rr1 0.1000000000E-02 # default value
+psml.chlocal.build.exp_al 1.012000000 # default value
+psml.chlocal.build.poly_order_rofi 7 # default value
+PAO.EnergyShift 0.2000000000E-01 Ry # default value
+PAO.SplitTailNorm F # default value
+PAO.FixSplitTable F # default value
+PAO.NewSplitCode F # default value
+PAO.Filter F # default value
+PAO.Filter F # default value
+PAO.Filter F # default value
+PAO.Filter F # default value
+PAO.OldStylePolorbs T # default value
+PAO.SplitTailNorm F # default value
+PAO.FixSplitTable F # default value
+PAO.NewSplitCode F # default value
+PAO.Filter F # default value
+Vna.Filter F # default value
+PAO.BasisType split # default value
+Debug.Elec.Corr F # default value
+Atom-Setup-Only F # default value
+UseStructFile F # default value
+MD.UseStructFile F # default value
+#:block? LatticeParameters F
+%block LatticeVectors
+LatticeConstant 4.648728119 Bohr
+# above item originally: LatticeConstant 2.460000000 Ang
+ 1.0000000000 0.0000000000 0.0000000000
+ 0.5000000000 0.8660254038 0.0000000000
+ 0.0000000000 0.0000000000 8.9430894309
+%endblock LatticeVectors
+AtomicCoordinatesFormat Fractional
+NumberOfAtoms 2
+#:block? AtomicCoordinatesOrigin F
+#:defined? AtomicCoordinatesOrigin F
+ZM.UnitsLength Bohr # default value
+ZM.UnitsAngle rad # default value
+ZM.ForceTolLength 0.1555740000E-02 Ry/Bohr # default value
+ZM.ForceTolAngle 0.3565490000E-02 Ry/rad # default value
+ZM.MaxDisplLength 0.2000000000 Bohr # default value
+ZM.MaxDisplAngle 0.3000000000E-02 rad # default value
+ZM.CalcAllForces F # default value
+%block AtomicCoordinatesAndAtomicSpecies
+ 0.3333333333 0.3333333333 0.1020678295 1
+ 0.6666666667 0.6666666667 0.1020678295 1
+%endblock AtomicCoordinatesAndAtomicSpecies
+MD.UseSaveXV T
+MD.UseSaveZM F # default value
+WriteCoorInitial T
+MD.TypeOfRun Broyden
+MD.TypeOfRun Broyden
+MD.InitialTimeStep 1 # default value
+MD.FinalTimeStep 1 # default value
+MD.TypeOfRun Broyden
+MaxBondDistance 6.000000000 Bohr # default value
+Output-Structure-Only F # default value
+WriteCoorXmol F # default value
+#:physical? MaxWalltime F
+MaxWalltime 0.1797693135+309 # default value
+#:physical? MaxWalltime.Slack F
+MaxWalltime.Slack 5.000000000 # default value
+HSetupOnly F # default value
+LongOutput F # default value
+WriteDenchar F # default value
+WriteMullikenPop 1
+WriteOrbMom F # default value
+WriteHirshfeldPop F # default value
+WriteVoronoiPop F # default value
+PartialChargesAtEveryGeometry F # default value
+PartialChargesAtEveryScfStep F # default value
+MeshCutoff 160.0000000 Ry
+# above item originally: MeshCutoff 160.0000000 Ry
+NetCharge 0.000000000 # default value
+MinSCFIterations 0 # default value
+MaxSCFIterations 1000
+SCF.MustConverge T
+#:block? TS.MixH F
+#:defined? TS.MixH F
+#:block? MixHamiltonian F
+#:defined? MixHamiltonian F
+#:block? MixCharge F
+#:defined? MixCharge F
+TS.MixH T # default value
+MixHamiltonian T # default value
+MixCharge F # default value
+SCF.Mix Hamiltonian
+Compat-pre-v4-DM-H F # default value
+SCF.MixAfterConvergence F # default value
+SCF.Recompute-H-After-Scf F # default value
+DM.NumberPulay 0 # default value
+DM.NumberBroyden 0 # default value
+DM.FIRE.Mixing F # default value
+DM.MixSCF1 T # default value
+SCF.Mix.First T # default value
+SCF.Mix.First.Force F # default value
+DM.PulayOnFile F # default value
+DM.MixingWeight 0.2500000000 # default value
+DM.OccupancyTolerance 0.1000000000E-11 # default value
+DM.NumberKick 0 # default value
+DM.KickMixingWeight 0.5000000000 # default value
+DM.RequireHarrisConvergence F # default value
+SCF.Harris.Converge F # default value
+DM.HarrisTolerance 0.7349806700E-05 Ry # default value
+SCF.Harris.Tolerance 0.7349806700E-05 Ry # default value
+SCF.DM.Converge T
+DM.Tolerance 0.1000000000E-03 # default value
+SCF.DM.Tolerance 0.1000000000E-07
+SCF.EDM.Converge F # default value
+SCF.EDM.Tolerance 0.7349806700E-04 Ry # default value
+SCF.H.Converge T # default value
+SCF.H.Tolerance 0.7349806700E-04 Ry # default value
+DM.RequireEnergyConvergence F # default value
+SCF.FreeE.Converge F # default value
+DM.EnergyTolerance 0.7349806700E-05 Ry # default value
+SCF.FreeE.Tolerance 0.7349806700E-05 Ry # default value
+MonitorForcesInSCF F # default value
+SCF.MonitorForces F # default value
+DFTD3 F # default value
+UseSaveData F # default value
+DM.UseSaveDM F
+NeglNonOverlapInt F # default value
+SolutionMethod diagon
+ElectronicTemperature 0.7349798845E-04 Ry
+# above item originally: ElectronicTemperature 0.1000000000E-02 eV
+FixSpin F # default value
+Spin.Fix F # default value
+ON.MaxNumIter 1000 # default value
+ON.etol 0.1000000000E-07 # default value
+ON.eta 0.000000000 Ry # default value
+ON.eta_alpha 0.000000000 Ry # default value
+ON.eta_beta 0.000000000 Ry # default value
+On.RcLWF 9.500000000 Bohr # default value
+ON.UseSaveLWF F # default value
+ON.functional kim # default value
+ON.ChemicalPotentialUse F # default value
+ON.ChemicalPotential F # default value
+ON.ChemicalPotentialRc 9.500000000 Bohr # default value
+ON.ChemicalPotentialTemperature 0.5000000000E-01 Ry # default value
+ON.ChemicalPotentialOrder 100 # default value
+TDED.WF.Initialize F # default value
+TDED.Saverho F # default value
+TDED.Nsaverho 100 # default value
+TDED.Write.Etot T # default value
+TDED.Write.Eig F # default value
+TDED.Write.Dipole F # default value
+TDED.Extrapolate F # default value
+TDED.TimeStep 0.1000000000E-02 fs # default value
+TDED.Nsteps 1 # default value
+TDED.Extrapolate.Substeps 3 # default value
+TDED.Inverse.Linear T # default value
+TDED.WF.Save F # default value
+MD.VariableCell F
+compat-pre-v4-dynamics F # default value
+MD.TypeOfRun Broyden
+MD.NumCGsteps 0 # default value
+MD.Steps 0
+MD.MaxCGDispl 0.2000000000 Bohr # default value
+MD.MaxDispl 0.2000000000 Bohr # default value
+MD.MaxForceTol 0.3889348769E-03 Ry/Bohr
+# above item originally: MD.MaxForceTol 0.1000000000E-01 eV/Ang
+MD.MaxStressTol 0.6797730000E-04 Ry/Bohr**3 # default value
+GeometryMustConverge F # default value
+MD.InitialTimeStep 1 # default value
+#:defined? MD.Steps T
+MD.FinalTimeStep 1 # default value
+MD.LengthTimeStep 1.000000000 fs # default value
+MD.Quench F # default value
+MD.FireQuench F # default value
+MD.InitialTemperature 0.000000000 K # default value
+MD.TargetTemperature 0.000000000 K # default value
+#:block? MD.TargetPressure F
+#:defined? MD.TargetPressure F
+MD.TargetPressure 0.000000000 Ry/Bohr**3 # default value
+Target.Pressure 0.000000000 Ry/Bohr**3 # default value
+MD.NoseMass 100.0000000 Ry*fs**2 # default value
+MD.ParrinelloRahmanMass 100.0000000 Ry*fs**2 # default value
+MD.AnnealOption TemperatureAndPressure # default value
+MD.TauRelax 100.0000000 fs # default value
+MD.BulkModulus 0.6797730000E-02 Ry/Bohr**3 # default value
+MD.FCDispl 0.4000000000E-01 Bohr # default value
+MD.FCfirst 1 # default value
+MD.FClast 2 # default value
+UseSpatialDecomposition F # default value
+UseDomainDecomposition F # default value
+SCF.Mix.Spin all # default value
+Mixer.Debug F # default value
+Mixer.Debug.MPI F # default value
+DM.NumberPulay 2 # default value
+DM.NumberBroyden 0 # default value
+DM.MixingWeight 0.2500000000 # default value
+DM.NumberKick 0 # default value
+DM.KickMixingWeight 0.5000000000 # default value
+SCF.LinearMixingAfterPulay F # default value
+SCF.MixingWeightAfterPulay 0.2500000000 # default value
+SCF.Mixer.History 10
+SCF.Mixer.Weight 0.3000000000
+SCF.Mixer.Kick 0 # default value
+SCF.Mixer.Kick.Weight 0.5000000000 # default value
+SCF.Mixer.Restart 0 # default value
+SCF.Mixer.Restart.Save 1 # default value
+SCF.Mixer.Method Pulay
+SCF.Mixer.Variant original
+SCF.Mixer.Linear.After -1 # default value
+SCF.Mixer.Linear.After.Weight 0.2500000000 # default value
+#:block? ChargeGeometries F
+#:defined? ChargeGeometries F
+#:block? ChargeGeometries F
+#:defined? ChargeGeometries F
+BulkBias.V 0.000000000 Ry # default value
+BulkBias.Voltage 0.000000000 Ry # default value
+BulkBias.Tolerance 0.1000000000E-14 # default value
+BulkBias.Current T # default value
+Harris_functional F # default value
+ForceAuxCell F # default value
+#:block? Optim.Broyden.History.Steps F
+#:defined? Optim.Broyden.History.Steps F
+#:block? Optim.Broyden.Cycle.On.Maxit F
+#:defined? Optim.Broyden.Cycle.On.Maxit F
+#:block? Optim.Broyden.Variable.Weight F
+#:defined? Optim.Broyden.Variable.Weight F
+#:block? Optim.Broyden.Debug F
+#:defined? Optim.Broyden.Debug F
+#:block? Optim.Broyden.Initial.Inverse.Jacobian F
+#:defined? Optim.Broyden.Initial.Inverse.Jacobian F
+Write.Kpoints F # default value
+Write.Forces T
+Write.DM T
+Write.DM.End.Of.Cycle T # default value
+Write.H F
+Write.H.End.Of.Cycle F # default value
+Write.DM.NetCDF F # default value
+WriteDM.History.NetCDF F # default value
+WriteDMHS.NetCDF F # default value
+WriteDMHS.History.NetCDF F # default value
+SCF.Read.Charge.NetCDF F # default value
+SCF.Read.Deformation.Charge.NetCDF F # default value
+Write.TSHS.History F # default value
+SaveInitialChargeDensity F # default value
+AnalyzeChargeDensityOnly F # default value
+UseNewDiagk F # default value
+Diag.WFS.Cache none # default value
+WriteBands F # default value
+WriteKbands F # default value
+WriteEigenvalues T
+WriteCoorStep T
+WriteMDhistory F # default value
+WriteMDXmol F # default value
+WriteOrbitalIndex T # default value
+Write.Graphviz none # default value
+WriteCoorStep T
+SaveHS F
+ReInitialiseDM T # default value
+DM.AllowReuse T # default value
+DM.AllowExtrapolation T # default value
+DM.History.Depth 1 # default value
+DM.NormalizationTolerance 0.1000000000E-04 # default value
+DM.NormalizeDuringSCF T # default value
+MullikenInSCF F # default value
+SpinInSCF F # default value
+WarningMinimumAtomicDistance 1.000000000 Bohr # default value
+BornCharge F # default value
+ChangeKgridInMD F # default value
+MD.RelaxCellOnly F # default value
+MD.RemoveIntraMolecularPressure F # default value
+COOP.Write F # default value
+SaveRho T
+SaveDeltaRho F
+SaveRhoXC T
+SaveElectrostaticPotential T
+SaveNeutralAtomPotential F
+SaveTotalPotential T
+SaveIonicCharge F
+SaveBaderCharge F
+SaveTotalCharge F
+Siesta2Wannier90.WriteMmn F # default value
+Siesta2Wannier90.WriteUnk F # default value
+Siesta2Wannier90.WriteAmn F # default value
+Siesta2Wannier90.WriteEig F # default value
+#:block? Siesta2Wannier90.NumberOfBandsUp F
+#:defined? Siesta2Wannier90.NumberOfBandsUp F
+#:block? Siesta2Wannier90.NumberOfBandsDown F
+#:defined? Siesta2Wannier90.NumberOfBandsDown F
+#:block? Siesta2Wannier90.NumberOfBands F
+#:defined? Siesta2Wannier90.NumberOfBands F
+Siesta2Wannier90.NumberOfBandsUp 0 # default value
+Siesta2Wannier90.NumberOfBandsDown 0 # default value
+Siesta2Wannier90.NumberOfBands 0 # default value
+CDF.Save T
+CDF.Compress 0 # default value
+CDF.MPI F # default value
+CDF.Read.Parallel F # default value
+CDF.Grid.Precision double
+DM.AllowReuse T # default value
+DM.AllowExtrapolation T # default value
+DM.AllowExtrapolation F # default value
+NumberOfEigenStates 26 # default value
+RcSpatial 0.000000000 Bohr # default value
+ProcessorGridX 1 # default value
+ProcessorGridY 1 # default value
+ProcessorGridZ 1 # default value
+FFT.ProcessorY.traditional F # default value
+processorY 2 # default value
+blocksize 1 # default value
+Spin.Spiral F # default value
+TimeReversalSymmetryForKpoints T # default value
+%block kgrid.MonkhorstPack
+ 6 0 0 0.0
+ 0 6 0 0.0
+ 0 0 1 0.0
+%endblock kgrid.MonkhorstPack
+#:block? ProjectedDensityOfStates F
+#:block? LocalDensityOfStates F
+Diag.ParallelOverK T
+Diag.ProcessorY 4 # default value
+Diag.BlockSize 1 # default value
+Diag.Use2D T # default value
+Diag.UpperLower lower # default value
+Diag.DivideAndConquer T # default value
+Diag.MRRR F # default value
+Diag.NoExpert F # default value
+Diag.Algorithm Divide-and-Conquer # default value
+Diag.AbsTol 0.1000000000E-15 # default value
+Diag.OrFac 0.1000000000E-05 # default value
+Diag.Memory 1.000000000 # default value
+#:block? BandLines T
+#:defined? BandLines T
+#:block? BandPoints F
+#:defined? BandPoints F
+BandLinesScale ReciprocalLatticeVectors
+%block BandLines
+ 1 0.0000000 0.00000000 0.000 \Gamma
+ 30 0.3333333 0.66666666 0.000 K
+ 15 0.5000000 0.50000000 0.000 M
+ 26 0.0000000 0.00000000 0.000 \Gamma
+%endblock BandLines
+#:block? BandLines T
+#:defined? BandLines T
+#:block? BandPoints F
+#:defined? BandPoints F
+BandLinesScale ReciprocalLatticeVectors
+%block BandLines
+ 1 0.0000000 0.00000000 0.000 \Gamma
+ 30 0.3333333 0.66666666 0.000 K
+ 15 0.5000000 0.50000000 0.000 M
+ 26 0.0000000 0.00000000 0.000 \Gamma
+%endblock BandLines
+LongOutput F # default value
+WriteWaveFunctions F # default value
+#:block-line-count? MetaForce (iirrr) 0
+#:block? TS.BufferAtomsLeft F
+#:defined? TS.BufferAtomsLeft F
+#:block? TS.BufferAtomsRight F
+#:defined? TS.BufferAtomsRight F
+#:list? TS.Atoms.Buffer F
+TS.HS.Save F # default value
+TS.DE.Save F # default value
+TS.onlyS F # default value
+TS.S.Save F # default value
+Spin.Spiral F # default value
+TimeReversalSymmetryForKpoints T # default value
+#:list? TS.kgrid.MonkhorstPack F
+#:block? TS.kgrid.Cutoff F
+#:defined? TS.kgrid.Cutoff F
+#:block? TS.kgrid.File F
+#:defined? TS.kgrid.File F
+AtomicCoordinatesFormat Fractional
+AtomCoorFormatOut Fractional # default value
+LatticeConstant 4.648728119 Bohr
+# above item originally: LatticeConstant 2.460000000 Ang
+debug-folding F # default value
+Save.Overlap.Gradient F # default value
+Sonly F # default value
+DM.Init atomic # default value
+DM.Init.RandomStates 0 # default value
+Sonly F # default value
+Debug.DHSCF F # default value
+MeshSubDivisions 2 # default value
+#:list? Mesh.Sizes F
+#:block? MeshSizes F
+#:defined? MeshSizes F
+CDF.Grid.Precision double
+#:block? LocalDensityOfStates F
+#:defined? LocalDensityOfStates F
+XC.Use.BSC.CellXC F # default value
+DirectPhi F # default value
+SimulateDoping F # default value
+Slab.DipoleCorrection none # default value
+Read-H-from-file F # default value
+timing-split-scf-steps F # default value
+SingleExcitation F # default value
+OccupationFunction MP
+OccupationMPOrder 1
+OccupationFunction MP
+OccupationMPOrder 1
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+timing-split-scf-steps F # default value
+compute-forces T # default value
+#:list? Grid.CellSampling F
+Read-H-from-file F # default value
+WriteCoorXmol F # default value
+WriteCoorCerius F # default value
+WFS.Write.For.Bands F # default value
+BasisPressure 0.2000000000 GPa # default value
+OpticalCalculation F # default value
diff --git a/graphene/siesta/SG15v1.2/ref/fort.14 b/graphene/siesta/SG15v1.2/ref/fort.14
new file mode 100644
index 0000000..7b3d90a
--- /dev/null
+++ b/graphene/siesta/SG15v1.2/ref/fort.14
@@ -0,0 +1,44 @@
+%YAML 1.2
+---
+
+siesta:
+ version: "MaX-1.0-55-g0612142bc"
+ arch: "----"
+ compiler: "GNU-10.3.0"
+ fflags: "-O3 -funroll-loops -funsafe-math-optimizations -fallow-argument-mismatch -fallow-argument-mismatch;"
+ fppflags: "----"
+ libs: "----"
+ build: "mpi"
+ openmp: "no"
+ gemm3m: "no"
+ netcdf: "yes"
+ netcdf4: "yes"
+ netcdf4_mpi: "no"
+ metis: "no"
+ chess: "no"
+ elpa: "no"
+ flook: "no"
+ pexsi: "no"
+
+energies:
+ Ebs: -0.76346259E+01
+ Eions: 0.67025869E+02
+ Ena: 0.33885912E+02
+ Ekin: 0.16619199E+02
+ Enl: 0.11502618E+01
+ Eso: 0.00000000E+00
+ Edftu: 0.00000000E+00
+ DEna: -0.51980083E+00
+ DUscf: 0.34721790E-01
+ DUext: 0.00000000E+00
+ Exc: -0.69589019E+01
+ Ecorrec: 0.00000000E+00
+ Emadel: 0.00000000E+00
+ Emeta: 0.00000000E+00
+ Emolmec: 0.00000000E+00
+ Ekinion: 0.00000000E+00
+ Eharris: -0.22814477E+02
+ Etot: -0.22814477E+02
+ FreeEng: -0.22814479E+02
+
+...
diff --git a/graphene/siesta/SG15v1.2/ref/graphene.BONDS b/graphene/siesta/SG15v1.2/ref/graphene.BONDS
new file mode 100644
index 0000000..c496df3
--- /dev/null
+++ b/graphene/siesta/SG15v1.2/ref/graphene.BONDS
@@ -0,0 +1,26 @@
+Neighbors of: 1 C at: 2.3244 1.3420 4.2434
+ 2 C 1.4203 Ang. Really at: 0.0000 2.6839 4.2434
+ 2 C 1.4203 Ang. Really at: 2.3244 -1.3420 4.2434
+ 2 C 1.4203 Ang. Really at: 4.6487 2.6839 4.2434
+ 1 C 2.4600 Ang. Really at: 6.9731 1.3420 4.2434
+ 1 C 2.4600 Ang. Really at: -2.3244 1.3420 4.2434
+ 1 C 2.4600 Ang. Really at: 4.6487 -2.6839 4.2434
+ 1 C 2.4600 Ang. Really at: 0.0000 5.3679 4.2434
+ 1 C 2.4600 Ang. Really at: 4.6487 5.3679 4.2434
+ 1 C 2.4600 Ang. Really at: -0.0000 -2.6839 4.2434
+ 2 C 2.8406 Ang. Really at: -2.3244 -1.3420 4.2434
+ 2 C 2.8406 Ang. Really at: 6.9731 -1.3420 4.2434
+ 2 C 2.8406 Ang. Really at: 2.3244 6.7099 4.2434
+Neighbors of: 2 C at: 4.6487 2.6839 4.2434
+ 1 C 1.4203 Ang. Really at: 6.9731 1.3420 4.2434
+ 1 C 1.4203 Ang. Really at: 4.6487 5.3679 4.2434
+ 1 C 1.4203 Ang. Really at: 2.3244 1.3420 4.2434
+ 2 C 2.4600 Ang. Really at: 9.2975 2.6839 4.2434
+ 2 C 2.4600 Ang. Really at: 0.0000 2.6839 4.2434
+ 2 C 2.4600 Ang. Really at: 6.9731 -1.3420 4.2434
+ 2 C 2.4600 Ang. Really at: 2.3244 6.7099 4.2434
+ 2 C 2.4600 Ang. Really at: 2.3244 -1.3420 4.2434
+ 2 C 2.4600 Ang. Really at: 6.9731 6.7099 4.2434
+ 1 C 2.8406 Ang. Really at: 9.2975 5.3679 4.2434
+ 1 C 2.8406 Ang. Really at: 0.0000 5.3679 4.2434
+ 1 C 2.8406 Ang. Really at: 4.6487 -2.6839 4.2434
diff --git a/graphene/siesta/SG15v1.2/ref/graphene.BONDS_FINAL b/graphene/siesta/SG15v1.2/ref/graphene.BONDS_FINAL
new file mode 100644
index 0000000..c496df3
--- /dev/null
+++ b/graphene/siesta/SG15v1.2/ref/graphene.BONDS_FINAL
@@ -0,0 +1,26 @@
+Neighbors of: 1 C at: 2.3244 1.3420 4.2434
+ 2 C 1.4203 Ang. Really at: 0.0000 2.6839 4.2434
+ 2 C 1.4203 Ang. Really at: 2.3244 -1.3420 4.2434
+ 2 C 1.4203 Ang. Really at: 4.6487 2.6839 4.2434
+ 1 C 2.4600 Ang. Really at: 6.9731 1.3420 4.2434
+ 1 C 2.4600 Ang. Really at: -2.3244 1.3420 4.2434
+ 1 C 2.4600 Ang. Really at: 4.6487 -2.6839 4.2434
+ 1 C 2.4600 Ang. Really at: 0.0000 5.3679 4.2434
+ 1 C 2.4600 Ang. Really at: 4.6487 5.3679 4.2434
+ 1 C 2.4600 Ang. Really at: -0.0000 -2.6839 4.2434
+ 2 C 2.8406 Ang. Really at: -2.3244 -1.3420 4.2434
+ 2 C 2.8406 Ang. Really at: 6.9731 -1.3420 4.2434
+ 2 C 2.8406 Ang. Really at: 2.3244 6.7099 4.2434
+Neighbors of: 2 C at: 4.6487 2.6839 4.2434
+ 1 C 1.4203 Ang. Really at: 6.9731 1.3420 4.2434
+ 1 C 1.4203 Ang. Really at: 4.6487 5.3679 4.2434
+ 1 C 1.4203 Ang. Really at: 2.3244 1.3420 4.2434
+ 2 C 2.4600 Ang. Really at: 9.2975 2.6839 4.2434
+ 2 C 2.4600 Ang. Really at: 0.0000 2.6839 4.2434
+ 2 C 2.4600 Ang. Really at: 6.9731 -1.3420 4.2434
+ 2 C 2.4600 Ang. Really at: 2.3244 6.7099 4.2434
+ 2 C 2.4600 Ang. Really at: 2.3244 -1.3420 4.2434
+ 2 C 2.4600 Ang. Really at: 6.9731 6.7099 4.2434
+ 1 C 2.8406 Ang. Really at: 9.2975 5.3679 4.2434
+ 1 C 2.8406 Ang. Really at: 0.0000 5.3679 4.2434
+ 1 C 2.8406 Ang. Really at: 4.6487 -2.6839 4.2434
diff --git a/graphene/siesta/SG15v1.2/ref/graphene.DM b/graphene/siesta/SG15v1.2/ref/graphene.DM
new file mode 100644
index 0000000..5eb4d7d
Binary files /dev/null and b/graphene/siesta/SG15v1.2/ref/graphene.DM differ
diff --git a/graphene/siesta/SG15v1.2/ref/graphene.EIG b/graphene/siesta/SG15v1.2/ref/graphene.EIG
new file mode 100644
index 0000000..d30a3a9
--- /dev/null
+++ b/graphene/siesta/SG15v1.2/ref/graphene.EIG
@@ -0,0 +1,68 @@
+ -0.388232477E+01
+ 26 1 22
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diff --git a/graphene/siesta/SG15v1.2/ref/graphene.FA b/graphene/siesta/SG15v1.2/ref/graphene.FA
new file mode 100644
index 0000000..232c265
--- /dev/null
+++ b/graphene/siesta/SG15v1.2/ref/graphene.FA
@@ -0,0 +1,3 @@
+ 2
+ 1 -0.488288403E-06 -0.894107724E-07 0.183733645E-03
+ 2 0.525082276E-06 -0.898987629E-07 0.183772360E-03
diff --git a/graphene/siesta/SG15v1.2/ref/graphene.KP b/graphene/siesta/SG15v1.2/ref/graphene.KP
new file mode 100644
index 0000000..f5fc0c0
--- /dev/null
+++ b/graphene/siesta/SG15v1.2/ref/graphene.KP
@@ -0,0 +1,23 @@
+ 22
+ 1 -0.450531E+00 0.260114E+00 0.000000E+00 0.555556E-01
+ 2 -0.225265E+00 0.130057E+00 0.000000E+00 0.555556E-01
+ 3 0.000000E+00 0.000000E+00 0.000000E+00 0.277778E-01
+ 4 0.675796E+00 -0.390171E+00 0.000000E+00 0.277778E-01
+ 5 -0.450531E+00 0.520228E+00 0.000000E+00 0.555556E-01
+ 6 -0.225265E+00 0.390171E+00 0.000000E+00 0.555556E-01
+ 7 0.000000E+00 0.260114E+00 0.000000E+00 0.555556E-01
+ 8 0.225265E+00 0.130057E+00 0.000000E+00 0.555556E-01
+ 9 0.450531E+00 -0.559538E-10 0.000000E+00 0.555556E-01
+ 10 0.675796E+00 -0.130057E+00 0.000000E+00 0.555556E-01
+ 11 -0.450531E+00 0.780342E+00 0.000000E+00 0.555556E-01
+ 12 -0.225265E+00 0.650285E+00 0.000000E+00 0.555556E-01
+ 13 0.000000E+00 0.520228E+00 0.000000E+00 0.555556E-01
+ 14 0.225265E+00 0.390171E+00 0.000000E+00 0.555556E-01
+ 15 0.450531E+00 0.260114E+00 0.000000E+00 0.555556E-01
+ 16 0.675796E+00 0.130057E+00 0.000000E+00 0.555556E-01
+ 17 -0.450531E+00 0.104046E+01 0.000000E+00 0.277778E-01
+ 18 -0.225265E+00 0.910399E+00 0.000000E+00 0.277778E-01
+ 19 0.000000E+00 0.780342E+00 0.000000E+00 0.277778E-01
+ 20 0.225265E+00 0.650285E+00 0.000000E+00 0.277778E-01
+ 21 0.450531E+00 0.520228E+00 0.000000E+00 0.277778E-01
+ 22 0.675796E+00 0.390171E+00 0.000000E+00 0.277778E-01
diff --git a/graphene/siesta/SG15v1.2/ref/graphene.ORB_INDX b/graphene/siesta/SG15v1.2/ref/graphene.ORB_INDX
new file mode 100644
index 0000000..4ca7be2
--- /dev/null
+++ b/graphene/siesta/SG15v1.2/ref/graphene.ORB_INDX
@@ -0,0 +1,672 @@
+ 26 650 = orbitals in unit cell and supercell. See end of file.
+
+ io ia is spec iao n l m z p sym rc isc iuo
+ 1 1 1 C 1 2 0 0 1 F s 4.192 0 0 0 1
+ 2 1 1 C 2 2 0 0 2 F s 3.432 0 0 0 2
+ 3 1 1 C 3 2 1 -1 1 F py 4.870 0 0 0 3
+ 4 1 1 C 4 2 1 0 1 F pz 4.870 0 0 0 4
+ 5 1 1 C 5 2 1 1 1 F px 4.870 0 0 0 5
+ 6 1 1 C 6 2 1 -1 2 F py 3.475 0 0 0 6
+ 7 1 1 C 7 2 1 0 2 F pz 3.475 0 0 0 7
+ 8 1 1 C 8 2 1 1 2 F px 3.475 0 0 0 8
+ 9 1 1 C 9 3 2 -2 1 T Pdxy 4.870 0 0 0 9
+ 10 1 1 C 10 3 2 -1 1 T Pdyz 4.870 0 0 0 10
+ 11 1 1 C 11 3 2 0 1 T Pdz2 4.870 0 0 0 11
+ 12 1 1 C 12 3 2 1 1 T Pdxz 4.870 0 0 0 12
+ 13 1 1 C 13 3 2 2 1 T Pdx2-y2 4.870 0 0 0 13
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+ 369 29 1 C 5 2 1 1 1 F px 4.870 -1 2 0 5
+ 370 29 1 C 6 2 1 -1 2 F py 3.475 -1 2 0 6
+ 371 29 1 C 7 2 1 0 2 F pz 3.475 -1 2 0 7
+ 372 29 1 C 8 2 1 1 2 F px 3.475 -1 2 0 8
+ 373 29 1 C 9 3 2 -2 1 T Pdxy 4.870 -1 2 0 9
+ 374 29 1 C 10 3 2 -1 1 T Pdyz 4.870 -1 2 0 10
+ 375 29 1 C 11 3 2 0 1 T Pdz2 4.870 -1 2 0 11
+ 376 29 1 C 12 3 2 1 1 T Pdxz 4.870 -1 2 0 12
+ 377 29 1 C 13 3 2 2 1 T Pdx2-y2 4.870 -1 2 0 13
+ 378 30 1 C 1 2 0 0 1 F s 4.192 -1 2 0 14
+ 379 30 1 C 2 2 0 0 2 F s 3.432 -1 2 0 15
+ 380 30 1 C 3 2 1 -1 1 F py 4.870 -1 2 0 16
+ 381 30 1 C 4 2 1 0 1 F pz 4.870 -1 2 0 17
+ 382 30 1 C 5 2 1 1 1 F px 4.870 -1 2 0 18
+ 383 30 1 C 6 2 1 -1 2 F py 3.475 -1 2 0 19
+ 384 30 1 C 7 2 1 0 2 F pz 3.475 -1 2 0 20
+ 385 30 1 C 8 2 1 1 2 F px 3.475 -1 2 0 21
+ 386 30 1 C 9 3 2 -2 1 T Pdxy 4.870 -1 2 0 22
+ 387 30 1 C 10 3 2 -1 1 T Pdyz 4.870 -1 2 0 23
+ 388 30 1 C 11 3 2 0 1 T Pdz2 4.870 -1 2 0 24
+ 389 30 1 C 12 3 2 1 1 T Pdxz 4.870 -1 2 0 25
+ 390 30 1 C 13 3 2 2 1 T Pdx2-y2 4.870 -1 2 0 26
+ 391 31 1 C 1 2 0 0 1 F s 4.192 0 -2 0 1
+ 392 31 1 C 2 2 0 0 2 F s 3.432 0 -2 0 2
+ 393 31 1 C 3 2 1 -1 1 F py 4.870 0 -2 0 3
+ 394 31 1 C 4 2 1 0 1 F pz 4.870 0 -2 0 4
+ 395 31 1 C 5 2 1 1 1 F px 4.870 0 -2 0 5
+ 396 31 1 C 6 2 1 -1 2 F py 3.475 0 -2 0 6
+ 397 31 1 C 7 2 1 0 2 F pz 3.475 0 -2 0 7
+ 398 31 1 C 8 2 1 1 2 F px 3.475 0 -2 0 8
+ 399 31 1 C 9 3 2 -2 1 T Pdxy 4.870 0 -2 0 9
+ 400 31 1 C 10 3 2 -1 1 T Pdyz 4.870 0 -2 0 10
+ 401 31 1 C 11 3 2 0 1 T Pdz2 4.870 0 -2 0 11
+ 402 31 1 C 12 3 2 1 1 T Pdxz 4.870 0 -2 0 12
+ 403 31 1 C 13 3 2 2 1 T Pdx2-y2 4.870 0 -2 0 13
+ 404 32 1 C 1 2 0 0 1 F s 4.192 0 -2 0 14
+ 405 32 1 C 2 2 0 0 2 F s 3.432 0 -2 0 15
+ 406 32 1 C 3 2 1 -1 1 F py 4.870 0 -2 0 16
+ 407 32 1 C 4 2 1 0 1 F pz 4.870 0 -2 0 17
+ 408 32 1 C 5 2 1 1 1 F px 4.870 0 -2 0 18
+ 409 32 1 C 6 2 1 -1 2 F py 3.475 0 -2 0 19
+ 410 32 1 C 7 2 1 0 2 F pz 3.475 0 -2 0 20
+ 411 32 1 C 8 2 1 1 2 F px 3.475 0 -2 0 21
+ 412 32 1 C 9 3 2 -2 1 T Pdxy 4.870 0 -2 0 22
+ 413 32 1 C 10 3 2 -1 1 T Pdyz 4.870 0 -2 0 23
+ 414 32 1 C 11 3 2 0 1 T Pdz2 4.870 0 -2 0 24
+ 415 32 1 C 12 3 2 1 1 T Pdxz 4.870 0 -2 0 25
+ 416 32 1 C 13 3 2 2 1 T Pdx2-y2 4.870 0 -2 0 26
+ 417 33 1 C 1 2 0 0 1 F s 4.192 1 -2 0 1
+ 418 33 1 C 2 2 0 0 2 F s 3.432 1 -2 0 2
+ 419 33 1 C 3 2 1 -1 1 F py 4.870 1 -2 0 3
+ 420 33 1 C 4 2 1 0 1 F pz 4.870 1 -2 0 4
+ 421 33 1 C 5 2 1 1 1 F px 4.870 1 -2 0 5
+ 422 33 1 C 6 2 1 -1 2 F py 3.475 1 -2 0 6
+ 423 33 1 C 7 2 1 0 2 F pz 3.475 1 -2 0 7
+ 424 33 1 C 8 2 1 1 2 F px 3.475 1 -2 0 8
+ 425 33 1 C 9 3 2 -2 1 T Pdxy 4.870 1 -2 0 9
+ 426 33 1 C 10 3 2 -1 1 T Pdyz 4.870 1 -2 0 10
+ 427 33 1 C 11 3 2 0 1 T Pdz2 4.870 1 -2 0 11
+ 428 33 1 C 12 3 2 1 1 T Pdxz 4.870 1 -2 0 12
+ 429 33 1 C 13 3 2 2 1 T Pdx2-y2 4.870 1 -2 0 13
+ 430 34 1 C 1 2 0 0 1 F s 4.192 1 -2 0 14
+ 431 34 1 C 2 2 0 0 2 F s 3.432 1 -2 0 15
+ 432 34 1 C 3 2 1 -1 1 F py 4.870 1 -2 0 16
+ 433 34 1 C 4 2 1 0 1 F pz 4.870 1 -2 0 17
+ 434 34 1 C 5 2 1 1 1 F px 4.870 1 -2 0 18
+ 435 34 1 C 6 2 1 -1 2 F py 3.475 1 -2 0 19
+ 436 34 1 C 7 2 1 0 2 F pz 3.475 1 -2 0 20
+ 437 34 1 C 8 2 1 1 2 F px 3.475 1 -2 0 21
+ 438 34 1 C 9 3 2 -2 1 T Pdxy 4.870 1 -2 0 22
+ 439 34 1 C 10 3 2 -1 1 T Pdyz 4.870 1 -2 0 23
+ 440 34 1 C 11 3 2 0 1 T Pdz2 4.870 1 -2 0 24
+ 441 34 1 C 12 3 2 1 1 T Pdxz 4.870 1 -2 0 25
+ 442 34 1 C 13 3 2 2 1 T Pdx2-y2 4.870 1 -2 0 26
+ 443 35 1 C 1 2 0 0 1 F s 4.192 2 -2 0 1
+ 444 35 1 C 2 2 0 0 2 F s 3.432 2 -2 0 2
+ 445 35 1 C 3 2 1 -1 1 F py 4.870 2 -2 0 3
+ 446 35 1 C 4 2 1 0 1 F pz 4.870 2 -2 0 4
+ 447 35 1 C 5 2 1 1 1 F px 4.870 2 -2 0 5
+ 448 35 1 C 6 2 1 -1 2 F py 3.475 2 -2 0 6
+ 449 35 1 C 7 2 1 0 2 F pz 3.475 2 -2 0 7
+ 450 35 1 C 8 2 1 1 2 F px 3.475 2 -2 0 8
+ 451 35 1 C 9 3 2 -2 1 T Pdxy 4.870 2 -2 0 9
+ 452 35 1 C 10 3 2 -1 1 T Pdyz 4.870 2 -2 0 10
+ 453 35 1 C 11 3 2 0 1 T Pdz2 4.870 2 -2 0 11
+ 454 35 1 C 12 3 2 1 1 T Pdxz 4.870 2 -2 0 12
+ 455 35 1 C 13 3 2 2 1 T Pdx2-y2 4.870 2 -2 0 13
+ 456 36 1 C 1 2 0 0 1 F s 4.192 2 -2 0 14
+ 457 36 1 C 2 2 0 0 2 F s 3.432 2 -2 0 15
+ 458 36 1 C 3 2 1 -1 1 F py 4.870 2 -2 0 16
+ 459 36 1 C 4 2 1 0 1 F pz 4.870 2 -2 0 17
+ 460 36 1 C 5 2 1 1 1 F px 4.870 2 -2 0 18
+ 461 36 1 C 6 2 1 -1 2 F py 3.475 2 -2 0 19
+ 462 36 1 C 7 2 1 0 2 F pz 3.475 2 -2 0 20
+ 463 36 1 C 8 2 1 1 2 F px 3.475 2 -2 0 21
+ 464 36 1 C 9 3 2 -2 1 T Pdxy 4.870 2 -2 0 22
+ 465 36 1 C 10 3 2 -1 1 T Pdyz 4.870 2 -2 0 23
+ 466 36 1 C 11 3 2 0 1 T Pdz2 4.870 2 -2 0 24
+ 467 36 1 C 12 3 2 1 1 T Pdxz 4.870 2 -2 0 25
+ 468 36 1 C 13 3 2 2 1 T Pdx2-y2 4.870 2 -2 0 26
+ 469 37 1 C 1 2 0 0 1 F s 4.192 -2 -2 0 1
+ 470 37 1 C 2 2 0 0 2 F s 3.432 -2 -2 0 2
+ 471 37 1 C 3 2 1 -1 1 F py 4.870 -2 -2 0 3
+ 472 37 1 C 4 2 1 0 1 F pz 4.870 -2 -2 0 4
+ 473 37 1 C 5 2 1 1 1 F px 4.870 -2 -2 0 5
+ 474 37 1 C 6 2 1 -1 2 F py 3.475 -2 -2 0 6
+ 475 37 1 C 7 2 1 0 2 F pz 3.475 -2 -2 0 7
+ 476 37 1 C 8 2 1 1 2 F px 3.475 -2 -2 0 8
+ 477 37 1 C 9 3 2 -2 1 T Pdxy 4.870 -2 -2 0 9
+ 478 37 1 C 10 3 2 -1 1 T Pdyz 4.870 -2 -2 0 10
+ 479 37 1 C 11 3 2 0 1 T Pdz2 4.870 -2 -2 0 11
+ 480 37 1 C 12 3 2 1 1 T Pdxz 4.870 -2 -2 0 12
+ 481 37 1 C 13 3 2 2 1 T Pdx2-y2 4.870 -2 -2 0 13
+ 482 38 1 C 1 2 0 0 1 F s 4.192 -2 -2 0 14
+ 483 38 1 C 2 2 0 0 2 F s 3.432 -2 -2 0 15
+ 484 38 1 C 3 2 1 -1 1 F py 4.870 -2 -2 0 16
+ 485 38 1 C 4 2 1 0 1 F pz 4.870 -2 -2 0 17
+ 486 38 1 C 5 2 1 1 1 F px 4.870 -2 -2 0 18
+ 487 38 1 C 6 2 1 -1 2 F py 3.475 -2 -2 0 19
+ 488 38 1 C 7 2 1 0 2 F pz 3.475 -2 -2 0 20
+ 489 38 1 C 8 2 1 1 2 F px 3.475 -2 -2 0 21
+ 490 38 1 C 9 3 2 -2 1 T Pdxy 4.870 -2 -2 0 22
+ 491 38 1 C 10 3 2 -1 1 T Pdyz 4.870 -2 -2 0 23
+ 492 38 1 C 11 3 2 0 1 T Pdz2 4.870 -2 -2 0 24
+ 493 38 1 C 12 3 2 1 1 T Pdxz 4.870 -2 -2 0 25
+ 494 38 1 C 13 3 2 2 1 T Pdx2-y2 4.870 -2 -2 0 26
+ 495 39 1 C 1 2 0 0 1 F s 4.192 -1 -2 0 1
+ 496 39 1 C 2 2 0 0 2 F s 3.432 -1 -2 0 2
+ 497 39 1 C 3 2 1 -1 1 F py 4.870 -1 -2 0 3
+ 498 39 1 C 4 2 1 0 1 F pz 4.870 -1 -2 0 4
+ 499 39 1 C 5 2 1 1 1 F px 4.870 -1 -2 0 5
+ 500 39 1 C 6 2 1 -1 2 F py 3.475 -1 -2 0 6
+ 501 39 1 C 7 2 1 0 2 F pz 3.475 -1 -2 0 7
+ 502 39 1 C 8 2 1 1 2 F px 3.475 -1 -2 0 8
+ 503 39 1 C 9 3 2 -2 1 T Pdxy 4.870 -1 -2 0 9
+ 504 39 1 C 10 3 2 -1 1 T Pdyz 4.870 -1 -2 0 10
+ 505 39 1 C 11 3 2 0 1 T Pdz2 4.870 -1 -2 0 11
+ 506 39 1 C 12 3 2 1 1 T Pdxz 4.870 -1 -2 0 12
+ 507 39 1 C 13 3 2 2 1 T Pdx2-y2 4.870 -1 -2 0 13
+ 508 40 1 C 1 2 0 0 1 F s 4.192 -1 -2 0 14
+ 509 40 1 C 2 2 0 0 2 F s 3.432 -1 -2 0 15
+ 510 40 1 C 3 2 1 -1 1 F py 4.870 -1 -2 0 16
+ 511 40 1 C 4 2 1 0 1 F pz 4.870 -1 -2 0 17
+ 512 40 1 C 5 2 1 1 1 F px 4.870 -1 -2 0 18
+ 513 40 1 C 6 2 1 -1 2 F py 3.475 -1 -2 0 19
+ 514 40 1 C 7 2 1 0 2 F pz 3.475 -1 -2 0 20
+ 515 40 1 C 8 2 1 1 2 F px 3.475 -1 -2 0 21
+ 516 40 1 C 9 3 2 -2 1 T Pdxy 4.870 -1 -2 0 22
+ 517 40 1 C 10 3 2 -1 1 T Pdyz 4.870 -1 -2 0 23
+ 518 40 1 C 11 3 2 0 1 T Pdz2 4.870 -1 -2 0 24
+ 519 40 1 C 12 3 2 1 1 T Pdxz 4.870 -1 -2 0 25
+ 520 40 1 C 13 3 2 2 1 T Pdx2-y2 4.870 -1 -2 0 26
+ 521 41 1 C 1 2 0 0 1 F s 4.192 0 -1 0 1
+ 522 41 1 C 2 2 0 0 2 F s 3.432 0 -1 0 2
+ 523 41 1 C 3 2 1 -1 1 F py 4.870 0 -1 0 3
+ 524 41 1 C 4 2 1 0 1 F pz 4.870 0 -1 0 4
+ 525 41 1 C 5 2 1 1 1 F px 4.870 0 -1 0 5
+ 526 41 1 C 6 2 1 -1 2 F py 3.475 0 -1 0 6
+ 527 41 1 C 7 2 1 0 2 F pz 3.475 0 -1 0 7
+ 528 41 1 C 8 2 1 1 2 F px 3.475 0 -1 0 8
+ 529 41 1 C 9 3 2 -2 1 T Pdxy 4.870 0 -1 0 9
+ 530 41 1 C 10 3 2 -1 1 T Pdyz 4.870 0 -1 0 10
+ 531 41 1 C 11 3 2 0 1 T Pdz2 4.870 0 -1 0 11
+ 532 41 1 C 12 3 2 1 1 T Pdxz 4.870 0 -1 0 12
+ 533 41 1 C 13 3 2 2 1 T Pdx2-y2 4.870 0 -1 0 13
+ 534 42 1 C 1 2 0 0 1 F s 4.192 0 -1 0 14
+ 535 42 1 C 2 2 0 0 2 F s 3.432 0 -1 0 15
+ 536 42 1 C 3 2 1 -1 1 F py 4.870 0 -1 0 16
+ 537 42 1 C 4 2 1 0 1 F pz 4.870 0 -1 0 17
+ 538 42 1 C 5 2 1 1 1 F px 4.870 0 -1 0 18
+ 539 42 1 C 6 2 1 -1 2 F py 3.475 0 -1 0 19
+ 540 42 1 C 7 2 1 0 2 F pz 3.475 0 -1 0 20
+ 541 42 1 C 8 2 1 1 2 F px 3.475 0 -1 0 21
+ 542 42 1 C 9 3 2 -2 1 T Pdxy 4.870 0 -1 0 22
+ 543 42 1 C 10 3 2 -1 1 T Pdyz 4.870 0 -1 0 23
+ 544 42 1 C 11 3 2 0 1 T Pdz2 4.870 0 -1 0 24
+ 545 42 1 C 12 3 2 1 1 T Pdxz 4.870 0 -1 0 25
+ 546 42 1 C 13 3 2 2 1 T Pdx2-y2 4.870 0 -1 0 26
+ 547 43 1 C 1 2 0 0 1 F s 4.192 1 -1 0 1
+ 548 43 1 C 2 2 0 0 2 F s 3.432 1 -1 0 2
+ 549 43 1 C 3 2 1 -1 1 F py 4.870 1 -1 0 3
+ 550 43 1 C 4 2 1 0 1 F pz 4.870 1 -1 0 4
+ 551 43 1 C 5 2 1 1 1 F px 4.870 1 -1 0 5
+ 552 43 1 C 6 2 1 -1 2 F py 3.475 1 -1 0 6
+ 553 43 1 C 7 2 1 0 2 F pz 3.475 1 -1 0 7
+ 554 43 1 C 8 2 1 1 2 F px 3.475 1 -1 0 8
+ 555 43 1 C 9 3 2 -2 1 T Pdxy 4.870 1 -1 0 9
+ 556 43 1 C 10 3 2 -1 1 T Pdyz 4.870 1 -1 0 10
+ 557 43 1 C 11 3 2 0 1 T Pdz2 4.870 1 -1 0 11
+ 558 43 1 C 12 3 2 1 1 T Pdxz 4.870 1 -1 0 12
+ 559 43 1 C 13 3 2 2 1 T Pdx2-y2 4.870 1 -1 0 13
+ 560 44 1 C 1 2 0 0 1 F s 4.192 1 -1 0 14
+ 561 44 1 C 2 2 0 0 2 F s 3.432 1 -1 0 15
+ 562 44 1 C 3 2 1 -1 1 F py 4.870 1 -1 0 16
+ 563 44 1 C 4 2 1 0 1 F pz 4.870 1 -1 0 17
+ 564 44 1 C 5 2 1 1 1 F px 4.870 1 -1 0 18
+ 565 44 1 C 6 2 1 -1 2 F py 3.475 1 -1 0 19
+ 566 44 1 C 7 2 1 0 2 F pz 3.475 1 -1 0 20
+ 567 44 1 C 8 2 1 1 2 F px 3.475 1 -1 0 21
+ 568 44 1 C 9 3 2 -2 1 T Pdxy 4.870 1 -1 0 22
+ 569 44 1 C 10 3 2 -1 1 T Pdyz 4.870 1 -1 0 23
+ 570 44 1 C 11 3 2 0 1 T Pdz2 4.870 1 -1 0 24
+ 571 44 1 C 12 3 2 1 1 T Pdxz 4.870 1 -1 0 25
+ 572 44 1 C 13 3 2 2 1 T Pdx2-y2 4.870 1 -1 0 26
+ 573 45 1 C 1 2 0 0 1 F s 4.192 2 -1 0 1
+ 574 45 1 C 2 2 0 0 2 F s 3.432 2 -1 0 2
+ 575 45 1 C 3 2 1 -1 1 F py 4.870 2 -1 0 3
+ 576 45 1 C 4 2 1 0 1 F pz 4.870 2 -1 0 4
+ 577 45 1 C 5 2 1 1 1 F px 4.870 2 -1 0 5
+ 578 45 1 C 6 2 1 -1 2 F py 3.475 2 -1 0 6
+ 579 45 1 C 7 2 1 0 2 F pz 3.475 2 -1 0 7
+ 580 45 1 C 8 2 1 1 2 F px 3.475 2 -1 0 8
+ 581 45 1 C 9 3 2 -2 1 T Pdxy 4.870 2 -1 0 9
+ 582 45 1 C 10 3 2 -1 1 T Pdyz 4.870 2 -1 0 10
+ 583 45 1 C 11 3 2 0 1 T Pdz2 4.870 2 -1 0 11
+ 584 45 1 C 12 3 2 1 1 T Pdxz 4.870 2 -1 0 12
+ 585 45 1 C 13 3 2 2 1 T Pdx2-y2 4.870 2 -1 0 13
+ 586 46 1 C 1 2 0 0 1 F s 4.192 2 -1 0 14
+ 587 46 1 C 2 2 0 0 2 F s 3.432 2 -1 0 15
+ 588 46 1 C 3 2 1 -1 1 F py 4.870 2 -1 0 16
+ 589 46 1 C 4 2 1 0 1 F pz 4.870 2 -1 0 17
+ 590 46 1 C 5 2 1 1 1 F px 4.870 2 -1 0 18
+ 591 46 1 C 6 2 1 -1 2 F py 3.475 2 -1 0 19
+ 592 46 1 C 7 2 1 0 2 F pz 3.475 2 -1 0 20
+ 593 46 1 C 8 2 1 1 2 F px 3.475 2 -1 0 21
+ 594 46 1 C 9 3 2 -2 1 T Pdxy 4.870 2 -1 0 22
+ 595 46 1 C 10 3 2 -1 1 T Pdyz 4.870 2 -1 0 23
+ 596 46 1 C 11 3 2 0 1 T Pdz2 4.870 2 -1 0 24
+ 597 46 1 C 12 3 2 1 1 T Pdxz 4.870 2 -1 0 25
+ 598 46 1 C 13 3 2 2 1 T Pdx2-y2 4.870 2 -1 0 26
+ 599 47 1 C 1 2 0 0 1 F s 4.192 -2 -1 0 1
+ 600 47 1 C 2 2 0 0 2 F s 3.432 -2 -1 0 2
+ 601 47 1 C 3 2 1 -1 1 F py 4.870 -2 -1 0 3
+ 602 47 1 C 4 2 1 0 1 F pz 4.870 -2 -1 0 4
+ 603 47 1 C 5 2 1 1 1 F px 4.870 -2 -1 0 5
+ 604 47 1 C 6 2 1 -1 2 F py 3.475 -2 -1 0 6
+ 605 47 1 C 7 2 1 0 2 F pz 3.475 -2 -1 0 7
+ 606 47 1 C 8 2 1 1 2 F px 3.475 -2 -1 0 8
+ 607 47 1 C 9 3 2 -2 1 T Pdxy 4.870 -2 -1 0 9
+ 608 47 1 C 10 3 2 -1 1 T Pdyz 4.870 -2 -1 0 10
+ 609 47 1 C 11 3 2 0 1 T Pdz2 4.870 -2 -1 0 11
+ 610 47 1 C 12 3 2 1 1 T Pdxz 4.870 -2 -1 0 12
+ 611 47 1 C 13 3 2 2 1 T Pdx2-y2 4.870 -2 -1 0 13
+ 612 48 1 C 1 2 0 0 1 F s 4.192 -2 -1 0 14
+ 613 48 1 C 2 2 0 0 2 F s 3.432 -2 -1 0 15
+ 614 48 1 C 3 2 1 -1 1 F py 4.870 -2 -1 0 16
+ 615 48 1 C 4 2 1 0 1 F pz 4.870 -2 -1 0 17
+ 616 48 1 C 5 2 1 1 1 F px 4.870 -2 -1 0 18
+ 617 48 1 C 6 2 1 -1 2 F py 3.475 -2 -1 0 19
+ 618 48 1 C 7 2 1 0 2 F pz 3.475 -2 -1 0 20
+ 619 48 1 C 8 2 1 1 2 F px 3.475 -2 -1 0 21
+ 620 48 1 C 9 3 2 -2 1 T Pdxy 4.870 -2 -1 0 22
+ 621 48 1 C 10 3 2 -1 1 T Pdyz 4.870 -2 -1 0 23
+ 622 48 1 C 11 3 2 0 1 T Pdz2 4.870 -2 -1 0 24
+ 623 48 1 C 12 3 2 1 1 T Pdxz 4.870 -2 -1 0 25
+ 624 48 1 C 13 3 2 2 1 T Pdx2-y2 4.870 -2 -1 0 26
+ 625 49 1 C 1 2 0 0 1 F s 4.192 -1 -1 0 1
+ 626 49 1 C 2 2 0 0 2 F s 3.432 -1 -1 0 2
+ 627 49 1 C 3 2 1 -1 1 F py 4.870 -1 -1 0 3
+ 628 49 1 C 4 2 1 0 1 F pz 4.870 -1 -1 0 4
+ 629 49 1 C 5 2 1 1 1 F px 4.870 -1 -1 0 5
+ 630 49 1 C 6 2 1 -1 2 F py 3.475 -1 -1 0 6
+ 631 49 1 C 7 2 1 0 2 F pz 3.475 -1 -1 0 7
+ 632 49 1 C 8 2 1 1 2 F px 3.475 -1 -1 0 8
+ 633 49 1 C 9 3 2 -2 1 T Pdxy 4.870 -1 -1 0 9
+ 634 49 1 C 10 3 2 -1 1 T Pdyz 4.870 -1 -1 0 10
+ 635 49 1 C 11 3 2 0 1 T Pdz2 4.870 -1 -1 0 11
+ 636 49 1 C 12 3 2 1 1 T Pdxz 4.870 -1 -1 0 12
+ 637 49 1 C 13 3 2 2 1 T Pdx2-y2 4.870 -1 -1 0 13
+ 638 50 1 C 1 2 0 0 1 F s 4.192 -1 -1 0 14
+ 639 50 1 C 2 2 0 0 2 F s 3.432 -1 -1 0 15
+ 640 50 1 C 3 2 1 -1 1 F py 4.870 -1 -1 0 16
+ 641 50 1 C 4 2 1 0 1 F pz 4.870 -1 -1 0 17
+ 642 50 1 C 5 2 1 1 1 F px 4.870 -1 -1 0 18
+ 643 50 1 C 6 2 1 -1 2 F py 3.475 -1 -1 0 19
+ 644 50 1 C 7 2 1 0 2 F pz 3.475 -1 -1 0 20
+ 645 50 1 C 8 2 1 1 2 F px 3.475 -1 -1 0 21
+ 646 50 1 C 9 3 2 -2 1 T Pdxy 4.870 -1 -1 0 22
+ 647 50 1 C 10 3 2 -1 1 T Pdyz 4.870 -1 -1 0 23
+ 648 50 1 C 11 3 2 0 1 T Pdz2 4.870 -1 -1 0 24
+ 649 50 1 C 12 3 2 1 1 T Pdxz 4.870 -1 -1 0 25
+ 650 50 1 C 13 3 2 2 1 T Pdx2-y2 4.870 -1 -1 0 26
+
+Column codes:
+ io = Orbital index in supercell
+ ia = Atom to which orbital belongs
+ is = Atomic species index
+spec = Atomic species label
+ iao = Orbital index within atom
+ n = Principal quantum number
+ l = Angular mumentum quantum number
+ m = Magnetic quantum number of (real) orbital:
+ m<0 => sin(m*phi), m>=0 => cos(m*phi)
+ z = Zeta index of orbital
+ p = Is this a polarization orbital? (False|True)
+ sym = Symmetry name of real orbital
+ rc = Cutoff radius of orbital (Bohr)
+ isc = Unit cell indexes to which orbital belongs:
+ center(io) = center(iuo) + sum_(i=1:3) cell_vec(i) * isc(i)
+ iuo = Equivalent orbital in first unit cell
+
diff --git a/graphene/siesta/SG15v1.2/ref/graphene.STRUCT_OUT b/graphene/siesta/SG15v1.2/ref/graphene.STRUCT_OUT
new file mode 100644
index 0000000..a195aea
--- /dev/null
+++ b/graphene/siesta/SG15v1.2/ref/graphene.STRUCT_OUT
@@ -0,0 +1,6 @@
+ 2.460000000 0.000000000 0.000000000
+ 1.230000000 2.130422494 0.000000000
+ 0.000000000 0.000000000 22.000000000
+ 2
+ 1 6 0.333333333 0.333333333 0.102067830
+ 1 6 0.666666667 0.666666667 0.102067830
diff --git a/graphene/siesta/SG15v1.2/ref/graphene.XV b/graphene/siesta/SG15v1.2/ref/graphene.XV
new file mode 100644
index 0000000..8510f43
--- /dev/null
+++ b/graphene/siesta/SG15v1.2/ref/graphene.XV
@@ -0,0 +1,6 @@
+ 4.648728119 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000
+ 2.324364060 4.025916647 0.000000000 0.000000000 0.000000000 0.000000000
+ 0.000000000 0.000000000 41.573991311 0.000000000 0.000000000 0.000000000
+ 2
+ 1 6 2.324364059 1.341972215 4.243367057 0.000000000 0.000000000 0.000000000
+ 1 6 4.648728120 2.683944431 4.243367057 0.000000000 0.000000000 0.000000000
diff --git a/graphene/siesta/SG15v1.2/ref/graphene.alloc b/graphene/siesta/SG15v1.2/ref/graphene.alloc
new file mode 100644
index 0000000..df3458f
--- /dev/null
+++ b/graphene/siesta/SG15v1.2/ref/graphene.alloc
@@ -0,0 +1,71 @@
+
+
+Allocation summary at 2023/07/03 19:17:33.543 -07:00
+
+Present memory all nodes : 0.000000 MB
+Added peak mem all nodes : 0.000000 MB
+Min peak memory in a node: 0.000000 MB
+Max peak memory in a node: 0.000000 MB
+
+Maximum peak of memory occurred in node: 0
+
+Present memory allocation: 0.000000 MB
+Maximum memory allocation: 0.000000 MB
+Occurred after allocating:
+In routine:
+
+Allocation summary at 2023/07/03 19:17:33.544 -07:00
+
+Present memory all nodes : 0.000000 MB
+Added peak mem all nodes : 0.000000 MB
+Min peak memory in a node: 0.000000 MB
+Max peak memory in a node: 0.000000 MB
+
+Maximum peak of memory occurred in node: 2
+
+Present memory allocation: 0.000000 MB
+Maximum memory allocation: 0.000000 MB
+Occurred after allocating:
+In routine:
+
+Allocation summary at 2023/07/03 19:17:33.544 -07:00
+
+Present memory all nodes : 0.000000 MB
+Added peak mem all nodes : 0.000000 MB
+Min peak memory in a node: 0.000000 MB
+Max peak memory in a node: 0.000000 MB
+
+Maximum peak of memory occurred in node: 13
+
+Present memory allocation: 0.000000 MB
+Maximum memory allocation: 0.000000 MB
+Occurred after allocating:
+In routine:
+
+Allocation summary at 2023/07/03 19:17:33.544 -07:00
+
+Present memory all nodes : 0.000000 MB
+Added peak mem all nodes : 0.000000 MB
+Min peak memory in a node: 0.000000 MB
+Max peak memory in a node: 0.000000 MB
+
+Maximum peak of memory occurred in node: 3
+
+Present memory allocation: 0.000000 MB
+Maximum memory allocation: 0.000000 MB
+Occurred after allocating:
+In routine:
+
+Allocation summary at 2023/07/03 19:17:33.544 -07:00
+
+Present memory all nodes : 0.000000 MB
+Added peak mem all nodes : 0.000000 MB
+Min peak memory in a node: 0.000000 MB
+Max peak memory in a node: 0.000000 MB
+
+Maximum peak of memory occurred in node: 11
+
+Present memory allocation: 0.000000 MB
+Maximum memory allocation: 0.000000 MB
+Occurred after allocating:
+In routine:
diff --git a/graphene/siesta/SG15v1.2/ref/graphene.bands b/graphene/siesta/SG15v1.2/ref/graphene.bands
new file mode 100644
index 0000000..90b40c7
--- /dev/null
+++ b/graphene/siesta/SG15v1.2/ref/graphene.bands
@@ -0,0 +1,225 @@
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diff --git a/graphene/siesta/SG15v1.2/ref/graphene.bib b/graphene/siesta/SG15v1.2/ref/graphene.bib
new file mode 100644
index 0000000..a2a26d9
--- /dev/null
+++ b/graphene/siesta/SG15v1.2/ref/graphene.bib
@@ -0,0 +1,13 @@
+# This file contains articles we encourage you to cite in case of publishing a paper.
+# Each entry corresponds to using a feature that has been enabled via FDF-flags
+# and which is based on a development paper as indicated.
+
+# Primary SIESTA paper
+@article{Soler2002,
+ journal = {{Journal of Physics: Condensed Matter}},
+ year = {2002},
+ volume = {14},
+ issue = {11},
+ doi = {10.1088/0953-8984/14/11/302},
+}
+
diff --git a/graphene/siesta/SG15v1.2/ref/graphene.nc b/graphene/siesta/SG15v1.2/ref/graphene.nc
new file mode 100644
index 0000000..8427e2a
Binary files /dev/null and b/graphene/siesta/SG15v1.2/ref/graphene.nc differ
diff --git a/graphene/siesta/SG15v1.2/ref/graphene.times b/graphene/siesta/SG15v1.2/ref/graphene.times
new file mode 100644
index 0000000..8c6b0c8
--- /dev/null
+++ b/graphene/siesta/SG15v1.2/ref/graphene.times
@@ -0,0 +1,88 @@
+
+timer: Number of nodes = 16
+timer: Busiest calculating node was node = 7
+timer: Times refer to node = 7
+timer: Total elapsed wall-clock time (sec) = 1.805
+timer: CPU times (sec):
+Calc: Sum, Avge, myNode, Avg/Max = 28.678 1.792 1.800 0.996
+Comm: Sum, Avge, myNode, Avg/Max = 0.000 0.000 0.000 NaN
+Tot: Sum, Avge, myNode, Avg/Max = 28.678 1.792 1.800 0.996
+Program times printed if > 0.000E+00 of total
+
+Program Calls Prg.com Prg.com Prg.tot Prg.tot Nod.avg
+ /Tot.com /Tot.tot/Nod.max
+siesta 1 0.000 0.0000 1.800 1.0000 0.996
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+geom_init 1 0.000 0.0000 0.132 0.0735 0.995
+state_init 1 0.000 0.0000 0.081 0.0451 0.996
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+naefs 2 0.000 0.0000 0.002 0.0013 0.930
+dnaefs 1 0.000 0.0000 0.000 0.0000 0.983
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+nlefsm 2 0.000 0.0000 0.007 0.0039 0.834
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+DHSCF1 1 0.000 0.0000 0.005 0.0030 0.616
+InitMesh 1 0.000 0.0000 0.005 0.0029 0.955
+INITMESH 3 0.000 0.0000 0.006 0.0034 0.763
+DHSCF2 1 0.000 0.0000 0.026 0.0146 0.949
+REMESH 1 0.000 0.0000 0.008 0.0047 0.856
+BuildDISTR 2 0.000 0.0000 0.006 0.0034 0.762
+meshCom-Ca 3 0.000 0.0000 0.000 0.0000 0.709
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+PHION 1 0.000 0.0000 0.006 0.0034 0.648
+dscfComm 1 0.000 0.0000 0.005 0.0029 0.739
+COMM_BSC 250 0.000 0.0000 0.103 0.0573 0.670
+POISON 63 0.000 0.0000 0.073 0.0406 0.946
+fft 126 0.000 0.0000 0.070 0.0390 0.946
+setup_H 60 0.000 0.0000 0.496 0.2754 1.000
+DHSCF 62 0.000 0.0000 0.542 0.3008 0.991
+DHSCF3 62 0.000 0.0000 0.533 0.2962 0.999
+rhoofd 62 0.000 0.0000 0.188 0.1042 0.772
+OtoM 63 0.000 0.0000 0.022 0.0121 0.865
+XC 62 0.000 0.0000 0.041 0.0226 0.793
+GXC-CellXC 62 0.000 0.0000 0.022 0.0123 0.868
+gridxc@cellXC 62 0.000 0.0000 0.022 0.0122 0.867
+vmat 61 0.000 0.0000 0.125 0.0694 0.906
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+compute_dm 59 0.000 0.0000 0.451 0.2507 1.000
+diagon 59 0.000 0.0000 0.449 0.2495 0.999
+cdiag 190 0.000 0.0000 0.268 0.1491 0.966
+cdiag1 190 0.000 0.0000 0.025 0.0139 0.955
+cdiag2 190 0.000 0.0000 0.054 0.0301 0.967
+cdiag3 190 0.000 0.0000 0.182 0.1012 0.966
+cdiag4 59 0.000 0.0000 0.000 0.0001 0.662
+MIXER 58 0.000 0.0000 0.010 0.0054 0.958
+PostSCF 1 0.000 0.0000 0.026 0.0144 0.901
+FINAL_HF 1 0.000 0.0000 0.026 0.0144 0.902
+DHSCF4 1 0.000 0.0000 0.008 0.0046 0.678
+dfscf 1 0.000 0.0000 0.006 0.0034 0.619
+overfsm 1 0.000 0.0000 0.000 0.0001 0.592
+state_analysis 1 0.000 0.0000 0.000 0.0001 0.173
+siesta_move 1 0.000 0.0000 0.000 0.0000 0.612
+Analysis 1 0.000 0.0000 0.289 0.1606 0.997
+c-eigval 72 0.000 0.0000 0.255 0.1417 1.000
+c-buildHS 72 0.000 0.0000 0.001 0.0008 0.767
+optical 1 0.000 0.0000 0.000 0.0000 0.873
+CDF-grid 4 0.000 0.0000 0.014 0.0079 0.745
+MPI total 0 0.000 1.0000 0.000 0.0000
+
+Definitions:
+Program: Name of a time-profiled routine (or code section)
+Calls: Number of profiled calls to a program
+Prg.com: CPU time in communications in one program in one node
+Tot.com: CPU time in communications in all progs. in one node
+Prg.tot: total CPU time in one program in one node
+Tot.tot: total CPU time in all programs in one node
+Nod.avg: average calculation time in one program across nodes
+Nod.max: maximum calculation time in one program across nodes
+Calculation time: CPU time excluding communications
+
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new file mode 100644
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diff --git a/graphene/siesta/SG15v1.2/ref/input.fdf b/graphene/siesta/SG15v1.2/ref/input.fdf
new file mode 100644
index 0000000..6744dce
--- /dev/null
+++ b/graphene/siesta/SG15v1.2/ref/input.fdf
@@ -0,0 +1,123 @@
+# SIESTA INPUT #
+SystemLabel graphene
+
+%include ./struct.fdf
+%include ./block-PAO.basis
+
+XC.functional LDA
+XC.authors PZ
+
+
+MeshCutoff 160.0 Ry
+OccupationFunction MP
+OccupationMPOrder 1
+ElectronicTemperature 0.001 eV
+
+%block kgrid_Monkhorst_Pack
+ 6 0 0 0.0
+ 0 6 0 0.0
+ 0 0 1 0.0
+%endblock kgrid_Monkhorst_Pack
+
+SolutionMethod diagon
+Diag.ParallelOverK T
+# Diag.Algorithm ELPA
+SolutionMethod ELSI
+ELSI.Solver ELPA
+#NumberOfEigenStates 4200
+
+DM.UseSaveDM F
+MD.UseSaveXV T
+
+MD.Steps 0
+MD.TypeOfRun Broyden
+MD.MaxForceTol 0.01 eV/Ang
+MD.VariableCell F
+
+MaxSCFIterations 1000
+SCF.DM.Converge T
+SCF.DM.Tolerance 1.0d-8
+SCF.MustConverge T
+SCF.Mix Hamiltonian
+SCF.Mixer.Method Pulay
+SCF.Mixer.Variant original
+SCF.Mixer.Weight 0.30
+SCF.Mixer.History 10
+
+Write.DM T
+Write.H F
+
+WriteMullikenPop 1
+WriteEigenvalues T
+WriteCoorInitial T
+WriteCoorStep T
+WriteForces T
+XML.Write T
+
+SaveHS F
+SaveRho T
+SaveDeltaRho F
+SaveRhoXC T
+SaveElectrostaticPotential T
+SaveNeutralAtomPotential F
+SaveTotalPotential T
+SaveIonicCharge F
+SaveBaderCharge F
+SaveTotalCharge F
+
+CDF.Save T
+CDF.Grid.Precision double
+
+##################
+# Band Structure #
+##################
+BandLinesScale ReciprocalLatticeVectors
+%block BandLines
+1 0.0000000 0.00000000 0.000 \Gamma
+30 0.3333333 0.66666666 0.000 K
+15 0.5000000 0.50000000 0.000 M
+26 0.0000000 0.00000000 0.000 \Gamma
+%endblock bandlinek
+
+#WFS.Write.For.Bands T
+#WFS.Band.Min 400
+#WFS.Band.Max 500
+#%block BandLines
+#1 0.0000000 0.00000000 0.000 \Gamma
+#60 7.0000000 -2.33333333 0.000 K
+#60 3.5000000 -3.50000000 0.000 M
+#60 0.0000000 0.00000000 0.000 \Gamma
+#%endblock BandLines
+
+################
+# Wavefunction #
+#################
+# WriteWaveFunctions F
+# WaveFuncKPointsScale ReciprocalLatticeVectors
+# %block WaveFuncKPoints
+# 0.000 0.000 0.000 from 1 to 10 # Gamma wavefuncs 1 to 10
+# 2.000 0.000 0.000 1 3 5 # X wavefuncs 1,3 and 5
+# 1.500 1.500 1.500 # K wavefuncs, all
+# %endblock WaveFuncKPoints
+
+########
+# PDOS #
+########
+# %block ProjectedDensityOfStates
+# -10.00 0.00 0.050 500 eV
+# %endblock ProjectedDensityOfStates
+# %block PDOS.kgrid_Monkhorst_Pack
+# 3 0 0 0.0
+# 0 3 0 0.0
+# 0 0 1 0.0
+# %endblock PDOS.kgrid_Monkhorst_Pack
+
+# %include grimme.fdf
+
+# Slab.DipoleCorrection vacuum
+# %block Geometry.Charge
+# plane 0
+# delta
+# 0.0 0.0 2.5 Ang # An intersection point, in the plane
+# 0.0 0.0 1.0 # The normal vector to the plane
+# %endblock Geometry.Charge
diff --git a/graphene/siesta/SG15v1.2/ref/plot_bands_siesta.py b/graphene/siesta/SG15v1.2/ref/plot_bands_siesta.py
new file mode 100644
index 0000000..1be0027
--- /dev/null
+++ b/graphene/siesta/SG15v1.2/ref/plot_bands_siesta.py
@@ -0,0 +1,76 @@
+from numpy import *
+import matplotlib.pyplot as plt
+import glob
+plt.rcParams["figure.figsize"] = (3.8/2.54,4.3/2.54)
+plt.rcParams["font.size"] = 8
+
+def main():
+ #ne = 3484
+ fn = glob.glob('*.bands')[0]
+ #fn = './WS2_temp.bands'
+ kpath, enk, xt, labels = read_bands(fn)
+
+ #vbm = max(enk[ne-1,:])
+# vbm = 0
+
+ for ek in enk:
+ plt.plot(kpath, ek, c='royalblue',lw=0.5)
+
+ ###Print band energy
+ #labels = ['X' , r'$\Gamma$','Y']
+
+ ### Plot styling
+ gridlinespec = { 'color': 'grey',
+ 'linestyle': 'dotted',
+ 'linewidth': 0.5 }
+ plt.grid(True, axis='x', **gridlinespec)
+ plt.axhline(0, **gridlinespec)
+ plt.ylabel('Energy (eV)')
+ plt.xticks(xt, labels)
+ plt.xlim(xt[0],xt[-1])
+ plt.ylim(-15,15)
+ plt.savefig('bands.png', dpi=400, bbox_inches='tight', pad_inches=0.01)
+ #plt.show()
+
+ return
+
+def read_bands(fname, ef=None):
+ Bohr_Ang = 0.529177
+ Ry_eV = 13.60580
+ f = open(fname, "r")
+ if ef:
+ f.readline()
+ else:
+ ef = float64(f.readline())
+
+ kmin, kmax = float64(f.readline().split())/Bohr_Ang # kpath min, max
+
+ emin, emax = float64(f.readline().split()) # energy min, max
+
+ nband, nspin, nkpts = int32(f.readline().split())
+
+ nlines = int((nband-1)/10)+1 # .EIG dumps 10 eigenvalues per one line
+
+ kpath = zeros(nkpts, dtype=float64)
+ enk_path = zeros((nband, nkpts), dtype=float64)
+ for ik in range(nkpts):
+ data = []
+ for il in range(nlines):
+ data += f.readline().split()
+ if len(data) != nband+1:
+ print ("[Error] Insufficient number of eigenvalues for ik=%d"%(ik+1))
+ return
+ kpath[ik] = data[0]
+ enk_path[:,ik] = array(data[1:], dtype=float64)-ef
+
+ nt = int(f.readline())
+ xt = []
+ labels = []
+ for i in range(nt):
+ row = f.readline().split()
+ xt.append(float(row[0]))
+ labels.append(row[1].strip("'"))
+ f.close()
+ return kpath, enk_path, xt, labels
+
+main()
diff --git a/graphene/siesta/SG15v1.2/ref/siesta.stdout b/graphene/siesta/SG15v1.2/ref/siesta.stdout
new file mode 100644
index 0000000..ffdf6ec
--- /dev/null
+++ b/graphene/siesta/SG15v1.2/ref/siesta.stdout
@@ -0,0 +1,848 @@
+Siesta Version : MaX-1.0-55-g0612142bc
+Architecture : ----
+Compiler version: GNU-10.3.0
+Compiler flags : -O3 -funroll-loops -funsafe-math-optimizations -fallow-argument-mismatch -fallow-argument-mismatch;
+PP flags : ----
+Libraries : ----
+Parallelisations: MPI
+NetCDF support
+NetCDF-4 support
+
+Runtime information:
+* Directory : /pscratch/sd/w/wkim94/graphene/siesta/SG15v1.2
+* Running on 16 nodes in parallel.
+>> Start of run: 3-JUL-2023 19:17:31
+
+ ***********************
+ * WELCOME TO SIESTA *
+ ***********************
+
+reinit: Reading from standard input
+reinit: Dumping input in INPUT_TMP.00246
+************************** Dump of input data file ****************************
+# SIESTA INPUT #
+SystemLabel graphene
+%include ./struct.fdf
+%include ./block-PAO.basis
+XC.functional LDA
+XC.authors PZ
+MeshCutoff 160.0 Ry
+OccupationFunction MP
+OccupationMPOrder 1
+ElectronicTemperature 0.001 eV
+%block kgrid_Monkhorst_Pack
+ 6 0 0 0.0
+ 0 6 0 0.0
+ 0 0 1 0.0
+%endblock kgrid_Monkhorst_Pack
+SolutionMethod diagon
+Diag.ParallelOverK T
+# Diag.Algorithm ELPA
+SolutionMethod ELSI
+ELSI.Solver ELPA
+#NumberOfEigenStates 4200
+DM.UseSaveDM F
+MD.UseSaveXV T
+MD.Steps 0
+MD.TypeOfRun Broyden
+MD.MaxForceTol 0.01 eV/Ang
+MD.VariableCell F
+MaxSCFIterations 1000
+SCF.DM.Converge T
+SCF.DM.Tolerance 1.0d-8
+SCF.MustConverge T
+SCF.Mix Hamiltonian
+SCF.Mixer.Method Pulay
+SCF.Mixer.Variant original
+SCF.Mixer.Weight 0.30
+SCF.Mixer.History 10
+Write.DM T
+Write.H F
+WriteMullikenPop 1
+WriteEigenvalues T
+WriteCoorInitial T
+WriteCoorStep T
+WriteForces T
+XML.Write T
+SaveHS F
+SaveRho T
+SaveDeltaRho F
+SaveRhoXC T
+SaveElectrostaticPotential T
+SaveNeutralAtomPotential F
+SaveTotalPotential T
+SaveIonicCharge F
+SaveBaderCharge F
+SaveTotalCharge F
+CDF.Save T
+CDF.Grid.Precision double
+##################
+# Band Structure #
+##################
+BandLinesScale ReciprocalLatticeVectors
+%block BandLines
+1 0.0000000 0.00000000 0.000 \Gamma
+30 0.3333333 0.66666666 0.000 K
+15 0.5000000 0.50000000 0.000 M
+26 0.0000000 0.00000000 0.000 \Gamma
+%endblock bandlinek
+#WFS.Write.For.Bands T
+#WFS.Band.Min 400
+#WFS.Band.Max 500
+#%block BandLines
+#1 0.0000000 0.00000000 0.000 \Gamma
+#60 7.0000000 -2.33333333 0.000 K
+#60 3.5000000 -3.50000000 0.000 M
+#60 0.0000000 0.00000000 0.000 \Gamma
+#%endblock BandLines
+################
+# Wavefunction #
+#################
+# WriteWaveFunctions F
+# WaveFuncKPointsScale ReciprocalLatticeVectors
+# %block WaveFuncKPoints
+# 0.000 0.000 0.000 from 1 to 10 # Gamma wavefuncs 1 to 10
+# 2.000 0.000 0.000 1 3 5 # X wavefuncs 1,3 and 5
+# 1.500 1.500 1.500 # K wavefuncs, all
+# %endblock WaveFuncKPoints
+########
+# PDOS #
+########
+# %block ProjectedDensityOfStates
+# -10.00 0.00 0.050 500 eV
+# %endblock ProjectedDensityOfStates
+# %block PDOS.kgrid_Monkhorst_Pack
+# 3 0 0 0.0
+# 0 3 0 0.0
+# 0 0 1 0.0
+# %endblock PDOS.kgrid_Monkhorst_Pack
+# %include grimme.fdf
+# Slab.DipoleCorrection vacuum
+# %block Geometry.Charge
+# plane 0
+# delta
+# 0.0 0.0 2.5 Ang # An intersection point, in the plane
+# 0.0 0.0 1.0 # The normal vector to the plane
+# %endblock Geometry.Charge
+************************** End of input data file *****************************
+
+reinit: -----------------------------------------------------------------------
+reinit: System Name:
+reinit: -----------------------------------------------------------------------
+reinit: System Label: graphene
+reinit: -----------------------------------------------------------------------
+
+initatom: Reading input for the pseudopotentials and atomic orbitals ----------
+Species number: 1 Atomic number: 6 Label: C
+
+
+---- Processing specs for species: C
+Ground state valence configuration: 2s02 2p02
+Reading pseudopotential information in PSML from:
+ C.psml
+PSML file version: 1.1
+Using libxc ids: 1 9
+LDA--CA XC_LDA_X--XC_LDA_C_PZ ca
+ Using ATOM defaults for log grid...
+PSML uuid: 54c8d220-1996-11ee-6c91-fcfe77fa0631
+
+---- Pseudopotential check for C
+
+Pseudized shells:
+2s( 2.00) rc: 1.42
+2p( 2.00) rc: 1.41
+Valence configuration for ps generation: 2s:2p: Total charge: 4.000000
+For C, standard SIESTA heuristics set lmxkb to 3
+ (one more than the basis l, including polarization orbitals).
+Use PS.lmax or PS.KBprojectors blocks to override.
+C pseudopotential only contains V_ls up to l=1 -- lmxkb reset.
+
+
+===============================================================================
+C Z= 6 Mass= 12.010 Charge= 0.17977+309
+Lmxo=2 Lmxkb= 1 BasisType=split Semic=F
+L=0 Nsemic=0 Cnfigmx=2
+ i=1 nzeta=2 polorb=0 (2s)
+ splnorm: 0.15000
+ vcte: 0.0000
+ rinn: 0.0000
+ qcoe: 0.0000
+ qyuk: 0.0000
+ qwid: 0.10000E-01
+ rcs: 0.0000 0.0000
+ lambdas: 1.0000 1.0000
+L=1 Nsemic=0 Cnfigmx=2
+ i=1 nzeta=2 polorb=1 (2p) (to be polarized perturbatively)
+ splnorm: 0.15000
+ vcte: 0.0000
+ rinn: 0.0000
+ qcoe: 0.0000
+ qyuk: 0.0000
+ qwid: 0.10000E-01
+ rcs: 0.0000 0.0000
+ lambdas: 1.0000 1.0000
+L=2 Nsemic=0 Cnfigmx=3
+ i=1 nzeta=0 polorb=0 (3d) (perturbative polarization orbital) (from 2p)
+-------------------------------------------------------------------------------
+L=0 Nkbl=1 erefs: 0.17977+309
+L=1 Nkbl=1 erefs: 0.17977+309
+===============================================================================
+
+
+atom: Called for C (Z = 6)
+NOTE: C pseudopotential has channels up to l= 1
+NOTE: PAOs with higher l will be generated with V_local
+
+read_vps: Pseudopotential generation method:
+read_vps: ONCVPSP-3.Hamann's oncvpsp
+Valence charge in pseudo generation: 4.00000
+
+xc_check: Exchange-correlation functional:
+xc_check: Ceperley-Alder
+Got Vlocal (oncv-fit) from psml data
+Choosing vlocal chloc cutoff: 5.249652
+qtot up to nchloc: 4.00001245
+atom: Maximum radius for chlocal: 5.24965
+atom: Maximum radius for r*vlocal+2*Zval: 5.24965
+Reading KB projs from C psml data
+Using scalar-relativistic projectors in PSML file
+
+PSML: Kleinman-Bylander projectors:
+ l= 0 rc= 1.448394 Ekb= 15.690435
+ l= 0 rc= 1.448394 Ekb= 1.334925
+ l= 1 rc= 1.430397 Ekb= -6.199647
+ l= 1 rc= 1.430397 Ekb= -1.887255
+
+PSML: Total number of Kleinman-Bylander projectors: 8
+atom: -------------------------------------------------------------------------
+
+atom: SANKEY-TYPE ORBITALS:
+atom: Selected multiple-zeta basis: split
+
+SPLIT: Orbitals with angular momentum L= 0
+
+SPLIT: Basis orbitals for state 2s
+
+SPLIT: PAO cut-off radius determined from an
+SPLIT: energy shift= 0.020000 Ry
+
+ izeta = 1
+ lambda = 1.000000
+ rc = 4.191849
+ energy = -0.984818
+ kinetic = 0.933770
+ potential(screened) = -1.918588
+ potential(ionic) = -5.522451
+
+ izeta = 2
+ rmatch = 3.431921
+ splitnorm = 0.150000
+ energy = -0.848814
+ kinetic = 1.407108
+ potential(screened) = -2.255922
+ potential(ionic) = -6.088993
+
+SPLIT: Orbitals with angular momentum L= 1
+
+SPLIT: Basis orbitals for state 2p
+
+SPLIT: PAO cut-off radius determined from an
+SPLIT: energy shift= 0.020000 Ry
+
+ izeta = 1
+ lambda = 1.000000
+ rc = 4.870301
+ energy = -0.378852
+ kinetic = 2.599214
+ potential(screened) = -2.978065
+ potential(ionic) = -6.490151
+
+ izeta = 2
+ rmatch = 3.475094
+ splitnorm = 0.150000
+ energy = -0.215245
+ kinetic = 3.915428
+ potential(screened) = -4.130673
+ potential(ionic) = -8.026919
+*Note: V_local used for l= 2
+
+** Using vlocal for PAOs with L= 2
+
+POLgen: Perturbative polarization orbital with L= 2
+
+POLgen: Polarization orbital for state 2p
+
+ izeta = 1
+ rc = 4.870301
+ energy = 1.279991
+ kinetic = 2.611691
+ potential(screened) = -1.331701
+ potential(ionic) = -4.271678
+atom: Total number of Sankey-type orbitals: 13
+
+atm_pop: Valence configuration (for local Pseudopot. screening):
+ 2s( 2.00)
+ 2p( 2.00)
+ 3d( 0.00)
+Vna: chval, zval: 4.00000 4.00000
+
+Vna: Cut-off radius for the neutral-atom potential: 4.870301
+
+atom: _________________________________________________________________________
+
+prinput: Basis input
+
+PAO.BasisType split
+
+%block ChemicalSpeciesLabel
+ 1 6 C # Species index, atomic number, species label
+%endblock ChemicalSpeciesLabel
+
+%block PAO.Basis # Define Basis set
+# WARNING: This information might be incomplete!
+C 2 # Species label, number of l-shells
+ n=2 0 2 # n, l, Nzeta
+ 4.192 3.432
+ 1.000 1.000
+ n=2 1 2 P 1 # n, l, Nzeta, Polarization, NzetaPol
+ 4.870 3.475
+ 1.000 1.000
+%endblock PAO.Basis
+
+prinput: ----------------------------------------------------------------------
+
+Dumping basis to NetCDF file C.ion.nc
+coor: Atomic-coordinates input format = Fractional
+
+ioxv: Reading coordinates and velocities from file
+! Info in XV file prevails over previous structure input
+
+siesta: Atomic coordinates (Bohr) and species
+siesta: 2.32436 1.34197 4.24337 1 1
+siesta: 4.64873 2.68394 4.24337 1 2
+
+siesta: System type = slab
+
+initatomlists: Number of atoms, orbitals, and projectors: 2 26 16
+
+siesta: ******************** Simulation parameters ****************************
+siesta:
+siesta: The following are some of the parameters of the simulation.
+siesta: A complete list of the parameters used, including default values,
+siesta: can be found in file out.fdf
+siesta:
+redata: Spin configuration = none
+redata: Number of spin components = 1
+redata: Time-Reversal Symmetry = T
+redata: Spin spiral = F
+redata: Long output = F
+redata: Number of Atomic Species = 1
+redata: Charge density info will appear in .RHO file
+redata: Write Mulliken Pop. = Atomic and Orbital charges
+redata: Matel table size (NRTAB) = 1024
+redata: Mesh Cutoff = 160.0000 Ry
+redata: Net charge of the system = 0.0000 |e|
+redata: Min. number of SCF Iter = 0
+redata: Max. number of SCF Iter = 1000
+redata: SCF convergence failure will abort job
+redata: SCF mix quantity = Hamiltonian
+redata: Mix DM or H after convergence = F
+redata: Recompute H after scf cycle = F
+redata: Mix DM in first SCF step = T
+redata: Write Pulay info on disk = F
+redata: New DM Occupancy tolerance = 0.000000000001
+redata: No kicks to SCF
+redata: DM Mixing Weight for Kicks = 0.5000
+redata: Require Harris convergence for SCF = F
+redata: Harris energy tolerance for SCF = 0.000100 eV
+redata: Require DM convergence for SCF = T
+redata: DM tolerance for SCF = 0.000000
+redata: Require EDM convergence for SCF = F
+redata: EDM tolerance for SCF = 0.001000 eV
+redata: Require H convergence for SCF = T
+redata: Hamiltonian tolerance for SCF = 0.001000 eV
+redata: Require (free) Energy convergence for SCF = F
+redata: (free) Energy tolerance for SCF = 0.000100 eV
+redata: Using Saved Data (generic) = F
+redata: Use continuation files for DM = F
+redata: Neglect nonoverlap interactions = F
+redata: Method of Calculation = Diagonalization
+redata: Electronic Temperature = 11.6044 K
+redata: Fix the spin of the system = F
+redata: Max. number of TDED Iter = 1
+redata: Number of TDED substeps = 3
+redata: Dynamics option = Single-point calculation
+mix.SCF: Pulay mixing = Pulay
+mix.SCF: Variant = stable
+mix.SCF: History steps = 10
+mix.SCF: Linear mixing weight = 0.300000
+mix.SCF: Mixing weight = 0.300000
+mix.SCF: SVD condition = 0.1000E-07
+redata: Save all siesta data in one NC = T
+redata: NC compression level = 0
+redata: ***********************************************************************
+
+%block SCF.Mixers
+ Pulay
+%endblock SCF.Mixers
+
+%block SCF.Mixer.Pulay
+ # Mixing method
+ method pulay
+ variant stable
+
+ # Mixing options
+ weight 0.3000
+ weight.linear 0.3000
+ history 10
+%endblock SCF.Mixer.Pulay
+
+DM_history_depth set to one: no extrapolation allowed by default for geometry relaxation
+Size of DM history Fstack: 1
+Total number of electrons: 8.000000
+Total ionic charge: 8.000000
+
+* ProcessorY, Blocksize: 2 1
+
+
+* Orbital distribution balance (max,min): 2 1
+
+k-point displ. along 1 input, could be: 0.00 0.50
+k-point displ. along 2 input, could be: 0.00 0.50
+ Kpoints in: 24 . Kpoints trimmed: 22
+
+siesta: k-grid: Number of k-points = 22
+siesta: k-points from Monkhorst-Pack grid
+siesta: k-cutoff (effective) = 7.380 Ang
+siesta: k-point supercell and displacements
+siesta: k-grid: 6 0 0 0.000
+siesta: k-grid: 0 6 0 0.000
+siesta: k-grid: 0 0 1 0.000
+
+diag: Algorithm = D&C
+diag: Parallel over k = T
+diag: Use parallel 2D distribution = T
+diag: Parallel block-size = 1
+diag: Parallel distribution = 4 x 4
+diag: Used triangular part = Lower
+diag: Absolute tolerance = 0.100E-15
+diag: Orthogonalization factor = 0.100E-05
+diag: Memory factor = 1.0000
+Using current reciprocal lattice vectors for BandLinesScale
+Beware any cell changes by the end of the run
+Using current reciprocal lattice vectors for BandLinesScale
+Beware any cell changes by the end of the run
+
+superc: Internal auxiliary supercell: 5 x 5 x 1 = 25
+superc: Number of atoms, orbitals, and projectors: 50 650 400
+
+
+ts: **************************************************************
+ts: Save H and S matrices = F
+ts: Save DM and EDM matrices = F
+ts: Only save the overlap matrix S = F
+ts: **************************************************************
+
+************************ Begin: TS CHECKS AND WARNINGS ************************
+************************ End: TS CHECKS AND WARNINGS **************************
+
+
+ ====================================
+ Single-point calculation
+ ====================================
+
+outcoor: Atomic coordinates (fractional):
+ 0.33333333 0.33333333 0.10206783 1 1 C
+ 0.66666667 0.66666667 0.10206783 1 2 C
+
+superc: Internal auxiliary supercell: 5 x 5 x 1 = 25
+superc: Number of atoms, orbitals, and projectors: 50 650 400
+
+outcell: Unit cell vectors (Ang):
+ 2.460000 0.000000 0.000000
+ 1.230000 2.130422 0.000000
+ 0.000000 0.000000 22.000000
+
+outcell: Cell vector modules (Ang) : 2.460000 2.460000 22.000000
+outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 60.0000
+outcell: Cell volume (Ang**3) : 115.2985
+
+
+refcount: 1>
+new_DM -- step: 1
+Initializing Density Matrix...
+DM filled with atomic data:
+
+
+refcount: 1>
+No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 16 157
+
+InitMesh: MESH = 18 x 18 x 180 = 58320
+InitMesh: Mesh cutoff (required, used) = 160.000 185.013 Ry
+New grid distribution: 1
+ 1 1: 9 1: 5 1: 12
+ 2 1: 9 1: 5 13: 24
+ 3 1: 9 1: 5 25: 35
+ 4 1: 9 1: 5 36: 46
+ 5 1: 9 1: 5 47: 57
+ 6 1: 9 1: 5 58: 68
+ 7 1: 9 1: 5 69: 79
+ 8 1: 9 1: 5 80: 90
+ 9 1: 9 6: 9 1: 12
+ 10 1: 9 6: 9 13: 24
+ 11 1: 9 6: 9 25: 35
+ 12 1: 9 6: 9 36: 46
+ 13 1: 9 6: 9 47: 57
+ 14 1: 9 6: 9 58: 68
+ 15 1: 9 6: 9 69: 79
+ 16 1: 9 6: 9 80: 90
+timer(meshCom-Ca) : 3.9935E-06 5.3709E-06 9.0003E-06
+timer(BuildDISTR) : 3.0300E-04 7.1686E-03 9.4920E-03
+New grid distribution: 2
+ 1 1: 5 1: 4 1: 6
+ 2 6: 9 1: 4 1: 6
+ 3 1: 4 5: 9 1: 6
+ 4 5: 9 5: 9 1: 6
+ 5 1: 4 1: 4 7: 9
+ 6 5: 9 1: 4 7: 9
+ 7 1: 5 5: 9 7: 9
+ 8 6: 9 5: 9 7: 9
+ 9 1: 4 1: 4 10: 12
+ 10 5: 9 1: 4 10: 12
+ 11 1: 5 5: 9 10: 12
+ 12 6: 9 5: 9 10: 12
+ 13 1: 9 1: 5 13: 14
+ 14 1: 9 6: 9 13: 14
+ 15 1: 9 1: 9 15: 15
+ 16 1: 9 1: 9 16: 90
+timer(meshCom-Ca) : 1.9968E-06 2.1886E-06 3.0100E-06
+timer(meshCom-Ca) : 1.9968E-06 2.3711E-06 3.0100E-06
+timer(BuildDISTR) : 2.3401E-04 2.6725E-04 2.8798E-04
+New grid distribution: 3
+ 1 1: 4 1: 4 1: 5
+ 2 5: 9 1: 4 1: 5
+ 3 1: 4 5: 9 1: 5
+ 4 5: 9 5: 9 1: 5
+ 5 1: 4 1: 4 6: 10
+ 6 5: 9 1: 4 6: 10
+ 7 1: 4 5: 9 6: 10
+ 8 5: 9 5: 9 6: 10
+ 9 1: 4 1: 4 11: 15
+ 10 5: 9 1: 4 11: 15
+ 11 1: 4 5: 9 11: 15
+ 12 5: 9 5: 9 11: 15
+ 13 1: 9 1: 4 16: 18
+ 14 1: 9 5: 9 16: 18
+ 15 1: 9 1: 9 19: 20
+ 16 1: 9 1: 9 21: 90
+Setting up quadratic distribution...
+
+stepf: Methfessel-Paxton step function
+ Using Hermite-Gauss polynomials of order 1
+
+siesta: Program's energy decomposition (eV):
+siesta: Ebs = -97.101158
+siesta: Eions = 911.940569
+siesta: Ena = 461.044942
+siesta: Ekin = 231.402177
+siesta: Enl = 15.239992
+siesta: Eso = 0.000000
+siesta: Edftu = 0.000000
+siesta: DEna = -11.260826
+siesta: DUscf = 0.726328
+siesta: DUext = 0.000000
+siesta: Ex = -83.519218
+siesta: Ec = -11.997339
+siesta: Exc = -95.516556
+siesta: EbV = 0.000000
+siesta: eta*DQ = 0.000000
+siesta: Emadel = 0.000000
+siesta: Emeta = 0.000000
+siesta: Emolmec = 0.000000
+siesta: Ekinion = 0.000000
+siesta: Eharris = -310.028268
+siesta: Etot = -310.304513
+siesta: FreeEng = -310.304545
+
+ iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
+ scf: 1 -310.028268 -310.304513 -310.304545 1.858236 -5.187288 2.935653
+timer(IterSCF ) : 1.8386E-02 1.8771E-02 2.3297E-02
+ scf: 2 -310.435770 -310.372575 -310.372606 0.032282 -4.582823 1.661705
+ scf: 3 -310.436041 -310.409059 -310.409090 0.047554 -3.822051 0.058198
+ scf: 4 -310.377942 -310.399104 -310.399104 0.035406 -3.892649 0.266123
+ scf: 5 -310.400157 -310.399630 -310.399620 0.001143 -3.909129 0.266601
+ scf: 6 -310.359359 -310.399196 -310.399196 0.066873 -3.896587 0.262316
+ scf: 7 -310.407326 -310.403543 -310.403552 0.007949 -3.883940 0.173861
+ scf: 8 -310.395889 -310.399968 -310.399964 0.006810 -3.881960 0.224384
+ scf: 9 -310.400180 -310.400070 -310.400066 0.000178 -3.882774 0.221220
+ scf: 10 -310.359226 -310.399062 -310.399058 0.065854 -3.876385 0.239212
+ scf: 11 -310.399528 -310.399295 -310.399292 0.000140 -3.888601 0.234984
+ scf: 12 -310.399742 -310.399519 -310.399516 0.000147 -3.886815 0.230104
+ scf: 13 -310.400687 -310.400104 -310.400100 0.000371 -3.882736 0.217893
+ scf: 14 -310.397484 -310.398818 -310.398815 0.000789 -3.874784 0.243302
+ scf: 15 -310.394978 -310.396933 -310.396933 0.000971 -3.876675 0.272358
+ scf: 16 -310.317467 -310.388464 -310.388464 0.072064 -3.878183 0.384703
+ scf: 17 -310.401461 -310.395219 -310.395219 0.002785 -3.876869 0.297694
+ scf: 18 -310.402077 -310.398767 -310.398767 0.001783 -3.876857 0.242319
+ scf: 19 -310.400054 -310.399415 -310.399412 0.000372 -3.876536 0.230755
+ scf: 20 -310.400328 -310.399875 -310.399871 0.000275 -3.879075 0.222212
+ scf: 21 -310.398456 -310.399168 -310.399156 0.001865 -3.881734 0.227655
+ scf: 22 -310.400897 -310.400046 -310.400043 0.001852 -3.880050 0.218941
+mix: Pulay -- inversion failed, > SVD [rank/size] 4 / 9
+ scf: 23 -310.361847 -310.399741 -310.399738 0.065327 -3.884672 0.224785
+ scf: 24 -310.400121 -310.399932 -310.399929 0.000117 -3.879382 0.221111
+mix: Pulay -- inversion failed, > SVD [rank/size] 4 / 9
+ scf: 25 -310.399592 -310.399758 -310.399751 0.000796 -3.881970 0.221030
+mix: Pulay -- inversion failed, > SVD [rank/size] 4 / 9
+ scf: 26 -310.361577 -310.399745 -310.399742 0.066006 -3.884591 0.224617
+mix: Pulay -- inversion failed, > SVD [rank/size] 4 / 9
+ scf: 27 -310.380859 -310.404323 -310.404335 0.056701 -3.881474 0.158352
+mix: Pulay -- inversion failed, > SVD [rank/size] 4 / 9
+ scf: 28 -310.364225 -310.399000 -310.398986 0.058559 -3.881486 0.229318
+mix: Pulay -- inversion failed, > SVD [rank/size] 4 / 9
+ scf: 29 -310.362172 -310.400073 -310.400070 0.067167 -3.880272 0.218284
+mix: Pulay -- inversion failed, > SVD [rank/size] 4 / 9
+ scf: 30 -310.373987 -310.402685 -310.402690 0.060273 -3.881487 0.183144
+mix: Pulay -- inversion failed, > SVD [rank/size] 4 / 9
+ scf: 31 -310.366022 -310.400058 -310.400050 0.060545 -3.881510 0.216871
+mix: Pulay -- inversion failed, > SVD [rank/size] 4 / 9
+ scf: 32 -310.412197 -310.407788 -310.407814 0.019871 -3.881502 0.086279
+mix: Pulay -- inversion failed, > SVD [rank/size] 3 / 9
+ scf: 33 -310.384242 -310.402926 -310.402932 0.040166 -3.881515 0.179747
+mix: Pulay -- inversion failed, > SVD [rank/size] 3 / 9
+ scf: 34 -310.399422 -310.407891 -310.407917 0.039694 -3.881525 0.083159
+mix: Pulay -- inversion failed, > SVD [rank/size] 3 / 9
+ scf: 35 -310.389208 -310.400277 -310.400270 0.019925 -3.881537 0.214071
+mix: Pulay -- inversion failed, > SVD [rank/size] 3 / 9
+ scf: 36 -310.372867 -310.402384 -310.402388 0.060786 -3.881529 0.187431
+mix: Pulay -- inversion failed, > SVD [rank/size] 3 / 9
+ scf: 37 -310.399487 -310.407950 -310.407977 0.040582 -3.881541 0.081283
+mix: Pulay -- inversion failed, > SVD [rank/size] 3 / 9
+ scf: 38 -310.404567 -310.408359 -310.408388 0.022205 -3.881544 0.066819
+mix: Pulay -- inversion failed, > SVD [rank/size] 3 / 9
+ scf: 39 -310.401834 -310.407555 -310.407580 0.023974 -3.881556 0.092864
+mix: Pulay -- inversion failed, > SVD [rank/size] 3 / 9
+ scf: 40 -310.409742 -310.409102 -310.409133 0.010354 -3.881561 0.024843
+mix: Pulay -- inversion failed, > SVD [rank/size] 4 / 9
+ scf: 41 -310.409152 -310.409128 -310.409159 0.000448 -3.881564 0.021895
+mix: Pulay -- inversion failed, > SVD [rank/size] 4 / 9
+ scf: 42 -310.408949 -310.409047 -310.409078 0.001286 -3.881575 0.030340
+ scf: 43 -310.409270 -310.409196 -310.409227 0.003009 -3.881461 0.010720
+mix: Pulay -- inversion failed, > SVD [rank/size] 4 / 9
+ scf: 44 -310.409187 -310.409192 -310.409223 0.000155 -3.881500 0.011681
+ scf: 45 -310.409165 -310.409206 -310.409237 0.002549 -3.881552 0.007257
+ scf: 46 -310.409039 -310.409140 -310.409171 0.002003 -3.881583 0.020387
+mix: Pulay -- inversion failed, > SVD [rank/size] 3 / 9
+ scf: 47 -310.409187 -310.409212 -310.409243 0.003388 -3.882112 0.003102
+ scf: 48 -310.409164 -310.409193 -310.409224 0.001138 -3.881467 0.011353
+ scf: 49 -310.409209 -310.409201 -310.409233 0.000371 -3.882024 0.008276
+ scf: 50 -310.409215 -310.409214 -310.409245 0.001099 -3.881884 0.001260
+ scf: 51 -310.409214 -310.409214 -310.409245 0.000077 -3.882305 0.000239
+ scf: 52 -310.409214 -310.409214 -310.409245 0.000042 -3.882159 0.000256
+ scf: 53 -310.409214 -310.409214 -310.409245 0.000009 -3.882323 0.000008
+ scf: 54 -310.409214 -310.409214 -310.409245 0.000002 -3.882325 0.000005
+ scf: 55 -310.409214 -310.409214 -310.409245 0.000000 -3.882325 0.000001
+ scf: 56 -310.409214 -310.409214 -310.409245 0.000000 -3.882325 0.000002
+ scf: 57 -310.409214 -310.409214 -310.409245 0.000000 -3.882325 0.000001
+ scf: 58 -310.409214 -310.409214 -310.409245 0.000000 -3.882325 0.000000
+ scf: 59 -310.409214 -310.409214 -310.409245 0.000000 -3.882325 0.000000
+
+SCF Convergence by DM+H criterion
+max |DM_out - DM_in| : 0.0000000088
+max |H_out - H_in| (eV) : 0.0000001962
+SCF cycle converged after 59 iterations
+
+Using DM_out to compute the final energy and forces
+ E_bs from EDM: -103.87519362570541
+No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 16 157
+
+siesta: E_KS(eV) = -310.4092
+
+siesta: E_KS - E_eggbox = -310.4092
+
+siesta: Atomic forces (eV/Ang):
+ 1 -0.000000 -0.000000 0.000184
+ 2 0.000001 -0.000000 0.000184
+----------------------------------------
+ Tot 0.000000 -0.000000 0.000368
+----------------------------------------
+ Max 0.000184
+ Res 0.000106 sqrt( Sum f_i^2 / 3N )
+----------------------------------------
+ Max 0.000184 constrained
+
+Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -2.26 -2.26 0.06 -0.00 0.00 -0.00
+(Free)E + p*V (eV/cell) -310.3024
+Target enthalpy (eV/cell) -310.4092
+
+mulliken: Atomic and Orbital Populations:
+
+Species: C
+Atom Qatom Qorb
+ 2s 2s 2py 2pz 2px 2py 2pz 2px
+ 3Pdxy 3Pdyz 3Pdz2 3Pdxz 3Pdx2-y2
+ 1 4.000 0.544 0.502 0.394 0.778 0.394 0.536 0.157 0.536
+ 0.046 0.032 0.002 0.032 0.046
+ 2 4.000 0.544 0.502 0.394 0.778 0.394 0.536 0.157 0.536
+ 0.046 0.032 0.002 0.032 0.046
+
+mulliken: Qtot = 8.000
+Computing bands...
+*** Note: ParallelOverK option not used for Bands
+
+diag: Algorithm = D&C
+diag: Parallel over k = F
+diag: Use parallel 2D distribution = T
+diag: Parallel block-size = 1
+diag: Parallel distribution = 4 x 4
+diag: Used triangular part = Lower
+diag: Absolute tolerance = 0.100E-15
+diag: Orthogonalization factor = 0.100E-05
+diag: Memory factor = 1.0000
+
+siesta: Eigenvalues (eV):
+ ik is eps
+ 1 1 -20.6509 -13.4748 -9.7464 -8.5089 1.1037 3.9956 10.7737 12.3579 12.9206 13.0535
+ 19.7286 21.1395 22.3462 29.9211 30.8463 38.4835 44.1341 53.3221 55.3302 65.0903
+ 65.9411 72.8643 80.3425 100.7127 141.3407 163.6026
+ 2 1 -22.5472 -10.7254 -9.2268 -8.1224 4.4867 5.5824 6.9740 8.3651 10.3556 12.2479
+ 22.9897 24.6098 24.8004 34.6003 34.7890 45.0288 47.4510 50.6154 51.2590 56.6106
+ 58.2720 73.7327 75.0582 92.4338 108.0097 153.4195
+ 3 1 -23.1673 -11.5046 -6.9832 -6.9832 4.4159 4.4159 7.6363 7.7503 9.3122 11.9758
+ 24.9374 28.0449 28.0449 42.6287 42.6287 44.2084 44.2084 45.6717 45.6717 54.9253
+ 63.9831 63.9832 72.8962 72.8962 76.6326 125.4727
+ 4 1 -17.9606 -17.1124 -10.3845 -6.2533 -2.1536 3.7113 12.6812 13.8217 14.4792 15.8976
+ 17.5600 19.9780 21.0438 27.9200 30.0710 34.5269 42.2186 57.4990 62.7156 63.2757
+ 69.6716 72.9527 83.9447 101.4613 136.1335 185.4750
+ 5 1 -18.8223 -15.2247 -11.9877 -6.5403 -1.3313 6.3136 11.0264 11.4106 12.8477 17.1555
+ 17.7064 20.8414 21.0996 24.4246 35.1838 39.0174 44.5933 51.3103 57.8865 65.7402
+ 75.7630 80.0156 97.1220 107.9767 143.1484 175.2075
+ 6 1 -21.2784 -11.6126 -10.3701 -9.2141 2.5591 6.1117 7.9129 10.0627 12.3905 13.6050
+ 19.0439 22.1811 23.9453 28.3025 36.9836 44.0533 45.9270 47.2614 53.7405 61.3169
+ 63.8245 74.5158 90.9327 101.0480 113.8662 164.4889
+ 7 1 -22.5472 -10.7254 -9.2268 -8.1224 4.4867 5.5824 6.9740 8.3651 10.3556 12.2479
+ 22.9897 24.6098 24.8004 34.6003 34.7890 45.0288 47.4510 50.6154 51.2590 56.6106
+ 58.2720 73.7327 75.0582 92.4338 108.0099 153.4194
+ 8 1 -22.5472 -10.7254 -9.2268 -8.1224 4.4867 5.5824 6.9740 8.3651 10.3556 12.2479
+ 22.9897 24.6098 24.8004 34.6003 34.7890 45.0288 47.4510 50.6154 51.2590 56.6106
+ 58.2720 73.7327 75.0582 92.4338 108.0097 153.4195
+ 9 1 -21.2784 -11.6126 -10.3701 -9.2141 2.5591 6.1117 7.9129 10.0627 12.3905 13.6050
+ 19.0439 22.1811 23.9453 28.3025 36.9836 44.0533 45.9270 47.2614 53.7405 61.3169
+ 63.8245 74.5158 90.9327 101.0480 113.8662 164.4888
+ 10 1 -18.8223 -15.2247 -11.9877 -6.5403 -1.3313 6.3136 11.0264 11.4106 12.8477 17.1555
+ 17.7064 20.8414 21.0996 24.4246 35.1838 39.0174 44.5933 51.3103 57.8865 65.7402
+ 75.7630 80.0156 97.1220 107.9767 143.1484 175.2074
+ 11 1 -16.3281 -16.3281 -14.5691 -3.8823 -3.8823 9.2516 10.3582 10.3582 12.1240 19.3112
+ 19.3112 20.0260 20.0260 20.5532 34.3064 45.1545 45.1545 53.8000 53.8000 77.5290
+ 77.5290 81.1266 117.3717 163.0699 163.0700 221.5087
+ 12 1 -18.8223 -15.2247 -11.9877 -6.5403 -1.3313 6.3136 11.0264 11.4106 12.8477 17.1555
+ 17.7064 20.8414 21.0996 24.4246 35.1838 39.0174 44.5933 51.3103 57.8865 65.7402
+ 75.7630 80.0156 97.1220 107.9767 143.1486 175.2074
+ 13 1 -20.6509 -13.4748 -9.7464 -8.5089 1.1037 3.9956 10.7737 12.3579 12.9206 13.0535
+ 19.7286 21.1395 22.3462 29.9211 30.8463 38.4835 44.1341 53.3221 55.3302 65.0903
+ 65.9411 72.8643 80.3425 100.7127 141.3411 163.6025
+ 14 1 -21.2784 -11.6126 -10.3701 -9.2141 2.5591 6.1117 7.9129 10.0627 12.3905 13.6050
+ 19.0439 22.1811 23.9453 28.3025 36.9836 44.0533 45.9270 47.2614 53.7405 61.3169
+ 63.8245 74.5158 90.9327 101.0480 113.8663 164.4889
+ 15 1 -20.6509 -13.4748 -9.7464 -8.5089 1.1037 3.9956 10.7737 12.3579 12.9206 13.0535
+ 19.7286 21.1395 22.3462 29.9211 30.8463 38.4835 44.1341 53.3221 55.3302 65.0903
+ 65.9411 72.8643 80.3425 100.7127 141.3407 163.6026
+ 16 1 -18.8223 -15.2247 -11.9877 -6.5403 -1.3313 6.3136 11.0264 11.4106 12.8477 17.1555
+ 17.7064 20.8414 21.0996 24.4246 35.1838 39.0174 44.5933 51.3103 57.8865 65.7402
+ 75.7630 80.0156 97.1220 107.9767 143.1484 175.2074
+ 17 1 -18.8223 -15.2247 -11.9877 -6.5403 -1.3313 6.3136 11.0264 11.4106 12.8477 17.1555
+ 17.7064 20.8414 21.0996 24.4246 35.1838 39.0174 44.5933 51.3103 57.8865 65.7402
+ 75.7630 80.0156 97.1220 107.9767 143.1484 175.2075
+ 18 1 -18.8223 -15.2247 -11.9877 -6.5403 -1.3313 6.3136 11.0264 11.4106 12.8477 17.1555
+ 17.7064 20.8414 21.0996 24.4246 35.1838 39.0174 44.5933 51.3103 57.8865 65.7402
+ 75.7630 80.0156 97.1220 107.9767 143.1486 175.2074
+ 19 1 -17.9606 -17.1124 -10.3845 -6.2533 -2.1536 3.7113 12.6812 13.8217 14.4792 15.8976
+ 17.5600 19.9780 21.0438 27.9200 30.0710 34.5269 42.2186 57.4990 62.7156 63.2756
+ 69.6716 72.9527 83.9447 101.4613 136.1338 185.4749
+ 20 1 -18.8223 -15.2247 -11.9877 -6.5403 -1.3313 6.3136 11.0264 11.4106 12.8477 17.1555
+ 17.7064 20.8414 21.0996 24.4246 35.1838 39.0174 44.5933 51.3103 57.8865 65.7402
+ 75.7630 80.0156 97.1220 107.9767 143.1486 175.2074
+ 21 1 -18.8223 -15.2247 -11.9877 -6.5403 -1.3313 6.3136 11.0264 11.4106 12.8477 17.1555
+ 17.7064 20.8414 21.0996 24.4246 35.1838 39.0174 44.5933 51.3103 57.8865 65.7402
+ 75.7630 80.0156 97.1220 107.9767 143.1484 175.2075
+ 22 1 -17.9606 -17.1124 -10.3845 -6.2533 -2.1536 3.7113 12.6812 13.8217 14.4792 15.8976
+ 17.5600 19.9780 21.0438 27.9200 30.0710 34.5269 42.2186 57.4990 62.7156 63.2756
+ 69.6716 72.9527 83.9447 101.4613 136.1335 185.4750
+siesta: Fermi energy = -3.882325 eV
+
+siesta: Program's energy decomposition (eV):
+siesta: Ebs = -103.875194
+siesta: Eions = 911.940569
+siesta: Ena = 461.044942
+siesta: Ekin = 226.117497
+siesta: Enl = 15.650232
+siesta: Eso = 0.000000
+siesta: Edftu = 0.000000
+siesta: DEna = -7.072306
+siesta: DUscf = 0.472418
+siesta: DUext = 0.000000
+siesta: Ex = -82.728243
+siesta: Ec = -11.953185
+siesta: Exc = -94.681428
+siesta: EbV = 0.000000
+siesta: eta*DQ = 0.000000
+siesta: Emadel = 0.000000
+siesta: Emeta = 0.000000
+siesta: Emolmec = 0.000000
+siesta: Ekinion = 0.000000
+siesta: Eharris = -310.409214
+siesta: Etot = -310.409214
+siesta: FreeEng = -310.409245
+
+siesta: Final energy (eV):
+siesta: Band Struct. = -103.875194
+siesta: Kinetic = 226.117497
+siesta: Hartree = 1736.200741
+siesta: Edftu = 0.000000
+siesta: Eso = 0.000000
+siesta: Ext. field = 0.000000
+siesta: Exch. = -82.728243
+siesta: Corr. = -11.953185
+siesta: Bulk bias = 0.000000
+siesta: Exch.-corr. = -94.681428
+siesta: Ion-electron = -3678.601238
+siesta: Ion-ion = 1500.555214
+siesta: Ekinion = 0.000000
+siesta: D3 dispersion = 0.000000
+siesta: Total = -310.409214
+siesta: Fermi = -3.882325
+
+siesta: Stress tensor (static) (eV/Ang**3):
+siesta: -0.001408 -0.000000 0.000000
+siesta: -0.000000 -0.001408 -0.000000
+siesta: 0.000000 -0.000000 0.000036
+
+siesta: Cell volume = 115.298465 Ang**3
+
+siesta: Pressure (static):
+siesta: Solid Molecule Units
+siesta: 0.00001009 0.00001009 Ry/Bohr**3
+siesta: 0.00092645 0.00092645 eV/Ang**3
+siesta: 1.48435227 1.48434938 kBar
+(Free)E+ p_basis*V_orbitals = -309.809386
+(Free)Eharris+ p_basis*V_orbitals = -309.809386
+
+siesta: Electric dipole (a.u.) = -0.000000 -0.000000 -0.000026
+siesta: Electric dipole (Debye) = -0.000000 -0.000000 -0.000066
+
+dhscf: Vacuum level (max, mean) = -0.111871 -0.114163 eV
+
+cite: Please see "graphene.bib" for an exhaustive BiBTeX file.
+cite: Please clearly indicate Siesta version in published work: MaX-1.0-55-g0612142bc
+cite: This calculation has made use of the following articles
+cite: which are encouraged to be cited in a published work.
+ Primary SIESTA paper
+ DOI: www.doi.org/10.1088/0953-8984/14/11/302
+
+
+>> End of run: 3-JUL-2023 19:17:33
+Job completed
diff --git a/graphene/siesta/SG15v1.2/ref/struct.fdf b/graphene/siesta/SG15v1.2/ref/struct.fdf
new file mode 100644
index 0000000..23d3b4c
--- /dev/null
+++ b/graphene/siesta/SG15v1.2/ref/struct.fdf
@@ -0,0 +1,19 @@
+
+NumberOfSpecies 1
+%block ChemicalSpeciesLabel
+ 1 6 C
+%endblock ChemicalSpeciesLabel
+
+LatticeConstant 2.46 Ang
+%block LatticeVectors
+1.0000000000 0.0000000000 0.0000000000
+0.5000000000 0.8660254038 0.0000000000
+0.0000000000 0.0000000000 8.9430894309
+%endblock LatticeVectors
+
+NumberOfAtoms 2
+AtomicCoordinatesFormat Fractional
+%block AtomicCoordinatesAndAtomicSpecies
+ 0.3333333333 0.3333333333 0.1020678295 1
+ 0.6666666667 0.6666666667 0.1020678295 1
+%endblock AtomicCoordinatesAndAtomicSpecies