diff --git a/examples/Li2GTH/README b/examples/Li2GTH/README new file mode 100644 index 00000000..f411a01e --- /dev/null +++ b/examples/Li2GTH/README @@ -0,0 +1,11 @@ +#Run MGmol +mpirun -np 4 mgmol-opt -c davidson.cfg -i li2.xyz > davidson.out + +#extract visit files from HDF5 file +python read_hdf5.py -bov li2.h5 Vtotal + +python read_hdf5.py -bov li2.h50 Function0002 + +Note: the eigenfunctions corresponding to the 3 occupied states are stored +in functions 2, 3 and 4 because they are the result of diagonalizing the DM +in Davidson algorithm, not H. diff --git a/examples/Li2GTH/davidson.cfg b/examples/Li2GTH/davidson.cfg new file mode 100644 index 00000000..d211b812 --- /dev/null +++ b/examples/Li2GTH/davidson.cfg @@ -0,0 +1,46 @@ +verbosity=2 +xcFunctional=PBE +FDtype=4th +[Mesh] +nx=96 +ny=96 +nz=96 +[Domain] +ox=-9. +oy=-9. +oz=-9. +lx=18. +ly=18. +lz=18. +[Potentials] +pseudopotential=pseudo.Li_GTH_PBE +[Poisson] +solver=CG +bcx=0 +bcy=0 +bcz=0 +[Run] +type=QUENCH +[Quench] +solver=Davidson +max_steps=200 +atol=1.e-8 +preconditioner_num_levels=3 +[Orbitals] +nempty=2 +initial_type=random +temperature=300. +bcx=0 +bcy=0 +bcz=0 +[ProjectedMatrices] +solver=exact +[DensityMatrix] +nb_inner_it=1 +mixing=1. +[Restart] +output_level=3 +output_filename=li2.h5 +output_type=single_file +[Coloring] +scope=global diff --git a/examples/Li2GTH/li2.xyz b/examples/Li2GTH/li2.xyz new file mode 100644 index 00000000..ccf3a3f1 --- /dev/null +++ b/examples/Li2GTH/li2.xyz @@ -0,0 +1,4 @@ +2 +Experimental geometry (Menconi and Tozer, Chem. Phys. Lett. 2002) +Li 1.3365 0.0 0.0 +Li -1.3365 0.0 0.0 diff --git a/potentials/pseudo.Li_GTH_PBE b/potentials/pseudo.Li_GTH_PBE new file mode 100644 index 00000000..7da944e0 --- /dev/null +++ b/potentials/pseudo.Li_GTH_PBE @@ -0,0 +1,332 @@ +# Goedecker, Teter, Hutter, Phys. rev. B 54 (3), 1996 +# Parameters from M. Krack, Theor. Chem. Acc. 114, 2005 +# Short description of the species type. One line only! +LithiumGTH_PBE +# +White +#radii of balls and covalent bonds +0.4 1.0 +# Nlcc flag +0 +# Atomic number +3 +# Atomic mass +3.0 +# Number of valence electrons +3.0 +# Gaussian core charge parameter rc +1. +# Number of potentials +1 +# l-value for state which is local +0 0 +# Local potential radius +3. +# Non-local potential radius +3. +# number of points in radial grid +301 +# log mesh parameter +0. +# radial grid, reference state, and potential for l=0 +0.0 -20.06528920602149 +0.01 -20.054252432503986 +0.02 -20.021181949571293 +0.03 -19.966197051499293 +0.04 -19.889495835016746 +0.05 -19.791354114111485 +0.06 -19.672123911517346 +0.07 -19.53223153752974 +0.08 -19.372175269684018 +0.09 -19.192522649601603 +0.1 -18.993907415941983 +0.11 -18.777026094871008 +0.12 -18.54263427174855 +0.13 -18.291542569831762 +0.14 -18.02461236366824 +0.15 -17.742751256501393 +0.16 -17.446908352415903 +0.17 -17.138069355105003 +0.18 -16.81725152603506 +0.19 -16.485498535412276 +0.2 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B 54 (3), 1996 +# Parameters from M. Krack, Theor. Chem. Acc. 114, 2005 +from math import exp, erf, sqrt, pi + +#coefficients for H +rloc = 0.4 +c1 = -14.081155 +c2 = 9.626220 +c3 = -1.783616 +c4 = 0.085152 +zion = 3. +anumber = 3 +name = "LithiumGTH_PBE" +mass = 3. + +def radialfunction(r): + alpha = (r/rloc)**2 + val = exp(-0.5*alpha)*(c1+c2*alpha+c3*alpha*alpha+c4*alpha*alpha*alpha) + if r>1.e-8: + val = val - zion*erf(r/(sqrt(2.)*rloc))/r + else: + #print("special case for r = {}".format(r)) + val = val -zion*sqrt(2.)/(sqrt(pi)*rloc) + + return val + +npts = 301 + +#header +print("# Short description of the species type. One line only!") +print(name) +print("#") +print("White") +print("#radii of balls and covalent bonds") +print("0.4 1.0") +print("# Nlcc flag") +print("0") +print("# Atomic number") +print(anumber) +print("# Atomic mass") +print(mass) +print("# Number of valence electrons") +print(zion) +print("# Gaussian core charge parameter rc") +print("1.") +print("# Number of potentials") +print("1") +print("# l-value for state which is local") +print("0 0") +print("# Local potential radius") +print("3.") +print("# Non-local potential radius") +print("3.") +print("# number of points in radial grid") +print(npts) +print("# log mesh parameter") +print("0.") +print("# radial grid, reference state, and potential for l=0") + +#potential +for i in range(npts): + r = round(0.01*i,2) + f = radialfunction(r) + print("{} {}".format(r,f))