Add Li2 example with local GTH potential

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.

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

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

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 -16.14387523971814
+0.21 -15.7934624196748
+0.22 -15.435351512330925
+0.23 -15.07063937052802
+0.24 -14.700423082322942
+0.25 -14.325794882014955
+0.26 -13.947837183265412
+0.27 -13.567617763419314
+0.28 -13.186185126555326
+0.29 -12.80456407102134
+0.3 -12.423751485274781
+0.31 -12.0447123937598
+0.32 -11.668376272337989
+0.33 -11.295633650466765
+0.34 -10.927333014911554
+0.35 -10.564278027307214
+0.36 -10.207225065372501
+0.37 -9.856881095051628
+0.38 -9.513901878330472
+0.39 -9.178890518973706
+0.4 -8.852396345973204
+0.41 -8.534914132107685
+0.42 -8.226883642706916
+0.43 -7.928689507508834
+0.44 -7.64066140641021
+0.45 -7.363074557955612
+0.46 -7.096150497598659
+0.47 -6.840058131114424
+0.48 -6.594915047052536
+0.49 -6.3607890708040955
+0.5 -6.1377000417180545
+0.51 -5.925621793748402
+0.52 -5.724484319343899
+0.53 -5.534176095708496
+0.54 -5.354546552160849
+0.55 -5.1854086571031885
+0.56 -5.026541603068161
+0.57 -4.877693568441651
+0.58 -4.73858453475222
+0.59 -4.60890913886544
+0.6 -4.488339540014026
+0.61 -4.376528282322026
+0.62 -4.273111134331415
+0.63 -4.17770988800058
+0.64 -4.089935100703225
+0.65 -4.009388764900398
+0.66 -3.935666891373983
+0.67 -3.868361993183916
+0.68 -3.807065458829906
+0.69 -3.751369804448444
+0.7 -3.7008707962442955
+0.71 -3.655169435730016
+0.72 -3.6138738017150143
+0.73 -3.5766007443361536
+0.74 -3.5429774277437494
+0.75 -3.512642719340314
+0.76 -3.4852484247051203
+0.77 -3.4604603685176145
+0.78 -3.4379593229091037
+0.79 -3.4174417857190456
+0.8 -3.3986206121036857
+0.81 -3.38122550383682
+0.82 -3.3650033614510035
+0.83 -3.3497185050904883
+0.84 -3.335152770582715
+0.85 -3.3211054877824484
+0.86 -3.307393348702202
+0.87 -3.293850173314738
+0.88 -3.2803265812005225
+0.89 -3.2666895774169027
+0.9 -3.2528220610898493
+0.91 -3.2386222652767795
+0.92 -3.224003136624447
+0.93 -3.208891663253622
+0.94 -3.1932281591472704
+0.95 -3.1769655131062664
+0.96 -3.160068410071886
+0.97 -3.142512532302873
+0.98 -3.1242837475424827
+0.99 -3.10537729092335
+1.0 -3.085796946940759
+1.01 -3.065554237383791
+1.02 -3.0446676206540504
+1.03 -3.0231617074287267
+1.04 -3.001066497143526
+1.05 -2.978416639286402
+1.06 -2.9552507230094722
+1.07 -2.931610598088238
+1.08 -2.9075407297881393
+1.09 -2.8830875897419252
+1.1 -2.8582990845006977
+1.11 -2.833224022999286
+1.12 -2.8079116237754826
+1.13 -2.7824110624044724
+1.14 -2.7567710592563195
+1.15 -2.7310395073568614
+1.16 -2.705263139831839
+1.17 -2.6794872361411723
+1.18 -2.653755366065358
+1.19 -2.628109170188997
+1.2 -2.60258817543732
+1.21 -2.57722964405972
+1.22 -2.552068454319101
+1.23 -2.527137011036365
+1.24 -2.50246518405455
+1.25 -2.4780802726257742
+1.26 -2.4540069936848927
+1.27 -2.430267491955173
+1.28 -2.4068813698318525
+1.29 -2.383865735007489
+1.3 -2.361235263837057
+1.31 -2.339002278488971
+1.32 -2.31717683598915
+1.33 -2.2957668273371157
+1.34 -2.274778084954434
+1.35 -2.2542144968149556
+1.36 -2.2340781257018256
+1.37 -2.2143693321366866
+1.38 -2.1950868996304913
+1.39 -2.176228161011706
+1.4 -2.1577891246951135
+1.41 -2.1397645998619574
+1.42 -2.1221483196287054
+1.43 -2.1049330613864585
+1.44 -2.0881107635950986
+1.45 -2.07167263841506
+1.46 -2.055609279654423
+1.47 -2.03991076559945
+1.48 -2.0245667563822187
+1.49 -2.0095665856193814
+1.5 -1.9948993461310054
+1.51 -1.9805539696177794
+1.52 -1.96651930023847
+1.53 -1.95278416208739
+1.54 -1.9393374206237712
+1.55 -1.9261680381514323
+1.56 -1.9132651234880866
+1.57 -1.900617975999247
+1.58 -1.8882161242021371
+1.59 -1.876049359170528
+1.6 -1.8641077629922906
+1.61 -1.8523817325479044
+1.62 -1.8408619988905475
+1.63 -1.8295396425169552
+1.64 -1.8184061048233324
+1.65 -1.807453196042526
+1.66 -1.796673099957719
+1.67 -1.786058375684427
+1.68 -1.7756019568068189
+1.69 -1.7652971481466952
+1.7 -1.7551376204340732
+1.71 -1.7451174031375227
+1.72 -1.7352308757004553
+1.73 -1.7254727574166897
+1.74 -1.7158380961650346
+1.75 -1.7063222562085625
+1.76 -1.696920905249867
+1.77 -1.6876300009190652
+1.78 -1.6784457768568064
+1.79 -1.6693647285401818
+1.8 -1.6603835989853395
+1.81 -1.6514993644468863
+1.82 -1.6427092202208944
+1.83 -1.6340105666456095
+1.84 -1.625400995381811
+1.85 -1.6168782760432898
+1.86 -1.608440343237089
+1.87 -1.6000852840630355
+1.88 -1.5918113261126972
+1.89 -1.5836168259992183
+1.9 -1.5755002584415392
+1.91 -1.567460205919256
+1.92 -1.5594953489078422
+1.93 -1.5516044566980827
+1.94 -1.54378637879836
+1.95 -1.5360400369138487
+1.96 -1.5283644174926794
+1.97 -1.5207585648257078
+1.98 -1.513221574683613
+1.99 -1.5057525884726553
+2.0 -1.4983507878884341
+2.01 -1.4910153900454863
+2.02 -1.4837456430593685
+2.03 -1.476540822057088
+2.04 -1.4694002255912106
+2.05 -1.4623231724327952
+2.06 -1.4553089987182684
+2.07 -1.4483570554256544
+2.08 -1.441466706155941
+2.09 -1.4346373251959794
+2.1 -1.4278682958400157
+2.11 -1.4211590089477848
+2.12 -1.4145088617179962
+2.13 -1.407917256657042
+2.14 -1.4013836007237732
+2.15 -1.3949073046322673
+2.16 -1.38848778229559
+2.17 -1.3821244503946528
+2.18 -1.3758167280573612
+2.19 -1.3695640366343098
+2.2 -1.3633657995583632
+2.21 -1.3572214422764575
+2.22 -1.3511303922429727
+2.23 -1.3450920789649687
+2.24 -1.3391059340904876
+2.25 -1.3331713915319947
+2.26 -1.3272878876178418
+2.27 -1.321454861265409
+2.28 -1.3156717541702987
+2.29 -1.3099380110066239
+2.3 -1.304253079634056
+2.31 -1.2986164113078702
+2.32 -1.2930274608887506
+2.33 -1.2874856870495992
+2.34 -1.2819905524770356
+2.35 -1.2765415240656612
+2.36 -1.271138073103527
+2.37 -1.2657796754475625
+2.38 -1.260465811688003
+2.39 -1.2551959673011142
+2.4 -1.2499696327897274
+2.41 -1.244786303811294
+2.42 -1.2396454812933442
+2.43 -1.2345466715363633
+2.44 -1.229489386304243
+2.45 -1.224473142902546
+2.46 -1.219497464244928
+2.47 -1.214561878908113
+2.48 -1.2096659211758896
+2.49 -1.204809131072622
+2.5 -1.1999910543868184
+2.51 -1.1952112426853008
+2.52 -1.1904692533185557
+2.53 -1.1857646494178307
+2.54 -1.1810969998845513
+2.55 -1.1764658793726301
+2.56 -1.1718708682642154
+2.57 -1.1673115526394273
+2.58 -1.1627875242406034
+2.59 -1.158298380431558
+2.6 -1.1538437241523383
+2.61 -1.149423163869939
+2.62 -1.1450363135254051
+2.63 -1.1406827924777474
+2.64 -1.1363622254450418
+2.65 -1.1320742424430907
+2.66 -1.1278184787219725
+2.67 -1.1235945747008054
+2.68 -1.1194021759010047
+2.69 -1.1152409328783188
+2.7 -1.1111105011538749
+2.71 -1.107010541144477
+2.72 -1.1029407180923525
+2.73 -1.0989007019945478
+2.74 -1.094890167532131
+2.75 -1.0909087939993736
+2.76 -1.0869562652330373
+2.77 -1.0830322695418986
+2.78 -1.079136499636622
+2.79 -1.0752686525600812
+2.8 -1.0714284296182166
+2.81 -1.067615536311507
+2.82 -1.0638296822671227
+2.83 -1.0600705811718185
+2.84 -1.0563379507056208
+2.85 -1.0526315124763437
+2.86 -1.0489509919549826
+2.87 -1.0452961184120013
+2.88 -1.0416666248545523
+2.89 -1.0380622479646329
+2.9 -1.0344827280382114
+2.91 -1.0309278089253149
+2.92 -1.0273972379711012
+2.93 -1.0238907659579113
+2.94 -1.0204081470483046
+2.95 -1.0169491387290766
+2.96 -1.013513501756257
+2.97 -1.0101010001010782
+2.98 -1.0067114008969125
+2.99 -1.0033444743871645
+3.0 -0.9999999938741118