In this exercise we will explore alternative ways to divide the electronic densities into orbitals. By requiring that orbitals should be as localized as possible one obtains a representation, which closely resembles the typical text-book pictures of molecular orbitals.
bsub -n 4.
Calculate the electronic ground state of the Caffeine molecule by running the provided input file. The simulation will output:
Repeat the previous calculation on a box of 64 water molecules. You can use the following SUBSYS-section. Since the water simulation uses periodic boundary condition, don't forget to turn off the Poisson solver.
&SUBSYS
&CELL
ABC 12.4544808085 12.4544808085 12.4544808085
&END CELL
&COORD
@INCLUDE '64water.coord'
&END COORD
...
&END SUBSYS
Initially VMD does not know about the dimensions of the simulations cell. To setup, e.g. a 15Å qubic box, just type the following into vmd's Tk-console:
vmd> pbc set {15.0 15.0 15.0}
vmd> pbc wrap
&GLOBAL
PROJECT caffeine
RUN_TYPE ENERGY
&END GLOBAL
&FORCE_EVAL
&DFT
! Output all occupied molecular orbitals as cube-files
&PRINT
&MO_CUBES
NHOMO -1
&END MO_CUBES
&END PRINT
! Calculate the maximally localized Wannier functions
&LOCALIZE
METHOD CRAZY
EPS_LOCALIZATION 1.0E-8
&PRINT
! Output the Wannier functions as cube-files
&WANNIER_CUBES
&END
! Output the centers of all Wannier functions as xyz-file
&WANNIER_CENTERS
IONS+CENTERS .TRUE.
&END
&END
&END
! exchange correlation functional
&XC
&XC_FUNCTIONAL PBE
&END XC_FUNCTIONAL
&END XC
! Poisson solver required for non-periodic calculation
&POISSON
PERIODIC NONE
PSOLVER WAVELET
&END POISSON
! ============ SCF fine tuning ============
&MGRID
CUTOFF 400
&END MGRID
&QS
EPS_DEFAULT 1.0E-10
&END QS
&SCF
SCF_GUESS ATOMIC
EPS_SCF 1.0E-7
MAX_SCF 30
&OT
MINIMIZER CG
PRECONDITIONER FULL_SINGLE_INVERSE
&END
&OUTER_SCF
EPS_SCF 1.0E-7
MAX_SCF 4
&END
&END SCF
! ============ End of SCF fine tuning ============
&END DFT
&SUBSYS
&CELL
ABC 15.0 15.0 15.0
PERIODIC NONE
&END CELL
&TOPOLOGY
&CENTER_COORDINATES
&END
&END TOPOLOGY
&COORD
H 4.4169009427 5.7654974925 7.9758408247
N 8.6708423642 5.8343946244 6.6347213084
C 7.7544572660 7.7275482372 7.8213939469
N 6.3919654318 5.8642629272 7.3568679126
C 6.4494839543 7.1525402940 7.9597387862
C 7.4402138371 5.1755331540 6.7117923744
C 8.8064058483 7.0850033638 7.1845597858
N 8.2778986769 8.9446280562 8.2382523594
O 7.2643506988 4.0529962930 6.2454118622
C 5.1156137682 5.1424213782 7.4120564649
O 5.4684099858 7.6593220497 8.5167253955
H 10.2341485900 9.7932463989 8.0304114260
C 9.7967248636 5.1907999513 5.9591641231
H 5.2562171072 4.1726515030 7.9014364748
H 4.7402775185 4.9652043967 6.3976240445
H 10.6401430351 5.0886560185 6.6519804958
H 10.1151718438 5.7973815083 5.1027558576
H 9.4549428018 4.2086990850 5.6240133244
C 7.5708564616 9.9966158796 8.9691451507
C 9.5777006425 8.9511038401 7.8331053451
N 9.9406928680 7.8388520756 7.1872221397
H 7.5517578349 10.9193467788 8.3771079019
H 8.0665429481 10.1847691445 9.9288020634
H 6.5474923450 9.6514720878 9.1444003294
&END COORD
&KIND H
BASIS_SET TZV2P-GTH
POTENTIAL GTH-PBE-q1
&END KIND
&KIND C
BASIS_SET TZV2P-GTH
POTENTIAL GTH-PBE-q4
&END KIND
&KIND N
BASIS_SET TZV2P-GTH
POTENTIAL GTH-PBE-q5
&END KIND
&KIND O
BASIS_SET TZV2P-GTH
POTENTIAL GTH-PBE-q6
&END KIND
&END SUBSYS
&END FORCE_EVAL
H TZV2P-GTH
2
1 0 0 5 3
10.8827241585 -0.0167058885 0.0000000000 0.0000000000
3.0968750876 -0.0627538300 0.0000000000 0.0000000000
0.9874518162 -0.1917521975 0.0000000000 0.0000000000
0.3450687533 -0.4173635232 1.0000000000 0.0000000000
0.1492693554 -0.4270508887 0.0000000000 1.0000000000
2 1 1 2 2
1.4070000000 1.0000000000 0.0000000000
0.3880000000 0.0000000000 1.0000000000
#
C TZV2P-GTH
2
2 0 1 5 3 3
5.3685662937 0.0974901974 0.0000000000 0.0000000000 -0.0510969367 0.0000000000 0.0000000000
1.9830691554 0.1041996677 0.0000000000 0.0000000000 -0.1693035193 0.0000000000 0.0000000000
0.6978346167 -0.3645093878 0.0000000000 0.0000000000 -0.3579933930 0.0000000000 0.0000000000
0.2430968816 -0.6336931464 1.0000000000 0.0000000000 -0.4327616531 1.0000000000 0.0000000000
0.0812865018 -0.1676727564 0.0000000000 1.0000000000 -0.2457672757 0.0000000000 1.0000000000
3 2 2 2 2
1.0970000000 1.0000000000 0.0000000000
0.3180000000 0.0000000000 1.0000000000
#
N TZV2P-GTH
2
2 0 1 5 3 3
7.6227447102 0.0983924689 0.0000000000 0.0000000000 -0.0561654555 0.0000000000 0.0000000000
2.7970605447 0.1045217098 0.0000000000 0.0000000000 -0.1798165209 0.0000000000 0.0000000000
0.9909765447 -0.3742661352 0.0000000000 0.0000000000 -0.3653986185 0.0000000000 0.0000000000
0.3417314862 -0.6278094034 1.0000000000 0.0000000000 -0.4259126207 1.0000000000 0.0000000000
0.1116822743 -0.1675236192 0.0000000000 1.0000000000 -0.2366040346 0.0000000000 1.0000000000
3 2 2 2 2
1.6540000000 1.0000000000 0.0000000000
0.4690000000 0.0000000000 1.0000000000
#
O TZV2P-GTH
2
2 0 1 5 3 3
10.2674419938 0.0989598460 0.0000000000 0.0000000000 -0.0595856940 0.0000000000 0.0000000000
3.7480495696 0.1041178339 0.0000000000 0.0000000000 -0.1875649045 0.0000000000 0.0000000000
1.3308337704 -0.3808255700 0.0000000000 0.0000000000 -0.3700707718 0.0000000000 0.0000000000
0.4556802254 -0.6232449802 1.0000000000 0.0000000000 -0.4204922615 1.0000000000 0.0000000000
0.1462920596 -0.1677863491 0.0000000000 1.0000000000 -0.2313901687 0.0000000000 1.0000000000
3 2 2 2 2
2.3140000000 1.0000000000 0.0000000000
0.6450000000 0.0000000000 1.0000000000
H GTH-PBE-q1
1
0.20000000 2 -4.17890044 0.72446331
0
#
C GTH-PBE-q4
2 2
0.33847124 2 -8.80367398 1.33921085
2
0.30257575 1 9.62248665
0.29150694 0
#
N GTH-PBE-q5
2 3
0.28379052 2 -12.41522559 1.86809592
2
0.25540500 1 13.63026257
0.24549453 0
#
O GTH-PBE-q6
2 4
0.24455430 2 -16.66721480 2.48731132
2
0.22095592 1 18.33745811
0.21133247 0