Atomic start guess¶
Initial SCF run¶
We consider the Hartree-Fock calculation of porphyrin with a mercury center
The SCF input file HF.inp reads:
**DIRAC
.WAVE FUNCTION
.ANALYZE
**WAVE FUNCTIONS
.SCF
*SCF
.MAXITR
20
.PRINT
2
.CLOSED SHELL
120 120
**ANALYZE
.MULPOP
*END OF
for an SCF calculation with a Mulliken population analysis. We specify the maximum number of iterations allowed for th caclulation to 20 and as we are chosing a molecule with inversion symmetry we specify the occupation number for both irreducible representations under the keyword CLOSED SHELL. The print level is set to 2 in order to have the eigenvlues printed for each iteration.
The molecular input hg-porphyrin.mol reads :
BASIS
6-31 and finite DK3 basis sets, geometry in au, ref ECP: Theor.Chim.Acta 1990,77,123 (from Gaussian)
--------------------------------------------------------
C 4 3 X Y Z
7. 2
N1 0.000000 4.1196801826 0.000000
N2 4.1196801826 0.000000 0.000000
LARGE BASIS 6-31G
6. 5
C1 4.642960672 4.642960672 0.000000
C2 2.127242869 5.577562894 0.000000
C3 1.2976452113 8.20576858026 0.000000
C4 8.20576858026 1.2976452113 0.000000
C5 5.577562894 2.127242869 0.000000
LARGE BASIS 6-31G
1. 3
H1 6.1040918256 6.1040918256 0.000000
H2 2.536971561 9.84908074236 0.000000
H3 9.84908074236 2.536971561 0.000000
LARGE BASIS 6-31G
80. 1
Hg 0.000000 0.000000 0.000000
LARGE 4 1 1 1 1
F 23 0 0 # s-functions
5.4107818D+07
1.2757417D+07
3.8200687D+06
1.2601464D+06
4.4355086D+05
1.6477405D+05
6.4498870D+04
2.6536057D+04
1.1391885D+04
5.0460108D+03
2.2877229D+03
1.0547293D+03
4.9377065D+02
2.3032535D+02
1.1057622D+02
4.7454363D+01
2.4814292D+01
1.0508682D+01
5.3690964D+00
1.7593797D+00
8.2178073D-01
1.6991016D-01
5.9613310D-02
F 23 0 0 # p-functions
2.1202540D+07
4.1579701D+06
1.0372139D+06
2.9906582D+05
9.5123364D+04
3.3364166D+04
1.2858845D+04
5.3680904D+03
2.3907706D+03
1.1241754D+03
5.5303069D+02
2.8249864D+02
1.4871000D+02
7.9474383D+01
4.3674317D+01
2.4527063D+01
1.4058201D+01
7.9450158D+00
4.5067591D+00
2.4440572D+00
1.2660103D+00
6.1522560D-01
2.5113161D-01
F 15 0 0 # d-functions
1.4315825D+04
3.7250818D+03
1.3315379D+03
5.5776192D+02
2.5656959D+02
1.2554901D+02
6.3698254D+01
3.3232923D+01
1.7367497D+01
8.9182853D+00
4.5159858D+00
2.1444878D+00
9.7876159D-01
4.1519292D-01
1.5886171D-01
F 10 0 0 # f-functions
1.3065007D+03
4.4185000D+02
1.8456705D+02
8.5884633D+01
4.2090822D+01
2.1327466D+01
1.0817659D+01
5.3881551D+00
2.5585604D+00
1.0775039D+00
FINISH
The calculations are carried out in D2h symmetry, so that the Fock matrix is real. From the output file we read:
Atoms and basis sets
--------------------
Number of atom types: 4
Total number of atoms: 37
label atoms charge prim cont basis
----------------------------------------------------------------------
N2 4 7 22 9 L - [10s4p|3s2p]
58 58 S - [4s10p4d|4s10p4d]
C5 20 5 22 9 L - [10s4p|3s2p]
58 58 S - [4s10p4d|4s10p4d]
H3 12 1 4 2 L - [4s|2s]
12 12 S - [4p|4p]
Hg 1 80 282 282 L - [23s23p15d10f|23s23p15d10f]
635 635 S - [23s38p33d15f10g|23s38p33d15f10g]
----------------------------------------------------------------------
858 522 L - large components
2171 2171 S - small components
----------------------------------------------------------------------
total: 37 220 3029 2693
showing that in AO-basis the Fock-matrix has the dimension 2693 x 2693 and thus requires 7252249 words. The SCF run will require something like three Fock matrices, so in this case 21 Mwords.
Unfortunately, this HF does not converge:
SCF - CYCLE
-----------
--------------------------------------------------------------------------------------------------------------------------------
Energy ERGVAL FCKVAL EVCVAL Conv.acc CPU Integrals Time stamp
--------------------------------------------------------------------------------------------------------------------------------
It. 1 -7794.747305914 0.00D+00 0.00D+00 0.00D+00 10.89634323s Scr. nuclei Fri Oct 19
It. 2 -20119.30505450 1.23D+04 -9.63D+01 1.29D+02 4min 6.910s LL SL Fri Oct 19
It. 3 -17230.23561991 -2.89D+03 1.95D+02 2.69D+02 DIIS 2 3min55.989s LL SL Fri Oct 19
It. 4 -20286.13741996 3.06D+03 -8.61D+01 9.85D+01 DIIS 3 3min42.372s LL SL Fri Oct 19
It. 5 -20126.54429484 -1.60D+02 -9.61D+01 4.27D+01 DIIS 4 3min52.176s LL SL Fri Oct 19
It. 6 -18673.18452215 -1.45D+03 1.36D+02 1.55D+02 DIIS 5 3min48.236s LL SL Fri Oct 19
It. 7 -18727.77909394 5.46D+01 -1.82D+00 1.48D+02 DIIS 6 3min53.450s LL SL Fri Oct 19
It. 8 -18755.21459721 2.74D+01 -8.49D-01 1.45D+02 DIIS 7 4min 4.378s LL SL Fri Oct 19
It. 9 -18760.27704618 5.06D+00 -1.58D-01 1.45D+02 DIIS 8 3min40.865s LL SL Fri Oct 19
It. 10 -18773.33929407 1.31D+01 -4.09D-01 1.44D+02 DIIS 9 3min51.322s LL SL Fri Oct 19
It. 11 -18779.70838778 6.37D+00 -1.28D-01 1.44D+02 DIIS 9 3min42.698s LL SL Fri Oct 19
It. 12 -18953.17392936 1.73D+02 -4.17D+00 1.33D+02 DIIS 9 3min52.510s LL SL Fri Oct 19
It. 13 -18938.57698783 -1.46D+01 5.29D-01 1.34D+02 DIIS 9 3min43.147s LL SL Fri Oct 19
It. 14 -18744.84737430 -1.94D+02 8.55D+00 1.59D+02 DIIS 9 3min56.082s LL SL Fri Oct 19
It. 15 -18164.22290167 -5.81D+02 -2.01D+02 4.93D+01 DIIS 9 3min48.373s LL SL Fri Oct 19
It. 16 -16110.21649469 -2.05D+03 2.64D+02 2.90D+02 DIIS 9 3min47.714s LL SL Fri Oct 19
It. 17 -16272.74479238 1.63D+02 -4.12D+00 2.75D+02 DIIS 9 3min49.219s LL SL Fri Oct 19
It. 18 -16280.64616752 7.90D+00 -2.09D-01 2.74D+02 DIIS 9 3min40.992s LL SL Fri Oct 19
It. 19 -16279.46291382 -1.18D+00 5.93D-02 2.75D+02 DIIS 9 3min37.488s LL SL Fri Oct 19
It. 20 -16289.37827128 9.92D+00 -2.58D-01 2.74D+02 DIIS 9 3min42.223s LL SL Fri Oct 19
We see that the corrected bare nucleus start is quite far from the energies of subsequent iterations. Although the energy in the second iteration drops considerably it bounces back and gets stuck. We will therefore switch to an atomic start [vanLenthe2006] . Observe that this caclulation will take more than an hour.
Preparing the atomic start¶
For each atom we now run a SCF calculation in full (linear) symmetry based on the atomic ground state configuration. For open-shell atoms this amounts to an average-of-configuration (AOC) calculation at the HF level, and a fractional occupation calculation at the DFT level.
Nitrogen atom¶
The input file N.inp reads:
**DIRAC
.WAVE FUNCTION
.ANALYZE
**GENERAL
.ACMOUT
**WAVE FUNCTIONS
.SCF
*SCF
.CLOSED SHELL
4 0
.OPEN SHELL
1
3/0,6
**ANALYZE
.MULPOP
*END OF
Note the keywords ACMOUT asking that the MO coeffcients transformed to no symmetry and written to file DFACMO. The open shell input specifies 1 open shell with 3 electrons in 0 and 6 spinors respectively for the two irriducible representations.
The molecular input N.mol is
BASIS
6-31 and finite DK3 basis sets, geometry in au, ref ECP: Theor.Chim.Acta 1990,77,123 (from Gaussian)
--------------------------------------------------------
C 1
7. 1
N 0.0 0.0 0.0
LARGE BASIS 6-31G
FINISH
The minimal pam command is
pam --mol=N.mol --inp=N.inp --get=DFACMO
mv DFACMO ac.N
Other atoms¶
The input file for the other atoms are prepared in similar manner. For carbon we use the occupation
.CLOSED SHELL
4 0
.OPEN SHELL
1
2/0,6
For mercury we use
.CLOSED SHELL
42 38
whereas the hydrogen atom is run as a one-electron system, meaning that the keyword for ignoring two-particle interactions ONESYS will be invoked
**DIRAC
.WAVE FUNCTION
.ANALYZE
**GENERAL
.ACMOUT
**HAMILTONIAN
.ONESYS
**WAVE FUNCTIONS
.SCF
*SCF
.CLOSED SHELL
2 0
**ANALYZE
.MULPOP
*END OF
(The occupation given above is simply to control orbitals printed in the subsequent Mulliken population analysis).
All atoms can be run in a single shot, e.g. using bash
for atom in H C N Hg
do
pam --mol=${atom}.mol --inp=${atom}.inp --get=DFACMO
mv DFACMO ac.${atom}
done
We are now ready to run the atomic start.
Running the atomic start¶
The input file atomstart.inp reads
**DIRAC
.WAVE FUNCTION
.ANALYZE
**WAVE FUNCTIONS
.SCF
*SCF
.ATOMST
AFNXXX 2
1,2
1.00
3..5
0.5
AFCXXX 2
1,2
1.00
3..5
0.33
AFHXXX 1
1
0.5
AFHGXX 1
1..40
1.00
.CLOSED SHELL
120 120
**ANALYZE
.MULPOP
*END OF
The keyword ATOMST is followed by input for each atomic type. The first input AFYYXX specifies the file to be read for an atomtype YY, and next to it a number specifying inversion symmtry (2) or not (1). Next, for each symmetry, the spinors of that symmetry is specified followed by the occupation of the spinors.
The occupations chosen corresponds to those of the atomic runs, but the user may
modify this at will. Please note that the order of atoms corresponds to the
order they appear in the molecule file.
Before running the calculation the user must make provide links to the atomic coefficient files
ln -s ac.N AFNXXX
ln -s ac.C AFCXXX
ln -s ac.H AFHXXX
ln -s ac.Hg AFHGXX
and the calculation is then run as
pam --mol=hg-porphyrin.mol --inp=atomstart.inp --copy="AF*" --outcmo
This calculation converges smoothly after 17 iterations
SCF - CYCLE
-----------
* Convergence on norm of error vector (gradient).
Desired convergence:1.000D-07
Allowed convergence:1.000D-06
* ERGVAL - convergence in total energy
* FCKVAL - convergence in maximum change in total Fock matrix
* EVCVAL - convergence in error vector (gradient)
--------------------------------------------------------------------------------------------------------------------------------
Energy ERGVAL FCKVAL EVCVAL Conv.acc CPU Integrals Time stamp
--------------------------------------------------------------------------------------------------------------------------------
It. 1 -20645.07067749 2.06D+04 0.00D+00 0.00D+00 Atomic s 32.88100123s LL SL Mon Mar 4
It. 2 -20633.15458108 -1.19D+01 6.07D-01 8.19D-01 1min11.442s LL SL Mon Mar 4
It. 3 -20633.38854493 2.34D-01 -2.13D-01 3.24D-01 DIIS 2 1min 9.861s LL SL Mon Mar 4
It. 4 -20633.41415475 2.56D-02 1.52D-01 1.72D-01 DIIS 3 1min 3.733s LL SL Mon Mar 4
It. 5 -20633.42153720 7.38D-03 -6.24D-02 2.79D-02 DIIS 4 1min 2.223s LL SL Mon Mar 4
It. 6 -20633.42175881 2.22D-04 -4.58D-03 8.00D-03 DIIS 5 1min 3.556s LL SL Mon Mar 4
It. 7 -20633.42178693 2.81D-05 2.31D-03 3.88D-03 DIIS 6 1min 1.382s LL SL Mon Mar 4
It. 8 -20633.42179098 4.05D-06 -1.68D-03 1.75D-03 DIIS 7 57.84219360s LL SL Mon Mar 4
It. 9 -20633.42179253 1.55D-06 3.91D-04 5.46D-04 DIIS 8 57.79122925s LL SL Mon Mar 4
It. 10 -20633.42179283 3.01D-07 -5.63D-05 2.16D-04 DIIS 9 55.75250244s LL SL Mon Mar 4
It. 11 -20633.42179286 3.30D-08 1.89D-05 7.63D-05 DIIS 9 53.37689209s LL SL Mon Mar 4
It. 12 -20633.42179287 4.12D-09 -1.74D-05 2.92D-05 DIIS 9 51.99108887s LL SL Mon Mar 4
It. 13 -20633.42179287 7.42D-10 6.49D-06 8.29D-06 DIIS 9 51.30120850s LL SL Mon Mar 4
It. 14 -20633.42179287 3.13D-10 -1.22D-06 2.61D-06 DIIS 9 48.06268311s LL SL Mon Mar 4
It. 15 -20633.42179287 -2.18D-10 5.07D-07 5.08D-07 DIIS 9 48.58166504s LL SL Mon Mar 4
It. 16 -20633.42179287 -2.15D-10 -2.13D-07 2.33D-07 DIIS 9 43.13543701s LL SL Mon Mar 4
It. 17 -20633.42179287 5.42D-10 1.06D-07 9.96D-08 DIIS 9 42.37854004s LL SL Mon Mar 4
--------------------------------------------------------------------------------------------------------------------------------
* Convergence after 17 iterations.