Example inputfiles¶
A set with many more examples is provided in the $AMSHOME/examples/quild directory.
Vibrational frequencies for multi-level QM/QM scheme¶
$AMSBIN/quild << eor
ATOMS
C -0.759255999 0.032048841 0.000000000
C 0.759255999 -0.032048841 0.000000000
H -1.179949313 -0.464915468 0.890460461
H -1.179949313 -0.464915468 -0.890460461
H -1.115011042 1.076188400 0.000000000
H 1.179949313 0.464915468 0.890460461
H 1.179949313 0.464915468 -0.890460461
H 1.115011042 -1.076188400 0.000000000
END
GEOMETRY
Frequencies
END
AnalyticalFreq
End
Integration 7.0 7.0
SCF
converge 1.0e-7 1.0e-7
diis ok=0.01
END
QUILD
NR_REGIONS=2
REGION 1
1-8
SUBEND
REGION 2
2 6-8
SUBEND
DESCRIPTION 1 ADF
BASIS
type DZ
core Large
END
SUBEND
DESCRIPTION 2 ADF ! adding NUMFREQ would use numerical Hessian
! (not necessary in this case,
! because Analytical Hessian is available)
BASIS
type TZP
core Large
END
SUBEND
INTERACTIONS
TOTAL description 1
REPLACE region 2 description 2 for description 1
SUBEND
END
END INPUT
eor
rm quildjob*
Symmetry rotation with Td symmetry for geometry and C2v for orbitals¶
$AMSBIN/quild << eor
Title JCTC systems
Occupations smearq=0.0 &
A1 10.0 // 9.0
A2 3.0 // 2.0
B1 6.0 // 5.0
B2 6.0 // 5.0
End
Symmetry C(2v)
QUILD
Symgeo T(d)
Symrot
-0.7071067811865475 -0.7071067811865475 0.0
-0.7071067811865475 0.7071067811865475 0.0
0.0 0.0 1.0
Subend
End
Atoms
Fe 0.000000000 0.000000000 0.000000000
Cl -1.326583289 1.326583289 1.326583289
Cl -1.326583289 -1.326583289 -1.326583289
Cl 1.326583289 1.326583289 -1.326583289
Cl 1.326583289 -1.326583289 1.326583289
End
Geometry
End
Charge -2 4
Unrestricted
XC
LDA VWN
GGA OPBE
END
BASIS
type TZ2P
core SMALL
END
SCF
converge 1.0e-6 1.0e-6
iterations 99
diis ok=0.01
END
INTEGRATION 6.0 6.0
EPRINT
SFO noeig noovl
END
endinput
eor
Optimization with B3LYP through the post-SCF METAGGA scheme¶
$AMSBIN/quild << eor
title Geometry optimization
EPRINT
SFO NOEIG NOOVL
END
XC
GGA BLYP
END
ATOMS
O .000000 .000000 .000000
C .000000 .000000 1.128100
END
BASIS
type DZ
core NONE
END
GEOMETRY
END
SCF
diis ok=0.01
converge 1.0e-5 1.0e-5
END
QUILD
cvg_grd 1.0e-4
numgrad 1
SMETAGGA B3LYP(VWN5)
END
METAGGA
HFEXCHANGE
INTEGRATION 5.0 5.0
endinput
eor
Optimization with B3LYP as SCF functional¶
$AMSBIN/quild << eor
title Geometry optimization
EPRINT
SFO NOEIG NOOVL
END
XC
HYBRID B3LYP
END
ATOMS
O .000000 .000000 .000000
C .000000 .000000 1.128100
END
BASIS
type DZ
core NONE
END
GEOMETRY
END
SCF
diis ok=0.01
converge 1.0e-5 1.0e-5
END
QUILD
cvg_grd 1.0e-4
numgrad 2
END
INTEGRATION 5.0 5.0
endinput
eor
Geometry optimization with QM/MM treatment of water dimer¶
TITLE QM/MM calculation setup by pdb2adf: M.Swart, 2005
GEOMETRY
END
ATOMS
O 0.0000 0.0000 0.0000
H -0.5220 0.2660 -0.7570
H -0.5220 0.2660 0.7570
O 0.0000 -3.2000 0.0000
H 0.0570 -2.2440 0.0000
H 0.9110 -3.4950 0.0000
END
QUILD
NR_REGIONS=2
INTERACTIONS
TOTAL description 1
REPLACE region 1 description 3 for description 2
SUBEND
REGION 1
1-3
SUBEND
REGION 2
4-6
SUBEND
DESCRIPTION 1 NEWMM
QMMM
FORCE_FIELD_FILE $AMSRESOURCES/ForceFields/amber95.ff
MM_CONNECTION_TABLE
1 OW QM 2 3
2 HW QM 1
3 HW QM 1
4 OW MM 5 6
5 HW MM 4
6 HW MM 4
SUBEND
CHARGES
1 -0.8340
2 0.4170
3 0.4170
4 -0.8340
5 0.4170
6 0.4170
SUBEND
END
SUBEND
DESCRIPTION 2 NEWMM
QMMM
FORCE_FIELD_FILE $AMSRESOURCES/ForceFields/amber95.ff
MM_CONNECTION_TABLE
1 OW QM 2 3
2 HW QM 1
3 HW QM 1
SUBEND
CHARGES
1 -0.8340
2 0.4170
3 0.4170
SUBEND
END
SUBEND
DESCRIPTION 3
EPRINT
SFO NOEIG NOOVL
END
XC
GGA Becke-Perdew
END
BASIS
type TZP
core small
END
SCF
Converge 1.0e-5 1.0e-5
Iterations 99
END
INTEGRATION 5.0 5.0 5.0
CHARGE 0.0
SUBEND
END
ENDINPUT
eor
LinearTransit run for bimolecular nucleophilic reaction of F- and CH3 Cl¶
$AMSBIN/quild << eor
Title LinearTransit for Sn2 reaction of F- + CH3Cl
XC
GGA OPBE
END
QUILD
nrlt 11
cvg_grd 1.0e-4
CONSTR
dist 1 6 2.5 1.5
SUBEND
END
ATOMS
C 0.000000 0.000000 0.000000
H -0.530807 0.919384693 0.112892
H -0.530807 -0.919384693 0.112892
H 1.061614 0.000000 0.112892
Cl 0.000000 0.000000 -1.724300
F 0.000000 0.000000 2.500000
END
Geometry
End
BASIS
type TZ2P
core NONE
END
INTEGRATION 6.0 6.0
SCF
converge 1.0e-6 1.0e-6
diis ok=0.01
iterations 99
END
Charge -1
EPRINT
SFO noeig noovl
END
endinput
eor
Geometry optimization of pure spin state for spin-contaminated system¶
$AMSBIN/quild << eor
Title InorgChimActa paper
EPRINT
SFO NOEIG NOOVL
END
XC
GGA OPBE
END
GEOMETRY
END
BASIS
type TZP
core SMALL
END
SCF
Iterations 99
Diis ok=0.01
Mix 0.1
converge 1.0e-6 1.0e-6
END
INTEGRATION 6.0 6.0 6.0
QUILD
INTERACTIONS
TOTAL description 1
S2CORR description 2
SUBEND
DESCRIPTION 1
Occupations smearq=0.0 &
AA1 4.0 // 5.0
AA2 0.0 // 0.0
EE1 8.0 // 8.0
EE2 6.0 // 4.0
AAA1 0.0 // 0.0
AAA2 4.0 // 4.0
EEE1 6.0 // 6.0
EEE2 4.0 // 4.0
End
CHARGE 0.0 1.0
Unrestricted
SUBEND
DESCRIPTION 2
Occupations smearq=0.0 &
AA1 5.0 // 4.0
AA2 0.0 // 0.0
EE1 8.0 // 8.0
EE2 6.0 // 4.0
AAA1 0.0 // 0.0
AAA2 4.0 // 4.0
EEE1 6.0 // 6.0
EEE2 4.0 // 4.0
End
CHARGE 0.0 3.0
Unrestricted
SUBEND
END
SYMMETRY D(5H)
ATOMS
V 0.00000 0.00000 0.00000
C 1.20500 -1.66000 0.00000
C 0.37237 -1.66000 1.14602
C -0.97487 -1.66000 0.70828
C -0.97487 -1.66000 -0.70828
C 0.37237 -1.66000 -1.14602
H 2.29965 -1.70014 0.00000
H 0.71063 -1.70014 2.18710
H -1.86046 -1.70014 1.35170
H -1.86046 -1.70014 -1.35170
H 0.71063 -1.70014 -2.18710
C -0.97487 1.66000 0.70828
C 0.37237 1.66000 1.14602
C 1.20500 1.66000 0.00000
C 0.37237 1.66000 -1.14602
C -0.97487 1.66000 -0.70828
H -1.86046 1.70014 1.35170
H 0.71063 1.70014 2.18710
H 2.29965 1.70014 0.00000
H 0.71063 1.70014 -2.18710
H -1.86046 1.70014 -1.35170
END
endinput
eor
LinearTransit run for water dimer¶
$AMSBIN/quild << eor
TITLE QUILD (QUantum-regions Interconnected by Local Descriptions) input
QUILD
Constr
dist 1 2 2.6 3.4
Subend
nrlt 9
cvg_grd 1.0e-4
END
XC
GGA PW91
END
BASIS
TYPE DZP
CORE small
END
INTEGRATION 6.0 6.0
SCF
converge 1.0e-6 1.0e-6
diis ok=0.01 n=5 bfac=0.2
iterations 99
END
GEOMETRY
END
Occupations smearq=0.0
ATOMS
O -1.262468 -0.389110 0.000000
O 1.537530 0.425178 0.000000
H -1.540482 0.138323 0.765971
H -1.540482 0.138323 -0.765971
H 0.654929 0.010487 0.000000
H 2.150974 -0.323200 0.000000
END
EPRINT
SFO NOEIG NOOVL
END
ENDINPUT
eor
Interface to the AMS driver¶
This is a simple geometry optimization, showing how to use the DFTB engine in Quild2019 through the AMS driver interface.
$AMSBIN/quild << eor
ATOMS
1 H 0.000000 2.182973 1.259286
2 H 0.000000 -2.182973 1.259286
3 H 0.000000 2.182973 -1.259286
4 H 0.000000 -2.182973 -1.259286
5 C 0.000000 0.000000 1.441079
6 C 0.000000 0.000000 -1.441079
7 C 0.000000 1.266644 0.674582
8 C 0.000000 -1.266644 0.674582
9 C 0.000000 1.266644 -0.674582
10 C 0.000000 -1.266644 -0.674582
11 O 0.000000 0.000000 2.678518
12 O 0.000000 0.000000 -2.678518
END
GEOMETRY
END
NOPRINT LOGFILE
QUILD
idcvg 1
logfile_quild 1
NR_REGIONS=1
REGION 1
GUIINFO Label All Show 0 MolVis {Balls And Sticks}
1-6
SUBEND
DESCRIPTION 1 AMS
Task SinglePoint
Properties
Gradients true
End
System
-> Atoms
End
Engine DFTB
ResourcesDir DFTB.org/3ob-3-1
EndEngine
SUBEND
INTERACTIONS
TOTAL description 1
SUBEND
END
eor