Usage

Command Line Usage

Generates an input for a computational chemistry package

usage: ccinput [-h] [--basis_set BASIS_SET] [--solvent SOLVENT]
               [--solvation_model SOLVATION_MODEL]
               [--solvation_radii SOLVATION_RADII]
               [--custom_solvation_radii CUSTOM_SOLVATION_RADII]
               [--specifications SPECIFICATIONS]
               [--density_fitting DENSITY_FITTING]
               [--custom_basis_sets CUSTOM_BASIS_SETS] [--xyz XYZ]
               [--file FILE [FILE ...]] [--output OUTPUT]
               [--constraints CONSTRAINTS] [--freeze ATOM [ATOM ...]]
               [--scan ATOM [ATOM ...]] [--from FROM] [--to TO]
               [--nsteps NSTEPS] [--step STEP] [--nproc NPROC] [--mem MEM]
               [--charge CHARGE] [--mult MULT] [--parse_name] [--trust_me]
               [--d3 | --d3bj] [--name NAME] [--aux_name AUX_NAME]
               [--header HEADER] [--save SAVE] [--preset [PRESET]]
               [--driver {none,ORCA,pysis}] [--version]
               [--fragments FRAGMENTS]
               [software] [type] [method]

Positional Arguments

software

Desired software package (Gaussian, ORCA, Q-Chem, …)

type

Calculation type (opt, freq, sp, …)

method

Computational method (HF, AM1, B3LYP, …)

Named Arguments

--basis_set, -bs

Basis set

Default: “”

--solvent, -s

Solvent for implicit solvation

Default: “”

--solvation_model, -sm

Solvation model for implicit solvation

Default: “”

--solvation_radii, -sr

Set of solvation radii for implicit solvation

Default: “”

--custom_solvation_radii, -csr

Specific solvation radii to modify

Default: “”

--specifications, -spec

Additional commands

Default: “”

--density_fitting, -df

Basis set for density fitting (Gaussian only)

Default: “”

--custom_basis_sets, -cbs

String specification of custom basis sets on a per-atom basis

Default: “”

--xyz, -x

XYZ structure as string

Default: “”

--file, -f

XYZ structure(s) as file(s)

--output, -o

Write the result to the specified file (single file) or using the specified pattern (multiple files)

Default: “”

--constraints, -co

String specification of constraints for certain calculations

Default: “”

--freeze

Freeze specified distance/angle/dihedral between the specified atoms

Default: []

--scan

Scan specified distance/angle/dihedral between the specified atoms (additional parameters required)

Default: []

--from

Initial distance (for –scan)

Default: []

--to

Final distance (for –scan)

Default: []

--nsteps

Number of steps (for –scan)

Default: []

--step

Step size in Å (for –scan)

Default: []

--nproc, -n

Number of CPU cores to use

Default: 1

--mem

Amount of memory to use (if no unit is provided, assumed to be in MB)

Default: “1000MB”

--charge, -c

Charge of the system

Default: 0

--mult, -m

Multiplicity of the system

Default: 1

--parse_name

Use filenames to assign the charge and multiplicity

Default: False

--trust_me

Unknown values will be accepted as given

Default: False

--d3

Use the D3(0) dispersion correction

Default: False

--d3bj

Use the D3 dispersion correction with Becke-Johnson damping

Default: False

--name

Name of the produced file (unused by some packages)

--aux_name

Name of the auxiliary file (some calculation types only)

--header

Header in produced file (unused by some packages)

Default: “File created by ccinput”

--save

Save the current parameters as a preset of the given name

--preset

Load parameters from the chosen preset

--driver

Possible choices: none, ORCA, pysis

Specify a computation driver other than the calculation package

Default: none

--version, -v

show program’s version number and exit

--fragments

Assign each atom to a fragment

Python Library Usage

When using ccinput as a Python library, the desired wrapper must be imported as such:

>>> from ccinput.wrapper import gen_input
>>> inp = gen_input(...)

The generated input can be directly written to files:

>>> from ccinput.wrapper import write_input
>>> inp = write_input(filename, ...)

The parameters to these two wrappers will be the same as in the command line usage, using their long name as named parameters. For example:

>>> from ccinput.wrapper import gen_input
>>> inp = gen_input(software="orca", type="ts", method="PBEh-3c", file="ethanol.xyz", nproc=16, solvent="ethanol", solvation_model="SMD")

Parameter Details

The parameters not case sensitive and ccinput recognizes several synonyms for each of them. For example, “Def2-TZVP” can be written in any of these forms:

• def2-TZVP

• DEF2TZVP

• def2tzvp

Spaces and symbols other than + and * will be ignored. The otherwise different synonyms will be listed for each parameter. If you believe that a common or useful synonym is missing, feel free to send a pull request.

Software

Software package for which the input should be generated. This can influence the availability of certain options.

As of version 1.0, the following packages are supported for most features:

Software id	Synonyms
gaussian	g16 gaussian16
nwchem
orca	orca5
psi4	psi4
qchem
xtb

Type

Type of calculation (e.g. single-point energy, geometrical optimization, transition state optimization…)

Calculation type	Code
Conformational Search	CalcType.CONF_SEARCH
Constrained Conformational Search	CalcType.CONSTR_CONF_SEARCH
Constrained Optimisation	CalcType.CONSTR_OPT
Frequency Calculation	CalcType.FREQ
Geometrical Optimisation	CalcType.OPT
MO Calculation	CalcType.MO
Minimum energy path	CalcType.MEP
NMR Calculation	CalcType.NMR
Opt+Freq Calculation	CalcType.OPTFREQ
Single-point Energy	CalcType.SP
TDA UV-Vis Calculation	CalcType.UVVIS_TDA
TS Optimisation	CalcType.TS
UV-Vis Calculation	CalcType.UVVIS

Method

Calculation method to use.

All computational methods

Method	Synonyms
am1
apfd
b1b95
b1lyp
b1p
b2gpplyp
b2kplyp
b2plyp
b2tplyp
b3lyp
b3p
b3p86
b97
b973c
b97d
b97d3
b98
bhandhlyp
blyp
bmk
bnl
bnull
bp
bvwn
camb3lyp
ccsd
ccsdt
dlpnoccsd
dlpnoccsdt
dlpnoqcisd
dlpnoqcisdt
g1lyp
g1p
g3lyp
g3p
gfn0xtb	xtb0 gfn0
gfn1xtb	xtb1 gfn1 gfnxtb
gfn2xtb	xtb2 gfn2
gfn2xtbgfnff	gfn2gfnff
gfnff
glyp
gp
hcth147
hcth407
hcth93
hf	hartreefock scf
hf3c
hfs
hissbpbe
hse06	hse1pbe
l7pnoqcisdt
lcblyp
lcpbe
lcpbe0	campbe0
lcwhpbe	lrcwpbeh
lcwpbe
lpnoccsd
lpnoccsdt
lpnoqcisd
lsd
m05
m052x
m06
m062x
m06hf
m06l
m08hx
m11
m11l
mcscf
mn12l
mn12sx
mn15
mn15l
mndo
mp2
mpw1lyp
mpw1pbe
mpw1pw
mpw1pw91
mpw2plyp
mpw3pbe
mpwlyp
mpwpw
n12
n12sx
o3lyp
ohse1pbe
ohse2pbe
olyp
opbe
pbe	pbe96
pbe0	pbe1pbe
pbeh1pbe
pbeh3c
pm3
pm6
pm7	pm7r6
pw6b95
pw6b95d3
pw86pbe
pw91
pw910
pwlda
pwp
pwp1
pwpb95
qcisd
qcisdt
qtp00
r2scan3c
revpbe
revtpss
rimp2
rpbe
rpw86pbe
scanfunc
sogga11
sogga11x
thcth
thcthhyb
tpss
tpss0
tpssh	xctpssh
vsxc
vwn3
vwn5
wb2gpplyp
wb2plyp
wb97
wb97x
wb97xd
wb97xd3
wb97xd3bj
wb97xv
x3lyp
xalpha
xlyp

Basis set (--basis_set, -bs)

Basis set used for the calculation. Required for most methods, except “-3c” methods (e.g. HF-3c, PBEh-3c) and semi-empirical methods (e.g. AM1, PM3, …), including tight-binding methods (e.g. GFN2-xTB).

All basis sets

Basis set	Synonyms
321g
321gsp
422gsp
431g
621g
631++g2d2p
631++g2df
631++g2df2p
631++g2df2pd
631++g2dp
631++gdp	631++g**
631+g2d
631+g2d2p
631+g2df
631+g2df2p
631+g2df2pd
631+g2dp
631+gd	631+g*
631+gdp	631+g**
6311++g2d
6311++g2d2p
6311++g2df
6311++g2df2p
6311++g2df2pd
6311++g2dp
6311++g3df
6311++g3df3pd
6311++gdp	6311++g**
6311+g2d
6311+g2d2p
6311+g2df
6311+g2df2p
6311+g2df2pd
6311+g2dp
6311+g3df
6311+g3df2p
6311+g3df3pd
6311+gd	6311+g*
6311+gdp	6311+g**
6311g2d
6311g2d,2p
6311g2df
6311g2df2p
6311g2df2pd
6311g2dp
6311g3df
6311g3df3pd
6311gd	6311g*
6311gdp	6311g**
631g
631g2d
631g2d2p
631g2df
631g2df2p
631g2df2pd
631g2dp
631gd	631g*
631gdp	631g**
anopv5z
anopv6z
anopvdz
anopvqz
anopvtz
anorccdzp
anorccfull
anorccqzp
anorcctzp
anosz
auganopv5z
auganopvdz
auganopvqz
auganopvtz
augccpcv5z
augccpcv5zpp
augccpcv6z
augccpcvdz
augccpcvdzpp
augccpcvqz
augccpcvqzpp
augccpcvtz
augccpcvtzpp
augccpv5+dz
augccpv5z
augccpv5zdk
augccpv5zpp
augccpv6+dz
augccpv6z
augccpvd+dz
augccpvdz
augccpvdzdk
augccpvdzpp
augccpvq+dz
augccpvqz
augccpvqzdk
augccpvqzpp
augccpvt+dz
augccpvtz
augccpvtzdk
augccpvtzj
augccpvtzpp
augccpwcv5z
augccpwcvdz
augccpwcvqz
augccpwcvtz
augccpwv5zdk
augccpwv5zpp
augccpwvdzdk
augccpwvdzpp
augccpwvqzdk
augccpwvqzpp
augccpwvtzdk
augccpwvtzpp
augpc0
augpc1
augpc2
augpc3
augpc4
augpcj0
augpcj1
augpcj2
augpcj3
augpcj4
augpcseg0
augpcseg1
augpcseg2
augpcseg3
augpcseg4
augpcsseg0
augpcsseg1
augpcsseg2
augpcsseg3
augpcsseg4
cbsb7
ccpcv5z
ccpcv5zpp
ccpcv6z
ccpcvdz
ccpcvdzf12
ccpcvdzpp
ccpcvqz
ccpcvqzf12
ccpcvqzpp
ccpcvtz
ccpcvtzf12
ccpcvtzpp
ccpv5+dz
ccpv5z
ccpv5zdk
ccpv5zpp
ccpv6z
ccpvd+dz
ccpvdz
ccpvdzdk
ccpvdzf12
ccpvdzpp
ccpvdzppf12
ccpvq+dz
ccpvqz
ccpvqzdk
ccpvqzf12
ccpvqzpp
ccpvqzppf12
ccpvt+dz
ccpvtz
ccpvtzdk
ccpvtzf12
ccpvtzpp
ccpvtzppf12
ccpwcv5z
ccpwcv5zdk
ccpwcvdz
ccpwcvdzdk
ccpwcvqz
ccpwcvqzdk
ccpwcvtz
ccpwcvtzdk
ccpwv5zpp
ccpwvdzpp
ccpwvqzpp
ccpwvtzpp
cep121g
cep31g
cep4g
cp
cpppp
d95
d95p
d95v
def2
def2msvp
def2mtzvp
def2mtzvpp
def2qzv
def2qzvp
def2qzvpd
def2qzvpp
def2qzvppd
def2sv
def2svp
def2svpd
def2svpp
def2tzv
def2tzvp
def2tzvpd
def2tzvpf
def2tzvpp
def2tzvppd
dgdzvp
dgdzvp2
dkhdef2qzvp
dkhdef2qzvpp
dkhdef2svp
dkhdef2tzvp
dkhdef2tzvpf
dkhdef2tzvpp
dkhqzvp
dkhqzvpp
dkhsvp
dkhtzvp
dkhtzvpp
eprii
epriii
gdtzvp
hav5+dz
havq+dz
havt+dz
igloii
igloiii
lanl08
lanl08f
lanl2dz
lanl2mb
lanl2tz
lanl2tzf
m631g
m631gd	m631g*
madef2msvp
madef2qzvp
madef2qzvpp
madef2svp
madef2tzvp
madef2tzvpf
madef2tzvpp
madkhdef2qzvp
madkhdef2qzvpp
madkhdef2svp
madkhdef2tzvp
madkhdef2tzvpf
madkhdef2tzvpp
mazoradef2qzvpp
mazoradef2svp
mazoradef2tzvp
mazoradef2tzvpf
mazoradef2tzvpp
midi
midix
mini
minis
minix
partridge1
partridge2
partridge3
partridge4
pc0
pc1
pc2
pc3
pc4
pcj0
pcj1
pcj2
pcj3
pcj4
pcseg0
pcseg1
pcseg2
pcseg3
pcseg4
pcsseg0
pcsseg1
pcsseg2
pcsseg3
pcsseg4
qzvp
qzvpp
sapporodkh3dzp2012
sapporodkh3qzp2012
sapporodkh3tzp2012
sapporodzp2012
sapporoqzp2012
sapporotzp2012
sarc
sarc2dkhqzv
sarc2dkhqzvp
sarc2zoraqzv
sarc2zoraqzvp
sarcdkhsvp
sarcdkhtzvp
sarcdkhtzvpp
sauganopv5z
sauganopvdz
sauganopvqz
sauganopvtz
sdd
sddall
shc
sto3g
sv
svp
tzv
tzvp
tzvpp
ugbs
w1dz
w1mtsmall
w1opt
w1qz
w1tz
wachters+f
x2c
zoradef2qzvp
zoradef2qzvpp
zoradef2svp
zoradef2tzvp
zoradef2tzvpf
zoradef2tzvpp
zoraqzvp
zoraqzvpp
zorasvp
zoratzvp
zoratzvpp

Custom basis sets (--custom_basis_sets, -cbs)

Specific basis sets for specific atoms. Uses the format “<Element>=<Basis set label>;…” (e.g. “I=Def2-TZVPD;”). To see all the valid basis set labels per element, visit the Basis Set Exchange. Nonetheless, ccinput will also detect close synonyms of the requested basis set.

If applicable, the effective core potential (ECP) corresponding to the requested basis set will also be added to the input file.

Density fitting (--density_fitting, -df)

Basis set to use for density fitting. For NWChem, specify the name of the basis set you want to use for density fitting.

Gaussian documentation about density fitting

Note

Only available (explicitly) for Gaussian 16 and NWChem for the moment. In NWChem, density fitting for DFT is only available for version 7.2.0.

Structure files (--file, -f)

Structure file(s) to use in the input. Only XYZ files are currently supported.

Multiple files can be specified at once when using from the command line:

$ ccinput [...] -f struct1.xyz struct2.xyz

If no output pattern is specified, each input file will be printed to the console sequentially separated by a header. With an output pattern, the files will be created in the chosen directory with the given prefix and extension. When specifying only one file, the exact output path will be used.

$ ccinput [...] -f struct1.xyz struct2.xyz -o calc_dir/sp.inp
Input file written to calc_dir/sp_struct1.inp
Input file written to calc_dir/sp_struct2.inp

$ ccinput [...] -f struct1.xyz struct2.xyz -o .com
Input file written to struct1.com
Input file written to struct2.com

$ ccinput [...] -f struct1.xyz -o my_struct.com
Input file written to my_struct.com

Solvent (--solvent, -s)

Solvent to model using implicit solvation.

All solvents

Solvent	Synonyms
111trichloroethane
112trichloroethane
124trimethylbenzene
12dibromoethane
12ethanediol
14dioxane
1bromo2methylpropane
1bromooctane
1bromopentane
1bromopropane
1butanol
1chlorohexane
1chloropentane
1chloropropane
1decanol
1fluorooctane
1heptanol
1hexanol
1hexene
1hexyne
1iodobutane
1iodohexadecane
1iodopentane
1iodopropane
1nitropropane
1nonanol
1pentanol
1pentene
1propanol
222trifluoroethanol
224trimethylpentane
24dimethylpentane
24dimethylpyridine
26dimethylpyridine
2bromopropane
2butanol
2chlorobutane
2heptanone
2hexanone
2methoxyethanol
2methyl1propanol
2methyl2propanol
2methylpentane
2methylpyridine
2nitropropane
2octanone
2pentanone
2propanol
2propen1ol
3methylpyridine
3pentanone
4heptanone
4methyl2pentanone
4methylpyridine
5nonanone
aceticacid
acetone	acetone
acetonitrile	acetonitrile acn ch3cn mecn
acetophenone
achlorotoluene
aniline
anisole
argon
benzaldehyde
benzene	benzene c6h6
benzonitrile
benzylalcohol
bromobenzene
bromoethane
bromoform
butanal
butanoicacid
butanone
butanonitrile
butylamine
butylethanoate
carbondisulfide
carbontetrachloride	ccl4 carbontetrachloride
chlorobenzene	phcl
chloroform	chcl3 trichloromethane
cis1,2dimethylcyclohexane
cisdecalin
cyclohexane
cyclohexanone
cyclopentane
cyclopentanol
cyclopentanone
decalinmixture
dibromomethane
dibutylether
dichloroethane	12dichloroethane
dichloromethane	ch2cl2 dcm
diethylamine
diethylether	ether et2o
diethylsulfide
diiodomethane
diisopropylether
dimethyldisulfide
dimethylformamide	dmf
dimethylsulfoxide	dmso
diphenylether
dipropylamine
e1,2dichloroethene
e2pentene
ethanethiol
ethanol
ethylbenzene
ethylethanoate
ethylmethanoate
ethylphenylether
fluorobenzene
formamide
formicacid
heptane
hexanoicacid
iodobenzene
iodoethane
iodomethane
isopropylbenzene
isoquinoline
krypton
mcresol
mesitylene
methanol	meoh
methylbenzoate
methylbutanoate
methylcyclohexane
methylethanoate
methylmethanoate
methylpropanoate
mxylene
nbutylbenzene
ndecane
ndodecane
nhexadecane
nhexane	hexane hex
nitrobenzene	phno2
nitroethane
nitromethane	meno2
nmethylaniline
nmethylformamidemixture
nndimethylacetamide
nndimethylformamide	dmf
nnonane
noctane
noctanol	1octanol octanol
npentadecane
npentane
nundecane
ochlorotoluene
ocresol
odichlorobenzene
onitrotoluene
oxylene
pentanal
pentanoicacid
pentylamine
pentylethanoate
perfluorobenzene
pisopropyltoluene
propanal
propanoicacid
propanonitrile
propylamine
propylethanoate
pxylene
pyridine
quinoline
secbutylbenzene
tertbutylbenzene
tetrachloroethene
tetrahydrofuran	thf
tetrahydrothiophenessdioxide
tetralin
thiophene
thiophenol
toluene	phme phch3
transdecalin
tributylphosphate
trichloroethene
triethylamine
water	h2o
xenon
xylenemixture
z12dichloroethene

Solvation model (--solvation_model, -sm)

Model used for implicit solvation.

Software	Models
Gaussian	SMD PCM CPCM
ORCA	SMD CPCM
xtb	GBSA ALPB
NWChem	SMD COSMO

Solvation radii (--solvation_radii, -sr)

Set of element radii to use in the solvation model.

Model	Sets of radii
SMD	Default SMD18 [SMD18]
All	UFF (g16 default) UA0 UAHF UAKS Pauling Bondi

[SMD18]

5. Engelage, N. Schulz, F. Heinen, S. M. Huber, D. G. Truhlar, C. J. Cramer, Chem. Eur. J. 2018, 24, 15983-15987.

Custom solvation radii (-custom_solvation_radii, -csr)

Specific solvation radii to use for some elements.

The format to use is “<ELEMENT>=<RADIUS>;…”, for example: “H=1.00;Li=1.70;”.

Parse Name (--parse_name)

Input files can have different charges or multiplicities, as long as the file name reflects this and the --parse_name option is used.

By default, inputs are assumed to be neutral and in the singlet state. Charges are indicated by having (tri/di)cation or (tri/di)anion in the file name. Doublet states are denoted with radical or doublet, and triplet states with triplet.

If a charge or multiplicity is also provided explicitly, it will be used as default state for all inputs. However, the charge and multiplicity in the file names have priority over the default state. As such, neutral can be added to the file name to ensure that the input will be considered neutral, even if the option --charge 1 is provided, for example.

Specifications (--specifications)

Custom keywords to add to the command of the input.

$ ccinput orca opt HF --xyz "Cl 0 0 0" -c -1 -bs Def2SVP
!OPT HF Def2-SVP
[...]

$ ccinput orca opt HF --xyz "Cl 0 0 0" -c -1 -bs Def2SVP --specifications "TIGHTSCF"
!OPT HF Def2-SVP tightscf
[...]

With Gaussian 16, this can also add parameters to the calculation keyword:

$ ccinput g16 opt HF --xyz "Cl 0 0 0" -c -1 -bs Def2SVP
[...]
#p opt HF/Def2SVP
[...]

$ ccinput g16 opt HF --xyz "Cl 0 0 0" -c -1 -bs Def2SVP --specifications "opt(maxstep=5)"
[...]
#p opt(maxstep=5) HF/Def2SVP
[...]

$ ccinput g16 opt HF --xyz "Cl 0 0 0" -c -1 -bs Def2SVP --specifications "opt(maxstep=5) SCF(restart)"
[...]
#p opt(maxstep=5) HF/Def2SVP scf(restart)
[...]

Note that the specifications are not checked for validity beyond simple syntax checks. This allows you to use all valid keywords of the software, but can also lead to invalid inputs.

In nwchem, the syntax for specifcations in the following:

$ ccinput g16 opt HF --xyz "Cl 0 0 0" -c -1 -bs Def2SVP --specifications "scf(maxiter 20);opt(tight)"

Constraints (--constraints, -co, --freeze, --scan, --from, --to, --nsteps, --step)

Constraints (freeze or scan) can be specified either as a string or as separate parameters.

The string representation allows to specified all the constraints at once in a relatively readable fashion:

# Freeze the bond between atoms 1 and 2 (starting at 1)
$ ccinput [...] --constraints "freeze/1_2;"

# Freeze the angle between atoms 1, 2 and 3
$ ccinput [...] --constraints "freeze/1_2_3;"

# Freeze the dihedral angle between atoms 1, 2, 3 and 4
$ ccinput [...] --constraints "freeze/1_2_3_4;"

# Different constraints are delimited by semi-colons
$ ccinput [...] --constraints "freeze/1_2;freeze/3_4_5;"

# Scans the bond 1-2 from 2 A to 1 A in 10 steps
# Note that Gaussian does not allow starting values other than those of the current structure.
# As such, the starting value is ignored with Gaussian.
$ ccinput [...] --constraints "scan_2_1_10/1_2;"

# Scans the angle 1-2-3 from 90 degrees to 0 degrees in 10 steps
$ ccinput [...] --constraints "scan_90_0_10/1_2_3;"

# Scans the angle 1-2-3 from its current value to 0 degrees in 10 steps
$ ccinput [...] --constraints "scan_auto_0_10/1_2_3;"

# Scans the dihedral angle 1-2-3-4 from 90 degrees to 0 degrees in 10 steps
$ ccinput [...] --constraints "scan_90_0_10/1_2_3_4;"

# Different types of constraint can be combined
$ ccinput [...] --constraints "scan_90_0_10/1_2_3;freeze/4_5;"

The library usage uses an identical syntax:

>>> from ccinput.wrapper import gen_input
>>> inp = gen_input([...], constraints="scan_90_0_10/1_2_3;freeze/4_5;")

With the string, scans always require the starting value, the final value as well as the number of steps. However, more convenient options are available using --scan, --from, --to, --nsteps and --step:

Note

Scans are not implemented in nwchem for the moment

# Also scans the bond 1-2 from 2 A to 1 A in 10 steps
$ ccinput [...] --scan 1 2 --from 2 --to 1 --nsteps 10

# Scans the bond 1-2 from its current value to 1 A in 10 steps
$ ccinput [...] --scan 1 2 --to 1 --nsteps 10

# Scans the bond 1-2 from its current value to 1 A in steps of 0.1 A
$ ccinput [...] --scan 1 2 --to 1 --step 0.1

# Equivalent to the above
$ ccinput [...] --scan 1 2 --to 1 --step -0.1

# Scans the bonds 1-2 and 3-4 from their current values to 1 A in steps of 0.1 A
$ ccinput [...] --scan 1 2 --to 1 --step 0.1 --scan 3 4 --to 1 --step 0.1

# The order of the sets of parameters matters:
# Scans the bond 1-2 from 1.9 A to 0.5 A by step of 0.15 and
# the bond 3-4 from 1.5 A to 1.0 A in step of 0.1 A
$ ccinput [...] --scan 1 2 --from 1.9 --to 0.5 --step 0.15 --scan 3 4 --from 1.5 --to 1 --step 0.1

# Scans the bond 1-2 from 1.5 A to 1.0 A in step of 0.1 A and
# the bond 3-4 from 1.9 A to 0.5 A by step of 0.15
$ ccinput [...] --scan 1 2 --from 1.5 --to 1 --step 0.1 --scan 3 4 --from 1.9 --to 0.5 --step 0.15

# However, the exact ordering of each different parameter does not matter
# Equivalent to the above
$ ccinput [...] --scan 1 2 --to 1 --from 1.5 --step 0.1 --scan 3 4 --step 0.15 --to 0.5 --from 1.9

# Moreover, coordinates can be frozen in a similar fashion
# Freezes the angle between atoms 1, 2 and 3
$ ccinput [...] --freeze 1 2 3

# Freezes the angle between atoms 1, 2 and 3 and
# scans the bond 1-2 from its current value to 1 A in steps of 0.1 A
$ ccinput [...] --freeze 1 2 3 --scan 1 2 --to 1 --step 0.1

# Equivalent to the above
$ ccinput [...] --scan 1 2 --to 1 --step 0.1 --freeze 1 2 3

# Also equivalent to the above (although confusing)
$ ccinput [...] --scan 1 2 --to 1 --freeze 1 2 3 --step 0.1

The library usage employs arrays for each parameter, with freeze and scan being arrays of arrays (for multiple constraints of multiple atoms each). The scanning parameters are prefixed by the letter “s” (for “scan”) due to the name clash with the Python keyword from.

>>> from ccinput.wrapper import gen_input
>>> inp = gen_input([...], freeze=[[1, 2]])

>>> inp = gen_input([...], scan=[[2, 3]], sfrom=[1.0], sto=[1.5], snsteps=[5])

>>> inp = gen_input([...], scan=[[2, 3]], sfrom=[1.0], sto=[1.5], sstep=[0.1])

>>> inp = gen_input([...], scan=[[2, 3], [1, 2, 3, 4]], sfrom=[1.0, 120], sto=[1.5, 160], sstep=[0.1, 5])

Presets

Presets offer a convenient way to save sets of parameters and reuse them easily in the command line:

$ ccinput gaussian opt m062x -bs def2tzvp --specifications "opt(maxstep=5) 5d nosymm" -sm smd -sr smd18 -s methanol --save my_preset
--- Saved preset 'my_preset'
software                      gaussian
type                          opt
method                        m062x
basis_set                     def2tzvp
version                       <Y.X.Z>
solvent                       methanol
solvation_model               smd
solvation_radii               smd18
specifications                opt(maxstep=5) 5d nosymm

$ ccinput --preset my_preset --xyz "Cl 0 0 0" -c -1
%chk=calc.chk
%nproc=1
%mem=1000MB
#p opt(maxstep=5) M062X/Def2TZVP 5d nosymm SCRF(SMD, Solvent=methanol, Read)

File created by ccinput

-1 1
Cl   0.00000000   0.00000000   0.00000000

modifysph

Br 2.60
I 2.74

All parameters can be saved in the preset, except the calculation name and the XYZ structure. To create a preset, simply enter all the desired parameters exactly like when creating an input file and append --preset <preset_name> to the command. This will not generate any input file and will instead same the parameters as JSON in an accessible user directory (generally ~/.local/share/ccinput or C:\\Users\\<username>\\AppData\\Local\\CYLlab\\ccinput).

Parameters in the preset file can be overwritten when creating the input file:

$ ccinput --preset my_preset --xyz "Cl 0 0 0" -c -1
%chk=calc.chk
%nproc=1
%mem=1000MB
#p opt(maxstep=5) M062X/Def2TZVP 5d nosymm SCRF(SMD, Solvent=methanol, Read)

File created by ccinput

-1 1
Cl   0.00000000   0.00000000   0.00000000

modifysph

Br 2.60
I 2.74


$ ccinput --preset my_preset --xyz "Cl 0 0 0" -c -1 -s vacuum
%chk=calc.chk
%nproc=1
%mem=1000MB
#p opt(maxstep=5) M062X/Def2TZVP 5d nosymm

File created by ccinput

-1 1
Cl   0.00000000   0.00000000   0.00000000

Specifications are the only parameters that are not overwritten, but combined:

$ ccinput --preset my_preset --xyz "Cl 0 0 0" -c -1 -s vacuum --specifications "Int(Ultrafinegrid)"

%chk=calc.chk
%nproc=1
%mem=1000MB
#p opt(maxstep=5) M062X/Def2TZVP 5d nosymm int(ultrafinegrid)

File created by ccinput

-1 1
Cl   0.00000000   0.00000000   0.00000000

Presets can be permanently modified by specifying new parameters and saving them in the same preset. Unspecified options will not be modified:

$ ccinput -s vacuum --save my_preset
--- Saved preset 'my_preset'
software                      gaussian
type                          opt
method                        m062x
basis_set                     def2tzvp
version                       1.2.2+7.g8e241e2.dirty
solvent                       vacuum
solvation_model               smd
solvation_radii               smd18
specifications                opt(maxstep=5) 5d nosymm

$ ccinput --preset my_preset --xyz "Cl 0 0 0" -c -1
%chk=calc.chk
%nproc=1
%mem=1000MB
#p opt(maxstep=5) M062X/Def2TZVP 5d nosymm

File created by ccinput

-1 1
Cl   0.00000000   0.00000000   0.00000000

Note that the parameters are not validated on preset creation.