Quantum chemistry¶

What you can do¶

Quantum chemical capabilities are:

SCF: Hartree-Fock and DFT, also in strong magnetic fields: moldft, nemo, znemo
analytical gradients for SCF: moldft, nemo, znemo
second nuclear derivatives for SCF (field-free case only), nemo
CIS, cis, zcis
response properties, molresponse
MP2, cc2
ADC(2), CIS(D), cc2
CC2 ground and excited states, cc2
PNO-MP2, pno
OEP/RKS, oep

Quickstart¶

All programs can read commandline options or an input file (by default this is named “input”). A full list of all available calculation parameters can be obtained by writing

qccode --help

where qccode stands for any of the qc codes (e.g. moldft, cc2, nemo, …)

Calculation parameters¶

All calculations require parameters, specifying the molecule, the quantum chemical model, charge etc. If no parameters are given, default parameters will be used. Only the molecule itself must be specified by the user. Parameters can be specified through an input file and/or command line options.

Some parameters depend on each other and are set automatically, e.g. certain numerical parameters, or the use of point group symmetry. Parameters set by the user are always respected.

In the output files of the calculations the complete set of input parameters are printed out, together with a short description and further information.

You can see the full list of parameters by typing

qccode --print_parameters

where, again, qccode stands for any of the qc codes

Input file¶

The input file consists of data groups, starting with the relevant keyword, e.g. “dft” and ending with “end”. All parameters in a data group are given as key/value pairs, where the value can be an integer, a double, a string even a vector or pair.

A sample input file looks like

dft
charge 1 # comment
ncf (slater,2.0) # value is a pair of string and double
end

geometry
O 0 0 0
H 0 1 1
H 0 1 -1
end

Blank lines are ignored, as is everything after a hashtag. The input file is case-insensitive. The key/value pairs can be separated by blanks or by the equal sign. Pairs and vectors must be encased in parantheses or brackets, their entries must be separated by commas.

All programs will output the complete list of input options. You can always run

qccode --help

which will output the input parameters and the copy/paste the options verbatim. Note the once an option appears in the input file it will be considered user-defined and will override all default or derived values.

Command line options¶

The data groups in the input file can also be set or augmented through the command line, e.g. the following line will pass the same calculation parameters as the input file above.

nemo --dft="charge=1; ncf=(slater,2.0)"

Different key/value pairs are separated by a semicolon to indicate a newline. If a given parameter is specified both in the input file and the command line, the command line parameters have priority over input file parameters.

The name of the input file can be changed by

nemo --input=customfile

Numerical parameters¶

Numerical parameters are specified in the dft block, the most important ones that will also be used is subsequent calculations (e.g. mp2) are

dft
k 5
L 20
end

The polynomial order k can be chosed between 2 and 30, for SCF calculations a value of 7 to 9 is advised, for correlated calculations it should be chosen 5 or 6.

The calculation box size L should be large enough to hold all relevant phyics. All wavefunctions should have decayed to practically zero at the box boundary. Note that excited states or anions can be quite large. The box size is given in atomic units (1 a.u. = 52 pm).

Generally it is advisable to use as few numerical parameters as possible, as they are usually dependent on each other

Geometry input¶

The geometry of the molecule is given in the geometry data group. By default atomic units are used, but angstrom can be switched on by adding the line

geometry
units angstrom
…
end

The following example will read an external xyz file, using angstrom by default

geometry
source_type xyz # optional
source_name h2o.xyz
end

or you can use the command line options using the convenience short option

nemo --geometry=h2o.xyz

A small number of geometries are stored in a library, accessible through

nemo --geometry="source_type=library; source_name=h2o"

If no source type is given it will be deduced from the file name, if the source is ambiguous, e.g. a structure in the library has the same same as an input file, the code will stop.

Geometry optimization¶

For the following codes/methods there are gradients implemented:

nemo, moldft, znemo

Native optimizer¶

Codes with gradients can use the built-in geometry optimizer by adding the gopt flag in the dft block, geometry optimization parameters are set in the geoopt block.

nemo --dft="k=8; econv=1.e-5; gopt=1" --geoopt="maxiter=10" --geometry="source_type=library; source_name=h2o"

External optimizers¶

External optimizers (e.g. pyberny, geometric ) can be used through Madness’s python wrapper. Details to follow.

from madness import madness
m=madcalc("/Users/fbischoff/devel/install/madness")
m.get_result()
print(m.data[0]["scf_energy"])
print(m.get_scf_energy())
print(m.data[0]["scf_k"])

Other electronic structure options¶

DFT functionals¶

Madness uses libxc for exchange-correlation functionals. The input parameters are located in the dft block

xc func

where func is a string defining the DFT XC functional. Predefined options are available as

func = hf, bp86, lda, pbe, b3lyp, pbe0

Other XC functionals can be created individually as in

xc "LDA_X 1.0 LDA_C_VWN 1.0"
xc "GGA_X_PBE 0.75 GGA_C_PBE 1.0 HF_X 0.25"

where the number after the functional determines its weight. The two lines define LDA and PBE0 functionals, respectively.

For more details see the libxc webpage.

PCM solvation model¶

Madness uses the Polarizable Continuum Model from PCMSolver for solvation effects. Details to come.

¶

Convenience short options¶

--optimize optimize the geometry
--geometry=file.xyz find the geometry in the xyz file (note Angstrom units!)

\( a=\frac{aa}{c}\)