Quantum chemistry¶
What you can do¶
Quantum chemical capabilities are:
SCF: Hartree-Fock and DFT, also in strong magnetic fields:
moldft, nemo, znemoanalytical gradients for SCF:
moldft, nemo, znemosecond nuclear derivatives for SCF (field-free case only),
nemoCIS,
cis, zcisresponse properties,
molresponseMP2,
cc2ADC(2), CIS(D),
cc2CC2 ground and excited states,
cc2PNO-MP2,
pnoOEP/RKS,
oep
What to expect from an MRA calculation¶
MRA provides results to your calculation at the complete basis set limit.
Due to its adaptive nature MRA has a low scaling with respect to system size, but a relatively high computational prefactor. Calculations on small systems are therefore computationally (much) more expensive than calculations in a (small) Gaussian basis set, while calculations on large systems and/or calculations aiming for high accuracy are (much) cheaper than calculations in a (large) Gaussian basis set.
Use MRA if you want to do
large systems using DFT or HF
anions or excited states
high-accuracy calculations
molecular properties esp magnetic properties
Don’t use MRA if you want to do
exploratory calculations with small basis sets
do a quick geometry optimization, as MRA requires tightly converged wave functions to avoid numerical noise on the PES
Don’t be discouraged when you run the Ne atom and it takes 20 seconds to get the total energy, while your favorite LCAO code gives you a similar number in less than a second.
MRA will give you few digits of the correct number, while LCAO will give you all digits of a (systematically) incorrect number.
Quickstart¶
The madqc program 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
madqc --help
A number of sample input files can be found at the bottom of this page
The quantum chemical calculations can be started by invoking the madqc program with the desired workflow, e.g. for a DFT calculation of water
madqc --wf=scf input
where input is the name of the input file. The workflow can be changed by using the --wf option, e.g. for a CIS calculation.
madqc --wf=cis input
The --wf option can be used to select the desired workflow, e.g. scf, nemo, cis, cc2, pno, oep, etc.
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
madqc --print_parameters
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
endgeometry
molecule
O 0 0 0
H 0 1 1
H 0 1 -1
end
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.
The program will output the complete list of input options. You can always run
madqc --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.
madqc --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
madqc --input=customfile
Numerical parameters: k and L¶
Numerical parameters are specified in the dft block, the most important ones that will also be used in subsequent calculations (e.g. mp2) are
dft
k 5
L 20
end
The calculation box size L should be large enough to hold all relevant physics. 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).
The polynomial order k will affect the computed numbers, but mostly the performance. Due to MRA adaptive nature a higher k will induce a less refined grid and vice versa. With a changing grid the numbers will change, but the significant ones will stay. Remember that MRA will give you few digits of the correct number, while LCAO will give you all digits of an incorrect number.
The k parameter can be chosen 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, as these are usually “sweet spots” for computational performance. If this parameters is not set it will be determined automatically.
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
madqc --wf=nemo --geometry=h2o.xyz
A small number of geometries are stored in a library, accessible through
madqc --wf=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 workflows 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.
madqc --wf=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.
SCF workflows¶
Madness has two SCF workflows, scf and nemo, that share most of their functionality.
Both can do
HF and DFT calculations
Only scf:
UHF calculations
being faster than nemo
nuclear gradients and optimizations
Only nemo:
regularized calculations with nuclear correlation factor
references for subsequent OEP calculations
preferred for reference calculations for MP2 and CC2
analytical second nuclear derivatives
Convenience short options¶
--optimize optimize the geometry
--geometry=file.xyz find the geometry in the xyz file (note Angstrom units!)
Example calculations¶
Hartree-Fock calculation of water¶
Input file named “input”
geometry
molecule O 0 0 0
H 0 1 1
H 0 1 -1
end end
Then run
moldft input
DFT geometry optimization of ammonia¶
input file name “input”
dft
xc pbe
k 7
econv 1.e-6
dconv 1.e-5 end
end
geometry
molecule n -0.000 0.000 -0.516
h -0.887 1.536 0.172
h -0.887 -1.536 0.172
h 1.774 0.000 0.172
end end
Then run
madqc –optimize input
CIS calculation of LiH¶
input file name “input”
dft
k 7
econv 1.e-5
endgeometry
molecule li 0.0 0.0 -0.529
h 0.0 0.0 2.529
end end
Then run
madqc –wf=cis input