Input

Niedoida’s input is specified in the yaml format. An example of an input file (single-point HF calculations for water molecule in a 6-31g basis set) is shown below:

# Results from CCCBDB
#   (<http://srdata.nist.gov/cccbdb/energy3.asp?method=1&basis=9&charge=0>)
#       Energy = -75.985359 hartrees
#       Nuclear repulsion energy = 9.252764 hartrees
#

title: water molecule

run_type: single_point
basis_set: 6-31g

units:
  length: angstrom
  energy: hartree

atoms: |
  O  0.0000  0.0000  0.1068
  H  0.0000  0.7852 -0.4273
  H  0.0000 -0.7852 -0.4273

Comments

Comments may appear anywhere in the input. Comment lines start with # sign.

Parameters

Parameters control calculations performed by niedoida. By setting them to specific values you decide what and how is calculated when the program is run. Parameters may be of simple, compound or list type. All parameter definitions have the yaml form key: value (key and value fields should be separated by a colon followed by a space). The order of parameter definitions is not significant.

Simple parameters

Simple parameter values are numbers or strings.

Examples:

title: water molecule
run_type: single_point
basis_set: 6-31g
multiplicity: 1

Sections

Sections are collections of parameters. Section names should be followed by a colon. Section members should be denoted by whitespace indentation (however tab characters are not allowed as indentation). Sections can be nested.

Examples:

units:
  length: angstrom
  energy: hartree

scf:
  method: uhf

properties:
  population_analyses:
    mulliken: false
    bader: true
  bond_order_analyses:
    mayer: false

Atom definitions

Atoms are defined in one simple parameter named atoms. Atoms value should contain a list of atom labels followed by cartesian coordinates. For multiline definition the | character followed by a newline should be used at the beginning of the value field. Multiline atom definition should also be denoted by indentation.

Examples:

atoms: h 0 0 0

atoms: |
  O  0.0000  0.0000  0.1068
  H  0.0000  0.7852 -0.4273
  H  0.0000 -0.7852 -0.4273

More examples

1. Unrestricted B3LYP/cc-pVTZ single-point calculations for methylene:

   run_type: single_point
   basis_set: cc-pvtz
   multiplicity: 3
   theory: b3lyp
   
   scf:
     method: uhf
   
   units:
     length: angstrom
     energy: hartree
   
   atoms:
   - C     0.000000     0.000000 -0.020583
   - H    -0.828840     0.707900  0.010292
   - H     0.828840     0.707900  0.010292
   

2. MP2/cc-pVDZ single-point calculations for benzene utilizing density fitting:

   run_type: single_point
   basis_set: cc-pvdz
   posthf_aux_basis_set: cc-pvdz-ri
   
   units:
     length: bohr
     energy: hartree
   
   moller_plesset:
       order: 2
   
   atoms:
   -  C               0.0000000000        2.6229244336        0.0000000000
   -  C               0.0000000000       -2.6229244336        0.0000000000
   -  C               2.2715093956        1.3114565033        0.0000000000
   -  C               2.2715093956       -1.3114565033        0.0000000000
   -  C              -2.2715093956        1.3114565033        0.0000000000
   -  C              -2.2715093956       -1.3114565033        0.0000000000
   -  H               0.0000000000        4.6669106833        0.0000000000
   -  H               0.0000000000       -4.6669106833        0.0000000000
   -  H               4.0416815230        2.3334040232        0.0000000000
   -  H               4.0416815230       -2.3334040232        0.0000000000
   -  H              -4.0416815230        2.3334040232        0.0000000000
   -  H              -4.0416815230       -2.3334040232        0.0000000000
   

3. Water molecule geometry optimization at the HF/cc-pVDZ level:

   basis_set: cc-pvdz
   theory: hf
   
   units:
     length: angstrom
     energy: hartree
   
   atoms:
   - O 0.0000 0.0000 0.1141
   - H 0.0000 0.7803 -0.4563
   - H 0.0000 -0.7803 -0.4563