.. input 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 # () # 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 .. _atoms: 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