The List of MQCP Datatypes

Datatypes specify the data format of inputs and outputs of modules, which are files in nature.

Input file (`inp`)

This datatype is used to set up runtime parameters for modules using human-readable format. It has a following format:

TITLE
MOLECULE DESCRIPTION SECTION
PARAMETERS SECTION

The title is a single line describing the calculation. It’s not used by modules.

In the MOLECULE DESCRIPTION SECTION the number of atoms, the atomic types and their coordinates are given. It resembles the chemical .xyz file format. First the number of atoms is given and then every atom is specified by its nucleic charge (Q) and Cartesian coordinates (X, Y and Z) in Angstrom:

NATOM=<number of atoms>
Q    X    Y    Z
...
Q    X    Y    Z

In the parameters section various options for modules are specified in the format OPTION=VALUE. Only one option per line is allowed.

Here is an example of input file:

C3H8 molecule
natom=11
0  -0.2814116433  -0.0914064155   0.0569146050
0  -0.0108420173   1.3451955038  -0.4302553427
0  -1.5164903822  -0.7099985842  -0.6138764961
0   0.5852250728  -0.7142140575  -0.1449089075
0  -0.3980187758  -0.0846805453   1.1288285918
0   0.2402967369   1.3696657263  -1.4851529300
0  -0.9033547396   1.9429289671  -0.2719580118
0   0.8176724909   1.7961170180   0.1140239055
0  -1.9541584238  -1.5030395028  -0.0171310512
0  -1.2780973834  -1.1336105793  -1.5855662126
0  -2.2852454650   0.0377688194  -0.7774286105
charge=0
scftype=rhf

Simulation metadata (`inf`)

This datatype contains common parameters of simulation which is shared among modules. It can be read and written as an unformatted Fortran 90 structure.

The corresponding Fortran 90 type is defined as follows:

type inf
    integer             :: natom      !< The number of atom
    integer             :: charge     !< Molecular charge
    integer             :: hamilton   !< The method of calculations,
                                      !< 1= EHT, 2=CNDO/2, 3=INDO, 10=HF, 20=DFT
    integer             :: scftype    !< Reference wavefunction,
                                      !< 1= RHF 2= UHF 3= ROHF
    integer             :: nelec      !< The number of electron
    integer             :: nelec_A    !< The number of alpha electron
    integer             :: nelec_B    !< The number of beta electron
    integer             :: mult       !< Spin multiplicity
    integer             :: nvelec     !< The number of valence electron
    integer             :: nocc       !< The number of occupied orbitals
                                      !< nOCC = nelec/2 for RHF
                                      !< nOCC = nelec_A for ROHF/UHF with mult=3
                                      !< nOCC = nelec/2 for ROHF/UHF with mult=1
    integer             :: maxit      !< The maximum number of iterations
    real(REAL64)        :: conv       !< Convergency criteria of SCF
    integer             :: idamp      !< Damp the density if idamp=1
    integer             :: mulliken   !< Print out Mulliken population charge if mulliken=1
    integer             :: nbasis     !< The number of basis set functions
    integer             :: n2basis    !< n2basis : nbasis*(nbasis+1)/2
    integer             :: l1         !< Used for compatibility, L1 = nbasis
    integer             :: l2         !< Used for compatibility, L2 = nbasis * (nbasis+1)/2 = n2basis
    integer             :: l3         !< Used for compatibility, L3 = nbasis * nbasis
    real(REAL64)        :: energy     !< Total energy
    real(REAL64)        :: enuc       !< Nuclear repulsion energy
    integer             :: nalpha     !<  Number of alpha electrons
    integer             :: nbeta      !<  Number of beta electrons
    character(len=20)   :: &
        basis_name = ''               !< The basis set name for ab initio method
    integer             :: npfunc     !< The number of p functions
    integer             :: mem        !< Available memory size in Mega Byte
    integer             :: runtype    !< Run type
                                      !<  1 - energy, 2 - gradient, 3 - geometry optimization
    integer             :: geomit     !< Maximum number of geometry optimization iteration
    integer             :: guess      !< Not used now
    real(REAL64)        :: xdamp      !< Not used now
    real(REAL64)        :: psinrm     !< Wavefunction normalization
    real(REAL64)        :: ehf1       !< One-electron energy
    real(REAL64)        :: vee        !< Two-electron energy
    real(REAL64)        :: nenergy    !< Nuclear repulsion energy
    real(REAL64)        :: etot       !< Total energy
    real(REAL64)        :: vne        !< Nucleus-electron potential energy
    real(REAL64)        :: vnn        !< Nucleus-nucleus potential energy
    real(REAL64)        :: vtot       !< Total potential energy
    real(REAL64)        :: tkin       !< Total kinetic energy
    real(REAL64)        :: virial     !< Virial ratio (v/t)
    real(REAL64)        :: olde       !< For geometry optimizations, energy of the previous step
    real(REAL64)        :: depre      !< For geometry optimizations, predicted energy change
    integer(I2B)        :: nolds      !< For geometry optimizations, number of steps performed
    integer             :: acell      !< Not used now
    real(REAL64)        :: ebot       !< Bottom bound of energy range in band calculations
    real(REAL64)        :: etop       !< Upper bound of energy range in band calculations
    real(REAL64)        :: &
        dfttyp(20)                    !< Parameters of XC functional
    character(len=1024) :: &
        XC_functional_name = ''       !< Name of the XC functional
    integer             :: &
        periodic_dim
end type

Todo

Replace with generic config format

Atomic information (`xyz`)

Describes molecular structure.

The xyz file contains the total number of atoms as well as the atomic information.

The formatting of the mqcp.xyz file format is as follows:

Natom=<N:=number of atoms>
ATOM(1)
ATOM(2)
...
ATOM(N)

The ATOM type is defined as follows

  TYPE atom
     INTEGER(INT32) :: &
!        The number of atomic basis set
         basis_n, &
!        The highest principal quantum number, n
         n_max, &
!        The real high principal quantum number, n:w
         nc_atm, &
!        The number of core electrons
         izcore
     REAL(REAL64) :: &
!        Atomic number or nuclear charge
         zn, &
!        Number of valence electrons
         ezn, &
!        Cartesian coordinates
         coord(3), &
!        The highest zeta
         zet_atm, &
!        Atomic mass
         mass, &
!        Gradient
         De(3)
     CHARACTER(LEN=2) :: &
!        Atomic symbol
         Symbol
  END TYPE atom

Atomic basis set (`bas`)

Provides basis set library.

This type of data is used to pass basis set library to the MQCP program. The library format is basically GAMESS(US)-style with minor adjustments. The basis set file contains several basis set entries for different elements separated by blank line. Symbols !, $, #, and & are recognized as in-line comment symbols and the rest of the line will be ignored. Comments can appear anywhere in the file.

! this is a comment
ATOM BASIS ENTRY
<blank line>
ATOM BASIS ENTRY
<blank line>
ATOM BASIS ENTRY
<blank line>

Note

The last blank line is mandatory.

Atom basis set entry starts from the line containing the element name or its chemical symbol (e.g. CARBON or C). Next, one or more shell entries appears. They must not be separated by blank lines. The atom basis entry format:

<Element name | symbol>
SHELL ENTRY
SHELL ENTRY
...
SHELL ENTRY

The shell entry contains information of the shell type, the contraction degree, and all exponents and contraction coefficients for every primitive Gaussian in the shell. Shell type denotes the angular momentum and is given as a letter S, P, D, F, G, H, or I, corresponding to angular momentum 0, 1, 2, 3, 4, 5, and 6 respectively.

Warning

In contrast to GAMESS(US) basis set format, Pople’s SP (or L) shell types are not supported. S and P components of these shells should be present as separate entries.

After the header, representing the shell type and contraction degree, the parameters of primitive Gaussians are give one at a line. Each primitive gaussian statement contains integer sequence number (which is ignored and is present only for compatibility), and two double precision numbers corresponding to the exponential and contraction coefficients respectively. Hereby, the shell entry format is as follows:

<shell type := {S,P,D,F,G,H,I}>      <N, contraction degree>
1        exponent 1       contraction coefficient 1
...
k        exponent k       contraction coefficient k
...
N        exponent N       contraction coefficient N

Here is an example of the 6-31G++ basis set entry for the carbon:

CARBON
S   6
1         0.3047524880E+04       0.1834737132E-02
2         0.4573695180E+03       0.1403732281E-01
3         0.1039486850E+03       0.6884262226E-01
4         0.2921015530E+02       0.2321844432E+00
5         0.9286662960E+01       0.4679413484E+00
6         0.3163926960E+01       0.3623119853E+00
S   3
1         0.7868272350E+01      -0.1193324198E+00
2         0.1881288540E+01      -0.1608541517E+00
3         0.5442492580E+00       0.1143456438E+01
S   1
1         0.1687144782E+00       0.1000000000E+01
S   1
1         0.4380000000E-01       0.1000000000E+01
P   3
1         0.7868272350E+01       0.6899906659E-01
2         0.1881288540E+01       0.3164239610E+00
3         0.5442492580E+00       0.7443082909E+00
P   1
1         0.1687144782E+00       0.1000000000E+01
P   1
1         0.4380000000E-01       0.1000000000E+01

The set pre-formatted basis sets is available here. All provided basis sets can be also downloaded from the Basis Set Exchange website.

One-electron integrals (`hst`)

In the hst data type the matrices of one-electron integrals are stored. They are namely:

Core hamiltonian matrix ($H_\mathrm{core}$)
Matrix of overlap integrals ($S$)
Matrix of electronic kinetic energy integrals ($T$)

The core hamiltonian matrix comprises both electron-nuclei Coulomb attraction integrals ($V^\mathrm{en}$) and electronic kinetic energy integrals and is virtually a sum of $T$ and $V^\mathrm{en}$ matrices:

\[H_\mathrm{core} = V^\mathrm{en} + T\]

$H_\mathrm{core}$, $S$, and $T$ are symmetric ($N\times N$) matrices. They are represented in the packed format where only an upper (U) triangle of a matrix is stored. Matrix dimensions $N$ is equal to the number of basis set function for the given molecule. In the output, these three matrices are written as a plain text sequentially one after another using Fortran 90 unformatted output. The order, in which matrices are written is precisely $H_\mathrm{core}$, then $S$, and finally $T$.

Wavefunction (`den`)

This datatype contains information about the molecular orbitals and electronic density for $\alpha$ and optionally $\beta$ spin. It includes the following components in order:

$\alpha$-spin density matrix ($D_\alpha$);
matrix $Q$ of orthonormal molecular orbitals constructed from the atomic basis set;
$\alpha$-spin molecular orbitals;
eigenvalues of the $\alpha$-spin molecular orbitals;
(optional) $\beta$-spin density matrix;
(optional) $\beta$-spin molecular orbitals

$D_\alpha$ and $D_\beta$ density are symmetric $N\times N$ matrices and are stored in a packed format (upper triangle). Here, $N$ denotes the number of basis set functions. $\alpha$ and $\beta$ molecular orbitals, as well as matrix $Q$ are $N\times N$ matrices which are stored in the full square format. $\alpha$-orbital energies is a vector of dimension $N$. All the data is written using the Fortran 90 unformatted I/O.

Shells data (`shl`)

This datatype contains a structured shell data for a given molecule. It can be read and written as an unformatted Fortran 90 structure.

The corresponding Fortran 90 type is defined as follows:

  TYPE shell_structure

     REAL(REAL64), DIMENSION(MXGTOT) :: &
!      Exponential coefficients for shells
       EX, &
!      Contraction coefficients for shells
       CS, CP, CD, CF, CG, CH, CI

     INTEGER(INT32), DIMENSION(MXSH) :: &
!      Location of the first exponent and the first
!      contraction coefficient contained in a particular shell
       KSTART, &
!      Atomic center indices
       KATOM, &
!      Shell types, 1,2,3,4,5,6,7 for S,P,D,F,G,H,I respectively
       KTYPE, &
!      Degrees of shell contraction
       KNG, &
!      Indices of first AO of the shell in the basis set
       KLOC, &
!      Starting and ending indices of the shell
!                   S    P    D    F   G   H   I   L
!            KMIN   1    2    5   11  21  36  57   1
!            KMAX   1    4   10   20  35  56  84   4
       KMIN, KMAX

!     Normalization constant
      REAL(REAL64) :: PNRM(84)

!     AO symbol
      CHARACTER(LEN=8) :: BFLAB(MXAO)
  END TYPE shell_structure

Log output (`log`)

This datatype is a simple text-based log file which contain status report of all modules. It has no specific format.

The List of MQCP Datatypes

Input file (inp)

Simulation metadata (inf)

Atomic information (xyz)

Atomic basis set (bas)

One-electron integrals (hst)

Wavefunction (den)

Shells data (shl)

Log output (log)