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This is the main module in TONTO. It is intenede to provide a quantum mechanocal repr4esentation of a molecule and all properties that can be interrogated from a molecule.
Because it is quite large, the module may be broken up into parts, each part being labelled by a particular working author. Thus for example, the current distribution contains mol_dylan, mol_daniel, mol_chris.
The main routine is mol_main and contains essentially just the read and process_input routines.
The online documentation may not work properly for routines which are under individual author names. Probably you should not be using these routines for production purposes.
There is no associated MOLVEC type; an input data order has not been defined.
Assign the natural orbitals to the currently defined molecular orbitals.
Evaluate the atomic Roby populations.
Enter data for a list of ATOM's. That is, concerning the number, type, and position of atoms in the molecule.
Example:
atoms= { O1 0.0 0.0 0.0 o-sto3g H2 1.0 0.0 0.0 h-sto3g H 0.0 1.0 0.0 h-sto3g } |
It is efficient to only specify a basis_label. Later, the entire basis set can be specified using the basis_sets command.
The basis_sets keyword may be used before or after the atoms keyword.
Before a QM calculation can begin, every basis_label must correspond to a defined basis set.
Use "units angstrom" to specify coordinates in angstrom units.
Use the axis_system command to specify coordinates in crystal axis system
The default units for thermal_tensors is angstrom -2.
Specify a partition of the numbers from 1 to the number of atoms in the molecule.
The GROUP module does not exist yet, so this keyword is not documented in the standard way yet
This is used for nonintegacting-group Hartree-Fock calculations
Within curly brackets { and } use the keywords atom_group= followed by an INTVEC list of atom indices; use atom_range= or range= followed by an INTVEC(2) indicating the range of atom indices, inclusive; use group_charges= array to enter an INTVEC describing the charge of each group.
Enter the cartesian components of an externally applied static magnetic field B.
The default value is (0,0,0)
It is assumed that B is in atomic units of flux.
This keyword is used for plots of the diamagnetic part of the current density.
Enter a directory where basis sets for each atom may be found.
This keyword must come before any atoms= keyword if basis sets are to be entered for those atoms
You must also specify a basis_set_kind=
The default value is "./basis_sets"
Not all basis sets are available. See the basis_sets directory and the contents of each file there for the list of available basis sets
Enter a the kind of basis set to be used.
This must correspond to an existing basis set file in the basis set directory
See basis_set_directory=
Enter data for a list of basis sets for use in quantum chemical calculations.
Example:
basis_sets= { { h-sto3g { S 3 3.42525091 0.15432897 0.62391373 0.53532814 0.16885540 0.44463454 } o-sto3g { S 3 130.70932000 0.15432897 23.80886100 0.53532814 6.44360830 0.44463454 S 3 5.03315130 -0.09996723 1.16959610 0.39951283 0.38038900 0.70011547 P 3 5.03315130 0.15591627 1.16959610 0.60768372 0.38038900 0.39195739 } } |
The basis_label need not correspond to any that are actually used in the atoms keyword.
Generate a fock matrix from the existing molecule orbitals in memory and diagonalise it over the occupied part only, and the virtual part only, producing "canonical" molecular orbitals.
The orbitals need not be converged for the existing kind of SCF
See scfdata= and especially the scf_kind= within this derived data keyword
Enter the charge on the molecule in atomic units of charge.
The charge on the molecule is used to work out the total number of electrons, and with the spin multiplicity, the number of alpha and beta electrons.
Create a cluster from the existing set of molecule information.
This keyword is not documented in the standard way
Refer to the online documentation
Enter the data for specifying a crystal, including the experimental data for measured structure factors
Delete the integrals files for the previous SCF calculation.
This must be done whenever a new geometry is specified.
This command has an effect for direct calculations, because the one electron integrals are always stored on disk.
Enter the data for specifying an integration grid for DFT functions.
Enter the cartesian components of an externally applied static electric field E.
The default value is (0,0,0)
It is assumed that E is in atomic units of flux.
Multiply certain atom basis set sized blocks of the density matrix by the specified factors
This keyword is not documented in the standard way
Refer to the online documentation
Optimise the thermal parameters so as to minimise the χ2 for the predicted vs. the experimental structure factors
Crystal data must be entered, and there must be an existing density matrix
Refer to crystal=
Force the thermal parameters on symmetry equivalent atoms to be equal. This is performed by averaging.
This keyword is undocumented
Enter the gauge origin for an externally applied static magnetic field.
The default value is (0,0,0)
This keyword will affect spin orbit and magnetic field calculations
Read the stored sum of spherically averaged atom densities from the archive stored on disk into the current density matrix.
Calculate the homoleptic bond index between two Roby fragments
This keyword remains undocumented
Refer to the online documentation
Calculate the Hartree-Fock energy gradient
Warning: this keyword is untested
Can you debug it?
Enter the data for specifying a rectilinear grid, for plots
Make the density matrix in the AO basis set from the current density matrix. (If the current density matrix of of the restricted kind, no operation is performed).
Make the matrix of the Sz operator in the AO basis set from the current density matrix. This is used to generate densities for use in calculating spin-only magnetic structure factors from UHF calculations.
Calculate the density matrix as a sum of spherically averaged atomic UHF densities.
The maximum multiplicity Hund's rule is assumed for the spin state of the atom.
Make and print out the Fermi mobility function on the specified vibrationally rectilinear plot grid.
Make an initial set of molecular orbitals and eigenvalues from the current fock matrix.
Make the fock matrix from a density matrix already in memory.
Make a density matrix which is the sum of non-interacting group densities
Refer to the atom_groups= keyword to define the groups
Only works for closed shell rhf group fragments at the moment
Can you fix the rest?
Make and print out the irrotational part of the paramagnetic current density on the specified rectilinear grid.
Make and print out the Mulliken population matrix.
Make the natural orbitals for the currently defined molecular orbitals.
Make the polarised neutron diffraction (pnd) scalar magnetic structure factors for the currently defined complex density matrix.
Make a promolecule density matrix from symmetrically orthonormalised group molecular orbitals
The promolecule orbitals are also made, and are ordered by group, including the virtual orbitals within each group i.e. the occupation number vector is not continguous
Refer to atom_groups= and make_promol_density
Only works for rhf fragment groups at the moment
Define the atomic natural orbitals for every atomn in the molecule
These are used to define the Roby aton projectors from Roby population analysis
Make a density matrix from the current set of molecular orbitals, for the currently defined type of SCF calculation (set in scfdata).
Make the structure factors for the currently defined density matrix.
Make the Sz spin only magnetic structure factors for the currently defined density matrix.
Make and print out the vubrationally averaged charge density for a diatomic molecule using adpative Simpson quadrature.
Calculate the parity violating weak force energy shift from a complex spin-orbit SCF calculation.
Enter the spin multiplicity value for the molecule, 2S+1, where S is the spin of the molecule.
The multiplicity values is used to define the number of alpha and beta electrons in unrestricted Hartree-Fock (UHF) calculations.
Input the name you wish to give to your molecule calculation.
The name= keyword must be the first one in any input file.
The value of the inputted string is used to define the start of archive file names, so do not use any spaces in it.
If set TRUE, the thermal parameters in an X-ray wavefunction fitting calculations are optimised to minimise the χ2 agreement statistic.
Output the Roby covalent orbital density for the specified orbital index.
Output the Roby ionic orbital density for the specified orbital index.
Output the Roby subspace density for the specified shared orbitals whose index is specified.
Specify th pointgroup symmetry of the molecule in Schoenflies notation.
The character table does not include complex irreps, but they are grouped into two dimensional modules.
The character table is not available for the Icosahedral groups. used in the atoms keyword.
Put out information concerning the current molecule to the stdout TEXTFILE.
Put the crystal Seitz operations which will generate a cluster for which no atom is more than a certain specified distance from the center of the molecule out to the stdout TEXTFILE.
Put out CRYSTAL information for the current molecule to the stdout TEXTFILE.
Put out all the atom coordinate information.
Put out the AO energy partition, which is a kind of Morokuma analysis
This is only available for two rhf fragment groups at the moment
The density matrix for each group is partitioned according to AO basis functions, and then the energy of each block os calculated separately, including the "interaction energy" EAB = E - EAA - EBB
Refer to put_sao_energy_partition and put_mo_energy_partition
Refer to atom_groups= command
Refer to make_promol_density_matrix and make_group_density_matrix command
Make a gnuplot table of the χ2 agreement statistic between calculated and experimental structure factors, and the binned sin &thetas;/λ values, where λ is the diffraction particle wavelength
This may be moved to the CRYSTAL module at a later date
Write out the cluster input details for a supercluster of the existing molecule
This keyword remains undcoumented
Refer to the online documentation
Put out all crystal information for this molecule
Put out only crystal reflection information for this molecule
This may be moved to the CRYSTAL module at a later data
Put the current time out to the stdout TEXTFILE.
Put out the density matrix to the stdout.
Put out the fock matrix to the stdout.
Put the calculated structure factors out to the stdout.
Put out a series of useful gnuplot files detailing the behaviour of the calculated structure factors
It produces the normalised deviates vs. sin&thetas;/λ; the normalised deviates vs. experimental structre factor magnitude; the normalised deviates vs. experimental structre factor magnitude; both of the above plots when the calculated structure factors include an extinction correction; and the mean value of the normalised deviate with and without extinction
Put out the fock matrix to the stdout.
Calculate and put out the g tensor information from an existing complex density matrix.
Write an archive of the QQ plot for the calculated structure factors data, including the h, k, l reflection data
This is a plot of the sorted experimental quantile versus the expected gaussian quantile
Refer to put_qq_plot
Put out the molecular orbitals and orbitals energies to the stdout.
Put out the molecular orbitals information to the stdout.
Put out the MO energy partition, which is a kind of Morokuma analysis
This is only available for two rhf fragment groups at the moment
The density matrix for each group is partitioned according to MO basis functions, and then the energy of each block os calculated separately, including the "interaction energy" EAB = E - EAA - EBB
Refer to put_ao_energy_partition and put_sao_energy_partition
Refer to atom_groups= command
Refer to make_promol_density_matrix and make_group_density_matrix command
Put out the symmetrix AO energy partition, which is a kind of Morokuma analysis
This is only available for two rhf fragment groups at the moment
The density matrix for each group is partitioned according to MO basis functions, and then the energy of each block os calculated separately, including the "interaction energy" EAB = E - EAA - EBB
Refer to put_ao_energy_partition and put_mo_energy_partition
Refer to atom_groups= command
Refer to make_promol_density_matrix and make_group_density_matrix command
Evaluate and put out the SCF energy
The kinetic energy is also outputted for information
Refer to scfdata= to set scf type
Evaluate and put out the SCF energy in an MO pairs like form
This decomposes the total SCF energy into one orbital in two orbital contributions in the expected way
Put out the plotgrid information
Refer to plotgrid= to set the plot information and plot type
Refer to plot to actually perform the plot calculation
Put out the polarised neutron diffraction (PND) structure factor information to the stdout.
Put out POINTGROUP information for the current molecule to the stdout.
Put the data for Hamilton's $QQ$ plot out to the stdout.
This is a plot of the sorted experimental quantile versus the expected gaussian quantile
Refer to put_labelled_qq_plot
Put out the Roby energies for every atom
This keyword is undocumented
Refer to the online documentation
Put out the Roby ionic energies for every atom
This keyword is undocumented
Refer to the online documentation
Output the Roby shared energy.
This keyword is undocumented
Refer to the online documentation
Output the Roby shared populations.
This keyword is undocumented
Refer to the online documentation
Output an approxintmation for the polarisability and hyperpolarisability tensors developed by Sylvian and Csizmadia.
Calculate and put out the SCF energy in molecular orbitals pairs for the current set of molecular orbitals.
Put the time taken since the start_timer command (or beginning of job, if the start_timer command is not present) to the stdout.
Put the total time since the start_timer command (or the beginning of job, if the start_timer command is not present) out to the stdout.
Put out a VRML graphics representation of the molecule
Read the specified binary archive, and its kind, into the program.
Only the possibilities molecular_orbitals, density_matrix, natural_orbitals, occupation_numbers and fock_matrix are allowed.
The kind must be one of the OPMATRIX kind types.
Read the specified ASCII archive into the program.
Only the possibilities molecular_orbitals, density_matrix, natural_orbitals, occupation_numbers and fock_matrix are allowed.
The kind must be one of the OPMATRIX kind types.
This command is useful for inputting data from other programs: simply rename the input into the appropriate archive file.
Read the gaussian94 checkpoint file, generated from the fchk command, into TONTO.
Atom positions, basis sets, molecular orbitals and density matrices are inputted.
Redirect the stdin to the name of the following input file
To come back to the original input file, use the revert command
See the revert command
Perform a Roby energy analysis on the previously calculated density matrix.
This keyword remains undocumented
Refer to the online documentation
Perform a Roby population analysis on the previously calculated density matrix.
This keyword remains undocumented
Refer to the online documentation
Perform an SCF calculation using the specified scfdata.
At the termination of the program the density matrix, molecular orbitals, and fock matrix hold the converged results for future calculations.
The results are also stored in archive files on disk for later use.
If a standard SCF calculation is performed, the integrals are stored ion disk and reused, if required.
Enter the data for the SCF calculation options, including the type of SCF, the initial guess, the convergence criteria, extrapolation methods, to name a few.
This does not perform a calculation. Only the required options are set. Use the scf keyword to invoke the SCF calculation.
Add a series of σ-variance gaussian random deviates to the experimental crystal structure factors
This may be moved to the CRYSTAL module at a later date
Start timing the program from the current point.
Write the specified binary archive into the program.
Only the possibilities molecular_orbitals, density_matrix, natural_orbitals, occupation_numbers and fock_matrix are allowed.
The kind is determined from the current type of object which is to be written.
Write the specified ASCII archive into the program.
Only the possibilities molecular_orbitals, density_matrix, natural_orbitals, occupation_numbers and fock_matrix are allowed.
The kind is determined from the current type of object which is to be written.
Write out a MORPHY98 .wfn input file.
This is useful for performing a Bader analysis on the current density matrix.