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Module Actions.pm - Index of actions

This file was generated from the file Actions.pm by the command gvib -w.

The following actions are available via the module Actions.pm:
(See gvib -? and the options -m and -a.) The following actions are available via the module Actions.pm:

all
Run the actions specified - i.e. all the implemented anharmonic methods.
cc
Run Gaussian to create force-field constants for the given geometry and all geometries with one of the atoms displaced along one of the three degrees of freedom. This action can be easily run on multiple processors, but this feature was not automated inside gvib, because it is very platform-dependent. The user has to take care of it and run it manually. See the action create-inputs and the scripts nondone-qsub and nondone-list. See also the action nm.
cc-ff34
Cubic and semidiagonal quartic terms of the Taylor expansion of the potential (V_ijk and W_ijkk) will be created and transformed to the normal modes. The higher derivatives will be calculated using geometries displaced along cartesian coordinates.
cff4-to-cff4b
Convert cff4 file to cff4b. The offdiagonal elements with all indices different will be replaced by zeros.
clean
Cleans the project directory by removing all temporary files which can be recalculated. Only log file, config, calculated frequencies and intensities will be left untouched.
  • [Perl code]
correct-ff2s
The force field (2nd order derivatives of the potential with respect to atomic displacement) should be translationaly invariant. Check this and try to correct the force field if being told so (i.e., if the option correct_ffs was set to 1 in the config file).
correct-ffs34
The force constants should be translationaly invariant. Check this and try to correct the force field if being told so (i.e., if the option correct_ffs was set to 1 in the config file). NOTE: Only cubic terms are checked, so far.
create-cc-edeqd2-constants
Calculates 2nd order derivatives of el.dipole-el.quadrupole tensor by numerical differentiation of the 1st order derivatives displaced along cartesian coordinates and transforms them into normal modes. See also the action create-nm-edeqd2-constants.
create-cc-edmdd2-constants
Calculates 2nd order derivatives of el.dipole-mg.dipole tensor by numerical differentiation of the 1st order derivatives displaced along cartesian coordinates and transforms them into normal modes. See also the action (create-nm-edmdd2-constants).
create-cc-inputs
Create Gaussian and PBS jobs for geometries displaced along cartesian coordinates.
create-cc-polard2-constants
Calculates 2nd order derivatives of electric polarizability by numerical differentiation of the 1st order derivatives displaced along cartesian coordinates and transforms them into normal modes. See also the action create-nm-polard2-constants.
create-cc-qdipd2-constants
Calculates 2nd order derivatives of electric dipole moment by numerical differentiation of the 1st order derivatives displaced along cartesian coordinates and transforms them into normal modes. See also the action create-nm-qdipd2-constants.
create-inputs
This script will generate Gaussian and PBS files for the given geometry and for geometries displaced either along cartesian coordinates or normal modes. The type of job depends on the variables along_cc and along_nm, which are set by gvib internaly in actions create-cc-inputs and create-nm-inputs. If none of them is set, only files for the original geometry will be generated.
create-nm-edeqd2-constants
Calculates 2nd order derivatives of el.dipole-el.quadrupole tensor by numerical differentiation of the 1st order derivatives displaced along normal modes. See also the action create-cc-edeqd2-constants.
create-nm-edmdd2-constants
Calculates 2nd order derivatives of el.dipole-mg.dipole tensor by numerical differentiation of the 1st order derivatives displaced along normal modes. See also the action create-cc-edmdd2-constants.
create-nm-inputs
Create Gaussian and PBS jobs for geometries displaced along normal modes.
create-nm-polard2-constants
Calculates 2nd order derivatives of electric polarizability by numerical differentiation of the 1st order derivatives displaced along normal modes. See also the action create-cc-polard2-constants.
create-nm-qdipd2-constants
Calculates 2nd order derivatives of electric dipole moment by numerical differentiation of the 1st order derivatives displaced along normal modes. See also the action create-cc-qdipd2-constants.
csf_evscf
Vibrational Self-Consistent-Field approach is an analog of electronic Hartree-Fock calculation. The vibrational mutlidimensional wavefunction is taken as product of independent one-dimensional wavefunctions which move in averaged potential created by the rest of the modes. More on the theory see in vibrations.ps.
Calculation of IR intensities may be requested by setting the variable ievscf; Raman by iraman_evscf; ROA by iroa_evscf and evscf+PT2 frequencies by cminv_evscfpt2.
csf_gvscf
Vibrational Self-Consistent-Field approach is an analog of electronic Hartree-Fock calculation. The vibrational mutlidimensional wavefunction is taken as product of independent one-dimensional wavefunctions which move in averaged potential created by the rest of the modes. More on the theory see in vibrations.ps.
Calculation of IR intensities may be requested by setting the variable igvscf; Raman by iraman_gvscf; ROA by iroa_gvscf and gVSCF+PT2 frequencies by cminv_gvscfpt2.
csf_harm_vci
If additional variables are specified, also intensities will be calculated: iharm_vci for IR intensities, iraman_harm_vci for Raman and iroa_harm_vci for ROA intensities. See also harm+vci.
csf_harmpt_freqs
See harm+pt.
csf_harmptb_freqs
See harm+ptb.
csf_nm_anim
Create list of geometries displaced along each of the normal mode. Good for visualizing via the mm (Molecule Maker) program.
default
Run the actions specified - i.e. all the implemented anharmonic methods with anharmonic force-field calculated along cartesian coordinates.
  • See also: cc all
  • [Gvib action]
evscf
VSCF with self-consistent but non-orthogonal excited solutions: During the VSCF iterations we choose to minimize excited state instead of ground state.
The 2nd order perturbation correction is calculated in the basis of the orthogonal solutions of the given excited state.
ff2
Create Gaussian and PBS job for non-displaced optimized geometry. Run Gaussian if necessary.
ff4b
Creates quartic constants with all indices different (V_ijkl).
g03-cc-ff34
Run Gaussian for all geometries displaced along cartesian coordinates.
g03-ff2
Run Gaussian to create 2nd derivatives of potential with respect to the nuclear displacements. Then dipole derivatives and the force-field constants are extracted and saved in the files cdipd1 and cff2.
g03-nm-ff34
Run Gaussian for all geometries displaced along normal modes.
gvscf
VSCF with orthogonal but self-inconsistent excited solutions.
harm+pt
Hamonic calculation corrected by 2nd order perturbation theory. The calculation is done in the basis of unperturbed solutions - linear harmonic oscillators.
harm+ptb
Hamonic calculation corrected by 2nd order perturbation theory. The calculation is done in the basis of unperturbed solutions - linear harmonic oscillators. In contrast to harm+pt, also off-diagonal quartic constants will be used.
harm+vci
Harmonic frequencies corrected by Vibrational Configuration Interaction approach. The anharmonic Hamiltonian (harmonic, cubic and semidiagonaly quartic potential terms) is diagonalized in the basis of variously excited linear harmonic oscillators. Because the dimension of the problem grows very fast, a cut-off limit must be specified. (See the vci_nbase, sparse_matrix_threshold and vci_state_threshold variables.)
harmonic-constants
Parse gaussian output file and extract force constants and create some requisite files required by other modules.
  • Skip if done: cff2
  • [Perl code]
harmonic-deps
When Gvib is run with a manually supplied force field, this action will determine number of atoms, atomic masses, etc. and create necessary files.
  • [Perl code]
harmonic-freqs
After creating all the prerequisities, harmonic frequencies are calculated. The normal modes can visualized by running the mm ("Molecule Maker") program on the output of csf_nm_anim. If specified in the configuration file, specified normal modes can be freezed and left out from the further anharmonic calculations. Six of the lowest frequencies are ignored by default, as they normaly correspond to translational and rotational movements.
harmonic-intensities
The harmonic intensities are calculated using the electric dipole moment approximated by the first order term of the Taylor expansion. (In linear harmonic approximation, the second order term is zero.) If the option iharm_dipd2 is set, also transitions 0->2 are evaluated.
harmonic-raman
Calculates the Raman scattering activities in harmonic approximation.
harmonic-roa
Calculates the Raman optical activity in harmonic approximation.
iharm-cc-dipd2
By default, harmonic intensities are calculated using only 1st order derivatives of electric dipole moment. However, if results for displaced geometries are available, 2nd order derivatives can be calculated and also the intensities for transitions 0->2 can be computed.
iharm-nm-dipd2
By default, harmonic intensities are calculated using only 1st order derivatives of electric dipole moment. However, if results for displaced geometries are available, 2nd order derivatives can be calculated and also the intensities for transitions 0->2 can be computed.
mrProper
Cleans the project directory by removing ALL files which can be recalculated. Thus, only config file, molecular geometry and gaussian outputs will be retained.
  • [Perl code]
nm
Create anharmonic constants by differentiating 2nd-order force-field derivatives in normal coordinates instead of cartesian coordinates. The obvious advantage is that instead of 2*3N+1 force-field evaluations, only 2*(3N-6)+1 are needed. For isotopic substitutions, the force-field must be recreated, though. See also the action cc.
nm-ff34
Cubic and semidiagonal quartic terms of the Taylor expansion of the potential (V_ijk and W_ijkk) will be created and transformed to the normal modes. The higher derivatives will be calculated using geometries displaced along cartesian coordinates.
nm_anim
Create list of geometries displaced along each of the normal mode. Good for visualizing via the mm (Molecule Maker) program.
pt2-intensities
The intensities for PT2 methods are not implemented. This routine will merge the PT2 frequencies with unperturbed intensities: gVSCF+PT2 with gVSCF intensities, eVSCF+PT2 with eVSCF intensities and Harm+PT2 with harmonic intensities.
  • [Perl code]
run_cdipd1_to_qdipd1
The harmonic intensities are calculated using the electric dipole moment approximated by the first order term of the Taylor expansion. (In linear harmonic approximation, the second order term is zero.) If the option iharm_dipd2 is set, also transitions 0->2 are evaluated.
run_cedeqd1_to_qedeqd1
Calculates the Raman optical activity in harmonic approximation.
run_cedmdd1_to_qedmdd1
Calculates the Raman optical activity in harmonic approximation.
run_cff2s_to_cff34
Takes 2nd order derivatives of the potential calculated in all displaced geometries along cartesian coordinates and calculates cubic and semidiagonal quartic constants (V_ijk and V_ijkk) by numerical differentiation.
run_cff3_to_qff3
Transform cubic terms of Taylor expansion of the potential (V_ijk) from cartesian coordinates into the normal modes.
run_cff4_to_qff4
Transform quartic semidiagonal terms of Taylor expansion of the potential (V_ijkk) from cartesian coordinates into the normal modes.
run_cff4b_to_qff4b
Transform semidiagonal quartic constants of Taylor expansion of the potential (V_ijkk) from cartesian coordinates into the normal modes. Unlike the action run_cff4_to_qff4, also off-diagonal elements with all indices different (V_ijkl) will be generated.
run_check_ff2
Check the translational symmetry of force-field constants.
run_check_ff3
Check translational symmetry of cubic constants.
run_check_ff4b
Check translational symmetry of quartic constants.
run_cpolard1_to_qpolard1
Calculates the Raman scattering activities in harmonic approximation.
run_dispcedeqd1_to_qedeqd2
Calculates 2nd order derivatives of el.dipole-el.quadrupole tensor by numerical differentiation of the 1st order derivatives displaced along cartesian coordinates and transforms them into normal modes. See also the action create-nm-edeqd2-constants.
run_dispcedmdd1_to_qedmdd2
Calculates 2nd order derivatives of el.dipole-mg.dipole tensor by numerical differentiation of the 1st order derivatives displaced along cartesian coordinates and transforms them into normal modes. See also the action (create-nm-edmdd2-constants).
run_dispcpolard_to_qpolard2
Calculates 2nd order derivatives of electric polarizability by numerical differentiation of the 1st order derivatives displaced along cartesian coordinates and transforms them into normal modes. See also the action create-nm-polard2-constants.
run_dispdipd_to_qdipd2
Calculates 2nd order derivatives of electric dipole moment by numerical differentiation of the 1st order derivatives displaced along cartesian coordinates and transforms them into normal modes. See also the action create-nm-qdipd2-constants.
run_gaussian_ff34
Run Gaussian in all the displaced geometries to find out 2nd derivatives of force-field constants. They will be later numerically differentiated to obtain higher order derivatives of the potential - cubic and semidiagonal quartic terms (V_ijk and V_ijkk). If the variable along_cc was set by gvib (i.e. the action was called from g03-cff34), displacement along cartesian coordinates is assumed. If the variable along_nm was set (the action was called from g03-qff34), normal mode displacements are assumed.
  • [Perl code]
run_harmonic
Reads the cartesian force constants, mass-weights them and diagonalizes the resulting matrix. On output are written: harmonic frequencies [1/cm]; the mass-weighted smatrix, which transforms cartesian coordinates into the normal modes; quadratic force constants in atomic units. For more on the theory, look at vibrations.ps file and the source code.
run_harmonic_intensities
The harmonic intensities are calculated using the electric dipole moment approximated by the first order term of the Taylor expansion. (In linear harmonic approximation, the second order term is zero.) If the option iharm_dipd2 is set, also transitions 0->2 are evaluated.
run_harmonic_raman
Calculates the Raman scattering activities in harmonic approximation.
run_harmonic_roa
Calculates the Raman optical activity in harmonic approximation.
run_harmonic_vzpe
Tiny program which calculated harmonic energy of the lowest vibrational state of the molecule. It just sums over the frequencies the well known formula for energy of the linear harmonic oscillator: E_0 = 0.5\hbar\omega.
run_nm_cff2s_to_qff34
Takes 2nd order derivatives of the potential calculated in all displaced geometries along normal modes and calculates cubic and semidiagonal quartic constants (V_ijk and V_ijkk) by numerical differentiation.
run_nm_dispcedeqd1_to_qedeqd2
Calculates 2nd order derivatives of el.dipole-el.quadrupole tensor by numerical differentiation of the 1st order derivatives displaced along normal modes. See also the action create-cc-edeqd2-constants.
run_nm_dispcedmdd1_to_qedmdd2
Calculates 2nd order derivatives of el.dipole-mg.dipole tensor by numerical differentiation of the 1st order derivatives displaced along normal modes. See also the action create-cc-edmdd2-constants.
run_nm_dispcpolard_to_qpolard2
Calculates 2nd order derivatives of electric polarizability by numerical differentiation of the 1st order derivatives displaced along normal modes. See also the action create-cc-polard2-constants.
run_nm_dispdipd_to_qdipd2
Calculates 2nd order derivatives of electric dipole moment by numerical differentiation of the 1st order derivatives displaced along normal modes. See also the action create-cc-qdipd2-constants.
run_project_cff2
The force field (2nd order derivatives of the potential with respect to atomic displacement) should be translationaly invariant. Check this and try to correct the force field if being told so (i.e., if the option correct_ffs was set to 1 in the config file).
run_project_cff3
The force constants should be translationaly invariant. Check this and try to correct the force field if being told so (i.e., if the option correct_ffs was set to 1 in the config file). NOTE: Only cubic terms are checked, so far.
run_project_cff4b
Correct translational and rotational symmetry of quartic constants.
sort_and_ignore_modes
Freeze the modes listed in the config file (i.e. leave them out from all calculations). The orignal files will be overwritten to reflect the change: smatrix, qff2, cminv_harm and nnmod_file.
  • [Perl code]
zero-out-cff2
Zeroes out constants which couple atoms separated by the distance larger than the given threshold.
zero-out-cff3
Zeroes out constants which couple atoms separated by the distance larger than the given threshold.
zero-out-cff4
Zeroes out constants which couple atoms separated by the distance larger than the given threshold.
zero_out_cff2
Zeroes out constants which couple atoms separated by the distance larger than the given threshold.
zero_out_cff3
Zeroes out constants which couple atoms separated by the distance larger than the given threshold.
zero_out_cff4
Zeroes out constants which couple atoms separated by the distance larger than the given threshold.