[ Gvib Home ]
Module Actions.pm  Index of actions
This file was generated from the file Actions.pm by the command gvib w.
 Actions.pm  Index
 Actions.pm  Tree
 Actions.conf
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 forcefield 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 platformdependent.
The user has to take care of it and run it manually. See the action
createinputs and the scripts nondoneqsub
and nondonelist. See also the action nm.
 ccff34

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.
 Variables: cff3 cff4 nat_file>natoms nnmod_file>nnmodes qff2 qff3 qff4 smatrix
 Skip if done: qff3 qff4
 See also: createccinputs g03ccff34 run_cff2s_to_cff34 correctffs34 zerooutcff3 zerooutcff4 run_cff3_to_qff3 run_cff4_to_qff4
 [Gvib action]
 cff4tocff4b

Convert cff4 file to cff4b. The offdiagonal elements with all indices different
will be replaced by zeros.
 Variables: cff4 cff4b nat_file>natoms
 Skip if done: cff4b
 [External program]
 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]
 correctff2s

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).
 Variables: cff2 geom nat_file>natoms pmatrix
 Skip if done: pmatrix
 Run if true: correct_ffs
 See also: run_check_ff2 run_project_cff2 run_check_ff2
 [Gvib action]
 correctffs34

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.
 Variables: cff3 cff4 nat_file>natoms pmatrix
 Run if true: correct_ffs
 See also: run_check_ff3 run_project_cff3 run_check_ff3
 [Gvib action]
 createccedeqd2constants

Calculates 2nd order derivatives of el.dipoleel.quadrupole tensor by numerical
differentiation of the 1st order derivatives displaced along cartesian coordinates
and transforms them into normal modes. See also the action createnmedeqd2constants.
 Variables: disp_cedeqd1 disp_stepsize nat_file>natoms nnmod_file>nnmodes qedeqd2 qff2 smatrix
 Skip if done: qedeqd2
 Run if exists: disp_cedeqd1
 See also: run_dispcedeqd1_to_qedeqd2
 [Gvib action]
 createccedmdd2constants

Calculates 2nd order derivatives of el.dipolemg.dipole tensor by numerical
differentiation of the 1st order derivatives displaced along cartesian coordinates
and transforms them into normal modes. See also the action (createnmedmdd2constants).
 Variables: disp_cedmdd1 disp_stepsize nat_file>natoms nnmod_file>nnmodes qedmdd2 qff2 smatrix
 Skip if done: qedmdd2
 Run if exists: disp_cedmdd1
 See also: run_dispcedmdd1_to_qedmdd2
 [Gvib action]
 createccinputs

Create Gaussian and PBS jobs for geometries displaced along cartesian coordinates.
 Variables: along_cc=1 disp_stepsize gcmd_displaced gcmd_harmonic gdisp_files geom
 Skip if done: qff3 qff4
 Optional: charge_multiplicity
 See also: createinputs
 [Gvib action]
 createccpolard2constants

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 createnmpolard2constants.
 Variables: disp_cpolard1 disp_stepsize nat_file>natoms nnmod_file>nnmodes qff2 qpolard2 smatrix
 Skip if done: qpolard2
 Run if exists: disp_cpolard1
 See also: run_dispcpolard_to_qpolard2
 [Gvib action]
 createccqdipd2constants

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 createnmqdipd2constants.
 Variables: disp_dipd disp_stepsize nat_file>natoms nnmod_file>nnmodes qdipd2 qff2 smatrix
 Skip if done: qdipd2
 Optional: 1st_dipd_derivs_only
 See also: run_dispdipd_to_qdipd2
 [Gvib action]
 createinputs

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 createccinputs and createnminputs. If none of them is set, only
files for the original geometry will be generated.
 Optional: gcmd_append harm_disp_differ
 [External program]
 createnmedeqd2constants

Calculates 2nd order derivatives of el.dipoleel.quadrupole tensor by numerical
differentiation of the 1st order derivatives displaced along normal modes.
See also the action createccedeqd2constants.
 Variables: disp_cedeqd1 disp_nmstep nat_file>natoms nnmod_file>nnmodes qedeqd2 qff2 smatrix
 Skip if done: qedeqd2
 Run if exists: disp_cedeqd1
 See also: run_nm_dispcedeqd1_to_qedeqd2
 [Gvib action]
 createnmedmdd2constants

Calculates 2nd order derivatives of el.dipolemg.dipole tensor by numerical
differentiation of the 1st order derivatives displaced along normal modes.
See also the action createccedmdd2constants.
 Variables: disp_cedmdd1 disp_nmstep nat_file>natoms nnmod_file>nnmodes qedmdd2 qff2 smatrix
 Skip if done: qedmdd2
 Run if exists: disp_cedmdd1
 See also: run_nm_dispcedmdd1_to_qedmdd2
 [Gvib action]
 createnminputs

Create Gaussian and PBS jobs for geometries displaced along normal modes.
 Variables: along_nm=1 disp_nmstep gcmd_displaced gcmd_harmonic gdisp_files geom nnmod_file>nnmodes smatrix
 Skip if done: qff3 qff4
 Optional: charge_multiplicity
 See also: createinputs
 [Gvib action]
 createnmpolard2constants

Calculates 2nd order derivatives of electric polarizability by numerical
differentiation of the 1st order derivatives displaced along normal modes.
See also the action createccpolard2constants.
 Variables: disp_cpolard1 disp_nmstep nat_file>natoms nnmod_file>nnmodes qff2 qpolard2 smatrix
 Skip if done: qpolard2
 Run if exists: disp_cpolard1
 See also: run_nm_dispcpolard_to_qpolard2
 [Gvib action]
 createnmqdipd2constants

Calculates 2nd order derivatives of electric dipole moment by numerical
differentiation of the 1st order derivatives displaced along normal modes.
See also the action createccqdipd2constants.
 Variables: disp_dipd disp_nmstep nat_file>natoms nnmod_file>nnmodes qdipd2 qff2 smatrix
 Skip if done: qdipd2
 See also: run_nm_dispdipd_to_qdipd2
 [Gvib action]
 csf_evscf

Vibrational SelfConsistentField approach is an analog of electronic
HartreeFock calculation. The vibrational mutlidimensional wavefunction is taken as
product of independent onedimensional 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.
 Variables: cminv_evscf nnmod_file>nnmodes qff2 qff3 qff4 sparse_matrix_threshold vscf_climit vscf_maxiter vscf_nbase
 Skip if done: cminv_evscf cminv_evscfpt2
 Optional: cminv_evscfpt2 ievscf iraman_evscf iroa_evscf non_funds pt_nexcited qdipd1 qdipd2 qedeqd1 qedeqd2 qedmdd1 qedmdd2 qpolard1 qpolard2 treat_degeneracy
 [External program]
 csf_gvscf

Vibrational SelfConsistentField approach is an analog of electronic
HartreeFock calculation. The vibrational mutlidimensional wavefunction is taken as
product of independent onedimensional 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.
 Variables: cminv_gvscf nnmod_file>nnmodes qff2 qff3 qff4 sparse_matrix_threshold vscf_climit vscf_maxiter vscf_nbase
 Skip if done: cminv_gvscf cminv_gvscfpt2
 Optional: cminv_gvscfpt2 igvscf iraman_gvscf iroa_gvscf non_funds pt_nexcited qdipd1 qdipd2 qedeqd1 qedeqd2 qedmdd1 qedmdd2 qpolard1 qpolard2 treat_degeneracy
 [External program]
 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.
 Variables: cminv_harm_vci nnmod_file>nnmodes qff2 qff3 qff4 sparse_matrix_threshold vci_nbase vci_nexcited
 Skip if done: cminv_harm_vci
 Optional: harm_vci_funds harm_vci_large_ir harm_vci_large_raman harm_vci_large_roa iharm_vci iraman_harm_vci iroa_harm_vci qdipd1 qdipd2 qedeqd1 qedeqd2 qedmdd1 qedmdd2 qpolard1 qpolard2 vci_basis_set vci_detect_gnd_state vci_ham vci_solutions vci_state_threshold vci_trans
 [External program]
 csf_harmpt_freqs

See harm+pt.
 Variables: cminv_harmpt2 nnmod_file>nnmodes pt_nexcited qff2 qff3 qff4 sparse_matrix_threshold
 Skip if done: cminv_harmpt2
 Optional: non_funds treat_degeneracy
 [External program]
 csf_harmptb_freqs

See harm+ptb.
 Variables: cminv_harmpt2b nnmod_file>nnmodes pt_nexcited qff2 qff3 qff4b sparse_matrix_threshold
 Skip if done: cminv_harmpt2b
 Optional: non_funds treat_degeneracy
 [External program]
 csf_nm_anim

Create list of geometries displaced along each of the normal mode.
Good for visualizing via the mm (Molecule Maker) program.
 Variables: geom ignore_modes nat_file>natoms nm_anim nm_step nnmod_file>nnmodes smatrix
 Skip if done: nm_anim
 [External program]
 default

Run the actions specified  i.e. all the implemented anharmonic
methods with anharmonic forcefield calculated along cartesian coordinates.
 evscf

VSCF with selfconsistent but nonorthogonal 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.
 See also: csf_evscf pt2intensities
 [Gvib action]
 ff2

Create Gaussian and PBS job for nondisplaced optimized geometry.
Run Gaussian if necessary.
 Variables: gcmd_harmonic geom
 Skip if done: qff2
 Optional: charge_multiplicity
 See also: createinputs g03ff2 harmonicconstants correctff2s zerooutcff2
 [Gvib action]
 ff4b

Creates quartic constants with all indices different (V_ijkl).
 Skip if done: qff4b
 See also: cc cff4tocff4b run_check_ff4b run_project_cff4b run_check_ff4b run_cff4b_to_qff4b
 [Gvib action]
 g03ccff34

Run Gaussian for all geometries displaced along cartesian coordinates.
 Variables: along_cc=1
 Skip if done: disp_cff2 disp_dipd
 See also: run_gaussian_ff34
 [Gvib action]
 g03ff2

Run Gaussian to create 2nd derivatives of potential
with respect to the nuclear displacements. Then dipole
derivatives and the forcefield constants are extracted
and saved in the files cdipd1 and cff2.
 Skip if done: gout_file
 [Perl code]
 g03nmff34

Run Gaussian for all geometries displaced along normal modes.
 Variables: along_nm=1
 Skip if done: disp_cff2 disp_dipd
 See also: run_gaussian_ff34
 [Gvib action]
 gvscf

VSCF with orthogonal but selfinconsistent excited solutions.
 See also: csf_gvscf pt2intensities
 [Gvib action]
 harm+pt

Hamonic calculation corrected by 2nd order perturbation theory. The calculation
is done in the basis of unperturbed solutions  linear harmonic oscillators.
 See also: csf_harmpt_freqs pt2intensities
 [Gvib action]
 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 offdiagonal quartic constants will be used.
 Skip if done: cminv_harmpt2b
 See also: ff4b csf_harmptb_freqs pt2intensities
 [Gvib action]
 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 cutoff limit must
be specified. (See the vci_nbase,
sparse_matrix_threshold and
vci_state_threshold variables.)
 See also: csf_harm_vci
 [Gvib action]
 harmonicconstants

Parse gaussian output file and extract force constants and create
some requisite files required by other modules.
 Skip if done: cff2
 [Perl code]
 harmonicdeps

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]
 harmonicfreqs

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.
 Variables: cminv_harm qff2 smatrix
 Skip if done: qff2 smatrix
 Optional: nat_file>natoms
 See also: harmonicdeps run_harmonic nm_anim sort_and_ignore_modes
 [Gvib action]
 harmonicintensities

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.
 Variables: cdipd1 iharm nat_file>natoms nnmod_file>nnmodes qdipd1 qff2 smatrix
 Skip if done: iharm
 Optional: iharm_dipd2=0 iharm_nexcited qdipd2
 See also: run_cdipd1_to_qdipd1 run_harmonic_intensities harmonicraman harmonicroa
 [Gvib action]
 harmonicraman

Calculates the Raman scattering activities in harmonic approximation.
 Variables: cpolard1 iraman_harm nat_file>natoms nnmod_file>nnmodes qff2 qpolard1 smatrix
 Skip if done: iraman_harm
 Run if exists: cpolard1
 See also: run_cpolard1_to_qpolard1 run_harmonic_raman
 [Gvib action]
 harmonicroa

Calculates the Raman optical activity in harmonic approximation.
 Variables: cedeqd1 cedmdd1 iroa_harm nat_file>natoms nnmod_file>nnmodes qedeqd1 qedmdd1 qff2 qpolard1 smatrix
 Skip if done: iroa_harm
 Run if exists: cedeqd1 cedmdd1
 See also: run_cedmdd1_to_qedmdd1 run_cedeqd1_to_qedeqd1 run_harmonic_roa
 [Gvib action]
 iharmccdipd2

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.
 Variables: iharm_nexcited qdipd2
 Run if true: iharm_dipd2
 See also: createccqdipd2constants
 [Gvib action]
 iharmnmdipd2

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.
 Variables: iharm_nexcited qdipd2
 Run if true: iharm_dipd2
 See also: createnmqdipd2constants
 [Gvib action]
 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 2ndorder forcefield derivatives
in normal coordinates instead of cartesian coordinates. The obvious advantage is that
instead of 2*3N+1 forcefield evaluations, only 2*(3N6)+1 are needed. For isotopic
substitutions, the forcefield must be recreated, though. See also the action cc.
 nmff34

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.
 Variables: cff3 cff4 nat_file>natoms nnmod_file>nnmodes qff2 qff3 qff4 smatrix
 Skip if done: qff3 qff4
 See also: createnminputs g03nmff34 run_nm_cff2s_to_qff34
 [Gvib action]
 nm_anim

Create list of geometries displaced along each of the normal mode.
Good for visualizing via the mm (Molecule Maker) program.
 Variables: geom ignore_modes nat_file>natoms nm_anim nm_step nnmod_file>nnmodes smatrix
 Skip if done: nm_anim
 See also: csf_nm_anim
 [Gvib action]
 pt2intensities

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.
 Variables: cdipd1 iharm nat_file>natoms nnmod_file>nnmodes qdipd1 qff2 smatrix
 Skip if done: iharm
 Optional: iharm_dipd2=0 iharm_nexcited qdipd2
 [External program]
 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.
 Variables: cff3 cff4 disp_cff2 disp_stepsize nat_file>natoms
 Skip if done: cff3 cff4
 [External program]
 run_cff3_to_qff3

Transform cubic terms of Taylor expansion of the potential (V_ijk)
from cartesian coordinates into the normal modes.
 Variables: cff3 nat_file>natoms nnmod_file>nnmodes qff2 qff3 smatrix
 Skip if done: qff3
 [External program]
 run_cff4_to_qff4

Transform quartic semidiagonal terms of Taylor expansion of the potential (V_ijkk)
from cartesian coordinates into the normal modes.
 Variables: cff4 nat_file>natoms nnmod_file>nnmodes qff2 qff4 smatrix
 Skip if done: qff4
 [External program]
 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 offdiagonal elements with all indices
different (V_ijkl) will be generated.
 Variables: cff4b nat_file>natoms nnmod_file>nnmodes qff2 qff4b smatrix
 Skip if done: qff4b
 [External program]
 run_check_ff2

Check the translational symmetry of forcefield constants.
 Variables: cff2 nat_file>natoms
 [External program]
 run_check_ff3

Check translational symmetry of cubic constants.
 Variables: cff3 nat_file>natoms
 [External program]
 run_check_ff4b

Check translational symmetry of quartic constants.
 Variables: cff4b nat_file>natoms
 [External program]
 run_cpolard1_to_qpolard1

Calculates the Raman scattering activities in harmonic approximation.
 Variables: cpolard1 iraman_harm nat_file>natoms nnmod_file>nnmodes qff2 qpolard1 smatrix
 Skip if done: iraman_harm
 Run if exists: cpolard1
 [External program]
 run_dispcedeqd1_to_qedeqd2

Calculates 2nd order derivatives of el.dipoleel.quadrupole tensor by numerical
differentiation of the 1st order derivatives displaced along cartesian coordinates
and transforms them into normal modes. See also the action createnmedeqd2constants.
 Variables: disp_cedeqd1 disp_stepsize nat_file>natoms nnmod_file>nnmodes qedeqd2 qff2 smatrix
 Skip if done: qedeqd2
 Run if exists: disp_cedeqd1
 [External program]
 run_dispcedmdd1_to_qedmdd2

Calculates 2nd order derivatives of el.dipolemg.dipole tensor by numerical
differentiation of the 1st order derivatives displaced along cartesian coordinates
and transforms them into normal modes. See also the action (createnmedmdd2constants).
 Variables: disp_cedmdd1 disp_stepsize nat_file>natoms nnmod_file>nnmodes qedmdd2 qff2 smatrix
 Skip if done: qedmdd2
 Run if exists: disp_cedmdd1
 [External program]
 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 createnmpolard2constants.
 Variables: disp_cpolard1 disp_stepsize nat_file>natoms nnmod_file>nnmodes qff2 qpolard2 smatrix
 Skip if done: qpolard2
 Run if exists: disp_cpolard1
 [External program]
 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 createnmqdipd2constants.
 Variables: disp_dipd disp_stepsize nat_file>natoms nnmod_file>nnmodes qdipd2 qff2 smatrix
 Skip if done: qdipd2
 Optional: 1st_dipd_derivs_only
 [External program]
 run_gaussian_ff34

Run Gaussian in all the displaced geometries to find
out 2nd derivatives of forcefield 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 g03cff34), displacement
along cartesian coordinates is assumed. If the variable along_nm was set
(the action was called from g03qff34), normal mode displacements
are assumed.
 [Perl code]
 run_harmonic

Reads the cartesian force constants, massweights them and diagonalizes
the resulting matrix. On output are written: harmonic frequencies [1/cm];
the massweighted 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.
 Variables: cff2 cminv_harm masses nat_file>natoms qff2 smatrix
 Skip if done: cminv_harm qff2 smatrix
 Optional: sort_modes=1
 [External program]
 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.
 Variables: cdipd1 iharm nat_file>natoms nnmod_file>nnmodes qdipd1 qff2 smatrix
 Skip if done: iharm
 Optional: iharm_dipd2=0 iharm_nexcited qdipd2
 [External program]
 run_harmonic_raman

Calculates the Raman scattering activities in harmonic approximation.
 Variables: cpolard1 iraman_harm nat_file>natoms nnmod_file>nnmodes qff2 qpolard1 smatrix
 Skip if done: iraman_harm
 Run if exists: cpolard1
 [External program]
 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.
 Variables: cminv_harm harm_vzpe nnmod_file>nnmodes
 Skip if done: harm_vzpe
 [External program]
 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.
 Variables: disp_cff2 disp_nmstep nat_file>natoms nnmod_file>nnmodes qff3 qff4 smatrix
 Skip if done: qff3 qff4
 [External program]
 run_nm_dispcedeqd1_to_qedeqd2

Calculates 2nd order derivatives of el.dipoleel.quadrupole tensor by numerical
differentiation of the 1st order derivatives displaced along normal modes.
See also the action createccedeqd2constants.
 Variables: disp_cedeqd1 disp_nmstep nat_file>natoms nnmod_file>nnmodes qedeqd2 qff2 smatrix
 Skip if done: qedeqd2
 Run if exists: disp_cedeqd1
 [External program]
 run_nm_dispcedmdd1_to_qedmdd2

Calculates 2nd order derivatives of el.dipolemg.dipole tensor by numerical
differentiation of the 1st order derivatives displaced along normal modes.
See also the action createccedmdd2constants.
 Variables: disp_cedmdd1 disp_nmstep nat_file>natoms nnmod_file>nnmodes qedmdd2 qff2 smatrix
 Skip if done: qedmdd2
 Run if exists: disp_cedmdd1
 [External program]
 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 createccpolard2constants.
 Variables: disp_cpolard1 disp_nmstep nat_file>natoms nnmod_file>nnmodes qff2 qpolard2 smatrix
 Skip if done: qpolard2
 Run if exists: disp_cpolard1
 [External program]
 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 createccqdipd2constants.
 Variables: disp_dipd disp_nmstep nat_file>natoms nnmod_file>nnmodes qdipd2 qff2 smatrix
 Skip if done: qdipd2
 [External program]
 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).
 Variables: cff2 geom nat_file>natoms pmatrix
 Skip if done: pmatrix
 Run if true: correct_ffs
 [External program]
 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.
 Variables: cff3 cff4 nat_file>natoms pmatrix
 Run if true: correct_ffs
 [External program]
 run_project_cff4b

Correct translational and rotational symmetry of quartic constants.
 Variables: cff4b nat_file>natoms pmatrix
 [External program]
 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]
 zerooutcff2

Zeroes out constants which couple atoms separated by the distance larger than the given threshold.
 Variables: cff2 cff2_dist_th=0 geom nat_file>natoms
 See also: zero_out_cff2
 [Gvib action]
 zerooutcff3

Zeroes out constants which couple atoms separated by the distance larger than the given threshold.
 Variables: cff3 cff3_dist_th=0 geom nat_file>natoms nat_file>natoms
 See also: zero_out_cff3
 [Gvib action]
 zerooutcff4

Zeroes out constants which couple atoms separated by the distance larger than the given threshold.
 Variables: cff4 cff4_dist_th=0 geom nat_file>natoms nat_file>natoms
 See also: zero_out_cff4
 [Gvib action]
 zero_out_cff2

Zeroes out constants which couple atoms separated by the distance larger than the given threshold.
 Variables: cff2 cff2_dist_th=0 geom nat_file>natoms
 [External program]
 zero_out_cff3

Zeroes out constants which couple atoms separated by the distance larger than the given threshold.
 Variables: cff3 cff3_dist_th=0 geom nat_file>natoms nat_file>natoms
 [External program]
 zero_out_cff4

Zeroes out constants which couple atoms separated by the distance larger than the given threshold.
 Variables: cff4 cff4_dist_th=0 geom nat_file>natoms nat_file>natoms
 [External program]