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Configuration file Actions.conf
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 Actions.pm  Tree
 Actions.conf
 1st_dipd_derivs_only

If set, only 1st el. dipole derivatives will be written
into qdipd2 by the action
run_dispdipd_to_qdipd2,
2nd derivatives will be replaced by zeros. This is good for
evaluating IR intensities without 2nd dipole derivatives.
by default commented out, otherwise = 1  JOB

Name of the job. If not specified, its value
will be set to match the value of WORK_DIR.
(It is safe to leave this blank.)
default value =  WORK_DIR

Where to put temporary and output files. If not
specified in the config file, it will be
determined from the command line arguments.
(It is safe to leave this blank.)
default value =  cdipd1

Dipole derivatives (of the optimized geometry)
in cartesian coordinates. (Sorted as disp_dipd.)
Atomic units: multiples of electron charge
[1/1.602176462e19 Coulombs].
default value = $(WORK_DIR)/cdipd1  cedeqd1

El.dipoleel.quadrupole derivatives in cartesian coordinates.
Ordered probably as
c1/x1..c18/x1,
c1/y1..c18/y1,
...
c1/zn..c18/zn. The constants c1..c18 are ordered as
xx/x, yy/x, zz/x, xy/x, xz/x, yz/x,
xx/y, yy/y, zz/y, xy/y, xz/y, yz/y,
xx/z, yy/z, zz/z, xy/z, xz/z, yz/z.
default value = $(WORK_DIR)/cedeqd1  cedmdd1

El. dipole  mg. dipole tensor derivatives in cartesian
coordinates. The derivatives are ordered as
c1/x1..c9/x1,
c1/y1..c9/y1,
...
c1/zn..c9/zn. The constants c1..c9 are ordered as xx,xy,xz,yx,yy,yz,zx,zy,zz.
default value = $(WORK_DIR)/cedmdd1  cff2

Where to put ff constants [Hartree/Bohr^2]. The order of the
constants is Vx1x1,Vy1x1,Vy1y1,Vz1x1...Vz1z1,...,VzNx1,
VzNy1,...,VzNzN.
default value = $(WORK_DIR)/cff2  cff2_dist_th

Threshold for zeroing out cff2 constants of too distant atoms. If set to 0,
all constants will be included. [Angstroms]
default value = 0  cff3

Cubic force constants in cartesian coordinates
[Hartree/Bohr^3]. The order of the coefficients
V(i,j,k) goes like k=1,n;j=1,k;i=1,j.
default value = $(WORK_DIR)/cff3  cff3_dist_th

The same as cff2_dist_th but for cff3 constants.
default value = 0  cff4

Semidiagonal quartic force constans in cartesian
coordinates [Hartree/Bohr^4]. The order of the
coefficients V(i,j,k,k) goes like
k=1,n;j=1,n;i=1,j. If both the files cff3 and
cff4 already exist, they will not be computed again.
default value = $(WORK_DIR)/cff4  cff4_dist_th

The same as cff2_dist_th but for cff4 constants.
default value = 0  cff4b

The same as cff4, but with the offdiagonal elements Vijkl present.
default value = $(WORK_DIR)/cff4b  charge_multiplicity

Charge and multiplicity as accepted by G03 input file.
by default commented out, otherwise = 0 1  cminv_evscf

A variant of VSCF, with selfconsistent (but
nonorthogonal) excited states. During the VSCF
iterations, not the energy of the ground state,
but of a specified excited state is minimized.
default value = $(WORK_DIR)/cminv_evscf  cminv_evscfpt2

If set, eVSCF+PT2 fundamental frequencies [1/cm] will
be calculated.
default value = $(WORK_DIR)/cminv_evscfpt2  cminv_gvscf

List of gVSCF fundamental frequencies [1/cm].
default value = $(WORK_DIR)/cminv_gvscf  cminv_gvscfpt2

If set, gVSCF+PT2 fundamental frequencies [1/cm] will
be calculated.
default value = $(WORK_DIR)/cminv_gvscfpt2  cminv_harm

List of harmonic frequencies [1/cm].
default value = $(WORK_DIR)/cminv_harm  cminv_harm_vci

List of VCI fundamental frequencies in the basis of LHOs.
default value = $(WORK_DIR)/cminv_harm_vci  cminv_harmpt2

List of harm+PT2 frequencies.
default value = $(WORK_DIR)/cminv_harmpt2  cminv_harmpt2b

List of harm+PT2 frequencies calculated with qff4b.
default value = $(WORK_DIR)/cminv_harmpt2b  correct_ffs

When defined, an effort will be made to correct
the input force field so that it will maintain
translational and rotational invariance.
default value = 1  cpolard1

Polarizability derivatives with respect to cartesian
coordinates. If c1,..,c6 are the polarizability
constants, then the derivatives are ordered as
c1/x1..c6/x1,
c1/y1..c6/y1,
...
c1/zn..c6/zn. The constants c1..c6 are ordered are ordered as xx,xy,yy,xz,yz,zz.
default value = $(WORK_DIR)/cpolard1  disp_cedeqd1

The same as disp_cpolard1 but for cedeqd1.
default value = $(WORK_DIR)/disp_cedeqd1  disp_cedmdd1

The same as disp_cpolard1 but for cedmdd1.
default value = $(WORK_DIR)/disp_cedmdd1  disp_cff2

List of the displaced force constants blocks separated
by a newline. For Natomic molecule, the file contains
2*3*N+1 blocks ordered as: original (optimized) geometry,
dx1,dy1,dz1,...,dzN,dx1,dy1,dz1,...,dzN.
These constants are used to calculate cubic and
semidiagonal quartic anharmonic constants.
NOTE: This file can hold also displacements along normal modes, depending on the route selected. If so, only 2*NNMODES+1 blocks are present.
default value = $(WORK_DIR)/disp_cff2  disp_cpolard1

List of the displaced polarizability derivatives in
cartesian coordinates. Each block is seperated
by a new line and the order of the blocks is the
same as in disp_cff2. The order of constants
inside a block is the same as cpolard1.
When undefined, only 1st derivatives will be used
for evaluating the intensitites.
NOTE: This file can hold also displacements along normal modes, depending on the route selected. If so, only 2*NNMODES+1 blocks are present.
default value = $(WORK_DIR)/disp_cpolard1  disp_dipd

List of the displaced dipole derivative blocks in
cartesian coordinates separated by a newline. The
order of the blocks is the same as for disp_cff2.
The derivatives in a block are in the order
mu_x/x1, mu_y/x1, mu_z/x1,
mu_x/y1, mu_y/y1, mu_z/y1, etc.
Atomic units: multiples of electron charge [1/1.602176462e19 Coulombs]
NOTE: This file can hold also displacements along normal modes, depending on the route selected. If so, only 2*NNMODES+1 blocks are present.
default value = $(WORK_DIR)/disp_dipd  disp_nmstep

A displacement step for calculating higher order
derivatives in normal modes. The number should be
given in the format e.g. 0.1, not as 1e1.
[Units: Angstroms*]
default value = 1  disp_stepsize

A displacement step for calculating higher order
derivatives in cartesian coordinates. The number
should be given in the format 0.025, not as
2.5e2. [Units: Angstroms*multiples of el.mass]
default value = 0.025  gauss_orientation

How to recognise the geometry field in the Gaussian output.
by default commented out, otherwise = "Input orientation:"  gchk_afile

Gaussian ascii check file  gzipped variant *.gz is ok.
If molecular properties should be read from the
checkpoint file, make sure that standard orientation
was used for molecular geometry!
default value = $(WORK_DIR)/gauss.achk  gchk_file

Gaussian check file  gzipped variant *.gz is ok.
If molecular properties should be read from the
checkpoint file, make sure that standard orientation
was used for molecular geometry!
default value = $(WORK_DIR)/gauss.chk  gcmd_append

A text file to be appended to every G03 input file by
the action createinputs.
by default commented out, otherwise = append.txt  gcmd_displaced

Gaussian command for calculating higher derivatives of
force field constants at displaced geometries. NOTE:
Even for a small molecule, this calculation is very
expensive. It is better to run the action
createinputs
separately and run the jobs in parallel on multiple
processors, using e.g. the
nondoneqsub
script.
For creating G03 force field with freezed cosmo cavities, append the "scrf=(cpcm,solvent=water,read)" to the command and set the gcmd_append option.
To speed up the calculations, do not evaluate Raman and ROA tensors in displaced geometries  the secondorder derivatives do not contribute significantly.
**************************************************
IMPORTANT NOTE: Set harm_disp_differ if the displaced calculations are performed at different level of theory or smaller basis set!
**************************************************
default value = \#B3LYP/631++G** freq  gcmd_harmonic

Gaussian command for calculating force field constants
of the optimized geometry.
default value = \#B3LYP/631++G** freq=roa  gdisp_files

Gaussian files for displaced geometries.
default value = $(WORK_DIR)/gaussdisps  geom

Geometry of the molecule extracted from the gout file.
default value = $(WORK_DIR)/$(JOB).x  geom_th

A threshold for rejecting molecular geometries which
differ this much from the expected geometry. Used in
sanity checks, to prevent user from absentmindedly
mixing different gaussian outputs.
default value = 1e7  ginp_file

Where to put input file for the gaussian.
default value = $(WORK_DIR)/gauss.inp  gout_file

Gaussian output  gzipped variant *.gz is ok.
default value = $(WORK_DIR)/gauss.out  harm_disp_differ

Set this option to 1, if the displaced geometries are
calculated at different level of theory, using different
basis set etc. than harmonic calculation. In this case, the
output file from calculation on optimized geometry using the
gcmd_displaced command is expected in the gdisp_files
directory under the standard name gauss.out[.gz] or gauss.achk[.gz].
default value = 0  harm_vci_funds

A list of most important contributions to the fundamental
frequencies. (Optional.) See the analyzevci utility.
default value = $(WORK_DIR)/harm_vci_funds  harm_vci_large_ir

If set, the peaks with large IR intensities will be
analyzed and a list of most important contrubutions
to these transitions will be saved.
default value = $(WORK_DIR)/harm_vci_large_ir  harm_vci_large_raman

Same as harm_vci_large_ir with Raman intensities.
default value = $(WORK_DIR)/harm_vci_large_raman  harm_vci_large_roa

Same as harm_vci_large_ir with ROA intensities.
default value = $(WORK_DIR)/harm_vci_large_roa  ievscf

Same as igvscf, but for eVSCF.
default value = $(WORK_DIR)/ir_evscf  ievscfpt2

If set, cminv_evscfpt2 will be merged with ievscf intensities.
default value = $(WORK_DIR)/ir_evscfpt2  ignore_chk

When set to a nonzero value, constants and molecular
properties will be read from Gaussian outputs and
Gaussian ascii checkpoint files will be ignored even
when available.
default value = 0  ignore_modes

Ignore 6 of the lowest normal modes (translation
and rotation). Any mode can be specified either
as range or commaseparated list: 13,5,710.
Tip: Use the "modenumbering" utility for painless
switching between absolute and relative numbering of
modes.
NOTE: When changed in an existing project, some actions
must be run again to update constants!
default value = 16  igvscf

VSCF intensities of fundamental frequencies [km/Mol].
default value = $(WORK_DIR)/ir_gvscf  igvscfpt2

If set, cminv_gvscfpt2 will be merged with igvscf intensities.
default value = $(WORK_DIR)/ir_gvscfpt2  iharm

Harmonic intensities [kM/Mol].
default value = $(WORK_DIR)/ir_harm  iharm_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.
default value = 0  iharm_vci

If set, Harmonic+VCI IR intensities will be calculated.
default value = $(WORK_DIR)/ir_harm_vci  iharmpt2

If set, cminv_harmpt2 will be merged with iharm intensities.
default value = $(WORK_DIR)/ir_harmpt2  input_file

A molecule geometry to be analyzed.
default value = $(WORK_DIR)/$(JOB).x  iraman_evscf

If set, Raman eVSCF scattering activity will be calculated. [A**4/AMU]
default value = $(WORK_DIR)/iraman_evscf  iraman_evscfpt2

If set, cminv_evscfpt2 will be merged with iraman_evscf intensities.
default value = $(WORK_DIR)/iraman_evscfpt2  iraman_gvscf

If set, Raman gVSCF scattering activity will be calculated. [A**4/AMU]
default value = $(WORK_DIR)/iraman_gvscf  iraman_gvscfpt2

If set, cminv_gvscfpt2 will be merged with iraman_gvscf intensities.
default value = $(WORK_DIR)/iraman_gvscfpt2  iraman_harm

If set, harmonic Raman scattering activity will be calculated. [A**4/AMU]
default value = $(WORK_DIR)/iraman_harm  iraman_harm_vci

If set, Harm+VCI Raman scattering activity will be calculated. [A**4/AMU]
default value = $(WORK_DIR)/iraman_harm_vci  iraman_harmpt2

If set, cminv_harmpt2 will be merged with iraman_harm intensities.
default value = $(WORK_DIR)/iraman_harmpt2  iroa_evscf

If set, eVSCF ROA intensities will be calculated. [10**4 A**5/AMU]
default value = $(WORK_DIR)/iroa_evscf  iroa_evscfpt2

If set, cminv_evscfpt2 will be merged with iroa_evscf intensities.
default value = $(WORK_DIR)/iroa_evscfpt2  iroa_gvscf

If set, gVSCF ROA intensities will be calculated. [10**4 A**5/AMU]
default value = $(WORK_DIR)/iroa_gvscf  iroa_gvscfpt2

If set, cminv_gvscfpt2 will be merged with iroa_gvscf intensities.
default value = $(WORK_DIR)/iroa_gvscfpt2  iroa_harm

If set, harmonic ROA intensities will be calculated. [10**4 A**5/AMU]
default value = $(WORK_DIR)/iroa_harm  iroa_harm_vci

If set, Harm+VCI ROA intensities will be calculated. [10**4 A**5/AMU]
default value = $(WORK_DIR)/iroa_harm_vci  iroa_harmpt2

If set, cminv_harmpt2 will be merged with iroa_harm intensities.
default value = $(WORK_DIR)/iroa_harmpt2  log

Where the logging messages will go.
default value = $(WORK_DIR)/log  masses

Atomic masses of the atoms in the molecule. (A subject
for isotopic substitution.) [atomic units
(multiples of electron mass)]
default value = $(WORK_DIR)/masses  nat_file

Number of atoms in the molecule.
default value = $(WORK_DIR)/natoms  nm_anim

List of normal modes and geometries. Good for
visualizing using the gmm program.
default value = $(WORK_DIR)/$(JOB).nmodes  nm_step

To visualize the normal modes in the gmm program,
use this big displacement of normal coordinates
(can be negative).
default value = 10  nnmod_file

Number of normal modes (3*nAtomsnIgnored).
default value = $(WORK_DIR)/nnmodes  non_funds

A file containing a list of nonfundamental product functions,
for which frequencies and intensities should be calculated.
Each state is expressed as a list of N integers,
where N equals to pt_nexcited. The numbers are indexes
of excited fundamental onemode functions in the same order
as given by the command nl path_to/cminv_harm.
If a fundamental is doubly excited, its index appears twice in the list.
The indexes must be sorted ascendently. If a state carries
less than N excitations, the list is zero padded on the right.
The option is used in gVSCF,eVSCF,+PT2 and Harm+PT2 methods.
by default commented out, otherwise = $(WORK_DIR)/non_funds  optimized_check

By default, sanity check will be performed to make sure
that the supplied Gaussian output file comes from
a calculation on an optimized geometry. Note that this
check is not bulletproof and may give a false alarm.
The output from the optimization job should be always
consulted if unsure.
default value = 1  pmatrix

A matrix for projecting translational and rotational
modes out of the force fields (correct_ffs option
above must be specified).
default value = $(WORK_DIR)/pmatrix  pt_nexcited

Maximal number of excitations in product functions
used in perturbation and VCI calculations.
Used in Harmonic+PT2, VSCF+PT2 and Harm+VCI methods.
default value = 5  qdipd1

Dipole derivatives in dimensionless normal modes. They
are ordered as:
mu_x/q1, mu_y/q1, mu_z/q1,
mu_x/q2, mu_y/q2, mu_z/q2, etc. The dimensionless coordinates are obtained as qdipd1(i)=qdipd_i/sqrt(omega_i). Atomic units.
default value = $(WORK_DIR)/qdipd1  qdipd2

2nd order dipole derivatives in dimensionless normal modes.
They are ordered as:
mu_x/q1q1, mu_y/q1q1, mu_z/q1q1,
mu_x/q2q1, mu_y/q2q1, mu_z/q2q1, etc. The dimensionless coordinates are obtained as qdipd2(i,j)=qdipd2(i,j)/sqrt(freq_i*freq_j). Atomic units.
default value = $(WORK_DIR)/qdipd2  qedeqd1

El.dipoleel.quadrupole derivatives transformed into normal modes.
Same order as cedeqd1.
default value = $(WORK_DIR)/qedeqd1  qedeqd2

Secondorder el.dip.el.quadrupole derivatives. The order
corresponds cedeqd1 and qpolard2.
default value = $(WORK_DIR)/qedeqd2  qedmdd1

El.dipolemg.dipole derivatives transformed into normal modes.
Same order as cedmdd1.
default value = $(WORK_DIR)/qedmdd1  qedmdd2

Secondorder el.dip.mg.dip. derivatives. The order corresponds
to cedmdd1 and qpolard2.
default value = $(WORK_DIR)/qedmdd2  qff2

Harmonic frequencies in [sqrt(Hartree/electron_mass)/Bohr].
The constants are weighted by frequency, so that proper
units are obtained when calculating overlaps
0.5*
*qff2. Please see the comments in anharmpotential.c.
default value = $(WORK_DIR)/qff2  qff3

Cubic force constants in normal coordinates in units
[Hartree/(Bohr*sqrt(multiples of el. mass))^3]. The
order is same as in cff3. If the file exists, it will
not be computed again.
The constants are weighted by frequency, so that proper
units are obtained when calculating overlaps
*qff3. Please see the comments in anharmpotential.c.
default value = $(WORK_DIR)/qff3  qff4

Quartic force constants in normal coordinates in units
[Hartree/(Bohr*sqrt(multiples of el. mass))^4]. The
order is same as in cff4. If the file already exists,
it will not be computed again.
The constants are weighted by frequency, so that proper
units are obtained when calculating overlaps
*qff4. Please see the comments in anharmpotential.c.
default value = $(WORK_DIR)/qff4  qff4b

The same as qff4, but with the offdiagonal elements Vijkl
present. Currently used only with the harm+ptb action.
default value = $(WORK_DIR)/qff4b  qpolard1

Polarizability derivatives transformed into normal modes.
Same order as cpolard1.
default value = $(WORK_DIR)/qpolard1  qpolard2

Secondorder polarizability derivatives. The order respects
cpolard1:
C1/q1q1 .. C6/q1q1
C1/q2q1 .. C6/q2q1
C1/q2q2 .. C6/q2q2
...
C1/qMq1 .. C6/qMq1
...
C1/qMqM .. C6/qMqM
...
C1/qNq1 .. C6/qNq1
...
C1/qNqN .. C6/qNqN.
default value = $(WORK_DIR)/qpolard2  smatrix

Transformation matrix from cartesians to normal modes
The matrix is massweighted. The columns
correspond to a constant normal mode index and rows to
a constant cartesian index. The matrix columns corresponding
to the modes specified in the ignore_modes option above will
be left out and the rest will be sorted ascendently
so that it stays consistent with the sorted qff2 file.
The sorting will not be done if sort_modes option is set
to false. Units: [1/sqrt(multiples of electron mass)]
default value = $(WORK_DIR)/smatrix  sort_modes

If sort_modes option is set to false, the constants
and modes will be left unsorted. The numbers in
the ignore_modes option are still assumed to
correspond to the order of sorted modes. The
default is "true".
NOTE: This option was introduced for debug purposes and
it is not supported any more  with updates, this code
is not being checked.
default value = 1  sparse_matrix_threshold

Cubic and quartic constants making up less then this
many % of the total sum of all constants will be
ignored. For more on this, look up in the output
lines containing the phrase 'size reduced from'
and check the source code of csf_matrix.c.
default value = 1e3  treat_degeneracy

0 .. do not treat, 1 .. simplified approach.
(See treatptdegeneracy.latex.)
Proper treatment not implemented.
By default, simplified approach will be employed.
default value = 1  vci_basis_set

Comment out this variable, if the states selected in the VCI
basis set should not be saved.
The format is:
<vci_nbase> <vci_nexcited>
<exc1> <exc2> .. <excvci_nexcited>
...,
see also the options vci_nbase and vci_nexcited.
by default commented out, otherwise = $(WORK_DIR)/vci_basis_set  vci_detect_gnd_state

If told so, csf_harm_vci will try to behave smartly and
detect ground state not as the lowest VCI solution, but as
the solution with the largest contribution from the
state 0000..<. If set, the option harm_vci_funds below
must be set as well (which is the default). This may correct
loosy performance of VCI with problematic nonfreezed modes.
default value = 1  vci_ham

Uncomment this variable, if the Hamiltonian matrix should be saved
for further analysis. It is saved in a binary format in the
order 11,21,22,..,M1,..,MM,N1,..,NN. See also the utility
print_matrix_el.
by default commented out, otherwise = $(WORK_DIR)/vci_hamiltonian  vci_nbase

A maximal dimension of the VCI basis. If there is
more basis functions, only those states a> with
the highest overlaps <fWa> will be included.
(The state f> is either a ground state or a
fundamental.)
default value = 1000  vci_nexcited
 default value = $(pt_nexcited)
 vci_solutions

Comment out this variable, if the diagonalized Harm+VCI
solutions should not be saved. (Saves some disk space.)
The binary format is:
<integer vci_nbase>
<double eigenvalue> <double coeff(1)> .. <double coeff(vci_nbase)>, see also the option vci_nbase and print_vci_state utility.
by default commented out, otherwise = $(WORK_DIR)/vci_solutions  vci_state_threshold

When calculating VCI IR and Raman intensities, the
parameter threshold specifies how large must be coefficients
of a given basis state to be included in the calculation. The
value of the parameter can be rougly interpreted as a
probability that the system can be found in the state.
Should be from interval (0,1), 0 means all states will be
included. Don't set this value too high, this evaluation
is not the bottleneck of VCI and the intensities are very
sensitive!
default value = 1e6  vci_trans

A list of transitions between states, for which frequencies and
intensities should be calculated. A transition should be specified
as two numbers  indexes to vci_basis_set, starting from 0.
The separator does not matter, can be a newline. The indexes can
obtained from vci_basis_set simply by running
nl v 1 vci_basis_set.
By default, the list 0 1,0 2,..,0 vci_nbase1 is considered.
The default list may be affected by the option
vci_detect_ground_state.
by default commented out, otherwise = $(WORK_DIR)/vci_transitions  vscf_climit

The convergence criteria for the VSCF energy [1/cm].
default value = 1e6  vscf_maxiter

Maximal count of VSCF iterations. (Set 0 for unlimited.)
default value = 50  vscf_nbase

A VSCF function is a Ndimensional product
function of N onedimensional functions, which are
expanded in the base of linear harmonic oscillators.
The vscf_nbase is the dimension of the LHO base.
(N stands for number of normal modes and it is equal
to nnmodes bellow.)
default value = 15