Actions.conf

Configuration file Actions.conf

This file was generated from the file Actions.pm by the command gvib -w.
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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 [1/1.602176462e-19 Coulombs].
default value = $(WORK_DIR)/cdipd1
cedeqd1: El.dipole-el.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 off-diagonal 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 self-consistent (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 N-atomic 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 [1/1.602176462e-19 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 1e-1. [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 2.5e-2. [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 create-inputs.
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 create-inputs separately and run the jobs in parallel on multiple processors, using e.g. the nondone-qsub 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 second-order 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/6-31++G** freq
gcmd_harmonic: Gaussian command for calculating force field constants of the optimized geometry.
default value = \#B3LYP/6-31++G** freq=roa
gdisp_files: Gaussian files for displaced geometries.
default value = $(WORK_DIR)/gauss-disps
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 = 1e-7
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 analyze-vci 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 comma-separated list: 1-3,5,7-10. Tip: Use the "mode-numbering" 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 = 1-6
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*nAtoms-nIgnored).
default value = $(WORK_DIR)/nnmodes
non_funds: A file containing a list of non-fundamental 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 one-mode 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 bullet-proof 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.dipole-el.quadrupole derivatives transformed into normal modes. Same order as cedeqd1.
default value = $(WORK_DIR)/qedeqd1
qedeqd2: Second-order el.dip.-el.quadrupole derivatives. The order corresponds cedeqd1 and qpolard2.
default value = $(WORK_DIR)/qedeqd2
qedmdd1: El.dipole-mg.dipole derivatives transformed into normal modes. Same order as cedmdd1.
default value = $(WORK_DIR)/qedmdd1
qedmdd2: Second-order 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 anharm-potential.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 anharm-potential.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 anharm-potential.c.
default value = $(WORK_DIR)/qff4
qff4b: The same as qff4, but with the off-diagonal 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: Second-order 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 mass-weighted. 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 = 1e-3
treat_degeneracy: 0 .. do not treat, 1 .. simplified approach. (See treat-pt-degeneracy.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> .. <exc-vci_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 non-freezed 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 <f|W|a> 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 = 1e-6
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_nbase-1 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 = 1e-6
vscf_maxiter: Maximal count of VSCF iterations. (Set 0 for unlimited.)
default value = 50
vscf_nbase: A VSCF function is a N-dimensional product function of N one-dimensional 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