# Release66:Properties

### From NWChem

(→Properties) |
(→Moldenfile) |
||

(14 intermediate revisions not shown) | |||

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* NMR indirect spin-spin coupling | * NMR indirect spin-spin coupling | ||

* Gshift | * Gshift | ||

- | * Response | + | * Response to electric and magnetic fields (static and dynamic) |

* Raman | * Raman | ||

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Most of the properties can be computed for Hartree-Fock (closed-shell RHF, open-shell ROHF, and open-shell UHF), and DFT (closed-shell and open-shell spin unrestricted) wavefunctions. The NMR hyperfine and indirect spin-spin coupling require a UHF or ODFT wave function. | Most of the properties can be computed for Hartree-Fock (closed-shell RHF, open-shell ROHF, and open-shell UHF), and DFT (closed-shell and open-shell spin unrestricted) wavefunctions. The NMR hyperfine and indirect spin-spin coupling require a UHF or ODFT wave function. | ||

+ | |||

+ | ==Vectors keyword== | ||

+ | |||

+ | VECTORS [ (<string input_movecs >)] | ||

+ | |||

+ | The VECTORS directive allows the user to specify the input molecular orbital vectors for the property calculation | ||

==Property keywords== | ==Property keywords== | ||

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SHIELDING [<integer> number_of_atoms <integer> atom_list] | SHIELDING [<integer> number_of_atoms <integer> atom_list] | ||

SPINSPIN [<integer> number_of_pairs <integer> pair_list] | SPINSPIN [<integer> number_of_pairs <integer> pair_list] | ||

+ | RESPONSE [<integer> response_order <real> frequency] | ||

ALL | ALL | ||

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com is the center of mass, coc is the center of charge, origin is (0.0, 0.0, 0.0) and arb is any arbitrary point which must be accompanied by the coordinated to be used. Currently the x, y, and z coordinates must be given in the same units as UNITS in [[Geometry|GEOMETRY]]. | com is the center of mass, coc is the center of charge, origin is (0.0, 0.0, 0.0) and arb is any arbitrary point which must be accompanied by the coordinated to be used. Currently the x, y, and z coordinates must be given in the same units as UNITS in [[Geometry|GEOMETRY]]. | ||

+ | === Response Calculations === | ||

Response calculations can be calculated as follows: | Response calculations can be calculated as follows: | ||

property | property | ||

- | response 1 7.73178E-2 # response order and frequency in | + | response 1 7.73178E-2 # response order and frequency in Hartree energy units |

velocity # use modified velocity gauge for electric dipole | velocity # use modified velocity gauge for electric dipole | ||

orbeta # calculate optical rotation 'beta' directly [2] | orbeta # calculate optical rotation 'beta' directly [2] | ||

Line 85: | Line 93: | ||

Response calculations are currently supported only for order 1 (linear response), single frequency, electric field and mixed electric-magnetic field perturbations. The output consists of the electric polarizability and optical rotation tensors (alpha, beta for optical rotation) in atomic units. If the 'velocity' or 'giao' keywords are absent, the dipole-length form will be used for the dipole integrals. This is a bit faster. The isotropic optical rotation is origin independent when using the velocity gauge or with GIAOs [1]. With the keyword 'bdtensor', a fully origin-invariant optical rotation tensor is calculated [1,6]. Note that 'velocity' and 'orbeta' are incompatible. An input line 'set prop:newaoresp 0' outside of the 'properties' block forces the use of an older version of the response code, which has fewer features (in particular, no working GIAO opetical rotation) | Response calculations are currently supported only for order 1 (linear response), single frequency, electric field and mixed electric-magnetic field perturbations. The output consists of the electric polarizability and optical rotation tensors (alpha, beta for optical rotation) in atomic units. If the 'velocity' or 'giao' keywords are absent, the dipole-length form will be used for the dipole integrals. This is a bit faster. The isotropic optical rotation is origin independent when using the velocity gauge or with GIAOs [1]. With the keyword 'bdtensor', a fully origin-invariant optical rotation tensor is calculated [1,6]. Note that 'velocity' and 'orbeta' are incompatible. An input line 'set prop:newaoresp 0' outside of the 'properties' block forces the use of an older version of the response code, which has fewer features (in particular, no working GIAO opetical rotation) | ||

- | but which has been tested more thoroughly. In the default newer version you may encounter undocumented features (bugs). 'analysis' triggers an analysis of the response tensors in terms of molecular orbitals. If the property input block also contains the keyword 'pmlocalization', then the analysis is performed in terms of Pipek-Mezey localized MOs, otherwise the canonical set is used (this feature | + | but which has been tested more thoroughly. In the default newer version you may encounter undocumented features (bugs). 'analysis' triggers an analysis of the response tensors in terms of molecular orbitals. If the property input block also contains the keyword 'pmlocalization', then the analysis is performed in terms of Pipek-Mezey localized MOs, otherwise the canonical set is used (this feature may currently not work, please check the sum of the analysis carefully). See Ref. [6] for an example. |

Works with HF and density functionals for which linear response kernels are implemented in NWChem. | Works with HF and density functionals for which linear response kernels are implemented in NWChem. | ||

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[ LAST < integer last default ‘number of normal modes’ > ] | [ LAST < integer last default ‘number of normal modes’ > ] | ||

[ WIDTH <double width default 20.0> ] | [ WIDTH <double width default 20.0> ] | ||

- | [ DQ | + | [ DQ <double dq default 0.01> ] |

END | END | ||

task dft raman | task dft raman | ||

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end | end | ||

+ | ====Raman Keywords==== | ||

+ | * NORMAL and RESONANCE: Type of Raman plot to make. | ||

+ | * LORENTZIAN and GAUSSIAN: Generation of smoothed spectra (rather than sticks) using either a Lorentzian function or a Gaussian function. The default is LORENTZIAN. | ||

+ | * LOW and HIGH: The default range in which to generate the Raman spectrum plot is (0.0, highest wavenumber normal mode) cm-1. The LOW and HIGH keywords modify the frequency range. | ||

+ | * FIRST and LAST: The default range of indices of normal modes used in the plot is (7, number of normal modes). The FIRST and LAST keywords modify the range of indices. | ||

+ | * WIDTH:Controls the width in the smoothed peaks, using Lorentzians or Gaussians, in the plot. The default value for WIDTH is 20.0. | ||

+ | * DQ: Size of the steps along the normal modes. The default value for DQ is 0.01. It is related to the step size dR used in numerical evaluation of polarizability derivative | ||

+ | |||

+ | ====Raman Output==== | ||

+ | Raman spectrum in stick format and smoothed using Lorentzians or Gaussians stored in a filename with format [fname].normal. | ||

+ | |||

+ | ====Raman References==== | ||

Please refer to the following papers for further details: | Please refer to the following papers for further details: | ||

- | # J. M. Mullin, J. Autschbach, G. C. Schatz, Computational and Theoretical Chemistry | + | # J. M. Mullin, J. Autschbach, G. C. Schatz, Computational and Theoretical Chemistry 987, 32 (2012). DOI: 10.1016/j.comptc.2011.08.027. |

- | # F. W. Aquino and G. C. Schatz, The Journal of Physical Chemistry A | + | # F. W. Aquino and G. C. Schatz, The Journal of Physical Chemistry A 118 , 517 (2014). DOI: 10.1021/jp411039m |

===Nbofile=== | ===Nbofile=== | ||

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start nacl | start nacl | ||

- | + | ||

- | + | ||

- | + | ||

- | + | ||

- | + | ||

geometry nocenter noautoz noautosym | geometry nocenter noautoz noautosym | ||

Na -0.00000000 0.00000000 -0.70428494 | Na -0.00000000 0.00000000 -0.70428494 | ||

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task dft property | task dft property | ||

+ | |||

+ | ==Moldenfile== | ||

+ | |||

+ | MOLDENFILE | ||

+ | [MOLDEN_NORM (JANPA | | NWCHEM)] | ||

+ | |||

+ | This keyword generates files using the [http://www.cmbi.ru.nl/molden/molden_format.html Molden format]. The resulting Molden file (.molden) should compatible with a variety of codes that can input Molden files, e.g. | ||

+ | * [http://www.cmbi.ru.nl/molden/ Molden] | ||

+ | * [http://janpa.sf.net JANPA] (the nwchem2molden step is no longer required when using .molden files and the <tt>MOLDEN_NORM JANPA</tt> keyword) | ||

+ | * [http://orbkit.github.io/ orbkit] | ||

+ | * [http://github.com/Konjkov/molden2qmc Molden2qmc] | ||

+ | * [http://zorkzou.github.io/Molden2AIM Molden2AIM] | ||

+ | |||

+ | The <tt>MOLDEN_NORM</tt> allows the renormalization of the basis set coefficients. By default, the coefficient values from input are not modified. Using the <tt> JANPA</tt> value coefficients are normalized following [https://sourceforge.net/p/janpa/wiki/nwchem2molden/ JANPA]'s convention, while the <tt>NWCHEM</tt> will produce coefficients normalized according to NWChem's convention. | ||

+ | |||

+ | Example input file for a scf calculation. The resulting Molden file will be named <tt>h2o.molden</tt> | ||

+ | |||

+ | start heat | ||

+ | |||

+ | geometry; he 0. 0. 0.; end | ||

+ | |||

+ | basis; * library 6-31g;end | ||

+ | |||

+ | task scf | ||

+ | |||

+ | property | ||

+ | vectors heat.movecs | ||

+ | moldenfile | ||

+ | molden_norm janpa | ||

+ | end | ||

+ | |||

+ | task scf property |

## Revision as of 12:40, 13 September 2017

## Contents |

# Properties

Properties can be calculated for both the Hartree-Fock and DFT wave functions. The properties that are available are:

- Natural bond analysis
- Dipole, quadrupole, and octupole moment
- Mulliken population analysis and bond order analysis
- Electrostatic potential (diamagnetic shielding) at nuclei
- Electric field and field gradient at nuclei
- Electric field gradients with relativistic effects
- Electron and spin density at nuclei
- NMR shielding (GIAO method)
- NMR hyperfine coupling (Fermi-Contact and Spin-Dipole expectation values)
- NMR indirect spin-spin coupling
- Gshift
- Response to electric and magnetic fields (static and dynamic)
- Raman

The properties module is started when the task directive TASK <theory> property is defined in the user input file. The input format has the form:

PROPERTY [property keyword] [CENTER ((com || coc || origin || arb <real x y z>) default coc)] END

Most of the properties can be computed for Hartree-Fock (closed-shell RHF, open-shell ROHF, and open-shell UHF), and DFT (closed-shell and open-shell spin unrestricted) wavefunctions. The NMR hyperfine and indirect spin-spin coupling require a UHF or ODFT wave function.

## Vectors keyword

VECTORS [ (<string input_movecs >)]

The VECTORS directive allows the user to specify the input molecular orbital vectors for the property calculation

## Property keywords

Each property can be requested by defining one of the following keywords:

NBOFILE DIPOLE QUADRUPOLE OCTUPOLE MULLIKEN ESP EFIELD EFIELDGRAD EFIELDGRADZ4 GSHIFT ELECTRONDENSITY HYPERFINE [<integer> number_of_atoms <integer> atom_list] SHIELDING [<integer> number_of_atoms <integer> atom_list] SPINSPIN [<integer> number_of_pairs <integer> pair_list] RESPONSE [<integer> response_order <real> frequency] ALL

The "ALL" keyword generates all currently available properties.

### NMR and EPR

Both the NMR shielding and spin-spin coupling have additional optional parameters that can be defined in the input. For the shielding the user can define the number of atoms for which the shielding tensor should be calculated, followed by the list of specific atom centers. In the case of spin-spin coupling the number of atom pairs, followed by the atom pairs, can be defined (i.e., spinspin 1 1 2 will calculate the coupling for one pair, and the coupling will be between atoms 1 and 2).

For both the NMR spin-spin and hyperfine coupling the isotope that has the highest abundance and has spin, will be chosen for each atom under consideration.

**Calculating EPR and paramagnetic NMR parameters:**
The following tutorial illustrates how to combine the hyperfine, gshift and shielding to calculate the EPR and paramagnetic NMR parameters of an open-shell system.

For theoretical and computational details, please refer to the following references:

- J. Autschbach, S. Patchkovskii, B. Pritchard, "Calculation of Hyperfine Tensors and Paramagnetic NMR Shifts Using the Relativistic Zeroth-Order Regular Approximation and Density Functional Theory", Journal of Chemical Theory and Computation 7, 2175 (2011)
- F. Aquino, B. Pritchard, J. Autschbach, "Scalar relativistic computations and localized orbital analysis of nuclear hyperfine coupling and paramagnetic NMR chemical shifts", J. Chem. Theory Comput. 2012, 8, 598–609.
- F. Aquino, N. Govind, J. Autschbach, "Scalar relativistic computations of nuclear magnetic shielding and g-shifts with the zeroth-order regular approximation and range-separated hybrid density functionals", J. Chem. Theory Comput. 2011, 7, 3278–3292.

The user also has the option to choose the center of expansion for the dipole, quadrupole, and octupole calculations.

[CENTER ((com || coc || origin || arb <real x y z>) default coc)]

com is the center of mass, coc is the center of charge, origin is (0.0, 0.0, 0.0) and arb is any arbitrary point which must be accompanied by the coordinated to be used. Currently the x, y, and z coordinates must be given in the same units as UNITS in GEOMETRY.

### Response Calculations

Response calculations can be calculated as follows:

property response 1 7.73178E-2 # response order and frequency in Hartree energy units velocity # use modified velocity gauge for electric dipole orbeta # calculate optical rotation 'beta' directly [2] giao # GIAO optical rotation [1,3,6], forces orbeta bdtensor # calculates B-tilde of Refs. [1,6] analysis # analyze response in terms of MOs [6] damping 0.007 # complex response functions with damping, Ref [5] convergence 1e-4 # set CPKS convergence criterion (default 1e-4) end

Response calculations are currently supported only for order 1 (linear response), single frequency, electric field and mixed electric-magnetic field perturbations. The output consists of the electric polarizability and optical rotation tensors (alpha, beta for optical rotation) in atomic units. If the 'velocity' or 'giao' keywords are absent, the dipole-length form will be used for the dipole integrals. This is a bit faster. The isotropic optical rotation is origin independent when using the velocity gauge or with GIAOs [1]. With the keyword 'bdtensor', a fully origin-invariant optical rotation tensor is calculated [1,6]. Note that 'velocity' and 'orbeta' are incompatible. An input line 'set prop:newaoresp 0' outside of the 'properties' block forces the use of an older version of the response code, which has fewer features (in particular, no working GIAO opetical rotation) but which has been tested more thoroughly. In the default newer version you may encounter undocumented features (bugs). 'analysis' triggers an analysis of the response tensors in terms of molecular orbitals. If the property input block also contains the keyword 'pmlocalization', then the analysis is performed in terms of Pipek-Mezey localized MOs, otherwise the canonical set is used (this feature may currently not work, please check the sum of the analysis carefully). See Ref. [6] for an example. Works with HF and density functionals for which linear response kernels are implemented in NWChem.

Please refer to the following papers for further details:

- J. Autschbach, ChemPhysChem 12 (2011), 3224-3235
- J. Autschbach, Comp. Lett. 3, (2007), 131
- M. Krykunov, J. Autschbach, J. Chem. Phys. 123 (2005), 114103
- J.R. Hammond, N. Govind, K. Kowalski, J. Autschbach, S.S. Xantheas, J. Chem. Phys. 131 (2009), 214103
- M. Krykunov, M. D. Kundrat, J. Autschbach, J. Chem. Phys. 125 (2006), 194110
- B. Moore II, M. Srebro, J. Autschbach, J. Chem. Theory Comput. 8 (2012), 4336-4346

### Raman

Raman calculations can be performed by specifying the Raman block. These calculations are performed in conjunction with polarizability calculations. Detailed description of input parameters at http://pubs.acs.org/doi/suppl/10.1021/jp411039m

RAMAN [ (NORMAL | | RESONANCE) default NORMAL ] [ (LORENTZIAN | | GAUSSIAN) default LORENTZIAN ] [ LOW <double low default 0.0> ] [ HIGH <double high default ‘highest normal mode’> ] [ FIRST <integer first default ‘7’> ] [ LAST < integer last default ‘number of normal modes’ > ] [ WIDTH <double width default 20.0> ] [ DQ <double dq default 0.01> ] END task dft raman

or

task dft raman numerical

Sample input block:

property response 1 8.8559E-2 damping 0.007 end raman normal lorentzian end

#### Raman Keywords

- NORMAL and RESONANCE: Type of Raman plot to make.
- LORENTZIAN and GAUSSIAN: Generation of smoothed spectra (rather than sticks) using either a Lorentzian function or a Gaussian function. The default is LORENTZIAN.
- LOW and HIGH: The default range in which to generate the Raman spectrum plot is (0.0, highest wavenumber normal mode) cm-1. The LOW and HIGH keywords modify the frequency range.
- FIRST and LAST: The default range of indices of normal modes used in the plot is (7, number of normal modes). The FIRST and LAST keywords modify the range of indices.
- WIDTH:Controls the width in the smoothed peaks, using Lorentzians or Gaussians, in the plot. The default value for WIDTH is 20.0.
- DQ: Size of the steps along the normal modes. The default value for DQ is 0.01. It is related to the step size dR used in numerical evaluation of polarizability derivative

#### Raman Output

Raman spectrum in stick format and smoothed using Lorentzians or Gaussians stored in a filename with format [fname].normal.

#### Raman References

Please refer to the following papers for further details:

- J. M. Mullin, J. Autschbach, G. C. Schatz, Computational and Theoretical Chemistry 987, 32 (2012). DOI: 10.1016/j.comptc.2011.08.027.
- F. W. Aquino and G. C. Schatz, The Journal of Physical Chemistry A 118 , 517 (2014). DOI: 10.1021/jp411039m

### Nbofile

The keyword NBOFILE does not execute the Natural Bond Analysis code, but simply creates an input file to be used as input to the stand-alone NBO code. All other properties are calculated upon request.

Following the successful completion of an electronic structure calculation, a Natural Bond Orbital (NBO) analysis may be carried out by providing the keyword NBOFILE in the PROPERTY directive. NWChem will query the rtdb and construct an ASCII file, <file_prefix>.gen, that may be used as input to the stand alone version of the NBO program, gennbo. <file_prefix> is equal to string following the START directive. The input deck may be edited to provide additional options to the NBO calculation, (see the NBO user's manual for details.)

Users that have their own NBO version can compile and link the code into the NWChem software. See the INSTALL file in the source for details.

## Gaussian Cube Files

Electrostatic potential (keyword *esp*) and the magnitude of the electric field (keyword *efield*) on the grid can be generated in the form of the Gaussian Cube File. This behavior is triggered by the inclusion of
grid keyword as shown below

grid [pad dx [dy dz]] [rmax x y z] [rmin x y z] [ngrid nx [ny nz]] [output filename]

where

- pad dx [dy dz] - specifies amount of padding (in angstroms) in x,y, and z dimensions that will be applied in the automatic construction of the rectangular grid volume based on the geometry of the system. If only one number is provided then the same amount of padding will be applied in all dimensions. The default setting is 4 angstrom padding in all dimensions.

- rmin x y z - specifies the coordinates (in angstroms) of the minimum corner of the rectangular grid volume. This will override any padding in this direction.

- rmax x y z - specifies the coordinates (in angstroms) of the maximum corner of the rectangular grid volume. This will override any padding in this direction.

- ngrid nx [ny nz] - specifies number of grid points along each dimension. If only one number is provided then the same number of grid points are assumed all dimensions. In the absence of this directive the number of grid points would be computed such that grid spacing will be close to 0.2 angstrom, but not exceeding 50 grid points in either dimension.

- output filename - specifies name of the output cube file. The default behavior is to use <prefix>-elp.cube or <prefix>-elf.cube file names for electrostatic potential or electric field respectively. Here <prefix> denotes the system name as specified in start directive. Note that Gaussian cube files will be written in the run directory (where the input file resides).

Example input file

echo start nacl geometry nocenter noautoz noautosym Na -0.00000000 0.00000000 -0.70428494 Cl 0.00000000 -0.00000000 1.70428494 end basis * library 6-31g* end #electric field would be written out to nacl.elf.cube file #with #ngrid : 20 20 20 #rmax : 4.000 4.000 5.704 #rmin :-4.000 -4.000 -4.704 property efield grid pad 4.0 ngrid 20 end task dft property #electrostatic potential would be written to esp-pad.cube file # with the same parameters as above property esp grid pad 4.0 ngrid 20 output esp-pad.cube end task dft property #illustrating explicit specification of minumum box coordinates property esp grid pad 4.0 rmax 4.000 4.000 5.704 ngrid 20 end task dft property

## Moldenfile

MOLDENFILE [MOLDEN_NORM (JANPA | | NWCHEM)]

This keyword generates files using the Molden format. The resulting Molden file (.molden) should compatible with a variety of codes that can input Molden files, e.g.

- Molden
- JANPA (the nwchem2molden step is no longer required when using .molden files and the
`MOLDEN_NORM JANPA`keyword) - orbkit
- Molden2qmc
- Molden2AIM

The `MOLDEN_NORM` allows the renormalization of the basis set coefficients. By default, the coefficient values from input are not modified. Using the ` JANPA` value coefficients are normalized following JANPA's convention, while the `NWCHEM` will produce coefficients normalized according to NWChem's convention.

Example input file for a scf calculation. The resulting Molden file will be named `h2o.molden`

start heat geometry; he 0. 0. 0.; end basis; * library 6-31g;end task scf property vectors heat.movecs moldenfile molden_norm janpa end task scf property