Keywords: user

Next: 38. Acknowledgments Up: user Previous: 36. Controlling NWChem with Contents
Subsections

- 37.1 `NBO` -- Natural Bond Orbital Analysis
- 37.2 `DIRDYVTST` -- DIRect Dynamics for Variational Transition State Theory
  - 37.2.1 Introduction
  - 37.2.2 Files
  - 37.2.3 Detailed description of the input
    - 37.2.3.1 Use of symmetry
    - 37.2.3.2 Basis specification
    - 37.2.3.3 Effective core potentials
    - 37.2.3.4 General input strings
    - 37.2.3.5 POLYRATE related options
      - 37.2.3.5.1 GENERAL section
      - 37.2.3.5.2 REACT1, REACT2, PROD1, PROD2, and START sections
      - 37.2.3.5.3 PATH section
    - 37.2.3.6 Restart
    - 37.2.3.7 Example

# 37. Interfaces to Other Programs

NWChem has interfaces to several different packages which are listed below. In general, the NWChem authors work with the authors of the other packages to make sure that the interface works. However, any problems with the interface should be reported to the `nwchem-users@emsl.pnl.gov` e-mail list.

#
37.1 `NBO` -- Natural Bond Orbital Analysis

      NBO
        ...
      END

This directive is used to run the NBO package within NWChem. (To only print out an input file for NBO, see Section 28.1.1.) The current version of NBO in NWChem is version 5.0.

Inside the NBO block are the typical commands that would be needed for NBO (Please see an NBO user's manual for more information.). The following directive is needed to execute NBO.

    task nbo

As an example:

    title "Methylamine...rhf/3-21g//Pople-Gordon standard geometry"

    start methylamine

    echo

    memory 8 mw

    basis
     C library 3-21g
     N library 3-21g
     H library 3-21g
    end

    geometry
     C            .052902     .711852     .000000
     N            .052902    -.758148     .000000
     H           -.974760    1.075185     .000000
     H            .566733    1.075185     .889981
     H            .566733    1.075185    -.889981
     H           -.423217   -1.094815     .824662
     H           -.423217   -1.094815    -.824662
     symmetry c1
    end

    task SCF energy

    nbo
     $nbo cmo $end
    end

    task nbo

#
37.2 `DIRDYVTST` -- DIRect Dynamics for Variational Transition State Theory

by Bruce C. Garrett,
Environmental Molecular Sciences Laboratory,
Pacific Northwest Laboratory, Richland, Washington
Yao-Yuan Chuang and Donald G. Truhlar,
Department of Chemistry and Super Computer Institute,
University of Minnesota, MN 55455-0431
and interfaced to NWChem by
Ricky A. Kendall,
Scalable Computing Laboratory,
Ames Laboratory and Iowa State University, Ames, IA 50011
Theresa L. Windus,
Environmental Molecular Sciences Laboratory,
Pacific Northwest Laboratory, Richland, Washington

If you use the DIRDYVTST portion of NWChem, please use following citation in addition to the usual NWChem citation from Section 1:

> DIRDYVTST, Yao-Yuan Chuang and Donald G. Truhlar, Department of Chemistry and Super Computer Institute, University of Minnesota; Ricky A. Kendall,Scalable Computing Laboratory, Ames Laboratory and Iowa State University; Bruce C. Garrett and Theresa L. Windus, Environmental Molecular Sciences Laboratory, Pacific Northwest Laboratory.

## 37.2.1 Introduction

By using DIRDYVTST, a user can carry out electronic structure calculations with NWChem and use the resulting energies, gradients, and Hessians for direct dynamics calculations with POLYRATE. This program prepares the file30 input for POLYRATE from NWChem electronic structure calculations of energies, gradients and Hessians at the reactant, product, and saddle point geometries and along the minimum energy path. Cartesian geometries for the reactants, products, and saddle points need to be input to this program; optimization of geometries is not performed in this program. Note that `DIRDYVTST` is based on the DIRDYGAUSS program and is similar to two other programs: DDUTILITIES and GAUSSRATE. Users of this module are encouraged to read the POLYRATE manual since they will need to create the file fu5 input to run calculations with POLYRATE.

Notes about the code:

Input. The code has been written to parallel, as much as possible, the `POLYRATE` code.

Output. There is one default output file for each `DIRDYVTST` run - .file30.

Integrators for following the reaction path. Currently the Euler and three Page-McIver (PM) methods are implemented. The PM methods are the local quadratic approximation (LQA), the corrected LQA (CLQA), and the cubic (CUBE) algorithm. The PM methods are implemented so that the Hessian can be reused at intermediate steps at which only the gradient is updated.

## 37.2.2 Files

Test runs are located in directories in `$NWCHEM_TOP/QA/tests`. Test runs are available for two systems: and .

The test uses the Euler integration method at the SCF/3-21G level of theory to calculate points along the reaction path. This test is located in the `$NWCHEM_TOP/QA/tests/h3tr1` directory.

The test uses the Page-McIver CUBE algorithm to calculate points on the SCF/3-21G surface and does additional single point calculations at the SCF/6-31G* level of theory. This test is located in the `$NWCHEM_TOP/QA/tests/oh3tr3` directory.

Note: These tests are set up with SCF, however, other levels of theory can be used. The initial hessian calculations at the reactants, products and saddle point can cause some problems when numerical hessians are required (especially when there is symmetry breaking in the wavefunction).

## 37.2.3 Detailed description of the input

The input consists of keywords for NWChem and keywords related to `POLYRATE` input. The first set of inputs are for NWChem with the general input block of the form:

      DIRDYVTST [autosym [real tol default 1d-2] | noautosym]
        [THEORY <string theory> [basis <string basis default "ao basis">] \
                             [ecp <string ecp>] [input <string input>]]
        [SPTHEORY <string theory> [basis <string basis default "ao basis">] \
                             [ecp <string ecp>] [input <string input>]]
        ...
      END

### 37.2.3.1 Use of symmetry

The use of symmetry in the calculation is controlled by the keyword `autosym | noautosym` which is used as described in the geometry directive (see Section 6). `Autosym` is on by default. A couple words of warning here. The tolerance related to `autosym` can cause problems when taking the initial step off of the transition state. If the tolerance is too large and the initial step relatively small, the resulting geometry will be close to a higher symmetry than is really wanted and the molecule will be symmetrized into the higher symmetry. To check this, the code prints out the symmetry at each geometry along the path. It is up to the user to check the symmetry and make sure that it is the required one. In preverse cases, the user may need to turn `autosym` off (`noautosym`) if changing the tolerance doesn't produce the desired results. In the case that autosym is used, the user does not need to worry about the different alignment of the molecule between NWChem and POLYRATE, this is taken care of internally in the DIRDYVTST module.

### 37.2.3.2 Basis specification

The basis name on the theory or sptheory directive is that specified on a basis set directive (see Section 7) and not the name of a standard basis in the library. If not specified, the basis set for the sptheory defaults to the theory basis which defaults to `"ao basis"`.

### 37.2.3.3 Effective core potentials

If an effective core potential is specified in the usual fashion (see Section 8) outside of the `DIRDYVTST` input then this will be used in all calculations. If an alternative ECP name (the name specified on the ECP directive in the same manner as done for basis sets) is specified on one of the theory directives, then this ECP will be used in preference for that level of theory.

### 37.2.3.4 General input strings

For many purposes, the ability to specify the theory, basis and effective core potential is adequate. All of the options for each theory are determined from their independent input blocks. However, if the same theory (e.g., DFT) is to be used with different options for theory and sptheory, then the general input strings must be used. These strings are processed as NWChem input each time the theoretical calculation is invoked. The strings may contain any NWChem input, except for options pertaining to `DIRDYVTST` and the task directive. The intent is that the strings be used just to control the options pertaining to the theory being used.

A word of caution. Be sure to check that the options are producing the desired results. Since the NWChem database is persistent, the input strings should fully define the calculation you wish to have happen.

For instance, if the theory model is DFT/LDA/3-21g and the sptheory model is DFT/B3LYP/6-311g**, the `DIRDYVTST` input might look like this

        dirdyvtst
          theory  dft basis 3-21g    input "dft\; xc\; end"
          sptheory dft basis 6-311g** input "dft\; xc b3lyp\; end"
          ....
        end

The empty `XC` directive restores the default LDA exchange-correlation option (see Section 11.3). Note that semi-colons and other quotation marks inside the input string must be preceded by a backslash to avoid special interpretation.

### 37.2.3.5 POLYRATE related options

These keyword options are simlar to the `POLYRATE` input format, except there are no ENERGETICS, OPTIMIZATION, SECOND, TUNNELING, and RATE sections.

#### 37.2.3.5.1 GENERAL section

The GENERAL section has the following format:

    *GENERAL
      [TITLE <string title>]
      ATOMS
        <integer num> <string tag> [<real mass>]
        ...
      END
      [SINGLEPOINT]
      [SAVEFILE (vecs || hess || spc)

Descriptions

TITLE is a keyword that allows the user to input a description of the calculation. In this version, the user can only have a single-line description.

For example: TITLE Calculation of D + HCl reaction

ATOMS is a list keyword that is used to input a list of the atoms. It is similar to `POLYRATE` in that the order of the atom and the atomic symbol are required in a single line. If isotope of the element is considered then the atomic mass is required in units of amu.

For example:

                              ATOMS
                                1     H     2.014
                                2     H
                                3     Cl
                              END

SINGLEPOINT is a keyword that specifies that a single point calculation is to be performed at the reactants, products and saddle point geometries. The type of single point calculation is specified in the `sptheory` line.

SAVEFILE is a keyword that specifies that NWChem files are to be saved. Allowed values of variable input to SAVEFILE are vecs, hess, and spc for saving the files base theory movecs, base theory hessian and singlepoint calculation movecs.

#### 37.2.3.5.2 REACT1, REACT2, PROD1, PROD2, and START sections

These sections have the following format:

    *(REACT1 || REACT2 || PROD1 || PROD2 || START)
      GEOM
        <integer num> <real x y z>
        ...
      END
      SPECIES (ATOMIC || LINRP || NONLINRP || LINTS || NONLINTS default NONLINRP)

REACT1 and REACT2 are input for each of the reactants and PROD1 and PROD2 are input for each of the products. REACT1 and PROD1 are required. START is the input for the transition state if one exists, or starting point to follow downhill the MEP.

Descriptions

GEOM is a list keyword that indicates the geometry of the molecule in Cartesian coordinates with atomic unit.

For example:

                              GEOM
                                 1      0.0     0.0     0.0
                                 2      0.0     0.0     1.5
                              END

SPECIES is a variable keyword that indicates the type of the molecule. Options are: ATOMIC (atomic reactant or product), LINRP (linear reactant or product), NONLINRP (nonlinear reactant or product), LINTS (linear transition state), and NONLINTS (nonlinear transition state).

For example: SPECIES atomic

#### 37.2.3.5.3 PATH section

The Path section has the format:

    *PATH
      [SCALEMASS <real scalemass default 1.0>]
      [SSTEP <real sstep default 0.01>]
      [SSAVE <real ssave default 0.1>]
      [SHESS <real shess default SSAVE>]
      [SLP <real slp default 1.0>]
      [SLM <real slm default -1.0>]
      [SIGN (REACTANT || PRODUCT default REACTANT)]
      [INTEGRA (EULER || LQA || CLQA || CUBE default EULER)]
      [PRINTFREQ (on || off default off)]

Descriptions

SCALEMASS is a variable keyword that indicates the arbitrary mass (in amu) used for mass-scaled Cartesian coordinates. This is the variable called mu in published papers. Normally, this is taken as either 1.0 amu or, for bimolecular reactions, as the reduced mass of relative translation of the reactants.

SSTEP is a variable keyword that indicates the numerical step size (in bohrs) for the gradient grid. This is the step size for following the minimum energy path.

SSAVE is a variable keyword that indicates the numerical step size (in bohrs) for saving the Hessian grid. At each save point the potential and its first and second derivatives are recalculated and written to the .file30 file. For example, if SSTEP=0.01 and SSAVE=0.1, then the potential information is written to .file30 every 10 steps along the gradient grid.

SHESS is a variable keyword that indicates the numerical step size (in bohrs) for recomputing the Hessian when using a Page-McIver integrator (e.g., LQA, CLQA, or CUBE). For Euler integration SHESS = SSAVE. For intermediate points along the gradient grid, the Hessian matrix from the last Hessian calculation is reused. For example, if SSTEP=0.01 and SHESS=0.05, then the Hessian matrix is recomputed every 5 steps along the gradient grid.

SLP is a variable keyword that indicates the positive limit of the reaction coordinate (in bohrs).

SLM is a variable keyword that indicates the negative limit of the reaction coordinate (in bohrs).

SIGN is a variable keyword used to ensure the conventional definition of the sign of s, for the reactant side and for the product side, is followed. `PRODUCT` should be used if the eigenvector at the saddle point points toward the product side and `REACTANT` if the eigenvector points toward the reactant side.

INTEGRA is a variable keyword that indicates the integration method used to follow the reaction path. Options are: EULER, LQA, CLQA, and CUBE.

PRINTFREQ is a variable keyword that indicates that projected frequencies and eigenvectors will be printed along the MEP.

### 37.2.3.6 Restart

`DIRDYVTST` calculations should be restarted through the normal NWChem mechanism (See Section 5.1). The user needs to change the `start` directive to a `restart` directive and get rid of any information that will overwrite important information in the RTDB. The `file.db` and `file.file30` need to be available for the calculation to restart properly.

### 37.2.3.7 Example

This is an example that creates the file30 file for POLYRATE for . Note that the multiplicity is that of the entire supermolecule, a doublet. In this example, the initial energies, gradients, and Hessians are calculated at the UHF/3-21G level of theory and the singlepoint calculations are calculated at the MP2/cc-pVDZ level of theory with a tighter convergence threshold than the first SCF.

    start h3test

    basis
     h library 3-21G
    end

    basis singlepoint
     h library cc-pVDZ
    end

    scf
       uhf
       doublet
       thresh 1.0e-6
    end

    dirdyvtst autosym 0.001
      theory scf input "scf; uhf; doublet; thresh 1.0e-06; end"
      sptheory mp2 basis singlepoint input \
        "scf; uhf; doublet; thresh 1.0e-07; end"
    *GENERAL
      TITLE
        Test run: H+H2 reaction, Page-McIver CLQA algorithm, no restart

      ATOMS
         1    H
         2    H
         3    H
      END

      SINGLEPOINT

    *REACT1
       GEOM
         1  0.0   0.0   0.0
         2  0.0   0.0   1.3886144
       END

       SPECIES LINRP

    *REACT2
      GEOM
        3    0.0   0.0 190.3612132
      END

      SPECIES  ATOMIC

    *PROD2
      GEOM
        1   0.0   0.0 190.3612132
      END

      SPECIES   ATOMIC

    *PROD1

      GEOM
        2  0.0   0.0   1.3886144
        3   0.0   0.0   0.0
      END

      SPECIES  LINRP

    *START

      GEOM
        1  0.0   0.0  -1.76531973
        2  0.0   0.0   0.0
        3  0.0   0.0   1.76531973
      END

      SPECIES  LINTS

    *PATH
      SSTEP  0.05
      SSAVE  0.05
      SLP    0.50
      SLM   -0.50
      SCALEMASS 0.6718993
      INTEGRA   CLQA
    end

    task dirdyvtst

Next: 38. Acknowledgments Up: user Previous: 36. Controlling NWChem with Contents