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<br><br>
<h1>NWChem FAQ</h1>

 <p><h2>Optimization Issues</h2></p>

<!--DO NOT REMOVE Begin Question and End Question Comments.-->
<ul>
<!--Begin Question-->
 	<li><a href="#0">I want to optimize the structure of my molecule. What should I try first?</a></li>
    <li><a href="#1">How do I accelerate a geometry optimization using information from a lower (cheaper) level of theory, and does this really help?</a></li>
    <li><a href="#2">When should I use STEPPER rather than DRIVER?</a></li>
    <li><a href="#3">AUTOZ fails to generate valid internal coordinates.  Now what?</a></li>
    <li><a href="#4">What initial guess is Driver using for the Hessian?</a></li>
    <li><a href="#5">My geometry optimization initially converged rapidly but now seems to be stuck.</a></li>
    <li><a href="#6">How do I keep some internal variables constant while optimizing the others?</a></li>
    <li><a href="#7">How do I constrain some internal variables to be the same value within a sign?</a></li>
    <li><a href="#8">How do I restart a geometry optimization?</a></li>
    <li><a href="#9">Can I use symmetry while optimizing the geometry?</a></li>
    <li><a href="#10">How do I adjust the value of (or change in any way) some internal coordinates in an existing geometry?</a></li>
    <li><a href="#11">How do I scan a potential energy surface?</a></li>
    <li><a href="#12">How do I find a transition state?</a></li>
<!--End Question-->
</ul>

   <hr>
   <p>
   <a name="0"></a>
   <font color="purple">I want to optimize the structure of my molecule.  What should I
       try first?
   </font>
   <p>
   The optimizer of first choice should be the default option of
       user-specified Cartesian coordinates and DRIVER using redundant
       internal coordinates (AUTOZ - automatic Z-matrix).  The example
       input optimizes the structure of H3C-COOH using 3-21g SCF.

   <pre>

            geometry
              c   -0.017    -0.030    -0.077
              c   -0.017    -0.030     1.422
              h    0.922    -0.030     1.764
              h   -0.487     0.783     1.764
              h   -0.487    -0.844     1.764
              o   -0.580    -1.005    -0.727
              o    0.545     0.944    -0.727
              h    0.545     0.944    -1.727
            end

            basis
              c library 3-21g; h library 3-21g; o library 3-21g
            end

            task scf optimize

   </pre>
   AUTOZ will generate a set of redundant internal coordinates
       for the optimization.  Under some circumstances AUTOZ will fail
       to generate a good set of coordinates, in which case Cartesians
       will be used.  If you specify the geometry with a Z-matrix then
       your coordinates will be used for the optimization.
   <p>
       Needless to say a good guess for the geometry is very important.
       If you don't have a good guess, then first optimize with an
       inexpensive level of theory to get a good guess.
   </p>

   <hr>
   <p>
   <a name="1"></a>
   <font color="purple">How do I accelerate a geometry optimization using information from
       a lower (cheaper) level of theory, and does this really help?
   </font>
   <p>
   It can help a lot and is especially worth doing for most large
       basis set calculations with correlated wavefunctions.
   <p>
       The geometry and Hessian information from a previous optimization
       are used by default --- if you saved them.  You should keep all
       of the files that NWChem puts into its permanent directory.
   <p>
   <ol>
   <li>Set the permanent directory to be somewhere permanent (sic).
          The default is the current directory, which for a batch job on the
          EMSL HP is /scratch.  If you plan on running both optimizations
          in the same input then you don't really need to do this, but if
          anything goes wrong you can only restart if you have saved the
          files.</li>
   <li>Run the first optimization with a low-level theory.
   <li>In the same job, or a subsequent one, specify the new
          wavefunction parameters and run the second optimization.  By
          default the calculation will restart from the previously
          converged geometry, but if you can estimate better values you
          can specify a new geometry (e.g., MP2 often predicts longer bond
          lengths than Hartree-Fock).
   </ol>
   <p>
       In the first example below, the geometry of H3C-COOH is first
       optimized using 3-21g SCF, and then, starting from the 3-21g SCF
       geometry and Hessian information, re-optimized with cc-pvdz MP2.
       The first optimization required 8 steps, taking 105s on a 360 MHz
       SUN Ultra-60.  The second optimization required 4 steps and 3882s.
       If the MP2 optimization is repeated starting again from the 3-21g
       SCF geometry, but not using the Hessian information then it takes 6
       steps and 4,900s.
   <p>
   <pre>

            permanent_dir /u/mydir

            geometry
              zmatrix
                c
                c 1 cc
                h 2 ch1 1 hcc1
                h 2 ch2 1 hcc2 3 t1
                h 2 ch3 1 hcc3 3 t2
                o 1 co1 2 occ1 3 t3
                o 1 co2 2 occ2 3 t4
                h 7 oh  1 hoc  6 t5
              variables
                cc     1.5;    ch1    1.0;    ch2     1.0
                ch3    1.0;    co1    1.3;    co2     1.3
                oh     1.0;    hcc1 110.0;    hcc2  110.0
                hcc3 110.0;    occ1 120.0;    occ2  120.0
                hoc  120.0;    t1   120.0;    t2   -120.0
                t3   120.0;    t4   -60.0;    t5      0.0
              end
            end

            basis
              c library 3-21g; h library 3-21g; o library 3-21g
            end

            scf; print low; end

            task scf optimize

            basis spherical
              c library cc-pvdz; h library cc-pvdz; o library cc-pvdz
            end

            mp2; freeze atomic; end

            task mp2 optimize

   </pre>
       This next example performs SCF geometry optimizations of the water
       dimer in a sequence of increasing basis sets.  Each calculation
       starts from the geometry and updated-Hessian from the previous one.
       The steps taken for each successive optimization are, 11, 6, 7, 9,
       4, 4, 4 and the total calculation took 966s.  If the Hessian
       information is not reused (but still using the previous geometry)
       the steps taken are 11, 11, 13, 13, 6, 11, 10, taking 2100s.
   <pre>

            driver; print low; end
            scf; print none; thresh 1e-6; end

            geometry autosym
               o     0.00000000     0.97541911     1.02217553
               h     0.75298271     0.97541911     1.58779814
               h    -0.75298271     0.97541911     1.58779814
               h     0.00000000    -0.44494805    -0.43332878
               o     0.00000000    -1.08950470    -1.12453116
               h     0.00000000    -0.59320543    -1.92342244
            end

            python
              basis = 'basis print spherical; o library %s; h library %s; end'
              for b in ('sto-3g','3-21g','6-31g','6-31g*','6-31g**',
                        '6-311g**','6-311G(2df,2pd)'):
                input_parse(basis % (b,b))
                task_optimize('scf')
            end

            task python

   </pre>
   </p>


   <hr>
   <p>
   <a name="2"></a>
   <font color="purple">When should I use STEPPER rather than DRIVER?
   </font>
   <p>
       In releases prior to 3.3, STEPPER was much more robust than DRIVER,
       especially for transition state searches, though when DRIVER did
       converge it was usually faster.  However, in release 3.3 DRIVER has
       been completely rewritten, AUTOZ has been extensively modified, and
       the diagonal guess for internal coordinates has also been
       substantially improved.  The net result is that if internal
       coordinates are available (AUTOZ or Z-matrix) then DRIVER is always
       preferable since STEPPER can only use Cartesians.  There is less
       data for the performance difference in Cartesians, but again DRIVER
       seems to have the edge, perhaps because it is less conservative and
       the use of a line search also enables it to take larger steps.
   <p>
       However, STEPPER was designed for stream-bed walking and has robust
       algorithms for following normal modes from a minimum up to
       transition states.  DRIVER can do this, but is not as robust.  So if
       you want to walk a long way along a mode, and are prepared to
       compute a full Hessian at the minimum geometry, then STEPPER is for
       you.
   </p>

   <hr>
   <p>
   <a name="3"></a>
   <font color="purple">AUTOZ fails to generate valid internal coordinates.  Now what?
   </font>
   <p>
       If AUTOZ fails, NWChem will default to using Cartesian coordinates
       (and ignore any zcoord data) so you don't have to do anything
       unless you really need to use internal coordinates. An exception are
       certain cases where we have a molecule that contains a linear chain
       of 4 or more atoms, in which case the code will fail (see item 2.
       for work arounds). For small
       systems you can easily construct a Z-matrix, but for larger systems
       this can be quite hard.
   <p>
       First check your input.  Are you using the correct units?  The
       default is Angstroms.  If you input atomic units but did not tell
       NWChem, then it's no wonder things are breaking.  Also, is the
       geometry physically sensible?  If atoms are too close to each other
       you'll get many unphysical bonds, whereas if they are too far
       apart AUTOZ will not be able to figure out how to connect things.
   <p>
       Once the obvious has been checked, there are several possible modes
       of failure, some of which may be worked around in the input.
   <ol>
   <li>Strictly linear molecules with 3 or more atoms.  AUTOZ does not
          generate linear bend coordinates, but, just as in a real
          Z-matrix, you can specify a dummy center that is not co-linear.
          There are two relevant tips:
     <ul>
     <li>constrain the dummy center to be not co-linear otherwise the
            center could become co-linear. Also, the inevitable small
            forces on the dummy center can confuse the optimizer.</li>
     <li>put the dummy center far enough away so that only one
            connection is generated.
     </ul>
   <pre>

          E.g., this input for acetylene will not use internals

          geometry
            h  0  0  0
            c  0  0  1
            c  0  0  2.2
            h  0  0  3.2
          end

          but this one will

          geometry
            zcoord
              bond    2 3  3.0  cx constant
              angle 1 2 3 90.0 hcx constant
            end
            h  0  0  0
            c  0  0  1
            x  3  0  1
            c  0  0  2.2
            h  0  0  3.2
          end

   </pre></li>
   <li>Larger molecules that contain a strictly linear chain of four or
          more atoms (that ends in a free atom). For these molecules the
          autoz will fail and the code can currently not recover by using
          cartesians. One has to explicitly define noautoz in the geometry
          input to make it work. If internal coordinates are required one
          can fix it in the same manner as described above. However, you can
          also force a connection to a real nearby atom.</li>
   <li>Very highly connected systems generate too many internal
          coordinates which can make optimization in redundant internals
          less efficient than in Cartesians.  For systems such as clusters
          of atoms or small molecules, try using a smaller value of the
          scaling factor for covalent radii
   <p>
          zcoord; cvr_scaling 0.9; end
   <p>
          In addition to this you can also try specifying a minimal set of
          bonds to connect the fragments.</li>
   </ol>
   <p>
          If these together don't work, then you're out of luck.  Use
          Cartesians or construct a Z-matrix.
   </p>

   <hr>
   <p>
   <a name="4"></a>
   <font color="purple">What initial guess is Driver using for the Hessian?
   </font>
   <p>
   <pre>

       If (restart file exists) then
         Attempt to use that data
       Endif

       If ((no restart file) or (could not use the file)) then
         If (requested use of Cartesian Hessian with INHESS=2) then
             Use the Hessian from a previous NWChem frequency calculation
         Else
           If ((you input a Z-matrix) or (input Cartesians with AUTOZ)) then
           .   Modified Fisher-Almlof rules are used to form a guess that is
           .   diagonal in the internal coordinate space.
           Else if (you input Cartesian coordinates) then
           .   0.5 * a unit matrix is used
           Endif
         Endif
       Endif

   </pre>
       Driver's restart information may be discarded by putting the CLEAR
       directive into the DRIVER input block, or by deleting the
       *.drv.hess file in the permanent directory.  Note that the CLEAR
       directive is not remembered, so that subsequent geometry
       optimizations will use restart info unless also preceded by a
       DRIVER input block with a CLEAR directive.
   <p>
       The restart filename expected by Driver is *.drv.hess, while the
       the filename when INHESS=2 is *.hess.
   </p>

   <hr>
   <p>
   <a name="5"></a>
   <font color="purple">My geometry optimization initially converged rapidly but now seems to
       be stuck.
   </font>
   <p>
   <ol>
   <li>One cause could be insufficient precision in the gradient.
          Sometimes higher precision than the default is necessary,
          especially if you have asked for tight convergence.  Also, if
          you are using DFT, or MP2 in a large diffuse basis, then the
          gradient itself may be not be sufficiently accurate by default.
          The precision in the gradient can be improved by
     <ol>
     <li> SCF ... simply decrease THRESH.  The default is 1d-4.  A value
            of 1d-6 should suffice. If you are asking for tight
            convergence, or in pathological cases such as strong linear
            dependence, then use 1d-8.</li>
     <li> DFT ... improve the resolution of the grid (try FINE or one of
            the Lebedev grids) and the convergence threshold for the
            density.  You can check if the grid resolution is adequate by
            looking at the value of the numerically integrated density.
            The error in this number is roughly the same magnitude as that
            in the gradients.  If this error is too large and you are
            already using a FINE or XFINE grid, try increasing the
            screening radius (e.g., TOLERANCES ACCQRAD 20).</li>
     <li> MP2 ... use the TIGHT keyword.  This tightens up thresholds in
            the SCF, CPHF and MP2.</li>
     </ol></li>
   <li>If the geometry has changed a lot and you are using AUTOZ the
          redundant internals generated at the initial geometry may no
          longer be appropriate.  Try restarting the optimization from the
          last good geometry generating new redundant variables using the
          directive REDOAUTOZ.</li>
   <li>Did you input your own Z-matrix or specify additional
          coordinates for AUTOZ?  If the variables don't correspond to
          standard molecular internal coordinates then the initial guess
          for the Hessian is not necessarily very good, and the actual
          Hessian may not be well conditioned.  You can switch from your
          own Z-matrix to redundant internals with this trick
   <pre>
          geometry
            zmatrix
              your z-matrix data
            end
          end

          geometry adjust    # Discards z-matrix and uses autoz
          end

   </pre></li>
   <li>Flat potential energy surfaces such as internal coordinates
          (e.g., some torsions) dominated by weak interactions, or floppy
          molecules/clusters are tough problems.  Try getting a better
          starting geometry and some more Hessian information by
          optimizing at the lowest acceptable level of theory before using
          more expensive models.</li>
   </ol>
   </p>

   <hr>
   <p>
   <a name="6"></a>
   <font color="purple">How do I keep some internal variables constant while optimizing
       the others?
   </font>
   <p>
   <ol>
   <li>
   If you are defining your own Z-matrix, then parameters specified
          in the constants section are frozen in any geometry optimization.
   <pre>

          E.g., water with the bond angle frozen

          geometry
            zmatrix
              o
              h 1 0.98
              h 1 0.98 2 hoh
            constants
              hoh 105.0
            end
          end

   </pre></li>
   <li>If you are using redundant internal coordinates then user
          defined internal coordinates flagged with the keyword constant
          are frozen during the optimization.  If no value is given for a
          user defined variable, then the value implicit in the Cartesian
          coordinates is used.  If a value is given, then it is imposed
          upon the Cartesian coordinates while attempting to make only
          minor changes in the other internal coordinates.
   <p>
          E.g., water with the bond angle frozen at the value defined
          by the Cartesian coordinates.
   <pre>

          geometry autosym
            zcoord; angle 3 1 2 constant; end
            O   0.000     0.0     0.119
            H   0.777     0.0    -0.477
            H  -0.777     0.0    -0.477
          end

   </pre>
          E.g., water with the bond angle held at 103 degrees.
   <pre>

          geometry autosym
            zcoord; angle 3 1 2 103.0 constant; end
            O   0.000     0.0     0.119
            H   0.777     0.0    -0.477
            H  -0.777     0.0    -0.477
          end

   </pre></li>
   </ol>
   </p>


   <hr>
   <p>
   <a name="7"></a>

   <font color="purple">How do I constrain some internal variables to be the same
       value within a sign?
   </font>
   <p>
       With either user-defined redundant internal coordinates, or a
       user-defined Z-matrix, variables with the same non-blank name are
       forced to have the same value even if they are not related by
       symmetry.  A sign may be optionally employed to orient torsion
       angles.
   <p>
       E.g. CH3-CF3 - related bonds, angles and torsions are forced to be
       equivalent.  Note the use of a sign on TOR1.
   <pre>

          geometry
            zmatrix
              C
              C 1 CC
              H 1 CH1 2 HCH1
              H 1 CH2 2 HCH2 3  TOR1
              H 1 CH2 2 HCH2 3 -TOR1
              F 2 CF1 1 CCF1 3  TOR3
              F 2 CF2 1 CCF2 6  FCH1  1
              F 2 CF2 1 CCF2 6  FCH2 -1
              variables
                CH1   1.08
                CH2   1.08
                CF1   1.37
                CF2   1.37
                HCH1  104.2
                HCH2  104.7
                CCF1  112.0
                CCF2  112.0
                TOR1  109.4
                FCH1  106.8
                FCH2  106.8
                CC    1.49
                TOR3  180.0
            end
          end

   </pre>
   </p>


   <hr>
   <p>
   <a name="8"></a>
   <font color="purple">How do I restart a geometry optimization?
   </font>
   <p>
       If you have saved the restart information that is kept in the
       permanent directory, then you can restart a calculation, as long as
       it did not crash while writing to the data base.
   <p>
       Following are two input files.  The first starts a geometry
       optimization for ammonia.  If this stops for nearly any reason such
       as it was interrupted, ran out of time or disk space, or exceeded
       the maximum number of iterations, then it may be restarted with the
       second job.
   <p>
       The key points are
   <ol>
   <li>The first job contains a START directive with a name for the
          calculation.</li>

   <li>All subsequent jobs should contain a RESTART directive with the
          same name for the calculation.</li>

   <li>All jobs must specify the same permanent directory.  The default
          permanent directory is the current directory.</li>

   <li>If you want to change anything in the restart job, just put the
          data before the task directive.  Otherwise, all options will be
          the same as in the original job.</li>
   </ol>
   <p>
       Job 1.
   <pre>

            start ammonia
            permanent_dir /u/myfiles

            geometry
              zmatrix
                n
                h 1 nh
                h 1 nh 2 hnh
                h 1 nh 2 hnh 3 hnh -1
              variables
                nh 1.
                hnh 115.
              end
            end

            basis
              n library 3-21g; h library 3-21g
            end

            task scf optimize

   </pre>
       Job 2.
   <pre>

            restart ammonia
            permanent_dir /u/myfiles

            task scf optimize

   </pre>
   </p>


   <hr>
   <p>
   <a name="9"></a>
   <font color="purple">Can I use symmetry while optimizing the geometry?
   </font>
   <p>
       Yes.
   <p>
       With Cartesian coordinates either
   <ul>
   <li>list all atoms in any orientation and use the AUTOSYM keyword for
       automatic detection of the point group, or </li>

   <li>list all, or just the unique, atoms in the standard NWChem
       orientation for the point group and specify the point group with
       the SYMMETRY directive. </li>
   </ul>
       If you are using a Z-matrix you can only use the AUTOSYM keyword.
   </p>

   <hr>
   <p>
   <a name="10"></a>
   <font color="purple">How do I adjust the value of (or change in any way) some internal
        coordinates in an existing geometry?
   </font>
   <p>
        NWChem provides the <tt>adjust</tt> keyword on the GEOMETRY directive
   <p>
        E.g., force the bond angle in an existing geometry for water to
        be 103.0 degrees.  Here, the initial geometry is input, but it could
        have come from any source, including a previous optimization.
   <pre>

        geometry
            O   0.000     0.0     0.119
            H   0.777     0.0    -0.477
            H  -0.777     0.0    -0.477
        end

        geometry adjust
            zcoord; angle 3 1 2 103.0 constant; end
        end

   </pre>
   </p>


   <hr>
   <p>
   <a name="11"></a>
   <font color="purple">How do I scan a potential energy surface?
   </font>
   <p>
        E.g., scanning the OH bond and HON bond angle in hydroxylamine in
        order to find a starting geometry for a transition state search.

   <ol>
   <li>You can do it manually:
   <pre>

           basis; n library 3-21g; h library 3-21g; o library 3-21g; end

           geometry # Hydroxylamine
             n  -0.239    -0.678   0.0
             o   0.237     0.710   0.0
             h  -0.579     1.226   0.0
             h   0.179    -1.084   0.822
             h   0.179    -1.084  -0.822
           end

           geometry adjust
             zcoord
               bond  3 2    1.2525 oh
               angle 3 2 1 84.3   hon constant
             end
           end
           task scf optimize

           geometry adjust
             zcoord
               bond  3 2    1.538 oh
               angle 3 2 1 65.3   hon constant
             end
           end
           task scf optimize

           geometry adjust
             zcoord
               bond  3 2    1.8235 oh
               angle 3 2 1 46.3   hon constant
             end
           end
           task scf optimize

   </pre></li>
   <li>Or, you can use a Python program.  The scan_input() procedure
           is defined in nwgeom.py and is documented there.
   <pre>

           basis; n library 3-21g; h library 3-21g; o library 3-21g; end

           geometry # Hydroxylamine
             n  -0.239    -0.678   0.0
             o   0.237     0.710   0.0
             h  -0.579     1.226   0.0
             h   0.179    -1.084   0.822
             h   0.179    -1.084  -0.822
           end

           python
             from nwgeom import *

             geom = '''
               geometry adjust
                 zcoord
                   bond  3 2 %f oh
                   angle 3 2 1 %f hon constant
                 end
               end
             '''

             results = scan_input(geom,
                                  [0.967, 103.3],
                                  [2.109,  26.96],
                                  3, 'scf', task_optimize)
           end

           task python

   </pre></li>
   </ol>
   </p>


   <hr>
   <p>
   <a name="12"></a>
   <font color="purple">How do I find a transition state?
   </font>
   <p>
        A fairly reliable approach is to
   <p>
   <ol>
   <li>Optimize the reactants and products</li>

   <li>Identify the key internal variables involved in the reaction</li>

   <li>Generate an initial guess for the saddle geometry by either
           guessing or scanning the coordinates.  Do a constrained
           minimization at this point to relax the geometry.</li>

   <li>From the relaxed initial guess, search for the saddle point
           using the default options (releasing unnecessary constraints).
           The default option is to take the first step uphill.  If this
           does not manage to locate the negative mode, then try taking
           the first step along one of the bonds being made/broken
           (using the DRIVER directive VARDIR).</li>
   </ol>
   <p>
        Steps 1) & 3) are covered elsewhere in the FAQ.  Step
        2) is your problem.  Step 4) is done as follows
   <p>
        E.g., find the transition state for CH3+HF <-> CH4 + F
        given a starting guess for the transition state.
   <pre>

          geometry autosym
             c    0.000   0.000  -1.220
             h    0.000   0.000   0.029
             h    1.063   0.000  -1.407
             h   -0.531  -0.921  -1.407
             h   -0.531   0.921  -1.407
             f    0.000   0.000   1.279
          end

          basis
            c library 3-21g; h library 3-21g; f library 3-21g
          end

          scf; doublet; uhf; thresh 1e-6; print none; end

          task scf saddle

   </pre>
          Note that it is often necessary to specify manually internal
          coordinates for the bonds being broken/made since the algorithms
          inside AUTOZ are optimized for geometries near minima.
   <p>
   Another useful tip is to tighten up the precision in the gradient, which
   can decrease the number of steps needed to reach the transition state.
          The precision in the gradient can be improved by
   <ul>
   <li>SCF ... simply decrease THRESH.  The default is 1d-4.  A value
            of 1d-6 should suffice. If you are asking for tight
            convergence, or in pathological cases such as strong linear
            dependence, then use 1d-8.</li>

   <li>DFT ... improve the resolution of the grid (try FINE or one of
            the Lebedev grids) and the convergence threshold for the
            density.  You can check if the grid resolution is adequate by
            looking at the value of the numerically integrated density.
            The error in this number is roughly the same magnitude as that
            in the gradients.  If this error is too large and you are
            already using a FINE or XFINE grid, try increasing the
            screening radius (e.g., TOLERANCES ACCQRAD 20).</li>

   <li>MP2 ... use the TIGHT keyword.  This tightens up thresholds in
            the SCF, CPHF and MP2.</li>
   </ul>
</p>
<p>
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Updated: February 22, 2005
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