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<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>
<hr>
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Updated: February 22, 2005
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