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NWChem FAQ
Optimization Issues
- I want to optimize the structure of my molecule. What should I try first?
- How do I accelerate a geometry optimization using information from a lower (cheaper) level of theory, and does this really help?
- When should I use STEPPER rather than DRIVER?
- AUTOZ fails to generate valid internal coordinates. Now what?
- What initial guess is Driver using for the Hessian?
- My geometry optimization initially converged rapidly but now seems to be stuck.
- How do I keep some internal variables constant while optimizing the others?
- How do I constrain some internal variables to be the same value within a sign?
- How do I restart a geometry optimization?
- Can I use symmetry while optimizing the geometry?
- How do I adjust the value of (or change in any way) some internal coordinates in an existing geometry?
- How do I scan a potential energy surface?
- How do I find a transition state?
I want to optimize the structure of my molecule. What should I try first?
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.
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
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.
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.
How do I accelerate a geometry optimization using information from a lower (cheaper) level of theory, and does this really help?
It can help a lot and is especially worth doing for most large basis set calculations with correlated wavefunctions.
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.
- 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.
- Run the first optimization with a low-level theory.
- 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).
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.
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
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.
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
When should I use STEPPER rather than DRIVER?
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.
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.
AUTOZ fails to generate valid internal coordinates. Now what?
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.
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.
Once the obvious has been checked, there are several possible modes of failure, some of which may be worked around in the input.
- 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:
- 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.
- put the dummy center far enough away so that only one connection is generated.
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 - 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.
- 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
zcoord; cvr_scaling 0.9; end
In addition to this you can also try specifying a minimal set of bonds to connect the fragments.
If these together don't work, then you're out of luck. Use Cartesians or construct a Z-matrix.
What initial guess is Driver using for the Hessian?
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
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.
The restart filename expected by Driver is *.drv.hess, while the the filename when INHESS=2 is *.hess.
My geometry optimization initially converged rapidly but now seems to be stuck.
- 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
- 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.
- 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).
- MP2 ... use the TIGHT keyword. This tightens up thresholds in the SCF, CPHF and MP2.
- 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.
- 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
geometry zmatrix your z-matrix data end end geometry adjust # Discards z-matrix and uses autoz end - 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.
How do I keep some internal variables constant while optimizing the others?
-
If you are defining your own Z-matrix, then parameters specified
in the constants section are frozen in any geometry optimization.
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 - 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.
E.g., water with the bond angle frozen at the value defined by the Cartesian coordinates.
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 endE.g., water with the bond angle held at 103 degrees.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
How do I constrain some internal variables to be the same value within a sign?
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.
E.g. CH3-CF3 - related bonds, angles and torsions are forced to be equivalent. Note the use of a sign on TOR1.
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
How do I restart a geometry optimization?
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.
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.
The key points are
- The first job contains a START directive with a name for the calculation.
- All subsequent jobs should contain a RESTART directive with the same name for the calculation.
- All jobs must specify the same permanent directory. The default permanent directory is the current directory.
- 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.
Job 1.
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
Job 2.
restart ammonia
permanent_dir /u/myfiles
task scf optimize
Can I use symmetry while optimizing the geometry?
Yes.
With Cartesian coordinates either
- list all atoms in any orientation and use the AUTOSYM keyword for automatic detection of the point group, or
- 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.
How do I adjust the value of (or change in any way) some internal coordinates in an existing geometry?
NWChem provides the adjust keyword on the GEOMETRY directive
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.
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
How do I scan a potential energy surface?
E.g., scanning the OH bond and HON bond angle in hydroxylamine in order to find a starting geometry for a transition state search.
- You can do it manually:
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 - Or, you can use a Python program. The scan_input() procedure
is defined in nwgeom.py and is documented there.
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
How do I find a transition state?
A fairly reliable approach is to
- Optimize the reactants and products
- Identify the key internal variables involved in the reaction
- 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.
- 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).
Steps 1) & 3) are covered elsewhere in the FAQ. Step 2) is your problem. Step 4) is done as follows
E.g., find the transition state for CH3+HF <-> CH4 + F given a starting guess for the transition state.
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
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.
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
- 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.
- 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).
- MP2 ... use the TIGHT keyword. This tightens up thresholds in the SCF, CPHF and MP2.
Contact: NWChem Support
Updated: February 22, 2005