1. General information about NWChem
   1. Where is the NWChem homepage?
   2. Where is the User's Manual?
   3. Where is the Programmer's Manual?
   4. How do I submit a job on NWMPP1?
   5. Is there any on-line training available?
   6. Where do I go for help with a GA problem?
   7. Where do I go for help with NWChem problems?
2. Input Problems
   1. I get the message: ! warning: processed input with no task. What is wrong?
3. Initial Guess and Convergence Problems
   1. I am having problems getting my initial guess in the correct order. How I do use the swap directive?
   2. I am having problems getting an open shell sytem to converge. What strategies will help me?
   3. I am having problems converging an ionic, extended system. What can I do?
   4. I am having convergence problems with the final iterations of a calculation using a large basis set. What can I do?
   5. Do you have an example of a complex fragment guess?
4. Basis Sets
   1. How do the basis sets get assigned to the atoms in my input deck?
5. Optimization Issues (including transition states)
   1. I want to optimize the structure of my molecule. What should I try first?
   2. How do I accelerate a geometry optimization using information from a lower (cheaper) level of theory, and does this really help?
   3. When should I use STEPPER rather than DRIVER?
   4. AUTOZ fails to generate valid internal coordinates. Now what?
   5. What initial guess is Driver using for the Hessian?
   6. My geometry optimization initially converged rapidly but now seems to be stuck.
   7. How do I keep some internal variables constant while optimizing the others?
   8. How do I constrain some internal variables to be the same value within a sign?
   9. How do I restart a geometry optimization?
   10. Can I use symmetry while optimizing the geometry?
   11. How do I adjust the value of (or change in any way) some internal coordinates in an existing geometry?
   12. How do I scan a potential energy surface?
   13. How do I find a transition state?
   14. I am getting different optimized structures between version 3.2 and 3.3. Why is this?
   15. I used the CVGOPT keyword in DRIVER in NWChem 3.2. How does this relate to the new convergence criteria in version 3.3?
6. MP2
1. How do I calculate MP2 properties?
2. My high symmetry MP2 calculation is taking longer that it should. Why is this?
7. SCF/DFT
1. How do I reproduce the XC numerical grid used in G9X?
2. Which Columb fitting basis set should I use?
3. How did the input for Lebedev grids changed from 3.3.1 to 4.0?
4. Are the DFT unoccupied orbital energies shifted?
5. I got the error message: "ao_replicated: insufficient memory XXXXXXXX"; what can I do?
8. GAPSS
1. Is the GAPSS module available?
2. I get the error message "gap_parse is not in this build of NWChem", how do I get GAPSS to work?
3. Can I do geometry optimizations with GAPSS?
9. QMMM
1. How do I run a QM/MM calculation?
10. Linux Clusters
1. What hardware configuration is suggested for running NWChem on Linux cluster?
2. How do I install and run NWChem on Myrinet clusters?
3. How do I install NWChem on Giganet clusters?
4. How do I increase the shared memory segment in FreeBSD?
11. IBM SP
1. What is the target for running NWChem on IBM SPs?
2. I have a lapi_init error. How do I fix this problem?
3. I have a load error when trying to run NWChem. How do I fix this problem?
4. Thread scheduling policy change from AIX 4.3 to 4.3.3 which effects performance.
5. How do I use more than 2 GB of disk space?
12. Windows 32
1. How do I compile NWChem on Windows NT and Windows 98?
13. DECOSF
1. What is causing a segmentation violation in DECOSF 4.0?
2. What is causing the ma_init failed error message?
14. SGI
1. How can I improve parallel performances under SGI?
2. How can I improve performances under SGITFP?
15. Useful Chemistry links
1. Computational Chemistry List
2. David Young's Computational Chemistry Topics
3. EMSL Gaussian Basis Set Order Form
4. Mike Colvin's Quantum Chemistry Tutorial
5. NIST WebBook
6. Protein Data Bank

Answers

General information about NWChem

NWChem homepage

NWChem User's Manual

NWChem Programmer's Manual

Check out the "Running NWChem" subsection in the LoadLeveler Description at MSCF" page.

The slides from the NWChem / Eccé Tutorial workshop, July 1999 are now available.

If you have problems with GA, please checkout the Global Arrays Support Page. If your problem is not resolved there, please send an e-mail to Jarek Nieplocha with a full description of your problem.

First, look at the FAQ (this page) and Known Bugs pages to see if your problem is described. If not, then please follow the directions on the Reporting Problems with NWChem page. This includes procedures for contacting the developers, directions for signing onto the nwchem-users list, and the archives of the nwchem-users list.

Input Problems

Have you used emacs to create your input file? Emacs usually does not put and an end-of-line as a last character of the file, therefore the NWChem input parser ignores the last line of your input (the one containing the task directive).

To fix the problem, add one more blank line after the task line and your task directive will be executed.

Initial Guess and Convergence Problems

Remember that you can (and should!) look at your initial orbitals by putting the line

print "initial vectors"

into the SCF block of your input deck. If the order isn't correct, you can use the "swap" directive to change the order of the orbitals.

For example:

vectors atomic swap 173 175 174 176 output end.movecs

Open shell systems, especially those containing transition metals or heavy elements with many unoccupied d and f orbitals, can be especially hard to converge. Running a spin unrestricted calculation can exacerbate the problem since all other possible spin states can mix into the wavefunction. It may also be true that your particular calculation has multireference character and, by using SCF or DFT, you are forcing it into a single determinate wavefunction.

That being said, to converge your system, you need to guide the code to the particular state that you want. This may be a very difficult task and different starting guesses can converge to different solutions, especially if there is symmetry breaking. Here are four different suggestions to help you with your problem:

1. Use Auf bau construction. Start by removing most or all of the open-shell electrons and converge the resulting closed-shell wavefunction. Incrementally add the missing electrons, maintaining a closed-shell form for the wavefunction until the last calculation. Once you have an ROHF wavefunction converged, then do the UHF calculation if desired (note that UHF is the only option with the DFT code). When adding electrons, pay attention to how well separated the virtual orbitals are in energy.
2. Converge a very high multiplicity state and then incrementally pair electrons until you get the state you want.
3. Converge in a minimal basis set where there is very little variational freedom and it is not as expensive to run many iterations. Then project to a larger basis set. It is also useful to use spherical functions since this tends to decrease the amount of linear dependence. This method isn't as reliable as the previous methods.
4. Use the fragment guess. This is especially useful if you know the configuration of the atoms. Prepare the atoms in the appropriate state and assemble the molecule from the fragments. If you want an antiferromagnetic state, this is the only way to do it.

This problem usually shows up when a minimum basis set is used and where a lot of charge has to be moved a long way but the minimal basis does not providea lot of coupling between the orbitals. The initial guess may be modified by

1. putting the charge on the atoms where it is believed to be,
2. look at the orbitals and swap the orbitals to obtain the correct occupation, or
3. ue the fragment guess.

This problem generally occurs when high precision is necessary because of near linear dependencies in the basis set and there is insufficient precision in the computed gradient or hessian vector product to converge to the requested threshold. The first item to check is to make sure that the convergence threshold is realistic (not below 1e^-7 or perhaps 1e^-8). If doing an MP2 gradient with the TIGHT directive, make sure the SCF input block is after the MP2 block and then in the SCF block put

SCF
  thresh 1e-7
  tol2e 1e-10
END

1. Run the calculation on enough nodes to run fully disk resident,
2. Run as before, but switch off the density screening with

   set fock:densityscreen f

3. Run the calculation fully direct.

The following is an advanced fragment guess (NOT for beginners!). It consists of two Fe³⁺ ions in a simulated lattice and the objective is to compute the energy difference between the ferro and anti-ferromagnetic states. This is accomplished by first using the atomic guess to do an ROHF calculation on an Fe³⁺ ion with d⁵ occupation. The next calculation is on the high spin system and it merely has to start from the two ions ... the open shell orbitals will automatically be contiguous and so nothing else is needed.

The final calculation is a UHF for which the 5 open shell electrons on one atom must be spin up and on the other spin down. The initial guess orbitals start off from the previous high spin solution. However, the d orbitals on the second atom must have the beta orbitals in the right place, hence the swap directive. The net result is a completely localized guess with the desired spin coupling.

start fe2

geometry noautoz autosym
  Fe  1.45 0.071  0.84
  Fe -1.45 0.071 -0.84

  Bq   3.02  0.84  0.03 charge -1.
  Bq  -0.00  1.04  0.03 charge -1.
  Bq   1.33 -1.67  0.03 charge -1.
  Bq   2.78 -0.69  2.33 charge -1.
  Bq   1.45  1.61  2.33 charge -1.
  Bq   0.11 -0.69  2.33 charge -1.
  Bq  -1.33 -1.67  0.03 charge -1.
  Bq  -3.02  0.84  0.03 charge -1.
  Bq  -0.12 -0.69 -2.25 charge -1.
  Bq  -1.45  1.61 -2.25 charge -1.
  Bq  -2.78 -0.69 -2.25 charge -1.
end

geometry Fe
  Fe  0 0 0
symmetry c2v
end

basis
  Fe library sto-3g
end

set atomscf:tags_z Fe
set atomscf:z      3.

title "Initial calculation on Fe3+"

set geometry Fe
charge 3
scf; rohf ; nopen 5; vectors atomic output fe.mos; end
task scf

title "Ferro-magnetic state"

unset geometry
charge -5

scf; print "initial vector analysis"; rohf; nopen 10
vectors fragment fe.mos fe.mos output feferr.mos; 
maxiter 0
print mulliken
end
task scf ignore

title "Anti-ferro-magnetic state"
scf; uhf; nopen 0;
  vectors input feferr.mos output feantif.mos\
     swap beta 19 24  20 25  21 26  22 27  23 28
maxiter 99
end
task scf

Basis Sets

The tags associated with atoms (e.g. H, H1, Hydrogen) are mapped to the tags used in the basis set definitions by:

1. If there is an exact match, then use it

   E.g., if H1 appears in both the geometry and the basis, then the H1 basis set is used.

2. If there is not an exact match, then if there is a basis set defined for that element, then use it

   E.g., if H1 appears in the geometry but not in the basis, then try to use a basis set for H or for Hydrogen. It will not try to match another tag such as H2 in the basis set.

3. If two definitions are given for an element in the basis set, then use the definition such that the basis set tag is completely matched (or is a substring) of the geometry tag.

   E.g., if H1, Hydrogen1, and Hydro1 appear in the geometry and H and Hydrogen appear in the basis, H1 will map to H, Hydrogen1 will map to Hydrogen, and Hydro1 will map to H. You are STRONGLY advised not to do perverse inputs such as Hydro1 which can only cause confusion.

Optimization Issues (including transition states)

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

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.

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.

1. Set the permanent directory to be somewhere permanent (sic). The default is the current directory, which for a batch job on the EMSL IBM 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.
2. Run the first optimization with a low-level theory.
3. 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

         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

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.

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.

1. 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
   
   

2. 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.
3. 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.

    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

The restart filename expected by Driver is *.drv.hess, while the the filename when INHESS=2 is *.hess.

1. 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
   1. 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.
   2. 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).
   3. MP2 ... use the TIGHT keyword. This tightens up thresholds in the SCF, CPHF and MP2.
2. 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.
3. 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
   
   

4. 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.

1. 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
   
   

2. 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
          end
   
   

   E.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
   
   

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

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

1. The first job contains a START directive with a name for the calculation.
2. All subsequent jobs should contain a RESTART directive with the same name for the calculation.
3. All jobs must specify the same permanent directory. The default permanent directory is the current directory.
4. 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

         restart ammonia
         permanent_dir /u/myfiles

         task scf optimize

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.

Version 3.3 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

E.g., scanning the OH bond and HON bond angle in hydroxylamine in order to find a starting geometry for a transition state search.

1. 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
   
   

2. 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
   
   

A fairly reliable approach is to

1. Optimize the reactants and products
2. Identify the key internal variables involved in the reaction
3. 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.
4. 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

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.

Driver in version 3.3 now takes several different criteria into account for convergence (GMAX, GRMS, XMAX and XRMS) whereas in version 3.2 it only took into account the maximum component of the gradient (CVGOPT which is now GMAX). Also, the default GMAX value has changed from 0.0008 to 0.00045. So, the default convergence in version 3.3 is tighter than it was in version 3.2 because these extra convergence criteria must be met. So, the optimizations will converge to slightly different geometries.

To get the previous default behavior of version 3.2, you will need to put

gmax 0.0008; grms 1; xrms 1; xmax 1

in your DRIVER block.

In version 3.3, CVGOPT is still an active keyword, although is is not encouraged since it will be discontinued in the next release. CVGOPT is being interpretted and essentially translated to GMAX in the new driver criteria. But now, driver takes several different criteria into account for convergence (GMAX, GRMS, XMAX and XRMS) whereas in version 3.2 it only took into account the maximum component of the gradient (CVGOPT which is now GMAX). It is very likely that the convergence for a given geometry will be tighter than it was in version 3.2 because of these extra convergence criteria that must be met. Also, the default GMAX value has changed from 0.0008 to 0.00045. This will mean that geometry optimizations will converge to slightly different geometries between the two versions when using the same value of CVGOPT or when using the default convergence criteria.

To get the previous default behavior of version 3.2, you will need to put

gmax 0.0008; grms 1; xrms 1; xmax 1

in your DRIVER block. The line

cvgopt 0.0008; grms 1; xrms 1; xmax 1

is equivalent, but should not be used as the user should get in the habit of using GMAX instead of CVGOPT.

MP2 Properties

The default molecular orbital file $file_prefix$.movecs is used unless a VECTORS subdirective is provided in the PROPERTY directive. It is therefore necessary to include a VECTORS directive if the MO vectors to be analyzed are not coming from the default file, e.g., if they have been previously redirected, or if MP2 natural orbitals (file extension ".mp2nos") are being anaylzed. So, to calculate MP2 properties, a PROPERTY block directive similar to the one in the following example would be appropriate:

     start h2o
     title; Water MP2 properties example

     geometry
       O 0  0     0
       H 0  1.430 1.107
       H 0 -1.430 1.107
     end

     basis
       H library sto-3g
       O library sto-3g
     end

     task mp2 

     property
       octupole 
       efield
       vectors h2o.mp2nos
     end

     task property

Currently MP2 can only use Abelian point groups and does not have descent of symmetry implemented (meaning that it does not know how to use a proper Abelian point group instead of an input non-Abelian group). The user must define the proper Abelian point group, orient the molecule into this point group, and then run the MP2.

SCF/DFT

G9X and NWChem default grids are different. To get a grid close to the default G9X grid you need the following input lines.

dft
 grid ssf euler lebedev 75 11
end

We strongly recommend use of the Ahlrichs Auxilliary basis sets for fitting the Coulomb potentatial in DFT calculations. The following is an example of an in input file using this basis set.

basis "cd basis"
 C library "Ahlrichs Coulomb Fitting"
end

Yes, in all versions of NWChem including 4.0 and below, the DFT unoccupied orbital energies are shifted by the amount of level-shifting used to converge the wavefunction. If you use these energies for any reason, you need to subtract out the level-shifting value. Check out the DFT Convergence section of the User Manual for more information about level-shifting.

You can fix this problem by having the code adopting the distributed data Fock build (that is less memory demanding compared to the default replicated data build). This is accomplished by adding the following line anywhere in you input file

 set fock:replicated logical .false.

GAPSS

The GAPSS module is available in NWChem 4.0. However, it is distributed only in the source tar file, the binaries do not include it.

Follow this procedure

1) cd $NWCHEM_TOP/src
2) make nwchem_config NWCHEM_MODULES="all gapss"
3) make 

No, the distributed version of GAPSS does not have analytical gradients.

QMMM

You need to have an nwchem input file (example for K(H₂O)₆), and an associated pdb file (example for K(H₂O)₆). The PDB file must be complete, containing both the QM and MM atoms. The nwchem input file must contain a prepare section and fields relative to the QM region and the md inputs. A template follows (Note that the memory and eatoms value are only examples.) The example for K(H₂O)₆ contains comments with more information.

start SYSTEM

memory  heap 8 mb  stack 54 mb  global 54 mb

prepare
   system SYSTEM_CALC
   Define quantum atoms 
   Add solvent
   update lists
end

basis
   basis set 
end

scf
   SCF input
   print low
end

md
   system SYSTEM_CALC
   MD input
   memory 15000
end
qmmm
   eatoms -190.0    
end
task qmmm scf ( energy | optimize | dynamics )

Linux Clusters

Most of the NWChem modules are not going to perform well on large Linux clusters that use just Fast Ethernet for communication. For optimal performance, you need to use either Giganet or Myrinet interconnects.

Prior to installing NWChem, you must have installed the GM and the MPICH over GM softwares on the system. Before starting the NWChem compilation, the following environmental variables must be defined

USE_MPI=y
GM_HOME="location of GM software"
GM_INCLUDE=$GM_HOME/include  
GM_LIB=$GM_HOME/lib
ARMCI_NETWORK=GM
MPI_LOC="location of MPICH-GM software"
MPI_LIB=$MPI_LOC/lib
MPI_INCLUDE=$MPI_LOC/include
LIBMPI=-lmpich             

#define GM_STRONG_TYPES 0

#include "gm.h"

GMPI_SHMEM_FILE /tmp/$USER.gm 

8
node1 2
node1 4
node2 2
node2 4
node3 2
node3 4
node4 2
node4 4

Before starting the NWChem compilation, the following environmental variables must be defined

ARMCI_NETWORK=VIA 
LIBMPI="-lmpipro -lpthread"

MPI_COMM=VIA 

To increase the shared memory segments on FreeBSD the following two sysctl's should be added to the startup scripts (e.g. /etc/rc.local):

sysctl -w kern.ipc.shmmax=67108864
sysctl -w kern.ipc.shmall=16384

IBM SP

The right target is

LAPI

If you get a message similar to:

  0: lapi_init failed 419(1a3)
system message: Operation not permitted.
ERRIR:  0031-250  task 0: terminated

setenv MP_MSG_API lapi

# @ network.lapi = css0, not_shared, US

If you get a message similar to:

exec(): 0509-036 Cannot load program /usr/local/NWChem/bin/nwchem because of the
 following errors:
        0509-023 Symbol kaio_rdwr in /usr/lpp/ppe.poe/lib/libc.a is not defined.
        0509-023 Symbol listio in /usr/lpp/ppe.poe/lib/libc.a is not defined.
        0509-023 Symbol acancel in /usr/lpp/ppe.poe/lib/libc.a is not defined.
        0509-023 Symbol iosuspend in /usr/lpp/ppe.poe/lib/libc.a is not defined.
        0509-022 Cannot load library libc.a[aio.o].
        0509-026 System error: Cannot run a file that does not have a valid format.

1. Enter smit
2. Go to "Devices"
3. Go to "Asynchronous I/O"
4. Go to "Change / Show Characteristics of Asynchronous I/O"
5. Change "State of fast path" to "enable"
6. Make sure "STATE to be configured at system restart" is set to "available"
7. Exit smit

The second solution is to compile GA without Asynchronous I/O turned on. This WILL slow down the performance of NWChem.

1. cd $NWCHEM_TOP/src/tools/pario
2. make TARGET=LAPI clean
3. make TARGET=LAPI CC="cc -DNOAIO" LARGE_FILES=y
4. cd $NWCHEM_TOP/src
5. make link

The default thread scheduling policy changed from AIX version 4.3 to 4.3.3 which effects MPI and LAPI programs that rely on switch packet arrival interrupts (such as NWChem). This directly effects the performance of NWChem. To change the default, you need to set the environment variable RT_GRQ. You can either do this in your environment:

setenv RT_GRQ ON

# @ environment      =    RT_GRQ=ON

# @ environment      =    COPY_ALL; MP_INFOLEVEL=3; MP_PULSE=0; 
MP_SINGLE_THREAD=yes; MP_WAIT_MODE=yield; RT_GRQ=ON; restart=no

During the compilation, the environment variable LARGE_FILES needs to be set (i.e. setenv LARGE_FILES TRUE). Also, you should make sure that the file sizes on your system are not limited to 2 GB (type "limit" and check the output). If the sizes are limited, ask your system adminitrator to change the limit for you.

Windows 32

The right target is WIN32. Before starting the compilation, you must have installed the Compaq Visual Fortran compiler (version 6.0 and 6.1 have been successfully tested) and the NT.MPICH library (http://www-unix.mcs.anl.gov/~ashton/mpich.nt/ ). Then, you need to have defined this series of variables (that you can set in autoexec.bat)

set NWCHEM_TOP=c:\nwchem
set NWCHEM_TARGET=WIN32
set MPI_INCLUDE=c:\PROGRA~1\ARGONN~1\MPICHN~1.4\SDK\INCLUDE
set MPI_LIB=c:\PROGRA~1\ARGONN~1\MPICHN~1.4\SDK\lib
set NWCHEM_EXTRA_LIBS=%MPI_LIB%\mpich.lib

nmake

DECOSF

The -automatic Fortran compiler option is causing this problem under DECOSF 4.0 using version 5.2 of the f77 compiler. To get a working executable, you need to edit $NWCHEM_TOP/src/config/makefile.h at line 1051. The modified line 1051 must therefore be

FOPTIONS = -i8 -align dcommons -math_library fast -fpe2 -check nounderflow \
-check nopower -check nooverflow -warn argument_checking -warn unused #-automatic

If NWChem crashes with the error message

MA error: MA_init: could not allocate XXXXXXXXX bytes
 ------------------------------------------------------------------------
 nwchem.F: ma_init failed (ga_uses_ma=T)      911 

limit datasize unlimited  

SGI

Use the MPI vendor library, after defining the usual environmental variable to replace TCGMSG with MPI

USE_MPI=y

Install the SCSL scientific library, freely available from the SGI web site , then link the code with the following environmental variable

BLASOPT=-lscs_blas_i8

Created by Theresa Windus
Last modified: January 4, 2001