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<table width="650"><tr><td>
<center><h1>NWChem Frequently Asked Questions</h1></center>
<ol>
<li> <a href="#geninf">General information about NWChem</a>
<ol>
<li> <a href="#0">Where is the NWChem homepage?</a></li>
<li> <a href="#1">Where is the User's Manual?</a></li>
<li> <a href="#2">Where is the Programmer's Manual?</a></li>
<li> <a href="#3">What citation should I use when publicizing results obtained from NWChem?</a></li>
<li> <a href="#4">How do I submit a job on MPP2?</a></li>
<li> <a href="#5">Is there any on-line training available?</a></li>
<li> <a href="#6">Where do I go for help with a GA problem?</a></li>
<li> <a href="#7">Where do I go for help with NWChem problems?</a></li>
</ol></li>
<li> <a href="#input">Input Problems</a>
<ol>
<li> <a href="#notask">I get the message:<tt> ! warning: processed input with no task</tt>. What is wrong?</a></li>
</ol></li>
<li> <a href="#initguess">Initial Guess and Convergence Problems</a>
<ol>
<li> <a href="#8">I am having problems getting my initial guess
in the correct order. How I do use the swap directive?</a></li>
<li> <a href="#openguess">I am having problems getting an open shell sytem to converge. What strategies will help me?</a></li>
<li> <a href="#minchargeguess">I am having problems converging an ionic, extended system. What can I do?</a></li>
<li> <a href="#accbbsconv">I am having convergence problems with the final iterations of a calculation using a large basis set. What can I do?</a></li>
<li> <a href="#compfragguess">Do you have an example of a complex fragment guess?</a></li>
</ol></li>
<li> <a href="#basissets">Basis Sets</a>
<ol>
<li> <a href="#basistags">How do the basis sets get assigned to the atoms in my input deck?</a></li>
</ol></li>
<li> <a href="#opt">Optimization Issues (including transition states)</a>
<ol>
<li> <a href="#first">I want to optimize the structure of my molecule.
What should I try first?
</a></li>
<li> <a href="#accel">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="#stepper">When should I use STEPPER rather than DRIVER?
</a></li>
<li> <a href="#autozfail">AUTOZ fails to generate valid internal coordinates. Now what?
</a></li>
<li> <a href="#inithess">What initial guess is Driver using for the Hessian?
</a></li>
<li> <a href="#stuck">My geometry optimization initially converged rapidly but
now seems to be stuck.
</a></li>
<li> <a href="#constant">How do I keep some internal variables constant while optimizing
the others?
</a></li>
<li> <a href="#sameval">How do I constrain some internal variables to be the same
value within a sign?
</a></li>
<li> <a href="#restart">How do I restart a geometry optimization?
</a></li>
<li> <a href="#symm">Can I use symmetry while optimizing the geometry?
</a></li>
<li> <a href="#adjust">How do I adjust the value of (or change in any way) some internal
coordinates in an existing geometry?
</a></li>
<li> <a href="#scan">How do I scan a potential energy surface?
</a></li>
<li> <a href="#findts">How do I find a transition state?
</a></li>
</ol></li>
<li><a href="#mp2"> MP2 </a></li>
<ol>
<li><a href="#howmp2prop">How do I calculate MP2 properties? </a></li>
<li><a href="#mp2symm">My high symmetry MP2 calculation is taking longer that it
should. Why is this?</a></li>
</ol>
<li><a href="#dft"> SCF/DFT</a></li>
<ol>
<li><a href="#g9xgrid">How do I reproduce the XC numerical grid used in G9X? </a></li>
<li><a href="#cdfit">Which Columb fitting basis set should I use?</a></li>
<li><a href="#lumoenergy">Are the DFT unoccupied orbital energies shifted?</a></li>
<li><a href="#aorepl">I got the error message: "<tt>ao_replicated: insufficient memory XXXXXXXX</tt>"; what can I do?</a></li>
<li><a href="#x3lyp">How can I do a X3LYP calculation in NWChem?</a></li>
<li><a href="#bqs">How do you address Bq's to get an integration grid?</a></li>
</ol>
<li><a href="#gapss"> GAPSS</a></li>
<ol>
<li><a href="#gapssdistr">Is the GAPSS module available? </a></li>
<li><a href="#gapsscomp">I get the error message "gap_parse is not in this build of NWChem", how do I get GAPSS to work? </a></li>
<li><a href="#gapssener">Can I do geometry optimizations with GAPSS?</a></li>
</ol>
<li><a href="#qmmm"> QMMM</a></li>
<ol>
<li><a href="#qmmminput">How do I run a QM/MM calculation?</a></li>
</ol>
<li><a href="#moldynam"> Molecular Dynamics</a></li>
<ol>
<li><a href="#moldynam_restart">How do I restart a Molecular Dynamics calculation?</a></li>
</ol>
<li><a href="#dirdyvtst"> DIRDYVTST</a></li>
<ol>
<li><a href="#dirdyexamples">How do I run a DIRDYVTST calculation?</a></li>
</ol>
<li><a href="#linuxclusters"> Linux Clusters</a></li>
<ol>
<li><a href="#linuxhw">What hardware configuration is suggested for running NWChem on Linux cluster? </a></li>
<li><a href="#myrinet">How do I install and run NWChem on Myrinet clusters?</a></li>
<li><a href="#giganet">How do I install NWChem on Giganet clusters?</a></li>
<li><a href="#freebsdmem">How do I increase the shared memory segment in FreeBSD?</a></li>
</ol>
<li><a href="#ibmsp"> IBM SP</a></li>
<ol>
<li><a href="#lapi">What is the target for running NWChem on IBM SPs? </a></li>
<li><a href="#lapiiniterr">I have a lapi_init error. How do I fix this problem?</a></li>
<li><a href="#asyncio">I have a load error when trying to run NWChem. How do I fix this problem?</a></li>
<li><a href="#rtgrqon">Thread scheduling policy change from AIX 4.3 to 4.3.3 which effects performance.</a></li>
<li><a href="#filelimit">How do I use more than 2 GB of disk space?</a></li>
</ol>
<li><a href="#ibm"> IBM </a></li>
<ol>
<li><a href="#ibm64python">How do I install a Python library
compatible with the NWCHEM_TARGET IBM64? </a></li>
</ol>
<li><a href="#win32"> Windows 32</a></li>
<ol>
<li><a href="#win32compile">How do I compile NWChem on Windows NT and
Windows 98? </a></li>
</ol>
<li><a href="#sgi"> SGI</a></li>
<ol>
<li><a href="#sgimpi">How can I improve parallel performances under SGI? </a></li>
<li><a href="#sgitfpscs">How can I improve performances under SGITFP? </a></li>
<li><a href="#sgitfpmpich">How do I install the MPI version of SGITFP? </a></li>
</ol>
<li><a href="#itanium"> Itanium</a></li>
<ol>
<li><a href="#itaniumcompiler">Which version of the Intel compiler should I use?</a></li>
</ol>
<li>Useful Chemistry links</li>
<ol>
<li><a href="http://www.ccl.net/chemistry/">Computational Chemistry List</a></li>
<li><a href="http://www.ccl.net/cca/documents/dyoung/topics-orig/">David Young's Computational Chemistry Topics</a></li>
<li><a href="http://www.emsl.pnl.gov/forms/basisform.html">EMSL Gaussian Basis Set Order Form</a></li>
<li><a href="http://webbook.nist.gov/">NIST WebBook</a></li>
<li><a href="http://www.rcsb.org/pdb/">Protein Data Bank</a></li>
<li><a href="http://www.webelements.com/">WebElements Periodic Table</a></li>
</ol>
</ol>
<pre>
</pre>
<a name="geninf"></a>
<h3>General information about NWChem</h3>
<hr>
<p>
<a name="0"></a>
<font color="purple">Where is the NWChem homepage?</font>
<p>
<a href="http://www.emsl.pnl.gov/docs/nwchem/nwchem_main.html">NWChem homepage</a>
</p>
<hr>
<p>
<a name="1"></a>
<font color="purple">Where is the User's Manual?</font>
<p>
<a href="http://www.emsl.pnl.gov/docs/nwchem/doc/user/index.html">
NWChem User's Manual</a>
</p>
<hr>
<p>
<a name="2"></a>
<font color="purple">Where is the Programmer's Manual?</font>
<p>
<a href="http://www.emsl.pnl.gov/docs/nwchem/doc/prog/index.html">
NWChem Programmer's Manual</a>
</p>
<hr>
<p>
<a name="3"></a>
<font color="purple">What citation should I use when publicizing results obtained from NWChem?</font>
<p>
Please see the <a href="../citation.html">NWChem Citation</a> page for the citation to use when publicizing
results obtained from NWChem.
</p>
<hr>
<p>
<a name="4"></a>
<font color="purple">How do I submit a job on MPP2?</font>
<p>
There is an <tt>llnw</tt> script used for submitting NWChem jobs on MPP2
located
in <tt>/home/scicons/bin</tt>.
Please refer to the <a href="http://mscf.emsl.pnl.gov/hardware/intro_paracomputers.shtml" target="_blank">MSCF website</a> for more details.
</p>
<hr>
<p>
<a name="5"></a>
<font color="purple">Is there any on-line training available?</font>
<p>
The slides from the <a href="http://www.emsl.pnl.gov/cgi-bin/mscf-training/pachelbel?HOME" target="_blank">
NWChem / Ecc&eacute Tutorial workshop, July 1999</a> are now
available.
</p>
<hr>
<p>
<a name="6"></a>
<font color="purple">Where do I go for help with a GA problem?</font>
<p>
If you have problems with GA, please checkout the
<a href="http://www.emsl.pnl.gov/docs/global/support.html" target="_blank">
Global Arrays Support Page</a>. If your problem is not resolved there,
please send an e-mail to <a href="mailto:hpctools@emsl.pnl.gov">
Global Arrays Support</a> with a full description of your problem.
</p>
<hr>
<p>
<a name="7"></a>
<font color="purple">Where do I go for help with NWChem problems?</font>
<p>
First, look at the <a href="NWChem_FAQ.html">FAQ</a> (this page) and
<a href="known_bugs.html">Known Bugs</a> pages to see if your problem is
described. If not, then please follow the directions on the
<a href="support.html">Reporting Problems with NWChem</a> page. This
includes procedures for contacting the developers, directions for signing
onto the nwchem-users list, and the archives of the nwchem-users list.
</p>
<hr>
<br><br>
<p>
<a name="input"></a>
<h3>Input Problems</h3>
</p>
<hr>
<p>
<a name="notask"></a>
<font color="purple">I get the message:<tt> ! warning: processed input with no task</tt>. What is wrong? </font>
<p>
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 <tt>task</tt> directive).
<p>
To fix the problem, add one more blank line
after the task line and your task directive will be executed.
</p>
<hr>
<br><br>
<p>
<a name="initguess"></a>
<h3>Initial Guess and Convergence Problems</h3>
</p>
<hr>
<p>
<a name="8"></a>
<font color="purple"> I am having problems getting my initial guess
in the correct order. How I do use the swap directive? </font>
<p>
Remember that you can <b>(and should!)</b> look at your initial orbitals
by putting the line<br>
<p>
print "initial vectors"
<p>
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.
<p>
For example:
<pre>
vectors atomic swap 173 175 174 176 output end.movecs
</pre>
will cause the orbitals 173 - 175 to be swapped to 175, 176, 173 and 174.
Note that the swaps are pairwise: first 173 and 175 are swapped, then the
the current orbitals 174 and 176 are swapped. More information on initial orbitals
can be obtained in <a href="http://www.emsl.pnl.gov/docs/nwchem/doc/user/node12.html#SECTION001250000000000000000" target="_blank">
Section 10.5</a> of the <a href="../doc/user/index.html" target="_blank">User's Manual</a>.
</p>
<hr>
<p>
<a name="openguess"></a>
<font color="purple"> I am having problems getting an open shell system to converge. What strategies will help me?</font>
<p>
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.
<p>
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:
<ol>
<li> 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.</li>
<li> Converge a very high multiplicity state and then incrementally
pair electrons until you get the state you want.</li>
<li> Converge in a minimal basis set where there is very little variational
freedom and it is not as expensive to run many iterations. Then
<a href="http://www.emsl.pnl.gov/docs/nwchem/doc/user/node12.html#SECTION001250000000000000000">project</a>
to a larger basis set (you can use this
<a href="http://www.emsl.pnl.gov/docs/nwchem/support/proj.nw">example</a>
as a model).
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.</li>
<li> Use the <a href="http://www.emsl.pnl.gov/docs/nwchem/doc/user/node12.html#SECTION001251000000000000000">fragment</a>
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.</li>
</ol>
</p>
<hr>
<p>
<a name="minchargeguess"></a>
<font color="purple"> I am having problems converging an ionic, extended system. What can I do?</font>
<p>
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
<ol>
<li><a href="http://www.emsl.pnl.gov/docs/nwchem/doc/user/node12.html#SECTION001252000000000000000">putting the charge on the atoms</a>
where it is believed to be,</li>
<li> look at the orbitals and
<a href="http://www.emsl.pnl.gov/docs/nwchem/doc/user/node12.html#SECTION001250000000000000000">swap the orbitals</a>
to obtain the correct occupation, or</li>
<li> ue the <a href="http://www.emsl.pnl.gov/docs/nwchem/doc/user/node12.h
tml#SECTION001251000000000000000">fragment</a> guess.</li>
</ol>
Better yet, use a better basis set which will allow for better coupling of
the orbitals!
</p>
<hr>
<p>
<a name="accbbsconv"></a>
<font color="purple"> I am having convergence problems with the final iterations of a calculation using a large basis set. What can I do?</font>
<p>
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
<a href="http://www.emsl.pnl.gov/docs/nwchem/doc/user/node12.html#SECTION001270000000000000000">threshold</a> is realistic (not below 1e<sup>-7</sup> or
perhaps 1e<sup>-8</sup>). If doing an MP2 gradient with the
<a href="http://www.emsl.pnl.gov/docs/nwchem/doc/user/node17.html#SECTION001712000000000000000">TIGHT</a> directive, make sure the SCF input block is
after the MP2 block and then in the SCF block put
<pre>
SCF
thresh 1e-7
tol2e 1e-10
END
</pre>
This may still not fix the problem if the calculation is using the semi-direct
algorithm. In this case:
<ol>
<li>Run the calculation on enough nodes to run fully disk resident,</li>
<li>Run as before, but switch off the density screening with<p>
set fock:densityscreen f<p></li>
<li>Run the calculation fully direct.</li>
</ol>
<hr>
<p>
<a name="compfragguess"></a>
<font color="purple"> Do you have an example of a complex fragment guess?</font>
<p>
The following is an advanced fragment guess (NOT for beginners!). It consists
of two Fe<sup>3+</sup> 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 Fe<sup>3+</sup> ion with d<sup>5</sup> 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.
<p>
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.
<pre>
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
</pre>
For DFT calculation you can either the same method just shown or a
different approach that is illustrated in this
<a href="http://www.emsl.pnl.gov/docs/nwchem/support/fe2dft.nw">example</a>.
</p>
<hr>
<br><br>
<p>
<a name="basissets"></a>
<h3>Basis Sets</h3>
</p>
<hr>
<p>
<a name="basistags"></a>
<font color="purple"> How do the basis sets get assigned to the atoms in my input deck?</font>
<p>
The tags associated with atoms (e.g. H, H1, Hydrogen) are mapped to the tags
used in the basis set definitions by:
<ol>
<li> If there is an exact match, then use it<p>
E.g., if H1 appears in both the geometry and the basis, then the H1
basis set is used.</li><p>
<li> If there is not an exact match, then if there is a basis set defined for
that element, then use it<p>
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.</li><p>
<li> 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.<p>
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.</li>
</ol>
</p>
<hr>
<br><br>
<p>
<a name="opt"></a>
<h3>Optimization Issues (including transition states)</h3>
</p>
<hr>
<p>
<a name="first"></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="accel"></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="stepper"></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="autozfail"></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="inithess"></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="stuck"></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="constant"></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="sameval"></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="restart"></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="symm"></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="adjust"></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="scan"></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="findts"></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>
<hr>
<br><br>
<p>
<a name="mp2"></a>
<h3>MP2 Properties</h3>
</p>
<hr>
<p>
<a name="howmp2prop"></a>
<font color="purple">How do I calculate MP2 properties?
</font>
<p>
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:
<pre>
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
</pre>
</p>
<hr>
<p>
<a name="mp2symm"></a>
<font color="purple">My high symmetry MP2 calculation is taking longer that it
should. Why is this?
</font>
<p>
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.
</p>
<hr>
<br><br>
<p>
<a name="dft"></a>
<h3>SCF/DFT</h3>
</p>
<hr>
<p>
<a name="g9xgrid"></a>
<font color="purple">How do I reproduce the XC numerical grid used in G9X?
</font>
<p>
G9X and NWChem default grids are different. To get a grid close to the default
G9X grid you need the following input lines.
<pre>
dft
grid ssf euler lebedev 75 11
end
</pre>
</p>
<hr>
<p>
<a name="cdfit"></a>
<font color="purple">Which Coulomb fitting basis set should I use?
</font>
<p>
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.
<pre>
basis "cd basis"
C library "Ahlrichs Coulomb Fitting"
end
</pre>
For analysis of the accuracy of this basis set, see <br>
Skylaris, C.-K.; Gagliardi, L.; Handy, N.C.; Ioannou, A.G.; Spencer, S.; Willetts, A.,
Journal of Molecular Structure: THEOCHEM <b>501-502</b>, 229 (2000).
</p>
<hr>
<p>
<a name="lumoenergy"></a>
<font color="purple"> Are the DFT unoccupied orbital energies shifted?</font>
<p>
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
<a href="http://www.emsl.pnl.gov/docs/nwchem/doc/user/node13.html#SECTION001350000000000000000">DFT Convergence</a> section of the User Manual for more
information about level-shifting.
</p>
<hr>
<p>
<a name="aorepl"></a>
<font color="purple">I got the error message: "<tt>ao_replicated: insufficient memory XXXXXXXX</tt>"; what can I do?</font>
<p>
<!There are two possible ways to fix this problem>
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
<pre>
set fock:replicated logical .false.
</pre>
<! 2) try to increase the memory allocation to make the replicated data
algorithm go. This can be done by introducing the memory line
as described in the Users Manual>
<! Option 1) is safer, but the replicated data algorithm (option 2) is
faster.>
</p>
<hr>
<p>
<a name="x3lyp"></a>
<font color="purple">How can I do an X3LYP calculation in NWChem?</font>
<p>The X3LYP functional is not available as a keyword. However, using section 11.3 (specifically 11.3.1 and 11.3.2)
of the NWChem user manual, and applying the parameters of the X3LYP paper on
<a href="http://www.pnas.org/cgi/content/full/101/9/2673" target="_blank">
http://www.pnas.org/cgi/content/full/101/9/2673</a> by Xu and Goddard you can define this exchange-correlation
functional using the following line in the DFT input block:</p>
<pre>XC vwn_1_rpa 0.129 lyp 0.871 Hfexch 0.218 slater 0.782 becke88 nonlocal 0.542 xperdew91 nonlocal 0.167</pre>
<hr>
<p>
<a name="bqs"></a>
<font color="purple">How do you address Bq's to get an integration grid?</font>
<p>Particular care is required to compute BSSE by the counter-poise method for the DFT module.
In order to include terms deriving from the numerical grid used in the XC integration, the user must label the
ghost atoms not just bq, but bq followed by the given atomic symbol. For example, the first component
needed to compute the BSSE for the water dimer, should be written as follows:</p>
<pre>
geometry h2o autosym units au
O 0.00000000 0.00000000 0.22143139
H 1.43042868 0.00000000 -0.88572555
H -1.43042868 0.00000000 -0.88572555
bqH 0.71521434 0.00000000 -0.33214708
bqH -0.71521434 0.00000000 -0.33214708
bqO 0.00000000 0.00000000 -0.88572555
end
basis
H library aug-cc-pvdz
O library aug-cc-pvdz
bqH library H aug-cc-pvdz
bqO library O aug-cc-pvdz
end
</pre>
<p>Please note that the ``ghost'' oxygen atom has been labeled bqO, and not just bq.</p>
<hr>
<br><br>
<p>
<a name="gapss"></a>
<h3>GAPSS</h3>
</p>
<hr>
<p>
<a name="gapssdistr"></a>
<font color="purple">Is the GAPSS module available?
</font>
<p>
The GAPSS module is available in the source code, however, we no
longer provide any support for this module.
</p>
<hr>
<p>
<a name="gapsscomp"></a>
<font color="purple"> I get the error message "gap_parse is not in this build of NWChem", how do I get GAPSS to work?
</font>
<p>
Follow this procedure
<pre>
1) cd $NWCHEM_TOP/src
2) make nwchem_config NWCHEM_MODULES="all gapss"
3) make
</pre>
</p>
<hr>
<p>
<a name="gapssener"></a>
<font color="purple">Can I do geometry optimizations with GAPSS?
</font>
<p>
No, the distributed version of GAPSS does not have analytical gradients.
</p>
<hr>
<br><br>
<p>
<a name="qmmm"></a>
<h3>QMMM</h3>
</p>
<hr>
<p>
<a name="qmmminput"></a>
<font color="purple">How do I run a QM/MM calculation?</font>
<p>
You need to have an nwchem input file (<a href="http://www.emsl.pnl.gov/docs/nwchem/support/qmmm.nw">example for K(H<sub>2</sub>O)<sub>6</sub></a>), and
an associated pdb file (<a href="http://www.emsl.pnl.gov/docs/nwchem/support/K6H2O.pdb">example for K(H<sub>2</sub>O)<sub>6</sub></a>).
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
<a href="http://www.emsl.pnl.gov/docs/nwchem/support/qmmm.nw">example for K(H<sub>2</sub>O)<sub>6</sub></a> contains comments with more information.
<pre>
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 )
</pre>
For detailes on the <tt>eatoms</tt> field, please have a look at the QM/MM section of
the Users' <a href="http://www.emsl.pnl.gov/docs/nwchem/doc/user/node31.html#SECTION003110000000000000000"> Manual</a>.
</p>
<hr>
<br><br>
<p>
<a name="moldynam"></a>
<h3>Molecular Dynamics</h3>
</p>
<hr><p>
<a name="moldynam_restart"></a>
<font color="purple">How do I restart a Molecular Dynamics calculation?
</font>
<p>
The restart file that was used to run the "task md dynamics" will contain the updated coordinates if you have a "record rest ###"
where ### is some number of steps (like 500). The restart file will have the prefix of the system name used in the md input block.
For example,
<pre>
# Start warming solute: initially at 50 K
# This file already exists: QJDa_md1.rst"
md
system QJDa_md1
cutoff 0.9
pme grid 64 order 4
leapfrog equil 0 data 10000 step 0.001
print step 1000 stat 10000
isotherm 50 trelax 0.1 0.1
update pairs 10 center 100 motion 100
record prop 50
record rest 500
record scoor 100
load pairs 20 size 0.75
end
task md dynamics
# Continue warming solute: at 100 K
task shell "cp QJDa_md1.rst QJDa_md2.rst"
md
system QJDa_md2
cutoff 0.9
pme grid 64 order 4
leapfrog equil 0 data 10000 step 0.001
print step 1000 stat 10000
isotherm 100 trelax 0.1 0.1
update pairs 10 center 100 motion 100
record prop 50
record rest 500
record scoor 100
load pairs 20 size 0.75
end
task md dynamics
</pre>
The QJDa_md2.rst file will have the final restart information.
</p>
<hr>
<br><br>
<p>
<a name="dirdyvtst"></a>
<h3>DIRDYVTST</h3>
</p>
<hr>
<p>
<a name="dirdyexamples"></a>
<font color="purple">How do I run a DIRDYVTST calculation?
</font>
<p>
Using the DIRDYVTST module is relatively straightforward and the user is referred to the
DIRDYVTST section of the Users' <a href="http://www.emsl.pnl.gov/docs/nwchem/doc/user/node39.html#SECTION003920000000000000000"> Manual</a>. A <a href="http://www.emsl.pnl.gov/docs/nwchem/support/examples/dirdyvtst/drdyvtst.tar"> set of examples </a> are available in a tar file.
</p>
<hr>
<br><br>
<p>
<a name="linuxclusters"></a>
<h3>Linux Clusters</h3>
</p>
<hr>
<p>
<a name="linuxhw"></a>
<font color="purple">What hardware configuration is suggested for running NWChem on Linux cluster?
</font>
<p>
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 <a href="#giganet">Giganet</a> or <a href="#myrinet"> Myrinet</a> interconnects.
</p>
<hr>
<p>
<a name="myrinet"></a>
<font color="purple">How do I install and run NWChem on Myrinet clusters?
</font>
<p>
Prior to installing NWChem, you must have installed the <a href="http://www.myri.com/scs/linux/index.html">GM</a> and the
<a href="http://www.myri.com/scs/index.html"> MPICH over GM</a>
softwares on the system.
<p>Before starting the NWChem compilation, the following environmental variables
must be defined
<pre>
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=$MPI_LOC/include
LIBMPI=-lmpich
</pre>
To run NWChem, you need to set the following enviromental variable
<pre>
GMPI_SHMEM_FILE /tmp/$USER.gm
</pre>
The next step is to launch the program. One way to do it is by using
the mpirun.ch_gm script supplied in the MPICH-GM tar file. The
command to execute is
<pre>
mpirun.ch_gm --gm-use-shmem $NWCHEM_TOP/bin/LINUX/nwchem
</pre>
or
<pre>
mpiexec $NWCHEM_TOP/bin/LINUX/nwchem
</pre>
<hr>
<p>
<a name="giganet"></a>
<font color="purple">How do I install NWChem on Giganet clusters?
</font>
<p>
Before starting the NWChem compilation, the following environmental variables
must be defined
<pre>
ARMCI_NETWORK=VIA
LIBMPI="-lmpipro -lpthread"
</pre>
To run NWChem, you need to set the following environmental variable
<pre>
MPI_COMM=VIA
</pre>
</p>
<hr>
<p>
<a name="freebsdmem"></a>
<font color="purple">How do I increase the shared memory segment in FreeBSD?</font>
<p>
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):
<pre>
sysctl -w kern.ipc.shmmax=67108864
sysctl -w kern.ipc.shmall=16384
</pre>
the first sysctl allocates 64Mbytes of memory, the second does
the same thing in 4k pages (4k * 16384 = 64M), you <b>must</b> set both
sysctl.
</p>
<hr>
<br><br>
<p>
<a name="ibmsp"></a>
<h3>IBM SP</h3>
</p>
<hr>
<p>
<a name="lapi"></a>
<font color="purple">What is the target for running NWChem on IBM SPs?
</font>
<p>
The right target is <pre>LAPI</pre>
IBM binaries are not going to work on IBM SP systems.
For further details, have a look at the Users's manual <a href="http://www.emsl.pnl.gov/docs/nwchem/doc/user/node40.html#SECTION004050000000000000000">Running on an IBM SP</a>.
</p>
<hr>
<p>
<a name="lapiiniterr"></a>
<font color="purple"> I have a lapi_init error. How do I fix this problem?</font>
<p>
If you get a message similar to:
<pre>
0: lapi_init failed 419(1a3)
system message: Operation not permitted.
ERRIR: 0031-250 task 0: terminated
</pre>
you need to set the environment variable MP_MSG_API. You can either do this in your environment:
<pre>
setenv MP_MSG_API lapi
</pre>
or you can set it in your LoadLeveller script:
<pre>
# @ network.lapi = css0, not_shared, US
</pre>
The LoadLeveller method is preferred since it sets several other useful
variables.
NOTE: If you are using SMP nodes (i.e. more than one processor per node),
change the "not_shared" to "shared".
</p>
<hr>
<p>
<a name="asyncio"></a>
<font color="purple"> I have a load error when trying to run NWChem. How do
I fix this problem?
</font>
<p>
If you get a message similar to:
<pre>
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.
</pre>
The problem is that Asynchronous I/O is not turned on for your system. There
are two possible solutions. The first and best solution is to have the
system administrator turn on Asynchronous I/O on all of the nodes. This can
be done by:
<ol>
<li> Enter smit </li>
<li> Go to "Devices" </li>
<li> Go to "Asynchronous I/O" </li>
<li> Go to "Change / Show Characteristics of Asynchronous I/O" </li>
<li> Change "State of fast path" to "enable" </li>
<li> Make sure "STATE to be configured at system restart" is set to "available" </li>
<li> Exit smit</li>
</ol>
The nodes will need to be rebooted for the change to take effect.
<p>
The second solution is to compile GA without Asynchronous I/O turned on.
This WILL slow down the performance of NWChem.
<ol>
<li>cd $NWCHEM_TOP/src/tools/pario</li>
<li>make TARGET=LAPI clean</li>
<li>make TARGET=LAPI CC="cc -DNOAIO" LARGE_FILES=y</li>
<li>cd $NWCHEM_TOP/src</li>
<li>make link</li>
</ol>
</p>
<hr>
<p>
<a name="rtgrqon"></a>
<font color="purple">Thread scheduling policy change from AIX 4.3 to 4.3.3 which
effects performance.
</font>
<p>
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:
<pre>
setenv RT_GRQ ON
</pre>
or you can set it in your LoadLeveller script:
<pre>
# @ environment = RT_GRQ=ON
</pre>
Note that you may have other variables to set with the environment line. Just
add the variable onto the existing line using a semi-colon as a separator. For
example:
<pre>
# @ environment = COPY_ALL; MP_INFOLEVEL=3; MP_PULSE=0;
MP_SINGLE_THREAD=yes; MP_WAIT_MODE=yield; RT_GRQ=ON; restart=no
</pre>
</p>
<hr>
<p>
<a name="filelimit"></a>
<font color="purple">How do I use more than 2 GB of disk space?</font>
<p>
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.
</p>
<hr>
<br><br>
<p>
<a name="ibm"></a>
<h3>IBM </h3>
</p>
<hr>
<p>
<a name="ibm64python"></a>
<font color="purple">How do I install a Python library
compatible with the NWCHEM_TARGET IBM64?
</font>
<p>
<ol>
<li> download the python source from <a href="http://www.python.org/ftp/python/src/py152.tgz">www.python.org</a> </li>
<li> extract the file from the source tar file and cd to the python
source directory
<li> tell the makefile framework the generate 64-bit object with xlc
<pre> setenv CFLAGS "-q64" </pre>
</li>
<li> configure python
<pre> ./configure --without-gcc </pre>
</li>
<li> instead of typing just <tt>make</tt>, type
<pre> make CC="xlc -q64" AR="ar -X64" </pre>
</li>
<li> instead of typing just <tt>make install</tt>, type
<pre> make CC="xlc -q64" AR="ar -X64" install </pre>
</li>
</ol>
</p>
<hr>
<br><br>
<p>
<a name="win32"></a>
<h3>Windows 32</h3>
</p>
<hr>
<p>
<a name="win32compile"></a>
<font color="purple">How do I compile NWChem on Windows NT and
Windows 98?</font>
<p>
The right target is <tt>WIN32.</tt> 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
(<a href="http://www-unix.mcs.anl.gov/~ashton/mpich.nt/">http://www-unix.mcs.anl.gov/~ashton/mpich.nt/</a> ).
Then, you need to have defined this series of variables (that you can
set in <tt> autoexec.bat</tt>)
<pre>
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
</pre>
To start the compilation, start the Microsoft makefile utility from
the top level source directory by typing
<pre>
nmake
</pre>
The name of the executable is <tt> nw32.exe </tt>
</p>
<hr>
<br><br>
<p>
<a name="sgi"></a>
<h3>SGI</h3>
</p>
<hr>
<p>
<a name="sgimpi"></a>
<font color="purple">How can I improve parallel performances under SGI?</font>
<p>Use the MPI vendor library, after defining the usual environmental
variable to replace TCGMSG with MPI
<pre>
USE_MPI=y
</pre>
<p>
<hr>
<a name="sgitfpscs"></a>
<font color="purple">How can I improve performances under SGITFP?</font>
<p>Install the SCSL scientific library, freely available from the <a href="http://www.sgi.com/software/scsl.html" target="_blank"> SGI web site </a>, then link the
code with the following environmental variable
<pre>
BLASOPT=-lscs_blas_i8
</pre>
</p>
<hr>
<p>
<a name="sgitfpmpich"></a>
<font color="purple">How do I install the MPI version of SGITFP?</font>
<p> You need to have installed a 64-bit version of MPICH. In order to
do that, you need to run configure with the following arguments
<pre>
./configure --with-arch=IRIX64 --with-device=ch_p4 ---prefix=/usr/local\
--disable-f90 --disable-f90modules
</pre>
</p>
<hr>
<br><br>
<p>
<a name="itanium"></a>
<h3>Itanium</h3>
</p>
<hr>
<p>
<a name="itaniumcompiler"></a>
<font color="purple">Which version of the Intel compiler should I use?</font>
<p>When compiling NWChem with the Intel compilers, we recommend using the Intel 7.0 compiler over the
6.0 compiler because of performance and stability issues.
</p>
<p><hr>
<i>Updated: Friday May 21 17:01:35 PDT 2004 <br>
Created by: Theresa Windus<br></i>
</p>
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