a new user of nwchem, several issue for help!!

Clicked A Few Times

2:13:11 PM PDT - Fri, Apr 25th 2014

(1) as usually I want to type make to only compile the file I just modified and then link to executable. But to my surprise, it goes over the whole compilation again, which takes a long time. Is there a way to avoid it?

(2) I am trying to work with fractional nuclear charge, so I used some input file as the following

start h2o

title "Water in 6-31g basis set"

geometry units au

  O      0.00000000    0.00000000    0.00000000

  Z      0.00000000    1.43042809   -1.10715266     charge 0.1

  H      0.00000000   -1.43042809   -1.10715266

end

basis

  Z library 6-31g

  H library 6-31g

  O library 6-31g

end

task scf

then, it complains

0:0:geom_input:center is neither atom nor bq:: -1

which is quite understandable if my interpretation is right to link the charge to a specified basis set file. So, how can I possibly fix this issue? (I want to use H library 6-31g for the factitious Z atom).

Thank you very much!

John

Forum Regular

2:32:35 PM PDT - Fri, Apr 25th 2014

Hi John,

Ad 1. Say you have changed nwchem/src/ddscf/rohf.F then of course you only want to recompile rohf.F and then relink. To do this you will need to have all the relevant environment variables set (the build_nwchem script in the development version will now write two files, nwchem/nwchem_make_env.sh and nwchem/nwchem_make_env.csh that contain a list of all relevant settings such that in C-shell you can just type

    source nwchem/nwchem_make_env.csh

and in Bash you can just type

   . nwchem/nwchem_make_env.sh

to load all the environment variables you need to compile NWChem in a way compatible with what the build_nwchem script found). Once you have all the relevant environment variables set you go into the directory where you changed the file (in our example nwchem/src/ddscf) and then issue the following command

    make FC=$FC; pushd $NWCHEM_TOP/src; make FC=$FC link; popd

and you will quickly get a new executable.

Best wishes, Huub

Forum Regular

2:54:59 PM PDT - Fri, Apr 25th 2014
Hi John, Ad 2. I think the following input will do what you want: start h2o title "Water in 6-31g basis set" geometry units au O 0.00000000 0.00000000 0.00000000 Bq_H 0.00000000 1.43042809 -1.10715266 charge 0.1 H 0.00000000 -1.43042809 -1.10715266 end charge 0.1 basis Bq_H library H 6-31g H library 6-31g O library 6-31g end scf doublet end task scf The program assumes that the number of electrons is integer. Therefore if I introduce a fractional nuclear charge I will also need a fractional charge overall. The basis set directives allow you to specify a particular basis set for a label in your geometry. For example "H library O 6-31g" puts the Oxygen 6-31g basis set on Hydrogen atoms (normally not a particularly useful thing to do, but you can). Finally, your idea with the label Z does not work. NWChem recognizes three kinds of centers: Atoms, Bq, or X. The label Z corresponds to none of those and so the program will crash. I hope this helps. Huub

Clicked A Few Times

5:34:31 PM PDT - Sat, Apr 26th 2014
what if I do fractional nuclear charge dft? it seems it failed
Thanks, it helped quite a lot. What I try to do is DFT calculation, the following is what I modified, but it complains "Last System Error Message from Task 0:: Numerical result out of range", any further help on that? Thanks, input.nw: start h2o title "Water in 6-31g basis set" geometry units au O 0.00000000 0.00000000 0.00000000 Bq_H 0.00000000 1.43042809 -1.10715266 charge 0.1 H 0.00000000 -1.43042809 -1.10715266 end charge -0.9 basis Bq_H library H 6-31g H library 6-31g O library 6-31g end dft xc pbe0 end task dft

Clicked A Few Times

5:39:04 PM PDT - Sat, Apr 26th 2014
and its output is ...
detailed output is ... Caching 1-el integrals General Information ------------------- SCF calculation type: DFT Wavefunction type: closed shell. No. of atoms : 3 No. of electrons : 10 Alpha electrons : 5 Beta electrons : 5 Charge : -1 (charge should be -0.9, but is shown as -1) Spin multiplicity: 1 Use of symmetry is: on ; symmetry adaption is: on Maximum number of iterations: 30 AO basis - number of functions: 13 number of shells: 9 Convergence on energy requested: 1.00D-06 Convergence on density requested: 1.00D-05 Convergence on gradient requested: 5.00D-04 XC Information -------------- ... Integral file = ./h2o.aoints.0 Record size in doubles = 65536 No. of integs per rec = 43688 Max. records in memory = 2 Max. records in file = 3249444 No. of bits per label = 8 No. of bits per value = 64 Last System Error Message from Task 0:: Numerical result out of range MPI_ABORT was invoked on rank 0 in communicator MPI COMMUNICATOR 4 DUP FROM 0 with errorcode 11. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. MA_verify_allocator_stuff: starting scan ... stack block 'DENS', handle 63, address 0x2b2c50e6a230: current checksum 13787195202806311060 != stored checksum 13799611636979891228

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