From NWChem
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| 2:13:11 PM PDT - Fri, Apr 25th 2014 |
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(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
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Huub Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop
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Forum Regular
Threads 1
Posts 185
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| 2:32:35 PM PDT - Fri, Apr 25th 2014 |
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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
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Huub Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop
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Forum Regular
Threads 1
Posts 185
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| 2:54:59 PM PDT - Fri, Apr 25th 2014 |
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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
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Posts 12
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| 5:34:31 PM PDT - Sat, Apr 26th 2014 |
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what if I do fractional nuclear charge dft? it seems it failed
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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
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Edited On 5:37:40 PM PDT - Sat, Apr 26th 2014 by Bsmile
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| 5:39:04 PM PDT - Sat, Apr 26th 2014 |
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and its output is ...
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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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Edited On 5:41:53 PM PDT - Sat, Apr 26th 2014 by Bsmile
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