geometry change between input and output as cube file using dplot

From NWChem

Viewed 189 times, With a total of 5 Posts
Jump to: navigation, search

Just Got Here
Threads 1
Posts 4
Dear All

I am currently comparing my own finite element DFT calculations for CH4,NH3,H20,C2H4,C2H6
with results of NWCHEM for the same functional and geometries.
In addition to comparing the total energies which agree to a few parts in 10^-4 between finite element and NWCHEM
I proceeded to also compare the densities obtained.
For CH4 this showed and angle of less then 1 degree between the densities of compatible cube files considered as vectors.
However for ammonia the angle came out much larger. On closer inspection I realized, that
the cube files from the different methods also had different geometries in their headers, although
the had been the same at input time. It seems some recentering and rotation had been applied by
nwchem at some point.

I would appreciate any assistance to get around that, since I really would like to compare the densities
for all five molecules!


Regards

Moritz

Just Got Here
Threads 1
Posts 4
geometry change between input and output : nocenter option in geometry section ignored
Dear All

I have now established, that the nocenter option in the geometry section is being ignored with version 6.8 of
NWCHEM

Regards

Moritz

Forum Vet
Threads 10
Posts 1632
Could you please post input and output files?
Thanks

Just Got Here
Threads 1
Posts 4
input output and header of cube file
Dear All

the input file is

Contents

===
memory stack 1500 mb heap 1000 mb global 1000 mb
start ammonia
geometry noautoz nocenter
n 0.0000 0.0000 0.0000
h 0.0000 -0.9377 -0.3816
h 0.8121 0.4689 -0.3816
h -0.8121 0.4689 -0.3816
end
basis
  • library cc-pvtz
end
dft
XC slater pw91lda
vectors output ammonia.movecs
end
task dft
dplot
 TITLE DENSITY
vectors ammonia.movecs
LimitXYZ units bohr
-6.0 6.0 200
-6.0 6.0 200
-6.0 6.0 200
spin total
gaussian
output density.cube
end
task dplot

==


the output of the run upto the
point where the
"output coordinates" are given is
==========
argument  1 = ammonia.nw




             Northwest Computational Chemistry Package (NWChem) 6.8
------------------------------------------------------


                   Environmental Molecular Sciences Laboratory
Pacific Northwest National Laboratory
Richland, WA 99352

                             Copyright (c) 1994-2017
Pacific Northwest National Laboratory
Battelle Memorial Institute

            NWChem is an open-source computational chemistry package
distributed under the terms of the
Educational Community License (ECL) 2.0
A copy of the license is included with this distribution
in the LICENSE.TXT file

                                 ACKNOWLEDGMENT
--------------

           This software and its documentation were developed at the
EMSL at Pacific Northwest National Laboratory, a multiprogram
national laboratory, operated for the U.S. Department of Energy
by Battelle under Contract Number DE-AC05-76RL01830. Support
for this work was provided by the Department of Energy Office
of Biological and Environmental Research, Office of Basic
Energy Sciences, and the Office of Advanced Scientific Computing.


          Job information
---------------

   hostname        = braunm-Latitude-5590
program = nwchem
date = Mon Feb 25 11:20:07 2019

   compiled        = Fri_Aug_10_20:13:27_2018
source = /build/nwchem-UgfcOn/nwchem-6.8+47+gitdf6c956
nwchem branch = 6.8
nwchem revision = v6.8-47-gdf6c956
ga revision = ga-5.6.3
use scalapack = T
input = ammonia.nw
prefix = ammonia.
data base = ./ammonia.db
status = startup
nproc = 1
time left = -1s



          Memory information
------------------

   heap     =  131071994 doubles =   1000.0 Mbytes
stack = 196607999 doubles = 1500.0 Mbytes
global = 131072000 doubles = 1000.0 Mbytes (distinct from heap & stack)
total = 458751993 doubles = 3500.0 Mbytes
verify = yes
hardfail = no


          Directory information
---------------------

 0 permanent = .
0 scratch = .




                               NWChem Input Module
-------------------



Scaling coordinates for geometry "geometry" by  1.889725989
(inverse scale = 0.529177249)

C3V symmetry detected


                            Geometry "geometry" -> ""
-------------------------

Output coordinates in angstroms (scale by  1.889725989 to convert to a.u.)

 No.       Tag          Charge          X              Y              Z
---- ---------------- ---------- -------------- -------------- --------------
1 n 7.0000 0.00000000 0.00000000 0.06776231
2 h 1.0000 0.66307724 0.66307724 -0.31383769
3 h 1.0000 -0.90578035 0.24270311 -0.31383769
4 h 1.0000 0.24270311 -0.90578035 -0.31383769

=============

Thus nwchem does recenter the molecule inspite of the keyword 'nocenter'
Thus I cannot compare the density with the density resulting from my finite element code.


Regards

Moritz

Forum Vet
Threads 10
Posts 1632
noautosym is likely to be what you are looking for


geometry noautoz nocenter noautosym
n  0.0000  0.0000  0.0000
h  0.0000 -0.9377 -0.3816
h  0.8121  0.4689 -0.3816
h -0.8121  0.4689 -0.3816



  No.       Tag          Charge          X              Y              Z
 ---- ---------------- ---------- -------------- -------------- --------------
    1 n                    7.0000     0.00000000     0.00000000     0.00000000
    2 h                    1.0000     0.00000000    -0.93770000    -0.38160000
    3 h                    1.0000     0.81210000     0.46890000    -0.38160000
    4 h                    1.0000    -0.81210000     0.46890000    -0.38160000
Edited On 10:40:32 AM PST - Fri, Mar 1st 2019 by Edoapra

Just Got Here
Threads 1
Posts 4
Thanks a Million
Dear Edopara

Thanks a million!

That is the solution.

Regards

Moritz


Forum >> NWChem's corner >> NWChem functionality



Who's here now Members 0 Guests 1 Bots/Crawler 0


AWC's: 2.5.10 MediaWiki - Stand Alone Forum Extension
Forum theme style by: AWC