From NWChem
Viewed 1164 times, With a total of 4 Posts
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Clicked A Few Times
Threads 3
Posts 9
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| 8:47:16 AM PST - Mon, Jan 18th 2016 |
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Hi,
I found a wrong output format for small values in cube files which were created by dplot-module when I was using NWChem 6.6.
A part of my cube file is shown:
0.14346E-35 0.55300E-38 0.14745E-40 0.27194E-43 0.34691E-46 0.30612E-49
0.18685E-52 0.78885E-56 0.23037E-59 0.46535E-63 0.65021E-67 0.62841E-71
0.42010E-75 0.19426E-79 0.62136E-84 0.13747E-88 0.21038E-93 0.22270E-98
0.16306-103 0.82585-109 0.28932-114 0.70108-120 0.11751-125 0.13624-131
0.10926-137 0.60610-144 0.23256-150 0.61724-157 0.11331-163
0.51661-283 0.66820-274 0.59782-265 0.36996-256 0.15836-247 0.46890-239
0.96033-231 0.13605-222 0.13331-214 0.90359-207 0.42364-199 0.13739-191
0.30818-184 0.47818-177 0.51321-170 0.38100-163 0.19564-156 0.69491-150
0.17073-143 0.29015-137 0.34107-131 0.27733-125 0.15598-119 0.60679-114
0.16329-108 0.30393-103 0.39131E-98 0.34848E-93 0.21467E-88 0.91469E-84
0.26959E-79 0.54960E-75 0.77502E-71 0.75597E-67 0.51005E-63 0.23803E-59
0.76839E-56 0.17157E-52 0.26499E-49 0.28310E-46 0.20920E-43 0.10693E-40
here, very small values (<1.0e-99) are written in wrong format, i.e., missing of "E".
Any comments are welcome.
Besides, I would like to ask anyone to post a patch file to fix this problem.
futofuji
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Edited On 8:53:28 AM PST - Mon, Jan 18th 2016 by Futofuji
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Edoapra Forum:Admin, Forum:Mod, bureaucrat, sysop
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Forum Vet
Threads 9
Posts 1401
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| 11:48:26 AM PST - Mon, Jan 18th 2016 |
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Could you please provide the input file that resulted in this cube file?
I have looked at the code that generates the cube output, and it should automatically set to zero tiny values.
Cheers, Edo
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Clicked A Few Times
Threads 3
Posts 9
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| 4:24:55 PM PST - Mon, Jan 18th 2016 |
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Hi, Edo
Thank you for your replying and checking.
>it should automatically set to zero tiny values.
Actually, almost all of tiny values are set as zero even if the "E"-missing occurs.
My input files are shown below:
TITLE "pcbm_pf12tbt-1_hf_631gs_ct2gs_homo-lumo"
restart pcbm_pf12tbt-1_hf_631gs_ct2gs_homo-lumo
permanent_dir ../perm
scratch_dir /work/users/uh4/
echo
memory stack 1000 heap 2000 global 1024 mb noverify
set geometry pcbm_pt12
dplot
TITLE chargeDensityDFT
vectors ../perm/gs.movecs
LimitXYZ
-30.0 30.0 150
-20.0 20.0 100
-20.0 20.0 100
spin total
gaussian
output chargeDensityDFT.cube
end
task dplot
dplot
TITLE chargeDensityCDFT
vectors ../perm/et.movecs
LimitXYZ
-30.0 30.0 150
-20.0 20.0 100
-20.0 20.0 100
spin total
gaussian
output chargeDensityCDFT.cube
end
task dplot
TITLE "pcbm_pf12tbt-1_hf_631gs_ct2gs_homo-lumo"
start pcbm_pf12tbt-1_hf_631gs_ct2gs_homo-lumo
permanent_dir ./perm
scratch_dir /work/users/uh4/
echo
memory stack 1000 heap 2000 global 1024 mb noverify
geometry pcbm_pt12 units angstroms print xyz noautoz noautosym
load format xyz /home/users/uh4/research-ccpg/OrgSolCells/pcbm_pf12tbt/pcbm_pf12tbtx2/pm3d_opt/optimized_structure/pcbm_pf12tbtx2fixed_pm3d_opted.xyz
end
basis
* library 6-31G*
end
set geometry pcbm_pt12
dft
xc HFexch
odft
iterations 1000
mult 1
direct
mulliken
vectors input atomic output ./perm/gs.movecs
end
charge 0
task dft
set geometry pcbm_pt12
dft
xc HFexch
odft
iterations 1000
mult 1
direct
convergence nolevelshifting
cdft 107 194 charge -1.0
mulliken
vectors input ./perm/gs.movecs swap beta 486 487 output ./perm/et.movecs
end
charge 0
task dft
et
vectors reactants et.movecs
vectors products gs.movecs
fock
end
task scf et
The structure file:
194
1-106:pf12tbt, 107-194:pcbm
C -1.938148e+01 1.909600e+00 -1.220630e+00
C -1.869910e+01 3.075380e+00 -9.877600e-01
S -1.835764e+01 5.201900e-01 -1.092950e+00
C -1.732568e+01 2.852860e+00 -7.104400e-01
C -1.695549e+01 1.519630e+00 -7.329400e-01
H -2.043347e+01 1.786760e+00 -1.445760e+00
H -1.915967e+01 4.057580e+00 -1.006650e+00
H -1.662834e+01 3.652260e+00 -4.862200e-01
C -1.284697e+01 2.579000e-02 -7.543000e-02
C -1.318604e+01 1.361700e+00 -2.523700e-01
C -1.396213e+01 -8.893600e-01 -1.307400e-01
C -1.450282e+01 1.823550e+00 -4.743100e-01
C -1.532186e+01 -4.057300e-01 -3.508700e-01
C -1.561222e+01 9.921000e-01 -5.236600e-01
H -1.463683e+01 2.889840e+00 -6.215400e-01
H -1.240244e+01 2.113430e+00 -2.284300e-01
N -1.389904e+01 -2.217430e+00 2.330000e-03
N -1.623227e+01 -1.381660e+00 -3.754400e-01
S -1.542989e+01 -2.793420e+00 -1.407000e-01
C -8.961250e+00 -5.253400e-01 4.450900e-01
C -9.590480e+00 -1.749800e+00 5.313500e-01
S -1.014061e+01 7.315500e-01 1.313800e-01
C -1.099378e+01 -1.693200e+00 3.614000e-01
C -1.147866e+01 -4.170100e-01 1.380300e-01
H -1.164471e+01 -2.555060e+00 4.080100e-01
H -9.050570e+00 -2.666650e+00 7.418400e-01
C -7.533830e+00 -2.390200e-01 5.669400e-01
C -7.061230e+00 1.040300e+00 9.303200e-01
C -6.595360e+00 -1.266270e+00 3.194500e-01
C -5.698920e+00 1.306090e+00 1.046800e+00
H -7.776970e+00 1.829800e+00 1.142530e+00
C -5.243320e+00 -1.005140e+00 4.423200e-01
H -6.943070e+00 -2.248010e+00 9.910000e-03
C -4.784600e+00 2.785900e-01 8.036600e-01
H -5.359190e+00 2.299000e+00 1.329850e+00
C -3.325750e+00 2.564600e-01 8.379000e-01
C -2.889210e+00 -1.040220e+00 4.962400e-01
C -2.393570e+00 1.255630e+00 1.126610e+00
C -1.540920e+00 -1.340860e+00 4.344900e-01
C -1.036060e+00 9.495500e-01 1.073620e+00
H -2.716310e+00 2.257830e+00 1.396660e+00
C -5.842300e-01 -3.426100e-01 7.271900e-01
H -1.209190e+00 -2.332390e+00 1.385600e-01
H -3.088200e-01 1.717700e+00 1.321410e+00
C -4.074270e+00 -1.952630e+00 2.121400e-01
C -4.049420e+00 -2.469870e+00 -1.238930e+00
H -4.942990e+00 -3.073380e+00 -1.440810e+00
H -4.022720e+00 -1.636440e+00 -1.949190e+00
H -3.164330e+00 -3.097160e+00 -1.401870e+00
C -4.115740e+00 -3.142170e+00 1.190350e+00
H -4.134140e+00 -2.792970e+00 2.228490e+00
H -5.011270e+00 -3.749420e+00 1.009210e+00
H -3.233000e+00 -3.778410e+00 1.050350e+00
C 8.397000e-01 -6.665000e-01 6.661400e-01
C 1.426170e+00 -1.913620e+00 7.680600e-01
S 2.061950e+00 5.650900e-01 4.415200e-01
C 2.833230e+00 -1.884640e+00 6.708700e-01
H 8.546400e-01 -2.818590e+00 9.434100e-01
C 3.361990e+00 -6.165300e-01 4.875100e-01
H 3.450380e+00 -2.772060e+00 7.565300e-01
C 4.768140e+00 -2.796300e-01 3.292600e-01
C 5.742740e+00 -1.257550e+00 1.775200e-01
C 5.266650e+00 1.070050e+00 3.165100e-01
C 7.119500e+00 -9.763400e-01 3.968000e-02
H 5.443260e+00 -2.299820e+00 1.508300e-01
C 6.688650e+00 1.365840e+00 1.709000e-01
N 4.508750e+00 2.162350e+00 4.314700e-01
C 7.658470e+00 3.055200e-01 3.110000e-02
H 7.783450e+00 -1.828120e+00 -7.611000e-02
N 6.949480e+00 2.676370e+00 1.835200e-01
S 5.515700e+00 3.456350e+00 3.608100e-01
C 9.082140e+00 5.605100e-01 -1.105300e-01
S 1.024421e+01 -7.651900e-01 -1.751400e-01
C 9.750030e+00 1.767900e+00 -2.105400e-01
C 1.159884e+01 3.314600e-01 -3.549100e-01
C 1.115155e+01 1.636280e+00 -3.472300e-01
H 9.229690e+00 2.715290e+00 -1.947300e-01
C 1.297647e+01 -1.413800e-01 -4.743400e-01
H 1.182174e+01 2.480480e+00 -4.677300e-01
C 1.328153e+01 -1.437770e+00 -9.404600e-01
C 1.403810e+01 7.223300e-01 -1.232200e-01
C 1.459919e+01 -1.875630e+00 -1.060460e+00
H 1.247178e+01 -2.101250e+00 -1.231810e+00
C 1.534554e+01 2.909100e-01 -2.509300e-01
H 1.381861e+01 1.712770e+00 2.658400e-01
C 1.563674e+01 -1.006810e+00 -7.173400e-01
H 1.480939e+01 -2.877810e+00 -1.425210e+00
C 1.662451e+01 1.049430e+00 7.238000e-02
C 1.708984e+01 -1.178040e+00 -7.369900e-01
C 1.768386e+01 1.466000e-02 -2.783700e-01
C 1.668577e+01 1.433670e+00 1.563350e+00
C 1.676151e+01 2.313110e+00 -7.985400e-01
C 1.787902e+01 -2.266350e+00 -1.115150e+00
C 1.906546e+01 1.270900e-01 -1.943000e-01
H 1.587432e+01 2.130040e+00 1.808710e+00
H 1.658864e+01 5.463000e-01 2.198270e+00
H 1.764133e+01 1.922990e+00 1.789090e+00
H 1.671801e+01 2.059030e+00 -1.863240e+00
H 1.595139e+01 3.017880e+00 -5.732400e-01
H 1.771808e+01 2.810600e+00 -5.961500e-01
C 1.926912e+01 -2.149220e+00 -1.029630e+00
H 1.742253e+01 -3.187320e+00 -1.469450e+00
C 1.985931e+01 -9.637400e-01 -5.729700e-01
H 1.952613e+01 1.046490e+00 1.600100e-01
H 1.989906e+01 -2.985890e+00 -1.320160e+00
H 2.094191e+01 -8.902500e-01 -5.119600e-01
C -1.167586e+00 3.008800e+00 -7.957601e+00
C -7.158734e-01 2.035727e+00 -8.926534e+00
C -1.485174e+00 9.396285e-01 -9.213686e+00
C -8.907681e-01 -3.845615e-01 -9.553629e+00
C -2.695175e-02 -6.913483e-01 -1.075076e+01
C 1.960282e-01 3.784706e-01 -1.179916e+01
H 8.677364e-01 -2.290909e-02 -1.257468e+01
C -1.062496e+00 9.368020e-01 -1.242737e+01
C -1.723260e+00 1.368885e-02 -1.342955e+01
H -2.050743e+00 5.849212e-01 -1.431046e+01
H -9.996112e-01 -7.315554e-01 -1.379799e+01
C -2.937223e+00 -6.938786e-01 -1.289054e+01
O -3.280392e+00 -1.741184e+00 -1.363529e+01
C -4.264555e+00 -2.603227e+00 -1.323516e+01
H -4.309139e+00 -3.299181e+00 -1.406620e+01
H -5.220558e+00 -2.105877e+00 -1.309837e+01
H -3.972675e+00 -3.117926e+00 -1.232148e+01
O -3.607074e+00 -4.470543e-01 -1.194210e+01
H -7.871243e-01 1.868224e+00 -1.294395e+01
H -1.768472e+00 1.236022e+00 -1.163429e+01
H 7.427631e-01 1.218633e+00 -1.133949e+01
C -1.558477e-02 -2.060035e+00 -1.132559e+01
C 1.185343e+00 -2.580358e+00 -1.180172e+01
C 1.217561e+00 -3.845551e+00 -1.236196e+01
H 2.157137e+00 -4.249892e+00 -1.272743e+01
C 5.534711e-02 -4.596158e+00 -1.245787e+01
H 8.274183e-02 -5.585906e+00 -1.290418e+01
C -1.139061e+00 -4.081913e+00 -1.198136e+01
H -2.058294e+00 -4.657220e+00 -1.205867e+01
H 2.096704e+00 -1.991273e+00 -1.172777e+01
C -1.173541e+00 -2.821658e+00 -1.140801e+01
H -2.113445e+00 -2.429494e+00 -1.101671e+01
C 6.372409e-01 -5.067097e-01 -9.407008e+00
C 1.363037e+00 7.086387e-01 -8.946820e+00
C 2.404006e+00 3.222563e-01 -8.031390e+00
C 2.264163e+00 -1.092665e+00 -7.760648e+00
C 2.544017e+00 -1.581902e+00 -6.500235e+00
C 1.680126e+00 -2.578459e+00 -5.913001e+00
C 5.796895e-01 -3.023714e+00 -6.617860e+00
C 3.021390e-01 -2.508512e+00 -7.940329e+00
C -1.153363e+00 -2.388291e+00 -8.072576e+00
C -1.745697e+00 -2.833307e+00 -6.831454e+00
C -2.870430e+00 -2.207380e+00 -6.332180e+00
C -3.442425e+00 -1.094881e+00 -7.052277e+00
C -2.863023e+00 -6.750058e-01 -8.233460e+00
C -3.908765e+00 -1.216818e-01 -6.081789e+00
C -3.775204e+00 1.224315e+00 -6.341430e+00
C -3.169087e+00 1.665147e+00 -7.584392e+00
C -3.346674e+00 2.127482e+00 -5.290915e+00
C -2.478027e+00 3.124979e+00 -5.886586e+00
C -1.379137e+00 3.584262e+00 -5.193266e+00
C -1.169004e-01 3.779023e+00 -5.881976e+00
C 9.515618e-01 3.395606e+00 -4.978465e+00
C 2.071173e+00 2.756685e+00 -5.466510e+00
C 2.178908e+00 2.466038e+00 -6.883686e+00
C 1.157753e+00 2.821054e+00 -7.742304e+00
C 2.646822e+00 1.641800e+00 -4.738292e+00
C 3.109215e+00 6.653876e-01 -5.705670e+00
C 2.070680e+00 1.220228e+00 -3.559115e+00
C 1.929660e+00 -1.977912e-01 -3.288774e+00
C 2.372733e+00 -1.126105e+00 -4.206261e+00
C 6.641613e-01 -3.990348e-01 -2.611866e+00
C -9.323548e-02 -1.518667e+00 -2.876034e+00
C 3.699233e-01 -2.491980e+00 -3.844948e+00
C -7.843386e-01 -2.970995e+00 -4.582060e+00
C -1.960622e+00 -2.300327e+00 -4.060332e+00
C -1.531438e+00 -1.398761e+00 -3.009725e+00
C -2.140574e+00 -1.701932e-01 -2.862997e+00
C -3.212190e+00 2.202804e-01 -3.758413e+00
C -1.343050e+00 1.005813e+00 -2.578046e+00
C -1.917064e+00 2.124008e+00 -3.301507e+00
C 2.444379e-02 8.932994e-01 -2.459169e+00
C 8.932077e-01 1.894043e+00 -3.046696e+00
C 3.484619e-01 2.956139e+00 -3.735669e+00
C -1.091861e+00 3.072648e+00 -3.867734e+00
C -3.072524e+00 1.638313e+00 -4.031122e+00
C -3.620731e+00 -6.380419e-01 -4.757477e+00
C -2.978565e+00 -1.929633e+00 -4.912178e+00
C -6.804886e-01 -3.227823e+00 -5.931693e+00
C 1.571244e+00 -2.300976e+00 -4.493135e+00
C 2.976054e+00 -6.811628e-01 -5.447387e+00
C 2.816813e+00 1.179332e+00 -7.030770e+00
C 1.136472e+00 -1.584242e+00 -8.509219e+00
C -1.711793e+00 -1.351501e+00 -8.771234e+00
C -2.723041e+00 7.390481e-01 -8.506362e+00
C 7.399499e-01 1.917995e+00 -8.790931e+00
C -1.545896e-02 3.497411e+00 -7.226802e+00
C -2.371176e+00 2.834864e+00 -7.304151e+00
May I send the output cubes?
Please tell me another way to send the cubes because the size of cube is ca. 20MB if you need the cubes.
Thank you very much for your kindness.
My best,
futofuji
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Edited On 4:37:14 PM PST - Mon, Jan 18th 2016 by Futofuji
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Edoapra Forum:Admin, Forum:Mod, bureaucrat, sysop
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Forum Vet
Threads 9
Posts 1401
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| 11:43:30 AM PST - Fri, Jan 22nd 2016 |
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Patch available
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Dear Futufuj
Thanks for providing the input file(s).
I was able to reproduce the bug.
Here is the patch the addresses this bug
http://www.nwchem-sw.org/images/Dplot_tolrho.patch.gz
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Clicked A Few Times
Threads 3
Posts 9
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| 12:01:05 PM PST - Fri, Jan 22nd 2016 |
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Dear Edoapra,
Thank you very much. I will try to use the patch.
My best,
futofuji
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