Wrong format for small values in cube files created by dplot

Clicked A Few Times

9:47:16 AM PST - Mon, Jan 18th 2016

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

Forum Vet

12:48:26 PM PST - Mon, Jan 18th 2016
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

Clicked A Few Times

5:24:55 PM PST - Mon, Jan 18th 2016

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

Forum Vet

12:43:30 PM PST - Fri, Jan 22nd 2016
Patch available
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://nwchemgit.github.io/images/Dplot_tolrho.patch.gz

Clicked A Few Times

1:01:05 PM PST - Fri, Jan 22nd 2016
Dear Edoapra, Thank you very much. I will try to use the patch. My best, futofuji

Forum >> NWChem's corner >> Running NWChem