Wrong format for small values in cube files created by dplot

From NWChem

Viewed 1013 times, With a total of 4 Posts
Jump to: navigation, search

Clicked A Few Times
Threads 3
Posts 9

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.

Edited On 9:53:28 AM PST - Mon, Jan 18th 2016 by Futofuji

Forum Vet
Threads 7
Posts 1354
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
Threads 3
Posts 9
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/
memory stack 1000 heap 2000 global 1024 mb noverify

set geometry pcbm_pt12
  TITLE chargeDensityDFT
  vectors ../perm/gs.movecs
 -30.0 30.0 150  
 -20.0 20.0 100 
 -20.0 20.0 100
  spin total
  output chargeDensityDFT.cube
task dplot

  TITLE chargeDensityCDFT
  vectors ../perm/et.movecs
 -30.0 30.0 150  
 -20.0 20.0 100 
 -20.0 20.0 100
  spin total
  output chargeDensityCDFT.cube
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/
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

 * library 6-31G*

set geometry pcbm_pt12
  xc HFexch
  iterations 1000
  mult 1
  vectors input atomic output ./perm/gs.movecs
charge 0
task dft

set geometry pcbm_pt12
  xc HFexch
  iterations 1000
  mult 1
  convergence nolevelshifting
  cdft 107 194 charge -1.0
  vectors input ./perm/gs.movecs swap beta 486 487 output ./perm/et.movecs
charge 0
task dft

  vectors reactants et.movecs
  vectors products  gs.movecs
task scf et

The structure file:
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,

Edited On 5:37:14 PM PST - Mon, Jan 18th 2016 by Futofuji

Forum Vet
Threads 7
Posts 1354
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


Clicked A Few Times
Threads 3
Posts 9
Dear Edoapra,

Thank you very much. I will try to use the patch.

My best,

Forum >> NWChem's corner >> Running NWChem

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

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