QuantumATK Forum
QuantumATK => General Questions and Answers => Topic started by: lihong on August 6, 2010, 12:02
-
Dear Sir:
I am new to use this powerful software ATK. I have some question which I could not solve by myself.
(1)The structure is displayed by “Ball” form. And I tried to change its form to “ball-stick” form but unfortunately it failed.
(2)Could I load the structure from the DMol3 directly to the ATK? If yes, how it can be transferred?
(3)When I construct the nanowires in ATK, I want to edit the structure and in your tutorials , it is mentioned an example that :
ribbon = NanoRibbon(3,0,dangling_atom=Boron,dangling_bond_length=1.5*Angstrom)
ribbon = ribbon.repeat(1,1,10)
Should this statement be saved by a vnl. fie and load it to where and then construct these nanostructures?
Lihong
-
Dear Sir:
I am new to use this powerful software ATK. I have some question which I could not solve by myself.
(1)The structure is displayed by “Ball” form. And I tried to change its form to “ball-stick” form but unfortunately it failed.
Ball-and-stick visualization is not implemented yet in ATK 10.8. But it has no influence on the calculations, and the bonding information is not used for the DFT or Huckel models.
(2)Could I load the structure from the DMol3 directly to the ATK? If yes, how it can be transferred?
If it's a molecule, then use XYZ format, which can be directly imported in ATK and VNL. For periodic structures, try the CAR file format which can also be read by VNL.
(3)When I construct the nanowires in ATK, I want to edit the structure and in your tutorials , it is mentioned an example that :
ribbon = NanoRibbon(3,0,dangling_atom=Boron,dangling_bond_length=1.5*Angstrom)
ribbon = ribbon.repeat(1,1,10)
Should this statement be saved by a vnl. fie and load it to where and then construct these nanostructures?
Maybe you meant .py file, but vnl files are not used anymore in ATK 10.8, and would anyway not be relevant. To use scripting commands, you can make a Python script and drop it on the relevant instrument, or just type the code above into the Editor and use the "Send to" button to transfer the structure to the Viewer or Builder.
-
Thanks for your expert answers. But I have another question.
In your reply, you mentioned that we can try car.file to tranfer to the VNL.
I use the "Script Generator" to open this car.file. But I find that there is an error. The error details is as follows:
traceback (most recent call last):
An error occurred
The following error message was generated when running the script:
invalid syntax (, line 1)
Typically this is caused by a syntax error or a spelling mistake; the message above should be helpful in correcting the issue in such cases.
I am not sure about this. Is the way to transfer this car.file to ATK wrong?
Lihong
-
Can you post the CAR file, could be something unsupported in it.
Also check the error message (click Details) and let us know what it says.
-
Oh, wait. How do you "open" it? You need to drop the file it on the Scripter icon, you cannot use "Send to" or any other method.
-
Ok, I will post this car file. If I drop it in the script generator. It will show the error.
!BIOSYM archive 3
PBC=ON
!DATE Aug 05 04:51:54 2010
PBC 21.7228 21.7228 21.7228 90.0000 90.0000 90.0000
Si1 6.951233118 8.179567417 -0.001159301 XXXX 1 xx Si 0.000
Ge1 8.454999167 6.533623326 3.491935756 XXXX 1 xx Ge 0.000
Ge2 8.403318787 9.619740340 1.183166948 XXXX 1 xx Ge 0.000
Ge3 9.870494273 8.132030697 2.391447693 XXXX 1 xx Ge 0.000
Si2 12.657601703 8.348256068 -0.306446793 XXXX 1 xx Si 0.000
Ge4 14.471521928 7.075743211 4.103237624 XXXX 1 xx Ge 0.000
Ge5 11.552724034 6.904457817 1.176992487 XXXX 1 xx Ge 0.000
Ge6 11.212260503 9.470686160 3.882962564 XXXX 1 xx Ge 0.000
Ge7 14.030866609 9.732042993 1.005461461 XXXX 1 xx Ge 0.000
Ge8 15.489440119 8.305017757 2.275940415 XXXX 1 xx Ge 0.000
Ge9 7.106976200 10.797366032 2.836002475 XXXX 1 xx Ge 0.000
Si3 7.302164570 13.851080918 0.074023049 XXXX 1 xx Si 0.000
Ge10 8.484516755 12.351124040 4.039462675 XXXX 1 xx Ge 0.000
Ge11 8.509246412 15.247027186 1.560299002 XXXX 1 xx Ge 0.000
Si4 9.832124411 11.058533013 -0.020219741 XXXX 1 xx Si 0.000
Ge12 9.966038351 13.806076509 2.822211318 XXXX 1 xx Ge 0.000
Ge13 12.646782732 10.915321271 2.590651424 XXXX 1 xx Ge 0.000
Si5 12.522276997 13.688256983 -0.157454179 XXXX 1 xx Si 0.000
Ge14 14.051549721 12.119480958 4.137728350 XXXX 1 xx Ge 0.000
Ge15 11.223639010 12.401016347 1.331521235 XXXX 1 xx Ge 0.000
Ge16 11.352377734 14.991984125 4.418834889 XXXX 1 xx Ge 0.000
Ge17 13.975875950 14.977201218 1.185525576 XXXX 1 xx Ge 0.000
Si6 15.273353817 11.294188033 -0.277924714 XXXX 1 xx Si 0.000
Ge18 15.256512475 13.831554104 2.906706520 XXXX 1 xx Ge 0.000
Ge19 7.254054371 7.507053662 5.338921194 XXXX 1 xx Ge 0.000
Ge20 8.103121938 6.678163567 9.312368480 XXXX 1 xx Ge 0.000
Ge21 8.482826869 9.209597557 6.564460341 XXXX 1 xx Ge 0.000
Ge22 9.815195084 7.883126321 8.081346650 XXXX 1 xx Ge 0.000
Ge23 12.595988211 8.088020917 5.287945596 XXXX 1 xx Ge 0.000
Ge24 13.629658285 6.445235923 9.943134585 XXXX 1 xx Ge 0.000
Ge25 11.238312015 6.566642238 6.603847240 XXXX 1 xx Ge 0.000
Ge26 11.019354771 9.287893310 9.628423576 XXXX 1 xx Ge 0.000
Ge27 13.846655125 9.338687831 6.931129404 XXXX 1 xx Ge 0.000
Ge28 14.858932831 7.463154114 8.115837376 XXXX 1 xx Ge 0.000
Ge29 6.942691917 10.582298308 7.800240111 XXXX 1 xx Ge 0.000
Ge30 6.989821701 13.862545195 5.185066161 XXXX 1 xx Ge 0.000
Ge31 8.128599533 11.968637691 9.396863682 XXXX 1 xx Ge 0.000
Ge32 8.072130847 14.944854341 7.034008839 XXXX 1 xx Ge 0.000
Ge33 9.825592456 10.804515410 5.332914703 XXXX 1 xx Ge 0.000
Ge34 9.583552002 13.450159287 8.179612325 XXXX 1 xx Ge 0.000
Ge35 12.463989882 10.722415539 8.336112436 XXXX 1 xx Ge 0.000
Ge36 12.725078485 13.451849173 5.654614659 XXXX 1 xx Ge 0.000
Ge37 13.802645345 12.064181769 9.827627307 XXXX 1 xx Ge 0.000
Ge38 11.130160632 12.109083586 6.886160297 XXXX 1 xx Ge 0.000
Ge39 11.137310010 14.827699842 9.383072525 XXXX 1 xx Ge 0.000
Ge40 14.427622380 14.680621671 6.880153806 XXXX 1 xx Ge 0.000
Ge41 15.368033804 10.696364027 5.615227760 XXXX 1 xx Ge 0.000
Ge42 15.401052716 13.479676875 8.727139244 XXXX 1 xx Ge 0.000
Ge43 6.957474824 7.958800092 11.033549424 XXXX 1 xx Ge 0.000
Si7 7.794031035 7.093255137 15.045527105 XXXX 1 xx Si 0.000
Si8 8.246419059 9.412399045 12.376529179 XXXX 1 xx Si 0.000
Si9 9.494323053 8.148758535 13.848383733 XXXX 1 xx Si 0.000
Ge44 12.202633049 7.903809433 11.213613539 XXXX 1 xx Ge 0.000
Si10 13.628447920 6.725104629 15.287806481 XXXX 1 xx Si 0.000
Si11 10.640488009 6.661322225 12.496999714 XXXX 1 xx Si 0.000
Si12 10.903157199 9.536272589 15.042857037 XXXX 1 xx Si 0.000
Si13 13.586419974 9.277074339 12.525521793 XXXX 1 xx Si 0.000
Si14 14.930321347 7.824933519 13.727725307 XXXX 1 xx Si 0.000
Si15 6.859669600 10.680962351 13.738946645 XXXX 1 xx Si 0.000
Ge45 6.687648856 13.425429630 10.658775998 XXXX 1 xx Ge 0.000
Si16 8.195425567 12.097265921 15.000922131 XXXX 1 xx Si 0.000
Si17 8.083595124 14.632511472 12.145051951 XXXX 1 xx Si 0.000
Ge46 9.533659695 10.711037032 10.887553765 XXXX 1 xx Ge 0.000
Si18 9.440570527 13.344471705 13.527302731 XXXX 1 xx Si 0.000
Si19 12.214595410 10.793309355 13.611221607 XXXX 1 xx Si 0.000
Ge47 12.314935702 13.531357255 11.035908052 XXXX 1 xx Ge 0.000
Si20 13.525837123 12.276545992 14.792889555 XXXX 1 xx Si 0.000
Si21 10.876143029 12.102551631 12.239294741 XXXX 1 xx Si 0.000
Si22 10.643607612 14.817768710 14.834553291 XXXX 1 xx Si 0.000
Si23 13.755108625 14.983442924 12.220234301 XXXX 1 xx Si 0.000
Ge48 15.030218225 10.381952008 11.042082513 XXXX 1 xx Ge 0.000
Si24 14.996129594 13.560121232 13.537078126 XXXX 1 xx Si 0.000
Si25 6.846616521 8.217265098 16.862015247 XXXX 1 xx Si 0.000
Si26 8.374554810 6.938546448 20.404796874 XXXX 1 xx Si 0.000
Si27 8.291824539 9.727687637 17.860778184 XXXX 1 xx Si 0.000
Si28 9.658130050 8.408838919 19.148985445 XXXX 1 xx Si 0.000
Si29 12.278511626 8.261685430 16.374233248 XXXX 1 xx Si 0.000
Si30 14.109742523 7.004354695 20.214149693 XXXX 1 xx Si 0.000
Si31 10.869453303 7.047506919 17.739966438 XXXX 1 xx Si 0.000
Si32 11.141366687 9.720080632 20.330653393 XXXX 1 xx Si 0.000
Si33 13.672990612 9.656164416 17.567641752 XXXX 1 xx Si 0.000
Si34 15.209571413 8.306228122 18.654068519 XXXX 1 xx Si 0.000
Si35 7.116907332 11.291068430 19.107321709 XXXX 1 xx Si 0.000
Si36 7.070952018 13.839805399 16.049370190 XXXX 1 xx Si 0.000
Si37 8.590204337 12.494105515 20.414572269 XXXX 1 xx Si 0.000
Si38 8.094870643 14.863724024 17.892504810 XXXX 1 xx Si 0.000
Si39 9.615047745 10.912588614 16.378728910 XXXX 1 xx Si 0.000
Si40 9.837410121 13.739250475 18.940952869 XXXX 1 xx Si 0.000
Si41 12.398403453 11.031518843 18.899017963 XXXX 1 xx Si 0.000
Si42 12.206988405 13.642851503 16.081096816 XXXX 1 xx Si 0.000
Si43 13.785917507 12.440352989 20.093491267 XXXX 1 xx Si 0.000
Si44 11.022087428 12.319628297 17.563146090 XXXX 1 xx Si 0.000
Si45 11.253713691 15.075006442 20.202928355 XXXX 1 xx Si 0.000
Si46 13.717410944 15.088059521 17.079859753 XXXX 1 xx Si 0.000
Si47 14.887169123 11.065222739 16.201908562 XXXX 1 xx Si 0.000
Si48 14.841420905 14.140645007 18.896347895 XXXX 1 xx Si 0.000
H1 6.177029481 7.362093884 0.990997736 XXXX 1 xx H 0.000
H2 5.966394233 8.929706670 -0.842812578 XXXX 1 xx H 0.000
H3 9.314998539 5.340046906 3.980696396 XXXX 1 xx H 0.000
H4 7.461864209 5.973464799 2.439428246 XXXX 1 xx H 0.000
H5 15.605485793 6.940060273 5.151908995 XXXX 1 xx H 0.000
H6 14.151098149 5.641678635 3.624617976 XXXX 1 xx H 0.000
H7 12.568257093 6.431093321 2.256645677 XXXX 1 xx H 0.000
H8 11.033260046 5.630150094 0.471366773 XXXX 1 xx H 0.000
H9 16.165876300 7.278817213 1.331757885 XXXX 1 xx H 0.000
H10 16.622061182 9.188435017 2.859146574 XXXX 1 xx H 0.000
H11 6.664665425 9.789597152 3.932789985 XXXX 1 xx H 0.000
H12 5.815631583 11.402465144 2.234705900 XXXX 1 xx H 0.000
H13 6.459520247 12.948573131 0.930749289 XXXX 1 xx H 0.000
H14 6.362068804 14.674894922 -0.758960245 XXXX 1 xx H 0.000
H15 9.309455392 16.339746690 0.818665645 XXXX 1 xx H 0.000
H16 7.525576739 15.972372969 2.510282436 XXXX 1 xx H 0.000
H17 12.200504975 16.064407592 3.692575213 XXXX 1 xx H 0.000
H18 10.408663275 15.736299394 5.398285972 XXXX 1 xx H 0.000
H19 14.989795035 15.771519639 0.324516265 XXXX 1 xx H 0.000
H20 13.101480028 16.031905331 1.909273648 XXXX 1 xx H 0.000
H21 16.359448331 10.611162469 -1.054576953 XXXX 1 xx H 0.000
H22 15.938066903 12.277294287 0.642170826 XXXX 1 xx H 0.000
H23 16.591271845 13.307860819 2.330046110 XXXX 1 xx H 0.000
H24 15.629683544 14.948202832 3.917601521 XXXX 1 xx H 0.000
H25 6.952185755 6.375001836 6.354443907 XXXX 1 xx H 0.000
H26 5.891717818 8.042599876 4.847136115 XXXX 1 xx H 0.000
H27 8.626815223 5.343404197 9.889028890 XXXX 1 xx H 0.000
H28 6.986473210 6.304992498 8.301473479 XXXX 1 xx H 0.000
H29 14.655858829 5.768799742 10.887317115 XXXX 1 xx H 0.000
H30 12.746241025 5.312614860 9.359928426 XXXX 1 xx H 0.000
H31 12.140993094 5.601087585 7.408082555 XXXX 1 xx H 0.000
H32 10.321389837 5.707450038 5.698004537 XXXX 1 xx H 0.000
H33 14.994615769 6.329190249 7.067166005 XXXX 1 xx H 0.000
H34 16.292997407 7.783577893 8.594457024 XXXX 1 xx H 0.000
H35 5.870268450 9.734171067 8.526499787 XXXX 1 xx H 0.000
H36 6.198376648 11.526012767 6.820789028 XXXX 1 xx H 0.000
H37 5.714515524 13.122300817 5.654445999 XXXX 1 xx H 0.000
H38 6.535531601 14.912790108 4.136890704 XXXX 1 xx H 0.000
H39 8.812375225 16.220160518 6.564629001 XXXX 1 xx H 0.000
H40 7.021885934 15.399144441 8.082184296 XXXX 1 xx H 0.000
H41 12.145078890 15.270010617 8.286285015 XXXX 1 xx H 0.000
H42 10.532210898 16.119044459 9.984369100 XXXX 1 xx H 0.000
H43 15.559674206 14.982490287 5.864631093 XXXX 1 xx H 0.000
H44 13.892076166 16.042958224 7.371938885 XXXX 1 xx H 0.000
H45 16.333588457 9.793682948 4.810992445 XXXX 1 xx H 0.000
H46 16.227226004 11.613286205 6.521070463 XXXX 1 xx H 0.000
H47 16.594629136 12.619677503 8.238378604 XXXX 1 xx H 0.000
H48 15.961211243 14.472811833 9.779646754 XXXX 1 xx H 0.000
H49 6.163156403 6.944881007 11.894558735 XXXX 1 xx H 0.000
H50 5.902770711 8.833196014 10.309801352 XXXX 1 xx H 0.000
H51 8.242979207 5.741592240 15.514262921 XXXX 1 xx H 0.000
H52 6.713648122 6.882899909 14.022335624 XXXX 1 xx H 0.000
H53 14.431556534 5.986737634 16.320515945 XXXX 1 xx H 0.000
H54 12.773876400 5.729822540 14.562313597 XXXX 1 xx H 0.000
H55 11.323513573 5.575227711 13.273651953 XXXX 1 xx H 0.000
H56 9.657381755 5.996609139 11.576904174 XXXX 1 xx H 0.000
H57 15.489280132 6.872356593 12.707280500 XXXX 1 xx H 0.000
H58 16.097162809 8.514209594 14.366581965 XXXX 1 xx H 0.000
H59 6.042008085 9.765110263 14.606316370 XXXX 1 xx H 0.000
H60 5.914012502 11.521826471 12.933254392 XXXX 1 xx H 0.000
H61 5.594929352 12.625220650 11.400409355 XXXX 1 xx H 0.000
H62 5.962303073 14.409099303 9.708792564 XXXX 1 xx H 0.000
H63 8.986102911 15.475155795 11.288325711 XXXX 1 xx H 0.000
H64 7.259781120 15.572607238 12.978035245 XXXX 1 xx H 0.000
H65 11.313727280 15.834765233 13.959905479 XXXX 1 xx H 0.000
H66 9.732703271 15.569063568 15.769426899 XXXX 1 xx H 0.000
H67 14.572582158 15.757646561 11.228077264 XXXX 1 xx H 0.000
H68 13.004969372 15.968281809 13.061887578 XXXX 1 xx H 0.000
H69 15.503582721 9.366418949 9.962429323 XXXX 1 xx H 0.000
H70 16.304525948 10.901415996 11.747708227 XXXX 1 xx H 0.000
H71 15.817130385 12.676442561 12.645688451 XXXX 1 xx H 0.000
H72 15.932507282 14.263227428 14.476400818 XXXX 1 xx H 0.000
H73 6.520719171 7.208024327 17.926268222 XXXX 1 xx H 0.000
H74 5.563840328 8.875152740 16.456458094 XXXX 1 xx H 0.000
H75 9.258233481 6.117545657 21.296186549 XXXX 1 xx H 0.000
H76 7.671448614 6.002168760 19.465474182 XXXX 1 xx H 0.000
H77 15.062319449 6.445395910 21.234594500 XXXX 1 xx H 0.000
H78 13.420466448 5.837513233 19.575293035 XXXX 1 xx H 0.000
H79 11.654901300 6.082745854 18.581734737 XXXX 1 xx H 0.000
H80 9.949464919 6.243193971 16.859949414 XXXX 1 xx H 0.000
H81 15.947938408 7.503119508 17.621359055 XXXX 1 xx H 0.000
H82 16.204853502 9.160799642 19.379561403 XXXX 1 xx H 0.000
H83 6.099910809 10.620948762 19.981969521 XXXX 1 xx H 0.000
H84 6.365612474 12.201972771 18.172448101 XXXX 1 xx H 0.000
H85 5.683363665 13.437184652 16.448705154 XXXX 1 xx H 0.000
H86 6.943911577 14.905697506 14.999474309 XXXX 1 xx H 0.000
H87 8.497491390 16.251312377 17.493169846 XXXX 1 xx H 0.000
H88 7.028978536 14.990764465 18.942400691 XXXX 1 xx H 0.000
H89 12.169565779 15.892667957 19.335558630 XXXX 1 xx H 0.000
H90 10.412849571 16.020663540 21.008620608 XXXX 1 xx H 0.000
H91 14.726651715 15.413956871 16.015606778 XXXX 1 xx H 0.000
H92 13.059523302 16.370835714 17.485416906 XXXX 1 xx H 0.000
H93 15.851930188 10.279774742 15.360140263 XXXX 1 xx H 0.000
H94 15.691482071 11.985211123 17.081925586 XXXX 1 xx H 0.000
H95 16.193083802 13.691696835 18.427612079 XXXX 1 xx H 0.000
H96 15.051776133 15.221027920 19.919539376 XXXX 1 xx H 0.000
end
end
-
Dear Sir:
There is a running error. The details are as follows:
Equivalent Bulk [Started Tue Aug 10 15:32:28 2010] |
| |
+------------------------------------------------------------------------------+
This application has requested the Runtime to terminate it in an unusual way.
Please contact the application's support team for more information.
NanoLanguageScript execution failure.
Lihong
-
I don't know which version you are running, but it works fine for me. Note that the file must be called .car, it recognizes the format by the extension.
The second issue means you are out of memory.
-
The first thing I have solved it. Thanks.