From: SourceForge.net <no...@so...> - 2011-12-02 00:12:45
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Bugs item #3156530, was opened at 2011-01-12 12:00 Message generated for change (Settings changed) made by hansonr You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=3156530&group_id=23629 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Applet Group: None >Status: Closed >Resolution: Fixed Priority: 5 Private: No Submitted By: Nobody/Anonymous (nobody) Assigned to: Bob Hanson (hansonr) Summary: isosurface display Initial Comment: Hello, I'm having problems displaying the homo and lumo from .cube files on the JMol applet. I have links below the applet that updates the displayed molecule so that the homo or lumo can be shown. Sometimes it works correctly. Other times only the positive or negative surface is displayed. Sometimes no surface is displayed. I am attaching screenshots of all three cases from the same molecule. I am also attaching a cube file that I use to get the isosurface info for the homo. Here is what the script looks like that updates the display of the molecule: <script type="text/javascript"> jmolInitialize("${jmol_url}"); jmolApplet(700, "load ${homo_cube_url}"); jmolSetLinkCssClass("jmol-link"); jmolBr(); jmolLink("isosurface off", "Clear"); jmolLink("isosurface off; isosurface pos color red cutoff ${doc.results.homo_contour} ${homo_cube_url}; isosurface neg color blue cutoff -${doc.results.homo_conto ur} ${homo_cube_url}", "HOMO"); jmolLink("isosurface off; isosurface pos color red cutoff ${doc.results.lumo_contour} ${lumo_cube_url}; isosurface neg color blue cutoff -${doc.results.lumo_conto ur} ${lumo_cube_url}", "LUMO"); </script> Craig ---------------------------------------------------------------------- Comment By: Nobody/Anonymous (nobody) Date: 2011-01-27 10:43 Message: I'm not sure what the problem could be. Something must go wrong when the file is grabbed from the server. It may be that it gets there too slow, because the file is actually stored as a blob in a database and served up by the web application. I'm sure that is slower than the file being served up statically via apache. The version is jmol-12.0.19. I have a nice pipeline for transforming our cube files to jvxl and storing that in the db instead. The web application is now working flawlessly. I'm not sure if this should be an open issue anymore. ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2011-01-25 13:30 Message: well, what do you suppose the problem is? The file you sent looks just fine to me. (See uploaded homo.png) What version of Jmol are you using? ---------------------------------------------------------------------- Comment By: https://www.google.com/accounts () Date: 2011-01-25 09:15 Message: I can't figure out how to attach another file, so I'm emailing it to the address you gave below. By the way, I have a problem with creating jvxl files and I'll post it on the users list. Craig ---------------------------------------------------------------------- Comment By: Nobody/Anonymous (nobody) Date: 2011-01-25 09:13 Message: Hello Bob, I have switched my db to use jvxl files and they are working very nicely. Thanks for the suggestion. I can't give you the file from below, but I can give you another one that displays incorrectly (sometimes). I think you are right about transmission being the problem. The java output for when the homo surface did not show up is below, and I'm attaching the file on the attachments for this bug report. isosurface SIGN color red blue cutoff 0.01263 http://scctest/opv/4ce2cb74cf265714e500077e/4ce2cb74cf265714e500077d/lumo-cube; reading isosurface data from http://scctest/opv/4ce2cb74cf265714e500077e/4ce2cb74cf265714e500077d/lumo-cube FileManager opening http://scctest/opv/4ce2cb74cf265714e500077e/4ce2cb74cf265714e500077d/lumo-cube 0:32 1:80 2:84 3:66 4:55 5:95 6:99 7:32 8:116 9:101 10:116 11:114 12:97 13:109 14:101 15:114 16:32 17:77 18:79 19:61 20:76 21:117 22:109 23:111 24:10 25:32 26:77 27:79 28:32 29:99 30:111 31:101 32:102 33:102 34:105 35:99 36:105 37:101 38:110 39:116 40:115 41:10 42:32 43:45 44:49 45:54 46:50 47:32 48:32 49:45 50:52 51:52 52:46 53:55 54:51 55:48 56:57 57:56 58:52 59:32 60:32 61:45 62:50 63:55 64:46 65:57 66:52 67:56 68:57 69:54 70:52 71:32 72:32 73:45 74:49 75:48 76:46 77:52 78:55 79:54 80:49 81:53 82:52 83:10 84:32 85:32 86:49 87:52 88:57 89:32 90:32 91:32 92:32 93:48 94:46 95:53 96:57 97:57 98:48 99:57 100:50 101:32 102:32 103:32 104:32 105:48 106:46 107:48 108:48 109:48 110:48 111:48 112:48 113:32 114:32 115:32 116:32 117:48 118:46 119:48 120:48 121:48 122:48 123:48 124:48 125:10 126:32 127:32 128:32 129:57 130:56 131:32 132:32 133:32 134:32 135:48 136:46 137:48 138:48 139:48 140:48 141:48 142:48 143:32 144:32 145:32 146:32 147:48 148:46 149:53 150:57 151:57 152:48 153:57 154:50 155:32 156:32 157:32 158:32 159:48 160:46 161:48 162:48 163:48 164:48 165:48 166:48 167:10 168:32 169:32 170:32 171:51 172:53 173:32 174:32 175:32 176:32 177:48 178:46 179:48 180:48 181:48 182:48 183:48 184:48 185:32 186:32 187:32 188:32 189:48 190:46 191:48 192:48 193:48 194:48 195:48 196:48 197:32 198:32 199:32 200:32 201:48 202:46 203:53 204:57 205:57 206:48 207:57 208:50 209:10 210:32 211:32 212:32 213:32 214:54 215:32 216:32 217:32 218:32 219:54 data file type was determined to be UNKNOWN Could not set the surface data isosurface1 created with cutoff=0.01263 min=-0.101685 max=0.13045299; number of isosurfaces = 1 isosurface full data range -1.0 to 1.0 with color scheme spanning -1.0 to 1.0 ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2011-01-24 10:24 Message: Great -- so that answers one question -- Jmol is not recognizing that as a CUBE file. All the numbers are a dump of a the first couple hundred bytes. That actually looks ok: acc0_D6_R1_A1_R1R4__n2 TD-DFT MO=Lumo MO coefficients -126 -44.854654 -17.399507 -11.815393 173 0.551322 0.000000 0.000000 63 0.000000 0.551322 0.000000 47 0.000000 0.000000 0.551... I don't know why Jmol is not identifying it as a CUBE file. Can you send me a few more lines of that test file, that would be great. BUT, actually, you aren't going to use CUBE files anymore -- still I would like to track this down. Just load the gaussian output file, making sure you have the GFPRINT option selected, and away you go. then just used the MO command. ---------------------------------------------------------------------- Comment By: https://www.google.com/accounts () Date: 2011-01-24 09:04 Message: Sorry Bob. Now I know what you are talking about for the java output. Here is the output from a failed case below. I really would like to depend on something besides CUBE files. Our cube files are generated by gaussian. I'm looking into generating the JVXL output instead. Here is that console output: 1/24/11 9:23:52 AM [0x0-0x22022].com.apple.Safari[480] isosurface SIGN color red blue cutoff 0.015 http://scctest:6543/All/4d39b3cacf26573a5c000446/4d39b3e3cf26573a5c000597/lumo-cube; 1/24/11 9:23:52 AM [0x0-0x22022].com.apple.Safari[480] reading isosurface data from http://scctest:6543/All/4d39b3cacf26573a5c000446/4d39b3e3cf26573a5c000597/lumo-cube 1/24/11 9:23:52 AM [0x0-0x22022].com.apple.Safari[480] FileManager opening http://scctest:6543/All/4d39b3cacf26573a5c000446/4d39b3e3cf26573a5c000597/lumo-cube 1/24/11 9:23:52 AM [0x0-0x22022].com.apple.Safari[480] 0:32 1:97 2:99 3:99 4:48 5:95 6:68 7:54 8:95 9:82 1/24/11 9:23:52 AM [0x0-0x22022].com.apple.Safari[480] 10:49 11:95 12:65 13:49 14:95 15:82 16:49 17:82 18:52 19:95 20:95 21:110 22:50 23:32 24:84 25:68 26:45 27:68 28:70 29:84 30:32 31:77 32:79 33:61 34:76 35:117 36:109 37:111 38:10 39:32 40:77 41:79 42:32 43:99 44:111 45:101 46:102 47:102 48:105 49:99 50:105 1/24/11 9:23:52 AM [0x0-0x22022].com.apple.Safari[480] 51:101 52:110 53:116 54:115 55:10 56:32 57:45 58:49 59:50 60:54 61:32 62:32 63:45 64:52 65:52 66:46 67:56 68:53 69:52 70:54 71:53 72:52 73:32 74:32 75:45 76:49 77:55 78:46 79:51 80:57 81:57 82:53 83:48 84:55 85:32 86:32 87:45 88:49 89:49 90:46 91:56 92:49 93:53 94:51 95:57 96:51 97:10 98:32 99:32 100:49 101:55 102:51 103:32 104:32 105:32 106:32 107:48 108:46 109:53 110:53 111:49 112:51 113:50 114:50 115:32 116:32 117:32 118:32 119:48 120:46 121:48 122:48 123:48 124:48 1/24/11 9:23:52 AM [0x0-0x22022].com.apple.Safari[480] 125:48 126:48 127:32 128:32 129:32 130:32 131:48 132:46 133:48 134:48 135:48 136:48 137:48 138:48 139:10 140:32 141:32 142:32 143:54 144:51 145:32 146:32 147:32 148:32 149:48 150:46 151:48 152:48 153:48 154:48 155:48 156:48 157:32 158:32 159:32 160:32 161:48 162:46 163:53 164:53 165:49 1/24/11 9:23:52 AM [0x0-0x22022].com.apple.Safari[480] 166:51 167:50 168:50 169:32 170:32 171:32 172:32 173:48 174:46 175:48 176:48 177:48 178:48 179:48 180:48 181:10 182:32 183:32 184:32 185:52 186:55 187:32 188:32 189:32 190:32 191:48 192:46 193:48 194:48 195:48 196:48 197:48 198:48 199:32 200:32 201:32 202:32 203:48 204:46 205:48 206:48 207:48 208:48 209:48 210:48 211:32 212:32 213:32 214:32 215:48 216:46 217:53 218:53 219:49 1/24/11 9:23:52 AM [0x0-0x22022].com.apple.Safari[480] data file type was determined to be UNKNOWN 1/24/11 9:23:52 AM [0x0-0x22022].com.apple.Safari[480] Could not set the surface data 1/24/11 9:23:52 AM [0x0-0x22022].com.apple.Safari[480] isosurface1 created with cutoff=0.015 min=-0.104662 max=0.115712; number of isosurfaces = 1 1/24/11 9:23:52 AM [0x0-0x22022].com.apple.Safari[480] isosurface full data range -1.0 to 1.0 with color scheme spanning -1.0 to 1.0 ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2011-01-23 11:08 Message: Craig, It's pretty hard to use CUBE files over the web. That's the whole reason I developed the JVXL format, and then later we built into Jmol an orbital generator. I'm guessing the real problem is just transmission time. It can take some time to generate CUBE file data. The output you have there is still just the Jmol console, not the Java console, where all the details are. See if you can track down how to open that. (On a Windows system, it's on your taskbar or under Java in the Control Panel. I can't be sure without seeing some actual files -- you could send them to me off list at ha...@st... -- but depending upon CUBE files is the last thing you what to do, just because they are so huge. I would use them only if no other way exists to create the orbital. You sure the MO command won't work in this case? What is the source of the CUBE files? Bob ---------------------------------------------------------------------- Comment By: Nobody/Anonymous (nobody) Date: 2011-01-22 06:39 Message: Oops, I missed the first line from the console output that shows I set debug : logLevel = 5 isosurface1 created with cutoff=0.025 min=-0.15647899 max=0.16178499; number of isosurfaces = 1 isosurface full data range -1.0 to 1.0 with color scheme spanning -1.0 to 1.0 isosurface1 created with cutoff=0.025 min=-0.15647899 max=0.16178499; number of isosurfaces = 1 isosurface full data range -1.0 to 1.0 with color scheme spanning -1.0 to 1.0 isosurface1 created with cutoff=0.025 min=-0.15647899 max=0.16178499; number of isosurfaces = 1 isosurface full data range -1.0 to 1.0 with color scheme spanning -1.0 to 1.0 isosurface1 created with cutoff=0.023 min=-0.180083 max=0.190436; number of isosurfaces = 1 isosurface full data range -1.0 to 1.0 with color scheme spanning -1.0 to 1.0 ---------------------------------------------------------------------- Comment By: Nobody/Anonymous (nobody) Date: 2011-01-22 06:37 Message: Here is the out put after the following happened: 1. I clicked the "HOMO" link and the homo surface displayed correctly. (see the script in my original bug submission) 2. I clicked the "LUMO" link and nothing appeared except the molecule. 3. I clicked the "LUMO" link again and nothing appeared except the molecule. 4. I clicked the "LUMO" link once again and the isosurface displayed correctly. isosurface1 created with cutoff=0.025 min=-0.15647899 max=0.16178499; number of isosurfaces = 1 isosurface full data range -1.0 to 1.0 with color scheme spanning -1.0 to 1.0 isosurface1 created with cutoff=0.025 min=-0.15647899 max=0.16178499; number of isosurfaces = 1 isosurface full data range -1.0 to 1.0 with color scheme spanning -1.0 to 1.0 isosurface1 created with cutoff=0.025 min=-0.15647899 max=0.16178499; number of isosurfaces = 1 isosurface full data range -1.0 to 1.0 with color scheme spanning -1.0 to 1.0 isosurface1 created with cutoff=0.023 min=-0.180083 max=0.190436; number of isosurfaces = 1 isosurface full data range -1.0 to 1.0 with color scheme spanning -1.0 to 1.0 ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2011-01-20 11:34 Message: We need to see that Java (not the Jmol) console output after one of the failures. From the Jmol script console, enter: set debug Then see if you can get it to fail. Copy the entire contents of the Java console. If you need to send this to me off-list, send that to me at ha...@st... ---------------------------------------------------------------------- Comment By: Jonathan Gutow (gutow) Date: 2011-01-20 10:22 Message: I have an idea from my experience running Jmol as the 3-D viewer in the SAGE math web interface. This sounds like a timing issue related to AJAX type calls. Are there requirements for updates from your server related to this? The code you are using does not seem to imply this, but intermittent behavior is what I saw when I didn't set things up to make sure the server or the applet was ready to respond to a request. Just and idea. ---------------------------------------------------------------------- Comment By: https://www.google.com/accounts () Date: 2011-01-20 08:56 Message: When the error happens, the console shows the exact same output as when the surface is correctly displayed. I don't think it is the cutoffs, because, in answer to your 'Third' point, the randomness happens like this. I go to a record for one of our molecules and and hit the HOMO link. That link may or may not cause the surface to correctly display. If I click the same exact link again, once again, the surface will display or not. In all cases the console shows the same exact output. I wish I could point you to a web site, but this is internal to our organization. ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2011-01-14 13:02 Message: First, if you can figure out how to open the Java console (not the Jmol console) you might find some sort of error there. Second -- could be the cutoffs. Third -- the randomness of this makes no sense. Not sure you mean sometimes with one molecule, sometimes with another, or sometimes with the same orbital and sometimes not, but with the same orbital. I can't imagine what is going on there, unless it's something about memory -- that you are not selecting out the specific subset of atoms or something. If you could point me to the web site, that might be best. ---------------------------------------------------------------------- Comment By: https://www.google.com/accounts () Date: 2011-01-14 07:48 Message: Thanks for pointing out the SIGN keyword. After switching to: jmolLink("isosurface off; isosurface SIGN color red blue cutoff ${doc.results.homo_contour} ${homo_cube_url}", "HOMO"); The behavior changed. Now I never get just a positive or negative surface, instead it is sometimes displayed correctly, or not at all. Just a rough estimate, but hitting the HOMO link gives me about a 1 in 3 chance of seeing the isosurface. When I watch the console, it will indicate that an isosurface was created even when it does not appear on the molecule: isosurface1 created with cutoff=0.017 min=-0.116008 max=0.11920901; number of isosurfaces = 1 isosurface full data range -1.0 to 1.0 with color scheme spanning -1.0 to 1.0 ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2011-01-12 15:54 Message: No need to use two surfaces -- just use the SIGN keyword. This applies your cutoff to both positive and negative cutoffs and gives you surfaces for both: isosurface SIGN yellow green cutoff 0.01 data/benzene-homo.cub.gz ---------------------------------------------------------------------- Comment By: https://www.google.com/accounts () Date: 2011-01-12 12:03 Message: Oops. I didn't get the other files attached that I meant to. I'm not sure how to upload the images that show the surface incorrectly displayed. If anyone needs them please let me know how to get them attached. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=3156530&group_id=23629 |