From: SourceForge.net <no...@so...> - 2012-09-06 09:30:27
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Feature Requests item #3565251, was opened at 2012-09-06 02:30 Message generated for change (Tracker Item Submitted) made by drdanj You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379136&aid=3565251&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: None Group: None Status: Open Priority: 5 Private: No Submitted By: Daniel Jones (drdanj) Assigned to: Nobody/Anonymous (nobody) Summary: Periodic repetition of coloured planes Initial Comment: If I have a system and I wish to display some function as a colour map projected on a plane, I can do this in Jmol using $ isosurface plane {x y z}{x1 y1 z1}{x2 y2 z2} map "data.dat" If the system is made periodic and I want to display a supercell, because it's easier to see the system when you look at more than a single repeat unit, I can reload a supercell in Jmol using e.g. $ load "<model_file>" { 2 2 2 } I now want to make a colour map onto a plane of some data $ isosurface plane {x y z}{x1 y1 z1}{x2 y2 z2} map "data.dat" This only plots a plane in the original repeat unit. If I then use $ isosurface lattice { 2 2 2 } This makes periodic repeats of the plane (and displays multiple planes) Is it possible to make periodic representation of the data, and map it to a larger single plane in the visualisation? Perhaps a 2D equivalent command for the $ isosurface lattice command. e.g. $ isosurface extendPlane { x y }. Might work. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379136&aid=3565251&group_id=23629 |
From: SourceForge.net <no...@so...> - 2012-09-08 11:54:27
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Feature Requests item #3565251, was opened at 2012-09-06 02:30 Message generated for change (Comment added) made by hansonr You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379136&aid=3565251&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: None Group: None Status: Open Priority: 5 Private: No Submitted By: Daniel Jones (drdanj) Assigned to: Nobody/Anonymous (nobody) Summary: Periodic repetition of coloured planes Initial Comment: If I have a system and I wish to display some function as a colour map projected on a plane, I can do this in Jmol using $ isosurface plane {x y z}{x1 y1 z1}{x2 y2 z2} map "data.dat" If the system is made periodic and I want to display a supercell, because it's easier to see the system when you look at more than a single repeat unit, I can reload a supercell in Jmol using e.g. $ load "<model_file>" { 2 2 2 } I now want to make a colour map onto a plane of some data $ isosurface plane {x y z}{x1 y1 z1}{x2 y2 z2} map "data.dat" This only plots a plane in the original repeat unit. If I then use $ isosurface lattice { 2 2 2 } This makes periodic repeats of the plane (and displays multiple planes) Is it possible to make periodic representation of the data, and map it to a larger single plane in the visualisation? Perhaps a 2D equivalent command for the $ isosurface lattice command. e.g. $ isosurface extendPlane { x y }. Might work. ---------------------------------------------------------------------- >Comment By: Bob Hanson (hansonr) Date: 2012-09-08 04:54 Message: Daniel, I think I have it. Please try the latest rendition of http://chemapps.stolaf.edu/jmol/Jmol-13.zip This version of Jmol includes a new isosurface option. You will use the LATTICE option after the MAP keyword to indicate that the mapped data itself is periodic and that you want to extend the plane over a translational lattice associated with that data set: isosurface plane {x y z}{x1 y1 z1}{x2 y2 z2} map LATTICE {2 2 2} "data.dat" Let's see if that does the trick. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379136&aid=3565251&group_id=23629 |
From: SourceForge.net <no...@so...> - 2012-09-10 15:03:33
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Feature Requests item #3565251, was opened at 2012-09-06 02:30 Message generated for change (Comment added) made by drdanj You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379136&aid=3565251&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: None Group: None Status: Open Priority: 5 Private: No Submitted By: Daniel Jones (drdanj) Assigned to: Nobody/Anonymous (nobody) Summary: Periodic repetition of coloured planes Initial Comment: If I have a system and I wish to display some function as a colour map projected on a plane, I can do this in Jmol using $ isosurface plane {x y z}{x1 y1 z1}{x2 y2 z2} map "data.dat" If the system is made periodic and I want to display a supercell, because it's easier to see the system when you look at more than a single repeat unit, I can reload a supercell in Jmol using e.g. $ load "<model_file>" { 2 2 2 } I now want to make a colour map onto a plane of some data $ isosurface plane {x y z}{x1 y1 z1}{x2 y2 z2} map "data.dat" This only plots a plane in the original repeat unit. If I then use $ isosurface lattice { 2 2 2 } This makes periodic repeats of the plane (and displays multiple planes) Is it possible to make periodic representation of the data, and map it to a larger single plane in the visualisation? Perhaps a 2D equivalent command for the $ isosurface lattice command. e.g. $ isosurface extendPlane { x y }. Might work. ---------------------------------------------------------------------- >Comment By: Daniel Jones (drdanj) Date: 2012-09-10 08:03 Message: Hi Bob, Sorry for the delay, just got round to trying it, works like a charm! Thanks very much, Dan ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2012-09-08 04:54 Message: Daniel, I think I have it. Please try the latest rendition of http://chemapps.stolaf.edu/jmol/Jmol-13.zip This version of Jmol includes a new isosurface option. You will use the LATTICE option after the MAP keyword to indicate that the mapped data itself is periodic and that you want to extend the plane over a translational lattice associated with that data set: isosurface plane {x y z}{x1 y1 z1}{x2 y2 z2} map LATTICE {2 2 2} "data.dat" Let's see if that does the trick. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379136&aid=3565251&group_id=23629 |
From: SourceForge.net <no...@so...> - 2012-09-10 17:51:58
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Feature Requests item #3565251, was opened at 2012-09-06 02:30 Message generated for change (Comment added) made by hansonr You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379136&aid=3565251&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: None Group: None Status: Open Priority: 5 Private: No Submitted By: Daniel Jones (drdanj) Assigned to: Nobody/Anonymous (nobody) Summary: Periodic repetition of coloured planes Initial Comment: If I have a system and I wish to display some function as a colour map projected on a plane, I can do this in Jmol using $ isosurface plane {x y z}{x1 y1 z1}{x2 y2 z2} map "data.dat" If the system is made periodic and I want to display a supercell, because it's easier to see the system when you look at more than a single repeat unit, I can reload a supercell in Jmol using e.g. $ load "<model_file>" { 2 2 2 } I now want to make a colour map onto a plane of some data $ isosurface plane {x y z}{x1 y1 z1}{x2 y2 z2} map "data.dat" This only plots a plane in the original repeat unit. If I then use $ isosurface lattice { 2 2 2 } This makes periodic repeats of the plane (and displays multiple planes) Is it possible to make periodic representation of the data, and map it to a larger single plane in the visualisation? Perhaps a 2D equivalent command for the $ isosurface lattice command. e.g. $ isosurface extendPlane { x y }. Might work. ---------------------------------------------------------------------- >Comment By: Bob Hanson (hansonr) Date: 2012-09-10 10:51 Message: Please be sure to get the latest version of Jmol -- http://chemapps.stolaf.edu/jmol/Jmol-13.zip It was while working on this that I discovered the problem with saving isosurface information in the state. ---------------------------------------------------------------------- Comment By: Daniel Jones (drdanj) Date: 2012-09-10 08:03 Message: Hi Bob, Sorry for the delay, just got round to trying it, works like a charm! Thanks very much, Dan ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2012-09-08 04:54 Message: Daniel, I think I have it. Please try the latest rendition of http://chemapps.stolaf.edu/jmol/Jmol-13.zip This version of Jmol includes a new isosurface option. You will use the LATTICE option after the MAP keyword to indicate that the mapped data itself is periodic and that you want to extend the plane over a translational lattice associated with that data set: isosurface plane {x y z}{x1 y1 z1}{x2 y2 z2} map LATTICE {2 2 2} "data.dat" Let's see if that does the trick. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379136&aid=3565251&group_id=23629 |