Gui uspex

[ovhpa]

Dear Prof. Rohl,

I update the USPEX implementation on GDIS in order to cope with its new 10.1 version.
I also made quite some changes:

• I modified slightly the graph system to include wild plain, dashed, dotted lines and symbols such as triangle, cross, square, diamond. The changes are presented here:
  ovhpa@5097a31#commitcomment-31146215
  Using that new system, the data is now represented a little differently from previous USPEX implementation: missing structures (for ex. from a restarted job) now appears as cross symbols, of course without the possibility to display the missing structure. I also added a basic convex hull representation for variable composition calculations.
  I will improve that graph system at a later time to get some more control (ie. zoom).

• I create a "carpet" (gui_defs.h) which holds the dust of gtk2 definitions, thanks to that it is much more easy to update GDIS when a gtk2 component goes obsolete... Maybe in the future we can rely on that method to upgrade to gtk3 or even switch to another graphical interface (in which case there would be ideally only one file to modify).
  For now it is just limited to vasp and uspex gui.

• I added a GUI to be able to launch USPEX jobs directly from GDIS. From a related structure or simply from an empty new model. Each panel have many options which may looks overwhelming.
  
  
  
  But I am happy to say that GDIS supports all options available in USPEX manual, plus some extra undocumented options. That is USPEX support in GDIS is over 100% ;)
  However, to launch USPEX calculations, one has to prepare a small script (since octave or matlab can be use). I have prepare an example of such script here:
  https://gist.github.com/ovhpa/59428fe32b9fd72c1ff3d9f2d3577190

• Last but not least I heavily modified previous support of reading USPEX results. The result for all calculation types but Transition Path Sampling (for which I need to understand more deeply what to represent) can be displayed. The graphs to analyse the data are however basically the same as in previous implementation:
  Uspex output #13
  But the best structures "BEST" graph now relies directly on USPEX BEST* files. Also, due to some mistake in the display of results by fitness, I have switch back to presenting only energy related results. I will provide an option to display fitness at a later time.

If you find something extra that would be nice to add, please don't hesitate.

[arohl]

Merged How do I get access to USPEX 10.1 to try it out? Thanks Andrew — Prof Andrew Rohl Director | Curtin Institute for Computation Professor of Computational Science | Department of Chemistry Curtin University PO Box U 1987 Perth, WA 6845 Ph: +61 8 9266 3124 Fax: +61 8 9266 2300 Web: http://computation.curtin.edu.au On 22 Nov 2018, at 9:46 pm, Okadome Valencia <notifications@github.com<mailto:notifications@github.com>> wrote: Dear Prof. Rohl, I update the USPEX implementation on GDIS in order to cope with its new 10.1 version. I also made quite some changes: * I modified slightly the graph system to include wild plain, dashed, dotted lines and symbols such as triangle, cross, square, diamond. The changes are presented here: ovhpa@5097a31#commitcomment-31146215<ovhpa@5097a31#commitcomment-31146215> Using that new system, the data is now represented a little differently from previous USPEX implementation: missing structures (for ex. from a restarted job) now appears as cross symbols, of course without the possibility to display the missing structure. I also added a basic convex hull representation for variable composition calculations. I will improve that graph system at a later time to get some more control (ie. zoom). * I create a "carpet" (gui_defs.h) which holds the dust of gtk2 definitions, thanks to that it is much more easy to update GDIS when a gtk2 component goes obsolete... Maybe in the future we can rely on that method to upgrade to gtk3 or even switch to another graphical interface (in which case there would be ideally only one file to modify). For now it is just limited to vasp and uspex gui. * I added a GUI to be able to launch USPEX jobs directly from GDIS. From a related structure or simply from an empty new model. Each panel have many options which may looks overwhelming. [panel_1]<https://user-images.githubusercontent.com/36496189/48905620-5ce00580-eea5-11e8-9de5-20c9b2501add.png> [panel_2]<https://user-images.githubusercontent.com/36496189/48905660-7da85b00-eea5-11e8-928f-688495d21c57.png> [panel_3]<https://user-images.githubusercontent.com/36496189/48905665-813be200-eea5-11e8-8b3a-20655dc95630.png> But I am happy to say that GDIS supports all options available in USPEX manual, plus some extra undocumented options. That is USPEX support in GDIS is over 100% ;) However, to launch USPEX calculations, one has to prepare a small script (since octave or matlab can be use). I have prepare an example of such script here: https://gist.github.com/ovhpa/59428fe32b9fd72c1ff3d9f2d3577190 * Last but not least I heavily modified previous support of reading USPEX results. The result for all calculation types but Transition Path Sampling (for which I need to understand more deeply what to represent) can be displayed. The graphs to analyse the data are however basically the same as in previous implementation: #13<#13> But the best structures "BEST" graph now relies directly on USPEX BEST* files. Also, due to some mistake in the display of results by fitness, I have switch back to presenting only energy related results. I will provide an option to display fitness at a later time. If you find something extra that would be nice to add, please don't hesitate.

…

________________________________ You can view, comment on, or merge this pull request online at: #16 Commit Summary * gui_uspex: prepare unified gui interface I + some warning fixes. * gui_uspex: prepare unified gui interface II. * gui_uspex: prepare unified gui interface III. * gui_uspex: prepare unified gui interface IV. * gui_uspex: prepare unified gui interface V. * gui_uspex: prepare unified gui interface VI. * gui_uspex: prepare unified gui interface VII + fix memory leaks I. * gui_uspex: prepare unified gui interface VIII + fix memory leaks II. * gui_uspex: FIX: prepare unified gui interface VII. * gui_uspex: prepare unified gui interface IX + fix memory leaks III. * gui_uspex: prepare unified gui interface X + fix memory leaks IV + minor fixes. * gui_uspex: prepare unified gui interface XI + fix memory leaks V. * gui_uspex: prepare unified gui interface XII + fix memory leaks VI. * gui_uspex: prepare unified gui interface (last) + fixes + uspex parameters I * gui_uspex: uspex parameters II * gui_uspex: uspex parameters III. * gui_uspex: uspex parameters IV. * gui_uspex: uspex parameters V. * gui_uspex: uspex parameters VI + valgrind debug. * gui_uspex: uspex parameters VII. * gui_uspex: FIX METADYNAMICS + uspex parameters VIII. * gui_uspex: gui_uspex 0. * gui_uspex: gui_uspex I. * gui_vasp: FIX & better poscar sync. * gui_uspex: FIX gui_uspex I + FIX gui_vasp + ADD anti_opt (for reverse USPEX optimization). * gui_uspex: gui_uspex II. * gui_uspex: gui_uspex III. * gui_uspex: gui_uspex IV + FIX uspex Parameters READ. * gui_uspex: FIX a _BUG_ where uninitialized _num_opt_steps can cause giant memory allocation. * gui_uspex: gui_uspex V. * file_uspex: update to USPEX version 10.1 (I) * file_uspex: update to USPEX version 10.1 (II) * file_uspex: update to USPEX version 10.1 (III) * file_uspex: update to USPEX version 10.1 (IV) * file_uspex: update to USPEX version 10.1 (V) + massive changes to file_uspex (1/2) + gl_graph cross symbols for missing data * file_uspex: update to USPEX version 10.1 (VI) + massive changes to file_uspex (2/2) + NEW graph system (symbols, line types, ...) * gui_uspex: uspex parameters I VER 10.1 * gui_uspex: uspex parameters II VER 10.1 * gui_uspex: uspex parameters III VER 10.1 * gui_uspex: uspex parameters IV VER 10.1 * gui_uspex: uspex parameters V VER 10.1 * file_uspex: fix incorrect reading of natoms with VER 10.1 * file_uspex: when relaxed information is present, data about unrelaxed individulals is now also displayed. * gui_uspex: uspex parameters VI VER 10.1 * gui_uspex: add variable composition cluster calculation + many fixes ; file_uspex: converge saving INPUT.txt with example cases + many fixes * file_uspex: deal with parenthesis for jobs mixing fixed and full relaxation. * file_uspex: proper handling of multiple commandExecutable lines. * gui_uspex: gui_sync 1/2 + fixes. * gui_uspex: gui_sync 2/3 + fixes + cosmetic changes. * gui_uspex: fix Latticevalues. * gui_uspex: fix IonDistances. * gui_uspex: improve molecular calculation settings. * gui_uspex: gui_sync 3/3 + fixes. * gui_uspex: fix calculation steps 1/2. * gui_uspex: fix calculation steps 1/2 + model integration with GDIS. * gui_uspex: task integration. File Changes * M src/file.h<https://github.com/arohl/gdis/pull/16/files#diff-0> (3) * M src/file_arc.c<https://github.com/arohl/gdis/pull/16/files#diff-1> (8) * M src/file_uspex.c<https://github.com/arohl/gdis/pull/16/files#diff-2> (3988) * M src/file_uspex.h<https://github.com/arohl/gdis/pull/16/files#diff-3> (342) * M src/file_vasp.c<https://github.com/arohl/gdis/pull/16/files#diff-4> (5) * M src/gl_graph.c<https://github.com/arohl/gdis/pull/16/files#diff-5> (725) * M src/gl_main.c<https://github.com/arohl/gdis/pull/16/files#diff-6> (3) * M src/graph.h<https://github.com/arohl/gdis/pull/16/files#diff-7> (63) * A src/gui_defs.h<https://github.com/arohl/gdis/pull/16/files#diff-8> (460) * M src/gui_main.c<https://github.com/arohl/gdis/pull/16/files#diff-9> (4) * M src/gui_setup.c<https://github.com/arohl/gdis/pull/16/files#diff-10> (27) * A src/gui_uspex.c<https://github.com/arohl/gdis/pull/16/files#diff-11> (4695) * A src/gui_uspex.h<https://github.com/arohl/gdis/pull/16/files#diff-12> (319) * M src/gui_vasp.c<https://github.com/arohl/gdis/pull/16/files#diff-13> (4056) * M src/gui_vasp.h<https://github.com/arohl/gdis/pull/16/files#diff-14> (489) * M src/interface.h<https://github.com/arohl/gdis/pull/16/files#diff-15> (3) * M src/main.c<https://github.com/arohl/gdis/pull/16/files#diff-16> (8) * M src/makefile.src<https://github.com/arohl/gdis/pull/16/files#diff-17> (2) * M src/pak.h<https://github.com/arohl/gdis/pull/16/files#diff-18> (7) * M src/project.c<https://github.com/arohl/gdis/pull/16/files#diff-19> (3) Patch Links: * https://github.com/arohl/gdis/pull/16.patch * https://github.com/arohl/gdis/pull/16.diff — You are receiving this because you are subscribed to this thread. 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[ovhpa]

Dear Prof. Rohl,

I think USPEX v.10.1 can be download from here: http://uspex-team.org/en/uspex/downloads
You will have to write a script similar to https://gist.github.com/ovhpa/59428fe32b9fd72c1ff3d9f2d3577190 to launch calculation directly from gdis, and name it run_uspex.
It will receive a -9 argument when "ver 10.1" is not selected in GDIS gui (at calculation page) and -m when "OCTAVE" is not selected (or both -9 -m if none are selected).

At present I'm not sure in what form USPEX is distributed. If you received a virtual disk version, you will have to either extract the source from it, or modify run_uspex script so it call USPEX through the virtual disk interface.

If you use 9.4.4, you can simply go to its src directory and prepare a src.tar.gz archive of it and place it under /opt/uspex/mat/944 and /opt/uspex/oct/944 directories if you plan to use my script. No modification should be required to run it from matlab or octave*

For 10.1, there are some modifications to run it from octave/matlab which I haven't report to USPEX team yet. I will do it after I come back from weekend (it is a 3-days long weekend in Japan right now).

In any case you can still save an INPUT.txt file with the save button of GDIS gui and launch USPEX from its usual command.

If you need further assistance, please let me know,

* however if you run USPEX with Octave, I recommend that you add the following line in the beginning (3rd line for ex.) of USPEX.m file:
warning('off', 'Octave:possible-matlab-short-circuit-operator');
to remove the numerous unnecessary warning ;)