Add XCrySDen xsf file reader and writer #52

cajfisher · 2021-11-12T08:04:17Z

Adds functionality for xsf format files, including animation files, used by XCrySDen, aenet, and other packages.

Refreshes bonds in model window when atom coordinates changed in Model:Editing box (same as already done for groups of selected atoms).

Enables reading and writing of structures in xsf format (including animation files)

Examples of single frame and animated xsf structures from XCrySDen website.

ovhpa · 2022-09-10T02:53:10Z

Hi,
I will review the XCrysDen file reader on this PR.

gcc and other compilers (icc, clang)
valgrind / libasan memory checks
static analysis
review

ovhpa · 2022-09-12T01:14:59Z

src/file.h

@@ -101,6 +101,7 @@ gint write_gmf(gchar *, struct model_pak *);
 gint write_planes(gchar *, struct model_pak *);
 gint write_marvin(gchar *, struct model_pak *);
 gint write_xml(gchar *, struct model_pak *);
+gint write_xsf(gchar *, struct model_pak *);


Already in PR #48

ovhpa · 2022-09-12T01:15:17Z

src/file.h

@@ -142,6 +143,7 @@ gint read_marvin(gchar *, struct model_pak *);
 gint read_mvnout(gchar *, struct model_pak *);
 gint read_sout(gchar *, struct model_pak *);
 gint read_xml(gchar *, struct model_pak *);
+gint read_xsf(gchar *, struct model_pak *);


Already in PR #48

ovhpa · 2022-09-12T01:15:25Z

src/file.h

@@ -189,6 +191,7 @@ gint read_qe_out_frame(FILE *, struct model_pak *);
 gint read_xyz_frame(FILE *, struct model_pak *);
 gint read_dlpoly_frame(FILE *, struct model_pak *);
 gint read_dmol_frame(FILE *, struct model_pak *);
+gint read_xsf_frame(FILE *, struct model_pak *);


Already in PR #48

ovhpa · 2022-09-12T01:16:16Z

src/file.c

+/****************************************/
+/* set up the recognized file type list */
+/****************************************/


Already in PR #48

ovhpa · 2022-09-12T01:16:56Z

src/gui_edit.c

@@ -438,6 +438,7 @@ printf("new dipole: %f\n", data->gulp.sdipole);
 sprintf(txt, "New surface dipole: %f\n", data->gulp.sdipole);
 gui_text_show(STANDARD, txt);

+gui_refresh(GUI_MODEL_PROPERTIES);


Already in PR #48

ovhpa · 2022-09-12T01:17:01Z

src/gui_edit.c

@@ -3050,18 +3051,21 @@ if (CEDIT.apd_core->shell)
    text = gtk_entry_get_text(GTK_ENTRY(CEDIT.apd_x));
    CEDIT.apd_core->x[0] = str_to_float(text);
    coords_compute(model);
+    connect_refresh(model);


Already in PR #48

ovhpa · 2022-09-12T01:17:06Z

src/gui_edit.c

    break;

  case COORD_Y:
    text = gtk_entry_get_text(GTK_ENTRY(CEDIT.apd_y));
    CEDIT.apd_core->x[1] = str_to_float(text);
    coords_compute(model);
+    connect_refresh(model);


Already in PR #48

ovhpa · 2022-09-12T01:17:24Z

src/gui_edit.c

    break;

  case COORD_Z:
    text = gtk_entry_get_text(GTK_ENTRY(CEDIT.apd_z));
    CEDIT.apd_core->x[2] = str_to_float(text);
    coords_compute(model);
+    connect_refresh(model);


Already in PR #48

ovhpa · 2022-09-12T01:18:34Z

src/file_xsf.c

+/*
+Copyright (C) 2000 by Sean David Fleming
+
+sean@ivec.org
+


Replace with your own header ;)

ovhpa · 2022-09-12T01:19:35Z

src/interface.h

@@ -60,7 +60,7 @@ GDIS, SGINFO, SYMMETRY, GPERIODIC, ELEM_EDIT, POVRAY, GENSURF,
 ABOUT, ANIM, PLOTS, SURF, DISPLAY, GEOMETRY, SPATIAL, TASKMAN, MANUAL, SETUP,
 FILE_SELECT, FILE_LOAD, FILE_SAVE, FILE_SAVE_AS,
 NODATA, DATA, BIOSYM, CIF, FDF, GULP, MONTY, MARVIN, MORPH,
-META_DATA, XML, XTL, XYZ, MOL2,
+META_DATA, XML, XSF, XTL, XYZ, MOL2,


Already in PR #48

ovhpa · 2022-09-12T01:19:50Z

src/makefile.src

@@ -10,7 +10,7 @@ SRC =	main.c model.c coords.c connect.c matrix.c module.c task.c \
 	ff.c ff_gulp.c test.c \
 	file.c file_cif.c file_gulp.c file_gmf.c file_marvin.c file_xtl.c \
 	file_arc.c file_xyz.c file_fdf.c file_vasp.c file_gms.c file_diff.c file_xml.c \
-	file_abinit.c file_pdb.c file_povray.c file_nwchem.c file_castep.c \
+	file_abinit.c file_pdb.c file_povray.c file_nwchem.c file_castep.c file_xsf.c \


Already in PR #48

ovhpa · 2022-09-12T04:16:57Z

Hi,
I finish reviewing, and almost everything looks OK.
I have just one little problem:
On animation, usually, I can turn the system to any orientation and the animation will be displayed given that point of view (POV), for ex:

However, when doing an animation of a xsf file, the orientation is reset at the first new frame displayed. For ex:

Or in the ZnS case:

Do you think you can fix that?

Best,

cajfisher added 5 commits October 8, 2021 13:17

Update bonds when atoms moved individually

87d8c7d

Refreshes bonds in model window when atom coordinates changed in Model:Editing box (same as already done for groups of selected atoms).

Add reader and writer for XCrysDen format (.xsf)

f33967d

Enables reading and writing of structures in xsf format (including animation files)

Fix xsf file reader

341ac53

Update manual with xsf reader and writer info

03ccf77

Add example xsf files

f09b9bb

Examples of single frame and animated xsf structures from XCrySDen website.

ovhpa self-assigned this Sep 4, 2022

ovhpa reviewed Sep 12, 2022

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Add XCrySDen xsf file reader and writer #52

Add XCrySDen xsf file reader and writer #52

cajfisher commented Nov 12, 2021

ovhpa commented Sep 10, 2022 •

edited

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ovhpa commented Sep 12, 2022

Add XCrySDen xsf file reader and writer #52

Are you sure you want to change the base?

Add XCrySDen xsf file reader and writer #52

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cajfisher commented Nov 12, 2021

ovhpa commented Sep 10, 2022 • edited Loading

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ovhpa commented Sep 12, 2022

ovhpa commented Sep 10, 2022 •

edited

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