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Add XCrySDen xsf file reader and writer #52

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87d8c7d
Update bonds when atoms moved individually
cajfisher Oct 8, 2021
f33967d
Add reader and writer for XCrysDen format (.xsf)
cajfisher Oct 29, 2021
341ac53
Fix xsf file reader
cajfisher Nov 12, 2021
03ccf77
Update manual with xsf reader and writer info
cajfisher Nov 12, 2021
f09b9bb
Add example xsf files
cajfisher Nov 12, 2021
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10 changes: 10 additions & 0 deletions models/ZnS.xsf
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Original file line number Diff line number Diff line change
@@ -0,0 +1,10 @@
# ZnS fixed cell
CRYSTAL
PRIMVEC
0.0000000 2.7100000 2.7100000
2.7100000 0.0000000 2.7100000
2.7100000 2.7100000 0.0000000
PRIMCOORD
2 1
16 0.0000000 0.0000000 0.0000000
30 1.3550000 -1.3550000 -1.3550000
15 changes: 15 additions & 0 deletions models/ZnS_fixed_cell.xsf
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Original file line number Diff line number Diff line change
@@ -0,0 +1,15 @@
# ZnS fixed cell
ANIMSTEPS 2
CRYSTAL
PRIMVEC
0.0000000 2.7100000 2.7100000
2.7100000 0.0000000 2.7100000
2.7100000 2.7100000 0.0000000
PRIMCOORD 1
2 1
16 0.0000000 0.0000000 0.0000000
30 1.3550000 -1.3550000 -1.3550000
PRIMCOORD 2
2 1
16 0.0000000 0.0000000 0.0000000
30 1.2550000 -1.2550000 -1.2550000
27 changes: 27 additions & 0 deletions models/ZnS_variable_cell.xsf
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Original file line number Diff line number Diff line change
@@ -0,0 +1,27 @@
# ZnS variable cell
ANIMSTEPS 2
CRYSTAL
PRIMVEC 1
2.7100000 2.7100000 0.00000000
2.7100000 0.0000000 2.71000000
0.0000000 2.7100000 2.71000000
CONVVEC 1
5.4200000 0.0000000 0.00000000
0.0000000 5.4200000 0.00000000
0.0000000 0.0000000 5.42000000
PRIMCOORD 1
2 1
16 0.0000000 0.0000000 0.00000000
30 1.3550000 -1.3550000 -1.35500000
PRIMVEC 2
2.9810000 2.9810000 0.00000000
2.9810000 0.0000000 2.98100000
0.0000000 2.9810000 2.98100000
CONVVEC 2
5.9620000 0.0000000 0.00000000
0.0000000 5.9620000 0.00000000
0.0000000 0.0000000 5.96200000
PRIMCOORD 2
2 1
16 0.0000000 0.0000000 0.00000000
30 1.5905000 -1.5905000 -1.59050000
6 changes: 6 additions & 0 deletions models/water.xsf
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Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
# Water molecule

ATOMS
8 0.0000 0.0000 0.0000 -0.0516 0.0000 -0.0399
1 0.0000 0.0000 1.0000 0.0176 0.0000 0.0304
1 0.9681 0.0000 -0.2503 0.0339 0.0000 0.0094
19 changes: 19 additions & 0 deletions models/water_anim.xsf
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Original file line number Diff line number Diff line change
@@ -0,0 +1,19 @@
# Water molecule animation

ANIMSTEPS 4
ATOMS 1
8 0.0000 0.0000 0.0000 -0.0516 0.0000 -0.0399
1 0.0000 0.0000 1.0000 0.0176 0.0000 0.0304
1 0.9681 0.0000 -0.2503 0.0339 0.0000 0.0094
ATOMS 2
8 -0.1480 0.0000 -0.1146 0.0020 0.0000 0.0015
1 -0.0468 0.0000 0.9134 -0.0069 0.0000 0.0069
1 0.8726 0.0000 -0.2740 0.0049 0.0000 -0.0084
ATOMS 3
8 -0.1032 0.0000 -0.0799 0.0013 0.0000 0.0010
1 -0.0319 0.0000 0.9591 0.0011 0.0000 -0.0028
1 0.9205 0.0000 -0.2710 -0.0025 0.0000 0.0018
ATOMS 4
8 -0.1102 0.0000 -0.0853 0.0001 0.0000 0.0000
1 -0.0345 0.0000 0.9503 -0.0000 0.0000 -0.0000
1 0.9114 0.0000 -0.2714 -0.0000 0.0000 -0.0000
19 changes: 16 additions & 3 deletions src/file.c
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Original file line number Diff line number Diff line change
Expand Up @@ -56,9 +56,9 @@ The GNU GPL can also be found at http://www.gnu.org
extern struct sysenv_pak sysenv;
extern struct elem_pak elements[];

/***************************************/
/* setup the recognized file type list */
/***************************************/
/****************************************/
/* set up the recognized file type list */
/****************************************/
Comment on lines +59 to +61

@ovhpa ovhpa Sep 12, 2022

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Already in PR #48

#define DEBUG_FILE_INIT 0
void file_init(void)
{
Expand Down Expand Up @@ -677,6 +677,19 @@ file_data->read_file = read_xml;
file_data->read_frame = NULL; /* frame reading */
sysenv.file_list = g_slist_prepend(sysenv.file_list, file_data);

/* supported file type */
file_data = g_malloc(sizeof(struct file_pak));
file_data->id = XSF;
file_data->group = XSF;
file_data->menu = TRUE;
file_data->label = g_strdup("XSF");
file_data->ext = NULL;
file_data->ext = g_slist_prepend(file_data->ext, "xsf");
file_data->write_file = write_xsf;
file_data->read_file = read_xsf;
file_data->read_frame = read_xsf_frame; /* frame reading */
sysenv.file_list = g_slist_prepend(sysenv.file_list, file_data);

/* supported file type */
file_data = g_malloc(sizeof(struct file_pak));
file_data->id = XTL;
Expand Down
3 changes: 3 additions & 0 deletions src/file.h
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Expand Up @@ -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 *);

@ovhpa ovhpa Sep 12, 2022

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Already in PR #48

gint write_xtl(gchar *, struct model_pak *);
gint write_xyz(gchar *, struct model_pak *);
gint write_gms(gchar *, struct model_pak *);
Expand Down Expand Up @@ -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 *);

@ovhpa ovhpa Sep 12, 2022

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Already in PR #48

gint read_xtl(gchar *, struct model_pak *);
gint read_xyz(gchar *, struct model_pak *);
gint read_using_babel(gchar *, struct model_pak *);
Expand Down Expand Up @@ -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 *);

@ovhpa ovhpa Sep 12, 2022

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Already in PR #48


/*NEW: track/update frames (TODO)*/
gint update_frame_uspex(gint idx,struct model_pak *model);
Expand Down
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