From 87d8c7d962967dae1e2158e51ec68753a6b882fc Mon Sep 17 00:00:00 2001
From: Craig Fisher <66772456+cajfisher@users.noreply.github.com>
Date: Fri, 8 Oct 2021 13:17:11 +0900
Subject: [PATCH 1/8] Update bonds when atoms moved individually

Refreshes bonds in model window when atom coordinates changed in Model:Editing box (same as already done for groups of selected atoms).
---
 src/gui_edit.c | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/gui_edit.c b/src/gui_edit.c
index 81511ed..4389638 100644
--- a/src/gui_edit.c
+++ b/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);
 redraw_canvas(SINGLE);
 }
 
@@ -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);
     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);
     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);
     break;
 
   case SOF:

From f33967d6cdf6a1a2c7ff317f16caa792de901a53 Mon Sep 17 00:00:00 2001
From: Craig Fisher <66772456+cajfisher@users.noreply.github.com>
Date: Fri, 29 Oct 2021 13:30:52 +0900
Subject: [PATCH 2/8] Add reader and writer for XCrysDen format (.xsf)

Enables reading and writing of structures in xsf format (including animation files)
---
 src/file.c       |  13 ++
 src/file.h       |   3 +
 src/file_xsf.c   | 459 +++++++++++++++++++++++++++++++++++++++++++++++
 src/interface.h  |   2 +-
 src/makefile.src |   2 +-
 5 files changed, 477 insertions(+), 2 deletions(-)
 create mode 100644 src/file_xsf.c

diff --git a/src/file.c b/src/file.c
index 243d00a..d2dca61 100644
--- a/src/file.c
+++ b/src/file.c
@@ -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;
diff --git a/src/file.h b/src/file.h
index 497e436..02aa147 100644
--- a/src/file.h
+++ b/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 *);
 gint write_xtl(gchar *, struct model_pak *);
 gint write_xyz(gchar *, struct model_pak *);
 gint write_gms(gchar *, struct model_pak *);
@@ -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 *);
 gint read_xtl(gchar *, struct model_pak *);
 gint read_xyz(gchar *, struct model_pak *);
 gint read_using_babel(gchar *, struct model_pak *);
@@ -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 *);
 
 /*NEW: track/update frames (TODO)*/
 gint update_frame_uspex(gint idx,struct model_pak *model);
diff --git a/src/file_xsf.c b/src/file_xsf.c
new file mode 100644
index 0000000..de9fcc8
--- /dev/null
+++ b/src/file_xsf.c
@@ -0,0 +1,459 @@
+/*
+Copyright (C) 2000 by Sean David Fleming
+
+sean@ivec.org
+
+This program is free software; you can redistribute it and/or
+modify it under the terms of the GNU General Public License
+as published by the Free Software Foundation; either version 2
+of the License, or (at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program; if not, write to the Free Software
+Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
+
+The GNU GPL can also be found at http://www.gnu.org
+*/
+
+#include <stdio.h>
+#include <string.h>
+
+#include "gdis.h"
+#include "coords.h"
+#include "model.h"
+#include "file.h"
+#include "matrix.h"
+#include "interface.h"
+#include "parse.h"
+
+/* main structures */
+extern struct sysenv_pak sysenv;
+
+/****************************/
+/* write a coordinate block */
+/****************************/
+gint write_xsf_frame(FILE *fp, struct model_pak *model)
+{
+gint i=0;
+gdouble vec[3];
+GSList *list;
+struct core_pak *core;
+
+/* header */
+if (model->periodic == 3)
+  {
+  for (list=model->cores ; list ; list=g_slist_next(list))
+    {
+    core = (struct core_pak *) list->data;
+
+    if (core->status & (DELETED | HIDDEN))
+      continue;
+    i++;
+    }
+  fprintf(fp,"%4d 1\n", i);
+  }
+
+/* coords */
+for (list=model->cores ; list ; list=g_slist_next(list))
+  {
+  core = (struct core_pak *) list->data;
+
+  if (core->status & (DELETED | HIDDEN))
+    continue;
+  if (core->primary)
+    {
+    ARR3SET(vec, core->x);
+    vecmat(model->latmat, vec);
+
+    fprintf(fp,"%4d %9.5f %9.5f %9.5f\n",
+            core->atom_code, vec[0], vec[1], vec[2]);
+    }
+  }
+return(0);
+}
+
+/**********************/
+/* save in XSF format */
+/**********************/
+#define DEBUG_WRITE_XSF 1
+gint write_xsf(gchar *filename, struct model_pak *data)
+{
+gint n, current, status;
+FILE *fp;
+GString *err_text;
+
+/* checks */
+g_return_val_if_fail(data != NULL, 1);
+g_return_val_if_fail(filename != NULL, 2);
+
+if( g_slist_length(data->cores) > 9999)
+  {
+  gui_text_show(ERROR, "Too many atoms for XSF format!\n");
+  return(1);
+  }
+
+if( data->periodic == 1)
+  {
+  gui_text_show(ERROR, "Model must be 0, 2 or 3 dimensional.n");
+  return(1);
+  }
+
+/* open the file */
+fp = fopen(filename,"w");
+if (!fp)
+  {
+  gui_text_show(ERROR, "Bad filename!\n");
+  return(1);
+  }
+
+if (data->frame_list)
+  {
+  data->afp = fopen(data->filename, "r");
+
+  if (!data->afp)
+    {
+    gui_text_show(ERROR, "Failed to open animation stream.\n");
+    return(0);
+    }
+
+  current = data->cur_frame; /* Remember current position */
+
+  fprintf(fp,"ANIMSTEPS %d\n", data->num_frames);
+
+  for (n=data->cur_frame ; n<data->num_frames ; n++)
+    {
+    status = read_raw_frame(data->afp, n, data);
+#if DEBUG_WRITE_XSF
+printf("Frame no: %d\n",n);
+#endif
+    if (status)
+      {
+      err_text = g_string_new("");
+      g_string_printf(err_text, "Error reading frame: %d\n", n);
+      gui_text_show(ERROR, err_text->str);
+      g_string_free(err_text, TRUE);
+      return(2);
+      }
+
+    if (data->periodic == 0)
+      {
+      fprintf(fp, "ATOMS %d\n", n+1);
+      }
+    else
+      {
+      if (data->periodic == 2)
+         fputs("SLAB\n", fp);
+      else
+         fputs("CRYSTAL\n", fp);
+
+      fprintf(fp, "PRIMVEC %d\n", n+1);
+      fprintf(fp,"%11.6f %11.6f %11.6f\n", data->latmat[0], data->latmat[1], data->latmat[2]);
+      fprintf(fp,"%11.6f %11.6f %11.6f\n", data->latmat[3], data->latmat[4], data->latmat[5]);
+      fprintf(fp,"%11.6f %11.6f %11.6f\n", data->latmat[6], data->latmat[7], data->latmat[8]);
+
+      if (data->periodic == 3)
+        {
+        fprintf(fp, "CONVVEC %d\n", n+1);
+        fprintf(fp,"%11.6f %11.6f %11.6f\n", data->latmat[0], data->latmat[1], data->latmat[2]);
+        fprintf(fp,"%11.6f %11.6f %11.6f\n", data->latmat[3], data->latmat[4], data->latmat[5]);
+        fprintf(fp,"%11.6f %11.6f %11.6f\n", data->latmat[6], data->latmat[7], data->latmat[8]);
+        }
+
+      fprintf(fp, "PRIMCOORD %d\n", n+1);
+      }
+
+    write_xsf_frame(fp, data);
+    }
+
+  /* Restore data for current frame */
+  read_raw_frame(data->afp, current, data);
+  connect_molecules(data);
+  fclose(data->afp);
+  }
+else
+  {
+  if (data->periodic == 0)
+    fputs("ATOMS\n", fp);
+  else
+    {
+    if (data->periodic == 2)
+      fputs("SLAB\n", fp);
+    else
+      fputs("CRYSTAL\n", fp);
+
+    fputs("PRIMVEC\n", fp);
+    fprintf(fp,"%11.6f %11.6f %11.6f\n", data->latmat[0], data->latmat[1], data->latmat[2]);
+    fprintf(fp,"%11.6f %11.6f %11.6f\n", data->latmat[3], data->latmat[4], data->latmat[5]);
+    fprintf(fp,"%11.6f %11.6f %11.6f\n", data->latmat[6], data->latmat[7], data->latmat[8]);
+
+    if (data->periodic == 3)
+      {
+      fputs("CONVVEC\n", fp);
+      fprintf(fp,"%11.6f %11.6f %11.6f\n", data->latmat[0], data->latmat[1], data->latmat[2]);
+      fprintf(fp,"%11.6f %11.6f %11.6f\n", data->latmat[3], data->latmat[4], data->latmat[5]);
+      fprintf(fp,"%11.6f %11.6f %11.6f\n", data->latmat[6], data->latmat[7], data->latmat[8]);
+      }
+    fputs("PRIMCOORD\n", fp);
+    }
+  write_xsf_frame(fp, data);
+  }
+
+/* done */
+gui_text_show(STANDARD, "File saved in XSF format\n");
+fclose(fp);
+return(0);
+}
+
+/*********************************************/
+/* read a xsf block into the model structure */
+/*********************************************/
+#define DEBUG_READ_XSF_BLOCK 0
+/* NB: assumes fp is one line before frame data */
+void read_xsf_block(FILE *fp, struct model_pak *data)
+{
+gint i, code, num_tokens;
+gint n = 0, num_atoms = 0;
+gchar **buff;
+struct core_pak *core;
+struct elem_pak elem_data;
+GSList *clist;
+
+g_assert(fp != NULL);
+g_assert(data != NULL);
+
+clist = data->cores;
+
+/* loop while there's data */
+for (;;)
+  {
+  buff = get_tokenized_line(fp, &num_tokens);
+  if (!buff)
+    break;
+
+  if (num_tokens)
+    {
+    if (num_tokens == 1)
+      {
+      if (!g_ascii_strcasecmp(*buff, "crystal"))
+        break;
+      else if (!g_ascii_strcasecmp(*buff, "slab"))
+        break;
+      }
+    if (!g_ascii_strcasecmp(*buff, "atoms"))
+      break;
+
+    if (!g_ascii_strcasecmp(*buff, "primvec"))
+      {
+      data->construct_pbc = TRUE;
+      for (i=0; i<3; i++)
+        {
+        g_strfreev(buff);
+        buff = get_tokenized_line(fp, &num_tokens);
+        if (num_tokens == 3)
+          {
+          data->latmat[3*i] = str_to_float(*(buff));
+          data->latmat[3*i+1] = str_to_float(*(buff+1));
+          data->latmat[3*i+2] = str_to_float(*(buff+2));
+          }
+#if DEBUG_READ_XSF_BLOCK
+P3MAT("Lattice:", data->latmat);
+#endif
+        }
+      }
+    if (!g_ascii_strcasecmp(*buff, "primcoord"))
+      {
+      g_strfreev(buff);
+      buff = get_tokenized_line(fp, &num_tokens);
+
+      if (num_tokens == 2)
+        num_atoms = (gint)str_to_float(*buff);
+      else
+        return;
+      }
+
+    if (num_tokens > 3)
+      {
+      code = (gint)str_to_float(*buff);
+      if (code > 0)
+        {
+        n++;
+/* overwrite existing core (if any) */
+        if (clist)
+          {
+          core = (struct core_pak *) clist->data;
+          clist = g_slist_next(clist);
+          }
+        else
+          {
+/* otherwise, add a new core */
+          get_elem_data(code, &elem_data, data);
+          core = core_new(elem_data.symbol, NULL, data);
+          data->cores = g_slist_append(data->cores, core);
+          }
+
+        core->x[0] = str_to_float(*(buff+1));
+        core->x[1] = str_to_float(*(buff+2));
+        core->x[2] = str_to_float(*(buff+3));
+        core->lookup_charge = TRUE;
+#if DEBUG_READ_XSF_BLOCK
+printf("Atom %d %s %f %f %f\n",n, core->atom_label, core->x[0],
+        core->x[1], core->x[2]);
+#endif
+        }
+      }
+    }
+  g_strfreev(buff);
+  }
+
+#if DEBUG_READ_XSF_BLOCK
+printf("Periodicity: %d\n", data->periodic);
+#endif
+
+if (n != g_slist_length(data->cores) || 
+   (data->periodic > 0 && num_atoms != n) ||
+   n == 0)
+  gui_text_show(ERROR, "Wrong number of atoms in xsf file.\n");
+
+/* convert input cartesian coords to fractional */
+if( data->periodic)
+  {
+  matrix_lattice_init(data);
+  coords_make_fractional(data);
+  data->fractional = TRUE;
+  }
+
+g_strfreev(buff);
+}
+/******************/
+/* xsf frame read */
+/******************/
+gint read_xsf_frame(FILE *fp, struct model_pak *data)
+{
+/* frame overwrite */
+read_xsf_block(fp, data);
+return(0);
+}
+/****************/
+/* read routine */
+/****************/
+#define DEBUG_READ_XSF 0
+gint read_xsf(gchar *filename, struct model_pak *data)
+{
+gint frame = 0, end_flag = 0;
+gint num_tokens;
+gchar **buff;
+fpos_t *offset;
+FILE *fp;
+
+/* checks */
+g_return_val_if_fail(data != NULL, 1);
+g_return_val_if_fail(filename != NULL, 1);
+
+if (strlen(filename) < FILELEN)
+  strcpy(data->filename, filename);
+else
+  {
+  gui_text_show(ERROR, "File name is too long.\n");
+  return(-1);
+  }
+
+fp = fopen(filename, "rt");
+if (fp == NULL)
+  return(2);
+
+/* inits */
+data->fractional = FALSE;
+
+for (;;)
+  {
+  buff = get_tokenized_line(fp, &num_tokens);
+  if (buff == NULL)
+    break;
+
+  /* first line should be type */
+  if (!g_ascii_strcasecmp(*buff, "animsteps"))
+    {
+    g_strfreev(buff);
+    buff = get_tokenized_line(fp, &num_tokens);
+    if (!buff)
+      break;
+    }
+
+  if (!g_ascii_strcasecmp(*buff, "atoms"))
+    {
+    data->periodic = 0;
+    end_flag++;
+    }
+  else if (!g_ascii_strcasecmp(*buff, "slab"))
+    {
+    data->periodic = 2;
+    end_flag++;
+    }
+  else if (!g_ascii_strcasecmp(*buff, "crystal"))
+    {
+    data->periodic = 3;
+    end_flag++;
+    }
+  else
+    end_flag = 0;
+
+/* coords search */
+  if ( end_flag == 1)
+    {
+    add_frame_offset(fp, data);
+
+/* increment counter */
+    frame++;
+    }
+
+  g_strfreev(buff);
+  }
+
+offset = g_list_nth_data(data->frame_list, 0);
+
+#if DEBUG_READ_XSF
+printf("Total frames: %d\n", g_list_length(data->frame_list));
+#endif
+
+if (!offset)
+  return(1);
+
+if (fsetpos(fp, offset))
+  {
+  printf("Error positioning file pointer.\n");
+  return(2);
+  }
+else
+  {
+/* use supplied routine (if available) */
+  read_xsf_frame(fp, data);
+  }
+
+/* got everything */
+data->num_asym = g_slist_length(data->cores);
+data->num_frames = frame;
+
+/* get rid of frame list if only one frame */
+if (data->num_frames == 1)
+  {
+  free_list(data->frame_list);
+  data->frame_list = NULL;
+  }
+
+#if DEBUG_READ_XSF
+printf("Found %d atoms.\n", n);
+#endif
+
+/* model setup */
+g_free(data->basename);
+data->basename = parse_strip(filename);
+
+model_prep(data);
+
+return(0);
+}
diff --git a/src/interface.h b/src/interface.h
index 251a1e5..5833655 100644
--- a/src/interface.h
+++ b/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,
 AUTO, CSSR, GAMOUT, PDB, GEOMVIEW_OFF, PROJECT, DOCKING,
 MDI, CREATOR, MVNOUT, GULPOUT, GULP_TRJ, SIESTA_OUT, VASP, CVASP,
 USPEX, CUSPEX, REPLACE_ATOMS, DYNAMICS, ZMATRIX,
diff --git a/src/makefile.src b/src/makefile.src
index 9394deb..209116c 100644
--- a/src/makefile.src
+++ b/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 \
 	file_gauss.c file_qe.c file_rietica.c file_geomview.c file_cssr.c file_cel.c \
 	file_dmol.c file_dlpoly.c file_bgf.c file_cgf.c file_dlp.c \
 	file_gromacs.c file_meta.c file_mol2.c file_uspex.c

From eaddb50e70a7cdb71fe27c57837fd3946ab60d81 Mon Sep 17 00:00:00 2001
From: Craig Fisher <66772456+cajfisher@users.noreply.github.com>
Date: Wed, 31 Aug 2022 14:06:07 +0900
Subject: [PATCH 3/8] Fix bug in meta file reader

Fixes bug in file_meta.c when parsing units
Replaces deprecated g_pattern_match_string with g_pattern_spec_match_string in file.c
Replace QE with Quantum Espresso in file type lists for clarity
Correct various spelling/punctuation errors
---
 src/analysis.c  |   2 +-
 src/file.c      | 127 +++++++++++++++++++++++++++++++++++++++++-------
 src/file_meta.c |  12 ++---
 src/gui_task.c  |   2 +-
 src/spatial.c   |   4 +-
 5 files changed, 119 insertions(+), 28 deletions(-)

diff --git a/src/analysis.c b/src/analysis.c
index 7824514..2842469 100644
--- a/src/analysis.c
+++ b/src/analysis.c
@@ -482,7 +482,7 @@ for (n=0 ; n<analysis->num_frames ; n++)
 */
 
 /* CURRENT - loop over all atoms - even duplicates so that we can record */
-/* distance between an atom and it's periodic images (NB: correct for double counting) */
+/* distance between an atom and its periodic images (NB: correct for double counting) */
   for (i=0 ; i<analysis->num_atoms ; i++)
     {
     corei = g_slist_nth_data(model->cores, i);
diff --git a/src/file.c b/src/file.c
index d2dca61..f6fbdcc 100644
--- a/src/file.c
+++ b/src/file.c
@@ -56,9 +56,74 @@ 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 */
-/***************************************/
+/**********************************************************/
+/* Check if file is binary or ascii                       */
+/**********************************************************/
+gint ascii_check(const gchar *filename)
+{
+FILE *fp;
+gchar c;
+gint flag = 0;
+
+fp = fopen(filename, "r");
+
+/* checks */
+g_assert(fp != NULL);
+
+c = fgetc(fp);
+
+while (c != EOF)
+  {
+  if (!isascii(c) ||
+     (iscntrl(c) && !isspace(c) &&
+     c != '\b' && c != '\032' && c != '\033'))
+      flag++;	/* not all ASCII */
+  c = fgetc(fp);
+  }
+
+fclose(fp);
+
+if (flag)
+  return 1;  /* Binary */
+else
+  return 0;  /* Ascii */
+}
+/**********************************************************/
+/* change model basename and update filenames & tree      */
+/**********************************************************/
+void change_basename(GtkWidget *w, struct model_pak *data)
+{
+g_assert(w != NULL);
+g_assert(data != NULL);
+
+/* de-alloc */
+g_free(data->basename);
+
+/* set the new basename & related info */
+data->basename = g_strdup(gtk_entry_get_text(GTK_ENTRY(w)));
+
+/* update the model tree */
+tree_model_add(data);
+}
+
+/********************************************/
+/* construct file name if path not included */
+/********************************************/
+gchar* construct_filename(gchar *filename)
+{
+gchar *fullname;
+
+/* construct complete filename */
+if( !g_ascii_strcasecmp(filename, g_path_get_basename(filename)) )
+  fullname = g_build_filename(sysenv.cwd, filename, NULL);
+else
+  fullname = g_strdup(filename);
+
+return fullname;
+}
+/****************************************/
+/* set up the recognized file type list */
+/****************************************/
 #define DEBUG_FILE_INIT 0
 void file_init(void)
 {
@@ -346,7 +411,7 @@ file_data = g_malloc(sizeof(struct file_pak));
 file_data->id = QE;
 file_data->group = QE;
 file_data->menu = TRUE;
-file_data->label = g_strdup("QE");
+file_data->label = g_strdup("Quantum Espresso");
 file_data->ext = NULL;
 file_data->ext = g_slist_append(file_data->ext, "qein");
 file_data->write_file = write_qe;
@@ -491,6 +556,45 @@ file_data->read_file = read_mol2;
 file_data->read_frame = NULL; 
 sysenv.file_list = g_slist_prepend(sysenv.file_list, file_data);
 
+/* supported file type */
+file_data = (struct file_pak *) g_malloc(sizeof(struct file_pak));
+file_data->id = MOLDY;
+file_data->group = MOLDY;
+file_data->menu = TRUE;
+file_data->label = g_strdup("Moldy");
+file_data->ext = NULL;
+file_data->ext = g_slist_prepend(file_data->ext, "in");
+file_data->ext = g_slist_prepend(file_data->ext, "min");
+file_data->ext = g_slist_prepend(file_data->ext, "mdy");
+file_data->read_file = read_moldy;
+file_data->write_file = write_moldy_sys;
+sysenv.file_list = g_slist_prepend(sysenv.file_list, file_data);
+
+/* supported file type */
+file_data = (struct file_pak *) g_malloc(sizeof(struct file_pak));
+file_data->id = MOLDY_POT;
+file_data->group = MOLDY;
+file_data->menu = FALSE;
+file_data->label = g_strdup("Moldy potentials");
+file_data->ext = NULL;
+file_data->ext = g_slist_prepend(file_data->ext, "pot");
+file_data->read_file = NULL;
+file_data->write_file = NULL;
+sysenv.file_list = g_slist_prepend(sysenv.file_list, file_data);
+
+/* supported file type */
+file_data = (struct file_pak *) g_malloc(sizeof(struct file_pak));
+file_data->id = MOLDY_RES;
+file_data->group = MOLDY;
+file_data->menu = TRUE;
+file_data->label = g_strdup("Moldy restart");
+file_data->ext = NULL;
+file_data->ext = g_slist_prepend(file_data->ext, "sav");
+file_data->ext = g_slist_prepend(file_data->ext, "mds");
+file_data->read_file = read_moldy_restart;
+file_data->write_file = NULL;
+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 = NWCHEM;
@@ -677,19 +781,6 @@ 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;
@@ -814,7 +905,7 @@ while (list)
   name = list->data;
   list = g_slist_next(list);
 
-  if (!g_pattern_match_string(ps, name))
+  if (!g_pattern_spec_match_string(ps, name))
     {
     files = g_slist_remove(files, name);
     g_free(name);
diff --git a/src/file_meta.c b/src/file_meta.c
index 4ca3c60..25a9064 100644
--- a/src/file_meta.c
+++ b/src/file_meta.c
@@ -35,21 +35,21 @@ extern struct elem_pak elements[];
 
 /* meta data for computational chemistry archiving */
 
-/*****************************************************************/
-/* split a string containing units into it's raw value and units */
-/*****************************************************************/
+/****************************************************************/
+/* split a string containing units into its raw value and units */
+/****************************************************************/
 void meta_parse_units(gchar **value, gchar **units, gchar *source)
 {
 gchar **buff;
 
 buff = g_strsplit(source, " ", 2);
 
-if (*buff+0)
-  *value = g_strdup(*(buff+0));
+if (*buff)
+  *value = g_strdup(*(buff));
 else
   *value = NULL;
 
-if (*buff+1)
+if (g_strv_length(buff) == 2)
   *units = g_strdup(*(buff+1));
 else
   *units = NULL;
diff --git a/src/gui_task.c b/src/gui_task.c
index 9b288ac..8fceeac 100644
--- a/src/gui_task.c
+++ b/src/gui_task.c
@@ -246,7 +246,7 @@ printf("%s", line);
 pclose(fp);
 
 /* Build the process hierarchy. Every process marks itself as first child */
-/* of it's parent or as sister of first child of its parent */
+/* of its parent or as sister of first child of its parent */
 /* algorithm taken from pstree.c by Fred Hucht */
 
 for (me = 0; me < psarray->len; me++)
diff --git a/src/spatial.c b/src/spatial.c
index 60c3e68..73d0cfd 100644
--- a/src/spatial.c
+++ b/src/spatial.c
@@ -399,8 +399,8 @@ struct core_pak *core1, *core2, *core3;
 /* FIXME - this only uses the 1st 3 points, in future - an average for n pts */
 /* http://www.geocities.com/CollegePark/Campus/1278/JBook/LSQ_Plane.html */
 /* shouldn't matter when this routine is properly implemented, as we'll go */
-/* through the atom_list in the usual fashoin & terminate when it is NULL, */
-/* not when it's data ptr is NULL */ 
+/* through the atom_list in the usual fashoin and terminate when it's NULL, */
+/* not when its data ptr is NULL */ 
 g_assert(cores != NULL);
 g_assert(g_list_length(cores) > 2);
 

From da5aa574a414edfe6e136191af58abc529eae635 Mon Sep 17 00:00:00 2001
From: Craig Fisher <66772456+cajfisher@users.noreply.github.com>
Date: Wed, 31 Aug 2022 14:10:19 +0900
Subject: [PATCH 4/8] Remove moldy files specs

---
 src/file.c | 104 -----------------------------------------------------
 1 file changed, 104 deletions(-)

diff --git a/src/file.c b/src/file.c
index f6fbdcc..6bc884c 100644
--- a/src/file.c
+++ b/src/file.c
@@ -56,71 +56,6 @@ The GNU GPL can also be found at http://www.gnu.org
 extern struct sysenv_pak sysenv;
 extern struct elem_pak elements[];
 
-/**********************************************************/
-/* Check if file is binary or ascii                       */
-/**********************************************************/
-gint ascii_check(const gchar *filename)
-{
-FILE *fp;
-gchar c;
-gint flag = 0;
-
-fp = fopen(filename, "r");
-
-/* checks */
-g_assert(fp != NULL);
-
-c = fgetc(fp);
-
-while (c != EOF)
-  {
-  if (!isascii(c) ||
-     (iscntrl(c) && !isspace(c) &&
-     c != '\b' && c != '\032' && c != '\033'))
-      flag++;	/* not all ASCII */
-  c = fgetc(fp);
-  }
-
-fclose(fp);
-
-if (flag)
-  return 1;  /* Binary */
-else
-  return 0;  /* Ascii */
-}
-/**********************************************************/
-/* change model basename and update filenames & tree      */
-/**********************************************************/
-void change_basename(GtkWidget *w, struct model_pak *data)
-{
-g_assert(w != NULL);
-g_assert(data != NULL);
-
-/* de-alloc */
-g_free(data->basename);
-
-/* set the new basename & related info */
-data->basename = g_strdup(gtk_entry_get_text(GTK_ENTRY(w)));
-
-/* update the model tree */
-tree_model_add(data);
-}
-
-/********************************************/
-/* construct file name if path not included */
-/********************************************/
-gchar* construct_filename(gchar *filename)
-{
-gchar *fullname;
-
-/* construct complete filename */
-if( !g_ascii_strcasecmp(filename, g_path_get_basename(filename)) )
-  fullname = g_build_filename(sysenv.cwd, filename, NULL);
-else
-  fullname = g_strdup(filename);
-
-return fullname;
-}
 /****************************************/
 /* set up the recognized file type list */
 /****************************************/
@@ -556,45 +491,6 @@ file_data->read_file = read_mol2;
 file_data->read_frame = NULL; 
 sysenv.file_list = g_slist_prepend(sysenv.file_list, file_data);
 
-/* supported file type */
-file_data = (struct file_pak *) g_malloc(sizeof(struct file_pak));
-file_data->id = MOLDY;
-file_data->group = MOLDY;
-file_data->menu = TRUE;
-file_data->label = g_strdup("Moldy");
-file_data->ext = NULL;
-file_data->ext = g_slist_prepend(file_data->ext, "in");
-file_data->ext = g_slist_prepend(file_data->ext, "min");
-file_data->ext = g_slist_prepend(file_data->ext, "mdy");
-file_data->read_file = read_moldy;
-file_data->write_file = write_moldy_sys;
-sysenv.file_list = g_slist_prepend(sysenv.file_list, file_data);
-
-/* supported file type */
-file_data = (struct file_pak *) g_malloc(sizeof(struct file_pak));
-file_data->id = MOLDY_POT;
-file_data->group = MOLDY;
-file_data->menu = FALSE;
-file_data->label = g_strdup("Moldy potentials");
-file_data->ext = NULL;
-file_data->ext = g_slist_prepend(file_data->ext, "pot");
-file_data->read_file = NULL;
-file_data->write_file = NULL;
-sysenv.file_list = g_slist_prepend(sysenv.file_list, file_data);
-
-/* supported file type */
-file_data = (struct file_pak *) g_malloc(sizeof(struct file_pak));
-file_data->id = MOLDY_RES;
-file_data->group = MOLDY;
-file_data->menu = TRUE;
-file_data->label = g_strdup("Moldy restart");
-file_data->ext = NULL;
-file_data->ext = g_slist_prepend(file_data->ext, "sav");
-file_data->ext = g_slist_prepend(file_data->ext, "mds");
-file_data->read_file = read_moldy_restart;
-file_data->write_file = NULL;
-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 = NWCHEM;

From 7a969760690555ee0911303ec7c02ea165800c9a Mon Sep 17 00:00:00 2001
From: Craig Fisher <66772456+cajfisher@users.noreply.github.com>
Date: Mon, 5 Sep 2022 11:43:17 +0900
Subject: [PATCH 5/8] Update copyright statement

---
 src/file_xsf.c | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/file_xsf.c b/src/file_xsf.c
index de9fcc8..3437b92 100644
--- a/src/file_xsf.c
+++ b/src/file_xsf.c
@@ -1,7 +1,7 @@
 /*
-Copyright (C) 2000 by Sean David Fleming
+Copyright (C) 2022 by Craig Andrew James Fisher
 
-sean@ivec.org
+c_fisher@jfcc.or.jp
 
 This program is free software; you can redistribute it and/or
 modify it under the terms of the GNU General Public License

From 43eb9325000b7e712d65d1490346313ed83106bc Mon Sep 17 00:00:00 2001
From: Craig Fisher <66772456+cajfisher@users.noreply.github.com>
Date: Mon, 5 Sep 2022 16:15:08 +0900
Subject: [PATCH 6/8] Fix bug in cif reader

---
 src/file_cif.c | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/file_cif.c b/src/file_cif.c
index 5eb03c5..bca09c1 100644
--- a/src/file_cif.c
+++ b/src/file_cif.c
@@ -182,7 +182,7 @@ return(0);
 /***************/
 /* CIF loading */
 /***************/
-#define DEBUG_LOAD_CIF 0
+#define DEBUG_LOAD_CIF 1
 gint read_cif(gchar *filename, struct model_pak *data)
 {
 gint i, j, n, natom, new, order, pos, keyword, loop_count=0;
@@ -776,7 +776,7 @@ else
     return(-1);
     }
 #if DEBUG_LOAD_CIF
-printf("Found %d atom%c.\n", natom, (natom != 1?'s':''));
+printf("Found %d atom%s\n", natom, (natom != 1 ? "s.":"."));
 printf("Found %d symmetry matrices.\n", data->sginfo.order);
 printf("Found %d model(s)\n", new);
 printf("Periodicity is %d\n", data->periodic);

From b36620ac7a48ce0f4d15aac44eebdc9fff46061a Mon Sep 17 00:00:00 2001
From: Craig Fisher <66772456+cajfisher@users.noreply.github.com>
Date: Mon, 26 Jun 2023 13:59:35 +0900
Subject: [PATCH 7/8] Add surface dipole option

Adds a button to "Region" window of "Model editing" dialog to calculate surface dipole of a 2D model and report it in message box
---
 src/coords.c   | 26 +++++++++++++++++
 src/coords.h   |  1 +
 src/file_cif.c |  2 +-
 src/gui_edit.c | 78 ++++++++++++++++++++++++++++++++++++++++++++++++++
 src/main.c     | 67 ++++++++++++++++++++++++++++++-------------
 src/pak.h      |  9 ++++++
 6 files changed, 162 insertions(+), 21 deletions(-)

diff --git a/src/coords.c b/src/coords.c
index 9d61406..7b0b3c0 100644
--- a/src/coords.c
+++ b/src/coords.c
@@ -47,6 +47,32 @@ The GNU GPL can also be found at http://www.gnu.org
 extern struct sysenv_pak sysenv;
 extern struct elem_pak elements[];
 
+#define DEBUG_CALC_CENTROID 0
+/*************************************/
+/* return centroid of selected atoms */
+/*************************************/
+void calc_centroid(gdouble *centroid, GSList *input)
+{
+GSList *list=NULL;
+struct core_pak *core;
+
+if (!input)
+  return;
+
+VEC3SET(centroid, 0.0, 0.0, 0.0);
+for (list=input ; list ; list=g_slist_next(list))
+  {
+  core = list->data;
+  ARR3ADD(centroid, core->x);
+  }
+
+VEC3MUL(centroid, 1.0 / (gdouble) g_slist_length(input));
+
+#if DEBUG_CALC_CENTROID
+   P3VEC("Centroid = ", centroid);
+#endif
+}
+
 /**********************/
 /* debugging routines */
 /**********************/
diff --git a/src/coords.h b/src/coords.h
index 29ca9e9..12f4ebc 100644
--- a/src/coords.h
+++ b/src/coords.h
@@ -291,3 +291,4 @@ GSList *connect_fragment_get(struct core_pak *,
                              struct model_pak *);
 GSList *connect_neighbours(struct core_pak *) ;
 
+void calc_centroid(gdouble *, GSList *);
diff --git a/src/file_cif.c b/src/file_cif.c
index bca09c1..424dee6 100644
--- a/src/file_cif.c
+++ b/src/file_cif.c
@@ -182,7 +182,7 @@ return(0);
 /***************/
 /* CIF loading */
 /***************/
-#define DEBUG_LOAD_CIF 1
+#define DEBUG_LOAD_CIF 0
 gint read_cif(gchar *filename, struct model_pak *data)
 {
 gint i, j, n, natom, new, order, pos, keyword, loop_count=0;
diff --git a/src/gui_edit.c b/src/gui_edit.c
index 4389638..c07e18d 100644
--- a/src/gui_edit.c
+++ b/src/gui_edit.c
@@ -63,6 +63,81 @@ extern struct elem_pak elements[];
 
 enum{AT_ANY, AT_SELECTED, AT_LATTICE};
 
+void show_surface_dipole(struct model_pak *data)
+{
+gchar txt[60];
+
+calc_emp(data);
+
+/* inform the user */
+sprintf(txt, "Surface dipole: %f e.Angs\n", data->gulp.sdipole);
+gui_text_show(STANDARD, txt);
+
+}
+
+/***************************************/
+/* hook for dipole moment button       */
+/***************************************/
+void surface_dipole(GtkWidget *w)
+{
+struct model_pak *data;
+
+data = sysenv.active_model;
+
+/* checks */
+if (!data)
+  return;
+
+if (data->periodic != 2) {
+  gui_text_show(WARNING, "Model must be 2D.\n");
+  return;
+  }
+
+show_surface_dipole(data);
+}
+
+/*********************************************/
+/* update widget values with internal values */
+/*********************************************/
+void update_centre(void)
+{
+/* set transformation matrix widget entries */
+gui_relation_update_widget(&CEDIT.edit_x[0]);
+gui_relation_update_widget(&CEDIT.edit_x[1]);
+gui_relation_update_widget(&CEDIT.edit_x[2]);
+}
+
+/*****************************************/
+/* set centre to centre of selected ions */
+/*****************************************/
+void set_centre(GtkWidget *w)
+{
+/* gint n; */
+struct model_pak *model;
+gdouble centroid[3];
+
+model = sysenv.active_model;
+if (!model)
+  return;
+
+/* list = model->selection;
+n = g_slist_length(list);
+if (!n)
+  return; */
+
+if (!model->selection)
+  return;
+
+calc_centroid(centroid, model->selection);
+
+if( model->periodic > 0 )
+   vecmat(model->latmat, centroid);
+
+ARR3SET(CEDIT.edit_x, centroid);
+
+update_centre();
+}
+
 /*********************************************/
 /* update widget values with internal values */
 /*********************************************/
@@ -2418,6 +2493,9 @@ gui_button_x("Add selected atoms to region 4", region_change, GINT_TO_POINTER(RE
 gui_button_x("Add selected atoms to growth slice", region_growth_slice, (gpointer) GROWTH_ADD, vbox);
 gui_button_x("Remove selected atoms from growth slice", region_growth_slice, (gpointer) GROWTH_DEL, vbox);
 
+vbox = gui_frame_vbox("Properties", FALSE, FALSE, box);
+gui_button_x("Calculate surface dipole", surface_dipole, NULL, vbox);
+
 /* if (model->periodic == 0 || model->periodic == 2)
   gtk_widget_set_sensitive(GTK_WIDGET(model->edit_regions_frame), TRUE);
 else
diff --git a/src/main.c b/src/main.c
index 1d6a6ea..83a7a49 100644
--- a/src/main.c
+++ b/src/main.c
@@ -423,27 +423,54 @@ sysenv.apb_on = TRUE;
 sysenv.lmb_on = FALSE;
 sysenv.pib_on = FALSE;
 
-/*edit_dialog*/
-sysenv.cedit.edit_anim_n=0;
-sysenv.cedit.edit_chirality[0]=6.;
-sysenv.cedit.edit_chirality[1]=6.;
-sysenv.cedit.edit_length=1.44;
-sysenv.cedit.edit_basis[0]=NULL;
-sysenv.cedit.edit_basis[1]=NULL;
-sysenv.cedit.edit_spatial_colour[0]=1.0;
-sysenv.cedit.edit_spatial_colour[1]=0.0;
-sysenv.cedit.edit_spatial_colour[2]=0.0;
-sysenv.cedit.edit_label_colour[0]=1.0;
-sysenv.cedit.edit_label_colour[1]=1.0;
-sysenv.cedit.edit_label_colour[2]=1.0;
-sysenv.cedit.spatial_list=NULL;
-sysenv.cedit.spatial_tree=NULL;
-sysenv.cedit.spatial_selected=NULL;
-sysenv.cedit.diffract_model=NULL;
+/* edit_dialog */
+sysenv.cedit.edit_anim_n = 0;
+sysenv.cedit.edit_chirality[0] = 6.;
+sysenv.cedit.edit_chirality[1] = 6.;
+sysenv.cedit.edit_length = 1.44;
+sysenv.cedit.edit_basis[0] = NULL;
+sysenv.cedit.edit_basis[1] = NULL;
+sysenv.cedit.edit_spatial_colour[0] = 1.0;
+sysenv.cedit.edit_spatial_colour[1] = 0.0;
+sysenv.cedit.edit_spatial_colour[2] = 0.0;
+sysenv.cedit.edit_label_colour[0] = 1.0;
+sysenv.cedit.edit_label_colour[1] = 1.0;
+sysenv.cedit.edit_label_colour[2] = 1.0;
+sysenv.cedit.spatial_list = NULL;
+sysenv.cedit.spatial_tree = NULL;
+sysenv.cedit.spatial_selected = NULL;
+sysenv.cedit.diffract_model = NULL;
 /*edit_widget*/
-sysenv.cedit.apd_data=NULL;
-sysenv.cedit.apd_core=NULL;
-
+sysenv.cedit.apd_data = NULL;
+sysenv.cedit.apd_core = NULL;
+
+/* edit miscellaneous functions dialog */
+sysenv.cedit.edit_x[0] = 0.0;
+sysenv.cedit.edit_x[1] = 0.0;
+sysenv.cedit.edit_x[2] = 0.0;
+/* sysenv.misc.edit_anim_n = 0;
+sysenv.misc.edit_length = 1.44;
+sysenv.misc.edit_percent = 0.0;
+sysenv.misc.edit_number = 1.0;
+sysenv.misc.edit_subdist = 0.0;
+sysenv.misc.edit_dist = 1.0;
+sysenv.misc.edit_shift_min = 0.0;
+sysenv.misc.edit_shift_max = 1.0;
+sysenv.misc.edit_length = 1.44;
+sysenv.misc.edit_construct;
+sysenv.misc.edit_basis[2] = {NULL, NULL};
+sysenv.misc.edit_type = NULL;
+sysenv.misc.edit_insert = NULL;
+sysenv.misc.elem_entry;
+sysenv.misc.grid_diml
+sysenv.misc.grid_sep;
+sysenv.misc.periodicity_spin;
+sysenv.misc.obj_reference;
+sysenv.misc.transmat[12];
+sysenv.misc.angle = 0.0;
+sysenv.misc.edit_radius = 10.0;
+sysenv.misc.edit_avcut = 0.8; 
+*/
 /* default to single model display */
 sysenv.mal = NULL;
 sysenv.displayed[0] = -1;
diff --git a/src/pak.h b/src/pak.h
index 07c5d3b..1c90ef6 100644
--- a/src/pak.h
+++ b/src/pak.h
@@ -153,6 +153,15 @@ GtkWidget *apd_element, *apd_label, *apd_type, *apd_charge, *apd_mass, *apd_sof,
 	  *apd_x, *apd_y, *apd_z, *apd_growth, *apd_region, *apd_translate;
 struct model_pak *apd_data;
 struct core_pak *apd_core;
+
+gdouble edit_percent, edit_number, edit_subdist;
+gdouble edit_dist, edit_shift_min, edit_shift_max;
+gchar *edit_type;
+gchar *edit_insert;
+GtkWidget *elem_entry, *grid_dim, *grid_sep;
+GtkWidget *obj_reference;
+gdouble angle, edit_radius, edit_avcut;
+gdouble edit_x[3];
 };
 
 /***********************/

From 514da97c325248ca7e39d8fdc4d1cedca08d17c2 Mon Sep 17 00:00:00 2001
From: Craig Fisher <66772456+cajfisher@users.noreply.github.com>
Date: Thu, 22 Feb 2024 10:26:41 +0900
Subject: [PATCH 8/8] Check GLIB version

Some OSs use older versions of glib, before g_pattern_spec_match_string replaced g_pattern_match_string (deprecated since v2.70)
---
 src/file.c | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/src/file.c b/src/file.c
index 6bc884c..e5bd3ae 100644
--- a/src/file.c
+++ b/src/file.c
@@ -33,6 +33,12 @@ The GNU GPL can also be found at http://www.gnu.org
 #include <sys/stat.h>
 #include <sys/types.h>
 
+#define GLIB_VERSION(major, minor, micro) \
+    (GLIB_MAJOR_VERSION > (major) || \
+    (GLIB_MAJOR_VERSION == (major) && GLIB_MINOR_VERSION > (minor)) || \
+    (GLIB_MAJOR_VERSION == (major) && GLIB_MINOR_VERSION == (minor) && \
+     GLIB_MICRO_VERSION >= (micro)))
+
 #include "gdis.h"
 #include "coords.h"
 #include "error.h"
@@ -801,7 +807,11 @@ while (list)
   name = list->data;
   list = g_slist_next(list);
 
+#if GLIB_VERSION(2, 7, 0)
   if (!g_pattern_spec_match_string(ps, name))
+#else
+  if (!g_pattern_match_string(ps, name))
+#endif
     {
     files = g_slist_remove(files, name);
     g_free(name);