/* Cleanup the data structures associated with recursive retrieving
(the variables above). */
void
recursive_cleanup (void)
{
free_slist (ulist);
ulist = NULL;
free_vec (forbidden);
forbidden = NULL;
free_slist (urls_html);
urls_html = NULL;
free_urlpos (urls_downloaded);
urls_downloaded = NULL;
FREE_MAYBE (base_dir);
FREE_MAYBE (robots_host);
first_time = 1;
}
void free_ramfli_data(Ramfli *rf)
{
free_slist((Slnode *)(rf->frames));
rf->frames = NULL;
pj_freez(&(rf->fhead));
}
void anim_free_all_frames(struct model_pak *model)
{
GSList *list;
struct frame_pak *frame;
g_assert(model != NULL);
for (list = model->frame_data_list ; list ; list=g_slist_next(list))
{
frame = list->data;
free_slist(frame->core_list);
free_slist(frame->shell_list);
g_free(frame);
}
g_slist_free(model->frame_data_list);
model->frame_data_list = NULL;
}
void file_cleanup(void)
{
/* NB: since the tree store is independant of the model's geom list */
/* it must be completely removed (and then restored) with the dialog */
gtk_list_store_clear(file_path_ts);
gtk_list_store_clear(file_name_ts);
free_slist(dir_list);
/* TODO - free row data (ie FILE_PATH/FILE_NAME strings) */
file_path_tv = NULL;
file_path_ts = NULL;
file_name_tv = NULL;
file_name_ts = NULL;
}
static void check_for_held(void)
{
struct state_list *slist;
struct sm_state *tmp;
slist = get_all_states(my_id);
FOR_EACH_PTR(slist, tmp) {
if (slist_has_state(tmp->possible, &held)) {
sm_msg("warn: '%s' held on error path.",
tmp->name);
}
} END_FOR_EACH_PTR(tmp);
free_slist(&slist);
}
void camera_rotate_animate(gint axis, gdouble *angle, gint overwrite, struct model_pak *model)
{
gdouble a, radian[3];
GSList *journey;
struct camera_pak *camera;
g_assert(model != NULL);
dialog_destroy_type(ANIM);
/* TODO - angle checks */
ARR3SET(radian, angle);
VEC3MUL(radian, D2R);
journey = NULL;
for (a=radian[0] ; a<radian[1]+0.5*radian[2] ; a+=radian[2])
{
camera = camera_dup(model->camera);
switch (axis)
{
case 1:
quat_concat_euler(camera->q, ROLL, a);
break;
case 2:
quat_concat_euler(camera->q, YAW, a);
break;
default:
quat_concat_euler(camera->q, PITCH, a);
}
journey = g_slist_prepend(journey, camera);
}
journey = g_slist_reverse(journey);
if (overwrite)
{
free_slist(model->transform_list);
model->transform_list = journey;
}
else
model->transform_list = g_slist_concat(model->transform_list, journey);
model->num_frames = g_slist_length(model->transform_list);
model->animation = TRUE;
redraw_canvas(SINGLE);
}
void zmat_free(gpointer data)
{
struct zmat_pak *zmat = data;
g_assert(zmat != NULL);
g_free(zmat->distance_units);
g_free(zmat->angle_units);
free_slist(zmat->zlines);
/* NB: zcores is a subset of the model's main core list - don't free its data */
g_slist_free(zmat->zcores);
g_hash_table_destroy(zmat->vars);
g_hash_table_destroy(zmat->consts);
g_free(zmat);
}
/* NB: leave symmetry / pbc structure intact */
void core_delete_all(struct model_pak *model)
{
g_assert(model != NULL);
/* free core reference lists */
free_mol_list(model);
wipe_bonds(model);
g_slist_free(model->unique_atom_list);
model->unique_atom_list = NULL;
/* free cores */
free_slist(model->cores);
model->cores = NULL;
/* redo dependancies */
zone_init(model);
calc_emp(model);
gui_refresh(GUI_MODEL_PROPERTIES);
model->state = 0;
}
// Generate a slist of directory entries in specified path. Then
// print the to stdout.
void list (char *path) {
DIR *dir = opendir (path);
struct dirent *ent;
slist_ref slist = new_slist ();
if (dir != NULL) {
for (;;) {
ent = readdir (dir);
if (ent == NULL) break;
insert (slist, path, ent->d_name);
}
closedir (dir);
if (flags.recursive) push_subdir (slist, path);
if (flags.opct > 1 && !flags.recursive)
printf ("%s:\n", path);
print_directory (slist);
}else {
print_error (path, strerror (errno));
}
free_slist (slist);
}
/* after argument number n combine all arguments to the curl type curl_slist */
static union luaValueT get_slist(lua_State* L, int n, const char** key)
{
int i;
union luaValueT v;
struct curl_slist *slist=0;
/* free the previous slist if any */
free_slist(L, key);
/* check if all parameters are strings */
for (i=n; i<lua_gettop(L); i++) luaL_checkstring(L, i);
for (i=n; i<lua_gettop(L); i++)
{
slist = curl_slist_append(slist, lua_tostring(L, i));
}
/* set the new slist in registry */
lua_pushlightuserdata(L, (void*)key);
lua_pushlightuserdata(L, (void *)slist);
lua_rawset(L, LUA_REGISTRYINDEX);
v.slist=slist;
return v;
}
gint update_file_pane(void)
{
gint filter;
gchar *name, *full;
GSList *list;
GtkTreeIter iter;
struct stat buff;
/* NEW */
filter = sysenv.file_type;
/* getting from this directory */
gtk_label_set_text(GTK_LABEL(curr_path), sysenv.cwd);
/* clear old data */
gtk_list_store_clear(file_path_ts);
gtk_list_store_clear(file_name_ts);
free_slist(dir_list);
/* get directory listing */
/* NB: success will always return something, even if only ".." */
dir_list = file_dir_list(sysenv.cwd, TRUE);
if (!dir_list)
{
gui_text_show(ERROR, "No directory listing; check your permissions.\n");
gtk_list_store_append(file_path_ts, &iter);
gtk_list_store_set(file_path_ts, &iter, FILE_PATH, "..", -1);
}
list = dir_list;
while (list)
{
/* stat the file (MUST have the full path) */
name = (gchar *) list->data;
full = g_build_filename(sysenv.cwd, list->data, NULL);
stat(full, &buff);
#if DEBUG_UPDATE_FILE_PANE
printf("[%s] : %d\n",full,buff.st_mode);
#endif
/* convert and check if directory */
if ((buff.st_mode & S_IFMT) == S_IFDIR)
{
gtk_list_store_append(file_path_ts, &iter);
gtk_list_store_set(file_path_ts, &iter, FILE_PATH, name, -1);
}
else
{
/* is it a recognized type? */
if (file_extension_valid(list->data))
{
gtk_list_store_append(file_name_ts, &iter);
gtk_list_store_set(file_name_ts, &iter, FILE_NAME, name, -1);
}
#if OLD_GOK /* FIXME: can it be deleted? I haven't changed this code
below to handle empty extensions */
file_data = get_file_info((gpointer *) list->data, BY_EXTENSION);
if (file_data)
{
/* display name if matches current file filter */
if (filter == DATA)
{
/* don't add filetypes with no read/write routines - pictures */
if (file_data->read_file || file_data->write_file)
{
gtk_list_store_append(file_name_ts, &iter);
gtk_list_store_set(file_name_ts, &iter, FILE_NAME, name, -1);
}
}
else
{
/* add if specifically requested (ie even if not in menu) */
if (filter == file_data->group)
{
gtk_list_store_append(file_name_ts, &iter);
gtk_list_store_set(file_name_ts, &iter, FILE_NAME, name, -1);
}
}
}
#endif
}
list = g_slist_next(list);
g_free(full);
}
return(TRUE);
}
Errcode load_ramfli(Ramfli *rfl, Flifile *flif)
{
Errcode err;
int frame_ix;
Ramframe frame;
Ramframe *rf;
Names first_one;
Ramframe *tail = (Ramframe *)&first_one;
LONG allocsize;
ULONG flags;
extern long mem_free;
long mem_needed;
Boolean ram_required = TRUE;
/* size to read in initially */
#define CHECK_SIZE (sizeof(Ramframe) - OFFSET(Ramframe,frame))
first_one.next = NULL;
free_ramfli_data(rfl);
/* load header from input one */
if((rfl->fhead = pj_malloc(sizeof(Fli_head))) == NULL)
{
err = Err_no_memory;
goto no_mem_error;
}
*(rfl->fhead) = flif->hdr;
/* read in the frames */
flags = rfl->flags;
clear_struct(&frame);
frame.frame.size = flif->hdr.frame1_oset;
frame_ix = -1;
mem_needed = flif->hdr.size;
while(++frame_ix <= (SHORT)(flif->hdr.frame_count))
{
frame.doff += frame.frame.size;
/* the last frame if it is an empty frame will only be
* sizeof(Fli_frame) so we may have an Err_eof on the last
* frame */
if((err = pj_readoset(flif->fd,&frame.frame,
frame.doff,CHECK_SIZE)) < Success)
{
if(frame_ix != flif->hdr.frame_count)
goto error;
if((err = pj_readoset(flif->fd,&frame.frame,
frame.doff,sizeof(frame.frame))) < Success)
{
goto error;
}
}
if( (!(flags & RF_LOAD_FIRST)) && frame_ix == 0)
goto add_empty_frame;
if( (!(flags & RF_LOAD_RING)) && frame_ix == flif->hdr.frame_count)
goto load_empty_frame;
/* simple memory test does not account for an un-needed ring frame */
if((mem_needed - frame.doff) >= mem_free)
goto no_mem_error;
allocsize = OFFSET(Ramframe,frame)+frame.frame.size;
if((rf = pj_malloc(allocsize)) == NULL)
{
if(ram_required)
goto no_mem_error;
goto add_empty_frame;
}
/* add next frame to list */
rf->next = NULL;
tail->next = rf;
tail = rf;
memcpy(rf,&frame,Min(allocsize,sizeof(frame)));
if(allocsize < sizeof(frame))
goto add_full_frame;
/* read in data: It there is a pstamp chunk we don't need it so
* bypass it and adjust frame data. Otherwise read whole chunk */
#ifdef DOESNT_WORK
if(frame.first_chunk.type == FLI_PSTAMP)
{
rf->frame.size -= frame.first_chunk.size;
rf->doff += frame.first_chunk.size;
if(rf->frame.size > sizeof(Fli_frame)
&& (err = pj_readoset(flif->fd,&(rf->first_chunk),
rf->doff + sizeof(Fli_frame),
rf->frame.size - sizeof(Fli_frame))) < Success)
{
goto error;
}
--rf->frame.chunks; /* one less chunk */
}
else
#endif
if(frame.frame.size > CHECK_SIZE
&& (err = pj_read_ecode(flif->fd,(rf + 1),
frame.frame.size - CHECK_SIZE)) < Success)
{
goto error;
}
add_full_frame:
rf->doff = -frame.doff; /* negative offset means we have a
* good ram record */
continue;
add_empty_frame:
if(rfl->fhead)
pj_freez(&(rfl->fhead));
load_empty_frame:
/* this is a little truncated ramframe only up to doff which is
* is positive in this case negative for a ram record */
if((rf = pj_malloc(POSTOSET(Ramframe,doff))) == NULL)
goto no_mem_error;
rf->doff = frame.doff;
rf->next = NULL;
tail->next = rf;
tail = rf;
}
rfl->frames = (Ramframe *)first_one.next;
return(Success);
no_mem_error:
/* if specified as required and not ok off disk ERROR out */
free_slist(first_one.next); /* we need enough ram to have requestor */
first_one.next = NULL;
if(ram_required && !ask_ok_off_disk(rfl))
err = Err_reported;
else
err = Success;
error:
pj_freez(&(rfl->fhead));
free_slist(first_one.next);
return(err);
#undef CHECK_SIZE
}
void command_main_loop(int argc, char **argv)
{
gint n, status, num_tokens;
gchar *inp, *out, *ext, *tmp, *line, *base, **buff;
gboolean exit=FALSE;
GSList *list, *files, *item, *structures;
struct file_pak *inp_pak, *out_pak;
struct model_pak *model;
if (argc < 2)
printf("gdis> Commandline interface. Enter ? for help.\n");
/* command line */
do
{
/* if additional keywords - process as single command line */
if (argc > 1)
{
/* convert options into single string for processing */
buff = g_malloc(argc*sizeof(gchar *));
for (n=1 ; n<argc ; n++)
*(buff+n-1) = g_strdup(argv[n]);
*(buff+argc-1) = NULL;
line = g_strjoinv(" ", buff);
g_strfreev(buff);
exit = TRUE;
}
else
{
/* standard repeating prompt */
printf("gdis> ");
line = file_read_line(stdin);
}
/* quit primitive */
if (g_ascii_strncasecmp("qu", line, 2) == 0 ||
g_ascii_strncasecmp("ex", line, 2) == 0)
exit=TRUE;
/* test primitive */
if (g_ascii_strncasecmp("te", line, 2) == 0)
{
buff = tokenize(line, &num_tokens);
for (n=1 ; n<num_tokens ; n++)
test_run(*(buff+n));
g_strfreev(buff);
}
/* copy primitive */
if (g_ascii_strncasecmp("co", line, 2) == 0 || g_ascii_strncasecmp("cp", line, 2) == 0)
{
buff = tokenize(line, &num_tokens);
if (num_tokens > 2)
{
out_pak = get_file_info(*(buff+2), BY_EXTENSION);
if (!out_pak)
{
printf("Error: unrecognized output filetype.\n");
break;
}
if (!out_pak->write_file)
{
printf("Error: write method for this filetype does not exist.\n");
break;
}
/* FIXME! - this is all wrong - should be no dependence on sysenv.cwd for path */
/* since this falls over with something like prompt:>gdis cp /tmp/gok.sot /tmp/dest/gok.meta */
ext = file_extension_get(*(buff+2));
files = file_dir_list_pattern(sysenv.cwd, *(buff+1));
for (list=files ; list ; list=g_slist_next(list))
{
inp_pak = get_file_info(list->data, BY_EXTENSION);
inp = g_build_filename(sysenv.cwd, list->data, NULL);
/* FIXME - changed to correct a problem with Florian's metadata store */
// base = parse_strip(list->data);
base = g_strdup(list->data);
if (inp_pak)
{
if (inp_pak->read_file)
{
model = model_new();
status = inp_pak->read_file(inp, model);
structures = g_slist_find(sysenv.mal, model);
#if DEBUG_COMMAND_MAIN_LOOP
printf("Items loaded = %d [status = %d]\n", g_slist_length(structures), status);
#endif
if (g_slist_length(structures) > 1)
{
/* multiple output for input files that contain more than one structure */
n = 1;
for (item=structures ; item ; item=g_slist_next(item))
{
model = item->data;
tmp = g_strdup_printf("%s_%d.%s", base, n, ext);
out = g_build_filename(sysenv.cwd, tmp, NULL);
status = out_pak->write_file(out, model);
#if DEBUG_COMMAND_MAIN_LOOP
printf("a [%s] -> [%s]\n", inp, out);
#endif
g_free(out);
g_free(tmp);
model_free(model);
n++;
}
}
else
{
tmp = g_strdup_printf("%s.%s", base, ext);
out = g_build_filename(sysenv.cwd, tmp, NULL);
g_free(tmp);
status = out_pak->write_file(out, model);
#if DEBUG_COMMAND_MAIN_LOOP
printf("b [%s] -> [%s]\n", inp, out);
#endif
g_free(out);
model_free(model);
}
}
else
printf("Error: read method for this filetype does not exist.\n");
}
else
{
printf("Error: unrecognized input filetype.\n");
}
g_free(base);
g_free(inp);
}
/* CURRENT hack */
if (!files)
{
/* FIXME */
}
g_free(ext);
free_slist(files);
}
else
printf("Error: insufficient tokens for <copy> command\n");
g_strfreev(buff);
}
if (g_ascii_strncasecmp("ls", line, 2) == 0)
{
buff = tokenize(line, &num_tokens);
if (num_tokens > 1)
files = file_dir_list_pattern(sysenv.cwd, *(buff+1));
else
files = file_dir_list(sysenv.cwd, FALSE);
for (list=files ; list ; list=g_slist_next(list))
{
printf("%s\n", (gchar *) list->data);
}
g_strfreev(buff);
}
if (g_ascii_strncasecmp("cd", line, 2) == 0)
{
buff = tokenize(line, &num_tokens);
if (num_tokens > 1)
{
inp = g_build_path(DIR_SEP, sysenv.cwd, *(buff+1), NULL);
set_path(inp);
g_free(inp);
}
printf("%s\n", sysenv.cwd);
g_strfreev(buff);
}
if (g_ascii_strncasecmp("pwd", line, 3) == 0)
{
printf("%s\n", sysenv.cwd);
}
if (g_ascii_strncasecmp("?", line, 1) == 0 || g_ascii_strncasecmp("h", line, 1) == 0)
{
printf("GDIS v%4.2f available commands\n\n", VERSION);
printf("cd <destination>\n");
printf(" - changes to target directory\n");
printf("pwd\n");
printf(" - prints the current working directory\n");
printf("ls\n");
printf(" - lists the files in the current working directory\n");
printf("copy <source> <destination>\n");
printf(" - convert between filetypes, based on extension (wildcards allowed)\n");
printf("quit\n");
printf(" - exit program\n");
}
/* done -> next line */
g_free(line);
}
while (!exit);
}
gint get_next_group(FILE *fp, struct model_pak *model, gint *have_basis)
{
gchar *line, *keyword;
gint ret;
GSList *keywords = NULL, *list;
line = file_read_line(fp);
if (!line)
return(FALSE);
/* TODO not a valid keyword so for the moment skip but could store */
if (g_ascii_strncasecmp(line, " $", 2) != 0)
return(TRUE);
if (g_ascii_strncasecmp(line, " $data", 6) == 0)
{
ret = get_data(fp, model, *have_basis);
}
else if (g_ascii_strncasecmp(line, " $basis", 7) == 0)
{
*have_basis = TRUE;
keywords = get_gamess_keywords(fp, line+7, &ret);
for (list=keywords ; list ; list=g_slist_next(list))
{
keyword = (gchar *) list->data;
ret = get_basis(keyword, model);
}
}
else if (g_ascii_strncasecmp(line, " $contrl", 8) == 0)
{
keywords = get_gamess_keywords(fp, line+8, &ret);
for (list=keywords; list ; list=g_slist_next(list))
{
keyword = (gchar *) list->data;
ret = get_control(keyword, model);
}
}
else if (g_ascii_strncasecmp(line, " $system", 8) == 0)
{
keywords = get_gamess_keywords(fp, line+8, &ret);
for (list=keywords; list ; list=g_slist_next(list))
{
keyword = (gchar *) list->data;
ret = get_system(keyword, model);
}
}
else if (g_ascii_strncasecmp(line, " $statpt", 8) == 0)
{
keywords = get_gamess_keywords(fp, line+8, &ret);
for (list=keywords; list ; list=g_slist_next(list))
{
keyword = (gchar *) list->data;
ret = get_statpt(keyword, model);
}
}
else if (g_ascii_strncasecmp(line, " $dft", 5) == 0)
{
model->gamess.dft = TRUE;
/* TODO - process functional */
}
else
{
/* TODO - Unknown keyword, just pass through */
}
free_slist(keywords);
g_free(line);
return(TRUE);
}
void camera_waypoint_animate(gint frames, gint overwrite, struct model_pak *model)
{
gint i;
gdouble a, af, v[3], e[3], o[3], tmp[3];
gdouble jf, jv[3], x[3], mat[9];
GSList *list, *journey;
struct camera_pak *cam, *cam1, *cam2;
/* checks */
g_assert(model != NULL);
g_assert(frames > 0);
if (g_slist_length(model->waypoint_list) < 2)
{
gui_text_show(ERROR, "You need to make at least 2 waypoint.\n");
return;
}
/* close any active animation dialog */
dialog_destroy_type(ANIM);
#if DEBUG_CAMERA_ANIMATE
printf("frames for each traversal: %d\n", frames);
#endif
list = model->waypoint_list;
cam1 = list->data;
list = g_slist_next(list);
/* create the camera journey */
journey = NULL;
while (list)
{
cam2 = list->data;
/* setup camera journey vector */
ARR3SET(jv, cam2->x);
ARR3SUB(jv, cam1->x);
/* add starting camera over journey leg */
for (i=0 ; i<frames ; i++)
{
/* journey fraction */
jf = i;
jf /= frames;
ARR3SET(x, jv);
VEC3MUL(x, jf);
cam = camera_dup(cam1);
ARR3ADD(cam->x, x);
journey = g_slist_prepend(journey, cam);
}
/* approx 5 degrees */
#define ROTATION_INCREMENT 0.08727
/* (v x e plane alignment) */
proj_vop(v, cam2->v, cam1->o);
a = via(v, cam1->v, 3);
/* compute rotation increment */
af = (gint) nearest_int(a / ROTATION_INCREMENT);
if (!af)
af = 1.0;
/* test rotation sense */
matrix_v_rotation(mat, cam1->o, a);
ARR3SET(tmp, cam1->v);
vecmat(mat, tmp);
if (via(tmp, v, 3) > 0.1)
a *= -1.0;
/* build rotaton */
matrix_v_rotation(mat, cam1->o, a/af);
/* apply to camera */
ARR3SET(v, cam1->v);
ARR3SET(e, cam1->e);
for (i=af ; i-- ; )
{
cam = camera_dup(cam1);
ARR3SET(cam->x, cam2->x);
vecmat(mat, v);
vecmat(mat, e);
ARR3SET(cam->v, v);
ARR3SET(cam->e, e);
journey = g_slist_prepend(journey, cam);
}
/* TODO - apply elevation to get v in complete coincidence */
/* rotate about e to achieve coincidence */
a = via(v, cam2->v, 3);
/* compute rotation increment */
af = (gint) nearest_int(a / ROTATION_INCREMENT);
if (!af)
af = 1.0;
/* test rotation sense */
matrix_v_rotation(mat, e, a);
ARR3SET(tmp, v);
vecmat(mat, tmp);
if (via(tmp, cam2->v, 3) > 0.1)
a *= -1.0;
/* build rotaton */
matrix_v_rotation(mat, e, a/af);
/* apply to camera */
ARR3SET(o, cam1->o);
for (i=af ; i-- ; )
{
cam = camera_dup(cam1);
ARR3SET(cam->x, cam2->x);
vecmat(mat, v);
vecmat(mat, o);
ARR3SET(cam->v, v);
ARR3SET(cam->o, o);
ARR3SET(cam->e, e);
journey = g_slist_prepend(journey, cam);
}
/* endpoint camera */
journey = g_slist_prepend(journey, camera_dup(cam2));
/* get next journey leg */
cam1 = cam2;
list = g_slist_next(list);
}
journey = g_slist_reverse(journey);
if (overwrite)
{
free_slist(model->transform_list);
model->transform_list = journey;
}
else
model->transform_list = g_slist_concat(model->transform_list, journey);
model->num_frames = g_slist_length(model->transform_list);
model->animation = TRUE;
redraw_canvas(SINGLE);
}
gint reaxmd_parse_properties(FILE *fp, struct model_pak *model, gpointer import)
{
gint i, j, k, n=1, time_column=0, num_tokens, num_properties;
gdouble frame_time=0.0, time, start, stop, value;
gchar *line, *label, **buff;
const gchar *xlabel, *ylabel;
GSList *item, *list;
GArray **property_array;
#if DEBUG_REAXMD_PARSE_PROPERTIES
printf("file_reaxmd(): parsing energy file...\n");
#endif
/* checks */
if (!fp)
return(FALSE);
if (!import)
return(FALSE);
/* setup internal frame counter */
if (model)
{
n = g_list_length(model->animate_list);
i=0;
frame_time = str_to_float(animate_frame_property_get(i, "Time", model));
}
// NB: file_read_line() skips comments by default, so it'll auto skip the header line
file_skip_comment(FALSE);
// process first line for column locations of time, energy, etc ...
line = file_read_line(fp);
// error handling
if (!line)
{
return(FALSE);
}
if (strlen(line) < 2)
{
return(FALSE);
}
buff = g_strsplit(&line[1], "|", -1);
list = NULL;
if (buff)
{
j=0;
while (buff[j])
{
label = g_strstrip(buff[j]);
if (strlen(label))
{
if (g_strrstr(label, "Time"))
{
time_column = j;
}
list = g_slist_prepend(list, g_strdup(label));
}
j++;
}
}
g_strfreev(buff);
g_free(line);
line = file_read_line(fp);
list = g_slist_reverse(list);
#if DEBUG_REAXMD_PARSE_PROPERTIES
for (item=list ; item ; item=g_slist_next(item))
{
printf("[%s]\n", (gchar *) item->data);
}
printf("Allocating %d property arrays, with start size %d\n", g_slist_length(list), n);
#endif
// NB: exclude the first - time
/* init arrays for properties */
num_properties = g_slist_length(list);
property_array = g_malloc(num_properties * sizeof(GArray));
for (k=0 ; k<num_properties ; k++)
{
property_array[k] = g_array_sized_new(FALSE, FALSE, sizeof(gdouble), n);
}
/* iterate over all output data lines */
while (line)
{
buff = tokenize(line, &num_tokens);
if (num_tokens > time_column)
{
time = str_to_float(buff[time_column]);
/* NEW - grab all values for property graphs */
for (j=0 ; j<num_tokens ; j++)
{
if (j < num_properties)
{
value = str_to_float(buff[j]);
g_array_append_val(property_array[j], value);
}
}
/* if output data time matches internal frame frame - store */
if (model)
{
if (time >= frame_time)
{
/* add current output data to the internally stored frame */
item = list;
for (j=0 ; j<num_tokens ; j++)
{
if (item)
{
//printf("[%d][%s][%s]\n", i, (gchar *) item->data, buff[j]);
// add to actual model property list (reference frame only)
// leave this out now, since we're auto constructing graphs anyway
/*
if (!i)
{
property_add_ranked(j, item->data, buff[j], model);
}
*/
animate_frame_property_put(i, item->data, buff[j], model);
}
else
break;
item = g_slist_next(item);
}
/* update the internal frame count */
i++;
frame_time = str_to_float(animate_frame_property_get(i, "Time", model));
}
}
}
g_strfreev(buff);
g_free(line);
line = file_read_line(fp);
}
/* iterate property arrays and construct graphs */
xlabel = g_slist_nth_data(list, time_column);
for (j=0 ; j<num_properties ; j++)
{
// don't graph time column
if (j != time_column)
{
gpointer data, graph;
k = property_array[j]->len;
data = g_array_free(property_array[j], FALSE);
start = g_array_index(property_array[time_column],gdouble,0);
stop = g_array_index(property_array[time_column],gdouble,k-1);
#if DEBUG_REAXMD_PARSE_PROPERTIES
printf("Building graph for: %s with %d data points and ", (gchar *) g_slist_nth_data(list, j), k);
printf("range: %f - %f\n", start, stop);
#endif
/* add graph if no ! prefix */
ylabel = g_slist_nth_data(list, j);
if (!g_strrstr(ylabel, "!"))
{
/* create and attach graph object */
label = g_strndup(ylabel, 8);
graph = graph_new(label);
g_free(label);
graph_set_data(k, data, start, stop, graph);
graph_x_label_set(xlabel, graph);
graph_y_label_set(ylabel, graph);
import_object_add(IMPORT_GRAPH, graph, import);
}
}
}
g_array_free(property_array[time_column], TRUE);
g_free(property_array);
/* cleanup */
free_slist(list);
return(0);
}
static void match_end_func(void)
{
free_slist(&start_states);
}
static void match_restore_states(struct expression *expr)
{
free_slist(&start_states);
start_states = pop_slist(&saved_stack);
}
void docking_project_create(GtkWidget *w, struct model_pak *model)
{
gint a, b, i, m, n, rx, ry, rz, size, rigid_save;
gint a_max, b_max, rx_max, ry_max, rz_max;
gchar *file, *dump, *dump_save, *rigid_move_save;
gdouble dx, dy, dz, x[3], scale[3], mat[9], dock_centroid[3], q[4];
GString *name, *rigid;
GSList *list, *core_list, *shell_list;
struct dock_pak *dock;
struct core_pak *core, *core2;
struct shel_pak *shell, *shell2;
FILE *fp;
/* checks */
g_assert(model != NULL);
size = g_slist_length(model->selection);
if (!size)
{
gui_text_show(WARNING, "Please select the subset you wish to dock.\n");
return;
}
/* create new docking project */
dock = g_malloc(sizeof(struct dock_pak));
/* NEW - setup project path */
/*
g_path_get_dirname(model->fullpath);
g_get_current_dir();
*/
/* seek a file name that doesn't exist (avoid background overwriting) */
name = g_string_new(NULL);
i=0;
do
{
g_string_sprintf(name, "project_%06d", i);
i++;
}
while (g_file_test(name->str, G_FILE_TEST_EXISTS));
dock->path = g_build_path(sysenv.cwd, name->str, NULL);
printf("creating new project: [%s]\n", dock->path);
#if WIN32
if (mkdir(dock->path))
#else
if (mkdir(dock->path, 0700))
#endif
{
gui_text_show(ERROR, "Failed to create project directory.\n");
g_free(dock->path);
g_free(dock);
return;
}
/* project control file */
g_string_sprintf(name, "%s%sproject.pcf", dock->path, DIR_SEP);
fp = fopen(name->str, "wt");
/* save original variables */
dump_save = model->gulp.dump_file;
model->gulp.dump_file = NULL;
rigid_save = model->gulp.rigid;
model->gulp.rigid = dock_rigid_on;
rigid_move_save = model->gulp.rigid_move;
model->gulp.rigid_move = NULL;
if (model->gulp.rigid)
{
rigid = g_string_new(NULL);
if (dock_rigid_x)
g_string_sprintf(rigid, "x");
if (dock_rigid_y)
g_string_sprintfa(rigid, "y");
if (dock_rigid_z)
g_string_sprintfa(rigid, "z");
model->gulp.rigid_move = g_string_free(rigid, FALSE);
}
/* duplicate selection for docking */
core_list = NULL;
shell_list = NULL;
VEC3SET(dock_centroid, 0.0, 0.0, 0.0);
for (list=model->selection ; list ; list=g_slist_next(list))
{
core2 = dup_core(list->data);
core_list = g_slist_prepend(core_list, core2);
if (core2->shell)
shell_list = g_slist_prepend(shell_list, core2->shell);
/* compute centroid */
ARR3ADD(dock_centroid, core2->x);
}
/* NB: lists must have the same order as original selection */
core_list = g_slist_reverse(core_list);
shell_list = g_slist_reverse(shell_list);
VEC3MUL(dock_centroid, 1.0/(gdouble) size);
/* fractional translation grid units */
scale[0] = dock_cell[0] / dock_grid[0];
scale[1] = dock_cell[1] / dock_grid[1];
/* rotational increments */
dx = PI/dock_rotate[0];
dy = PI/dock_rotate[1];
dz = PI/dock_rotate[2];
/* translational sampling */
if (dock_grid_on)
{
a_max = dock_grid[0];
b_max = dock_grid[1];
}
else
{
a_max = 1;
b_max = 1;
}
/* rotational sampling */
if (dock_rotate_on)
{
rx_max = dock_rotate[0];
ry_max = dock_rotate[1];
rz_max = dock_rotate[2];
}
else
{
rx_max = 1;
ry_max = 1;
rz_max = 1;
}
/* project header */
fprintf(fp, "%%title solvent mapping project\n");
fprintf(fp, "%%set %d %d %f %f\n", a_max, b_max, dock_cell[0], dock_cell[1]);
/* loop over all grid translations */
m = n = 0;
for (a=0 ; a<a_max ; a++)
{
for (b=0 ; b<b_max ; b++)
{
VEC3SET(x, a, b, 0.0);
x[0] *= scale[0];
x[1] *= scale[1];
/* loop over rotations */
VEC4SET(q, 1.0, 0.0, 0.0, 0.0);
for (rx=0 ; rx<rx_max ; rx++)
{
if (rx)
quat_concat_euler(q, PITCH, dx);
for (ry=0 ; ry<ry_max ; ry++)
{
if (ry)
quat_concat_euler(q, ROLL, dy);
for (rz=0 ; rz<rz_max ; rz++)
{
if (rz)
quat_concat_euler(q, YAW, dz);
/* build total rotation matrix */
quat_matrix(mat, q);
/* transform the cores and shells */
i = 0;
for (list=model->selection ; list ; list=g_slist_next(list))
{
core = list->data;
/* FIXME - should we restore this after? how? */
core->region = 2;
/* get original selection core coordinates */
core2 = g_slist_nth_data(core_list, i);
ARR3SET(core->x, core2->x);
/* perform the rotation (NB: must be done about origin in cartesian space) */
ARR3SUB(core->x, dock_centroid);
vecmat(model->latmat, core->x);
vecmat(mat, core->x);
vecmat(model->ilatmat, core->x);
ARR3ADD(core->x, dock_centroid);
/* add the current translation offset */
ARR3ADD(core->x, x);
/* as above, for the associated shell */
if (core->shell)
{
shell = core->shell;
shell->region = 2;
shell2 = core2->shell;
g_assert(shell2 != NULL);
ARR3SET(shell->x, shell2->x);
ARR3SUB(shell->x, dock_centroid);
vecmat(model->latmat, shell->x);
vecmat(mat, shell->x);
vecmat(model->ilatmat, shell->x);
ARR3ADD(shell->x, dock_centroid);
ARR3ADD(shell->x, x);
}
i++;
}
/* write docking configuration */
/*
file = g_strdup_printf("%s_%06d.gin", model->basename, n);
*/
/* m identifies grid points (for later minimum check) */
fprintf(fp, "%s_%06d.gin %f %f %d\n", model->basename, n, x[0], x[1], m);
file = g_strdup_printf("%s%s%s_%06d.gin", dock->path, DIR_SEP, model->basename, n);
dump = g_strdup_printf("%s_%06d.res", model->basename, n);
model->gulp.dump_file = dump;
write_gulp(file, model);
g_free(file);
g_free(dump);
n++;
}
}
}
m++;
}
}
/* restore original variables */
model->gulp.dump_file = dump_save;
model->gulp.rigid = rigid_save;
g_free(model->gulp.rigid_move);
model->gulp.rigid_move = rigid_move_save;
/* restore original selection (delete, then concat saved list) */
i = 0;
for (list=model->selection ; list ; list=g_slist_next(list))
{
core = list->data;
core2 = g_slist_nth_data(core_list, i);
ARR3SET(core->x, core2->x);
if (core->shell)
{
shell = core->shell;
shell2 = core2->shell;
g_assert(shell2 != NULL);
ARR3SET(shell->x, shell2->x);
}
i++;
}
/* free docking core/shell lists */
free_slist(core_list);
free_slist(shell_list);
g_string_free(name, TRUE);
fclose(fp);
/* run docking in background unless told to stop after setup */
/*
if (!dock_no_execute)
submit_task("Docking", &docking_execute, dock, &docking_cleanup, dock, model);
*/
}
void zmat_build(void)
{
gint i, j, k, n, type;
gdouble r, a, d, x[4][3], v[3];
gdouble zaxis[3] = {0.0, 0.0, 1.0};
gchar *line;
GSList *list, *species;
struct zmat_pak *zmat;
struct core_pak *core[4] = {NULL, NULL, NULL, NULL};
struct model_pak *model;
model = sysenv.active_model;
if (!model)
return;
/* CURRENT - using selection as our list of cores to generate a zmatrix from */
if (!model->selection)
{
gui_text_show(WARNING, "ZMATRIX: please select a molecule.\n");
return;
}
/* destroy old zmatrix */
/* TODO - prompt if non null */
zmat_free(model->zmatrix);
zmat = model->zmatrix = zmat_new();
zmat_angle_units_set(model->zmatrix, DEGREES);
/* setup SIESTA species type */
species = fdf_species_build(model);
/* sort the list so it follows molecular connectivity */
model->selection = zmat_connect_sort(model->selection);
n=0;
for (list=model->selection ; list ; list=g_slist_next(list))
{
/* current atom/zmatrix line init */
core[0] = list->data;
type = fdf_species_index(core[0]->atom_label, species);
line = NULL;
zmat->zcores = g_slist_append(zmat->zcores, core[0]);
/* build a ZMATRIX line for processing */
switch (n)
{
case 0:
if (core[0])
{
ARR3SET(x[0], core[0]->x);
vecmat(model->latmat, x[0]);
}
line = g_strdup_printf("%d 0 0 0 %f %f %f 0 0 0\n", type, x[0][0], x[0][1], x[0][2]);
break;
case 1:
if (core[0])
{
ARR3SET(x[0], core[0]->x);
vecmat(model->latmat, x[0]);
}
if (core[1])
{
ARR3SET(x[1], core[1]->x);
vecmat(model->latmat, x[1]);
}
r = measure_distance(x[0], x[1]);
/* angle with z axis */
ARR3SET(v, x[0]);
ARR3SUB(v, x[1]);
a = R2D * via(v, zaxis, 3);
/* angle between xy projection and x axis */
d = R2D * angle_x_compute(v[0], v[1]);
line = g_strdup_printf("%d 1 0 0 %f %f %f 0 0 0\n", type, r, a, d);
break;
case 2:
/* coords init */
for (i=3 ; i-- ; )
{
if (core[i])
{
ARR3SET(x[i], core[i]->x);
vecmat(model->latmat, x[i]);
}
else
g_assert_not_reached();
}
r = measure_distance(x[0], x[1]);
a = measure_angle(x[0], x[1], x[2]);
/* create a fake core -> 1 unit displaced in the z direction */
g_assert(core[3] == NULL);
core[3] = core_new("x", NULL, model);
ARR3SET(core[3]->rx, core[2]->rx);
ARR3ADD(core[3]->rx, zaxis);
d = measure_torsion(core);
core_free(core[3]);
line = g_strdup_printf("%d 2 1 0 %f %f %f 0 0 0\n", type,r,a,d);
break;
default:
/* connectivity test */
if (!zmat_bond_check(core[0], core[1]))
{
#if DEBUG_ZMAT_BUILD
printf("[%d] non-connected atoms [%f]\n", n, measure_distance(x[0], x[1]));
#endif
/* need to build a new connectivity chain starting from core[0] */
core[1] = core[2] = core[3] = NULL;
if (!zmat_connect_find(n, core, zmat))
{
gui_text_show(WARNING, "ZMATRIX: bad connectivity (molecule will be incomplete)\n");
goto zmat_build_done;
}
}
/* coords init */
for (i=3 ; i-- ; )
{
if (core[i])
{
ARR3SET(x[i], core[i]->x);
vecmat(model->latmat, x[i]);
}
else
g_assert_not_reached();
}
r = measure_distance(x[0], x[1]);
a = measure_angle(x[0], x[1], x[2]);
d = measure_torsion(core);
/* NB: indexing starts from 0, siesta starts from 1 (naturally) */
i = 1+g_slist_index(zmat->zcores, core[1]);
j = 1+g_slist_index(zmat->zcores, core[2]);
k = 1+g_slist_index(zmat->zcores, core[3]);
line = g_strdup_printf("%d %d %d %d %f %f %f 0 0 0\n", type,i,j,k,r,a,d);
}
/* process a successfully constructed ZMATRIX line */
if (line)
{
zmat_core_add(line, model->zmatrix);
g_free(line);
}
/* shuffle */
core[3] = core[2];
core[2] = core[1];
core[1] = core[0];
n++;
}
zmat_build_done:
/* do the species typing */
zmat_type(model->zmatrix, species);
free_slist(species);
}