gint anim_read_all_frames(struct model_pak *model)
{
gint i;
struct frame_pak *frame;
FILE *fp;
/* checks */
g_assert(model != NULL);
g_assert(model->animation == TRUE);
/* TODO - test is we have enough memory by using g_try_malloc() */
/* read in all frames and store relevant data */
fp = fopen(model->filename, "r");
if (!fp)
{
printf("Could not open source file.");
return(1);
}
for (i=0 ; i<model->num_frames ; i++)
{
/* NB: frames start at 1 */
read_raw_frame(fp, i+1, model);
matrix_lattice_init(model);
frame = g_malloc(sizeof(struct frame_pak *));
memcpy(frame->latmat, model->latmat, 9*sizeof(gdouble));
frame->core_list = dup_core_list(model->cores);
frame->shell_list = dup_shell_list(model->shels);
model->frame_data_list = g_slist_prepend(model->frame_data_list, frame);
}
model->frame_data_list = g_slist_reverse(model->frame_data_list);
return(1);
}
gint load_planes(gchar *filename, struct model_pak *data)
{
gint h, k, l, num_tokens;
gint cflag=FALSE, sflag=FALSE, gflag=FALSE;
gdouble m[3];
gchar **buff;
GSList *list, *new_planes;
struct plane_pak *plane=NULL;
struct shift_pak *shift=NULL;
FILE *fp;
fp = fopen(filename, "rt");
if (!fp)
return(1);
/* get next line */
new_planes = NULL;
for (;;)
{
buff = get_tokenized_line(fp, &num_tokens);
if (!buff)
break;
/* NB: only update space/cell etc. data if this call did */
/* not originate from an import planes call */
if (data->id == MORPH)
{
/* cell parameters */
if (g_ascii_strncasecmp(*buff,"cell",4) == 0)
{
if (num_tokens >= 7)
{
cflag=TRUE;
data->pbc[0] = str_to_float(*(buff+1));
data->pbc[1] = str_to_float(*(buff+2));
data->pbc[2] = str_to_float(*(buff+3));
data->pbc[3] = PI*str_to_float(*(buff+4))/180.0;
data->pbc[4] = PI*str_to_float(*(buff+5))/180.0;
data->pbc[5] = PI*str_to_float(*(buff+6))/180.0;
/* compute direct & reciprocal lattices */
/* NB: enables fn_make_plane() to correctly compute Dhkl */
matrix_lattice_init(data);
}
else
printf("load_planes() error: bad cell line.\n");
}
/* space group */
if (g_ascii_strncasecmp(*buff,"space",5) == 0)
{
if (num_tokens > 1)
{
sflag=TRUE;
data->sginfo.spacename = g_strjoinv(" ", buff+1);
data->sginfo.spacenum = 0;
}
}
/* default morphology type */
if (g_ascii_strncasecmp(*buff, "morph", 5) == 0)
{
if (num_tokens >= 3)
{
if (g_ascii_strncasecmp(*(buff+1), "unrelaxed", 9) == 0)
{
if (g_ascii_strncasecmp(*(buff+2), "equil", 5) == 0)
data->morph_type = EQUIL_UN;
if (g_ascii_strncasecmp(*(buff+2), "growth", 6) == 0)
data->morph_type = GROWTH_UN;
}
if (g_ascii_strncasecmp(*(buff+1), "relaxed", 7) == 0)
{
if (g_ascii_strncasecmp(*(buff+2), "equil", 5) == 0)
data->morph_type = EQUIL_RE;
if (g_ascii_strncasecmp(*(buff+2), "growth", 6) == 0)
data->morph_type = GROWTH_RE;
}
}
else
printf("load_planes() error: bad type line.\n");
}
}
/* process miller line */
if (g_ascii_strncasecmp(*buff,"miller",6) == 0)
{
/* init space group (latmat? - if so, remove the make_latmat() in cell parse) */
if (cflag && sflag)
{
if (!gflag)
{
if (space_lookup(data))
printf("Error in space group lookup.\n");
gflag = TRUE;
}
}
else
{
if (data->id == MORPH)
{
printf("load_planes() error: miller encountered before space or cell.\n");
return(2);
}
}
if (num_tokens >= 4)
{
h = (gint) str_to_float(*(buff+1));
k = (gint) str_to_float(*(buff+2));
l = (gint) str_to_float(*(buff+3));
#if DEBUG_LOAD_PLANES
printf("read plane: %d %d %d\n", h, k, l);
#endif
VEC3SET(m, h, k, l);
/* FIXME - signature change */
/*
plane = plane_find(m, data);
*/
if (!plane)
{
plane = plane_new(m, data);
if (plane)
new_planes = g_slist_prepend(new_planes, plane);
}
}
}
/* potential data */
if (num_tokens >= 8 && plane)
{
/* NB: use create_shift(), as it sets some important defaults */
shift = shift_new(0.0);
if (shift)
{
shift->shift = str_to_float(*(buff+0));
shift->region[0] = str_to_float(*(buff+1));
shift->region[1] = str_to_float(*(buff+2));
shift->esurf[0] = str_to_float(*(buff+3));
shift->eatt[0] = str_to_float(*(buff+4));
shift->esurf[1] = str_to_float(*(buff+5));
shift->eatt[1] = str_to_float(*(buff+6));
shift->gnorm = str_to_float(*(buff+7));
#if DEBUG_LOAD_PLANES
printf("adding shift: %f\n", shift->shift);
#endif
/* append to preserve order (eg import on existing plane set) */
plane->shifts = g_slist_append(plane->shifts, shift);
}
}
g_strfreev(buff);
}
data->planes = g_slist_concat(data->planes, g_slist_reverse(new_planes));
/* compute dhkl's for the plane's list */
for (list=data->planes ; list ; list=g_slist_next(list))
{
plane = list->data;
/* create default shift if none found */
if (!plane->shifts)
{
shift = shift_new(0.0);
if (shift)
plane->shifts = g_slist_append(plane->shifts, shift);
}
/* get best energy for the plane */
/* FIXME - signature changed */
/*
update_plane_energy(plane, data);
*/
}
/* compute symmetry related faces */
/* FIXME - new surface rewrite */
/*
surf_symmetry_generate(data);
*/
fclose(fp);
return(0);
}
void zmat_process(gpointer data, struct model_pak *model)
{
gint i, n;
gdouble r, a, d;
gdouble v1[3], v2[3], v3[3], m1[9], m2[9];
gpointer tmp;
GSList *list;
struct zmat_pak *zmat = data;
struct zval_pak *zval;
struct core_pak *core[4] = {NULL, NULL, NULL, NULL};
/* checks */
if (!zmat)
return;
matrix_lattice_init(model);
#if ZMAT_PROCESS_DEBUG
printf("distance scale = %f\n", zmat->distance_scale);
printf("angle scale = %f\n", zmat->angle_scale);
#endif
/* track the core # - 1st 3 items in zmatrix are exceptions */
n = 0;
for (list=zmat->zlines ; list ; list=g_slist_next(list))
{
zval = list->data;
/* check for variable names */
for (i=3 ; i-- ; )
{
if (zval->name[i])
{
/* hash table lookup for variable value */
zval->value[i] = zmat_table_lookup(zval->name[i], zmat);
}
}
/* create the core */
#if ZMAT_PROCESS_DEBUG
printf("[%d = %s] [%d %d %d]", zval->type, zval->elem,
zval->connect[0], zval->connect[1], zval->connect[2]);
P3VEC(" x: ", zval->value);
#endif
/* TODO - need to mark zmatrix generated cores as special */
/* probably have another list in the zmat struct that contains */
/* all the cores created below */
switch (n)
{
case 0:
/* TODO - convert to cartesian if fractional and enforce cart model */
core[0] = new_core(zval->elem, model);
model->cores = g_slist_prepend(model->cores, core[0]);
zmat->zcores = g_slist_prepend(zmat->zcores, core[0]);
ARR3SET(core[0]->x, zval->value);
if (zmat->fractional)
vecmat(model->latmat, core[0]->x);
else
{
VEC3MUL(core[0]->x, zmat->distance_scale);
}
break;
case 1:
core[1] = new_core(zval->elem, model);
model->cores = g_slist_prepend(model->cores, core[1]);
zmat->zcores = g_slist_prepend(zmat->zcores, core[1]);
r = zmat->distance_scale * zval->value[0];
/*
a = zmat->angle_scale * zval->value[1];
d = zmat->angle_scale * zval->value[2];
*/
/* SIESTA hack : z-axis angle is 2nd, and theta is 3rd (last) */
a = zmat->angle_scale * zval->value[2];
d = zmat->angle_scale * zval->value[1];
v1[0] = v1[1] = r * sin(d);
v1[0] *= cos(a);
v1[1] *= sin(a);
v1[2] = r * cos(d);
ARR3SET(core[1]->x, core[0]->x);
ARR3ADD(core[1]->x, v1);
break;
case 2:
/* check the connection order */
if (zval->connect[0] == 2)
{
tmp = core[0];
core[0] = core[1];
core[1] = tmp;
}
r = zmat->distance_scale * zval->value[0];
a = zmat->angle_scale * zval->value[1];
d = zmat->angle_scale * zval->value[2];
ARR3SET(v2, core[1]->x);
ARR3SUB(v2, core[0]->x);
/* get rotation axis for bond angle */
VEC3SET(v3, 0.0, 0.0, 1.0);
crossprod(v1, v3, v2);
/* rotate bondlength scaled vector into position */
matrix_v_rotation(m2, v1, a);
ARR3SET(v3, v2);
normalize(v3, 3);
VEC3MUL(v3, r);
vecmat(m2, v3);
/* rotate to give required dihedral */
matrix_v_rotation(m1, v2, d);
vecmat(m1, v3);
/* generate the atom position */
core[2] = new_core(zval->elem, model);
model->cores = g_slist_prepend(model->cores, core[2]);
zmat->zcores = g_slist_prepend(zmat->zcores, core[2]);
ARR3SET(core[2]->x, core[0]->x);
ARR3ADD(core[2]->x, v3);
break;
default:
/* get core connectivity (NB: prepending cores - hence n - number) */
core[0] = g_slist_nth_data(zmat->zcores, n-zval->connect[0]);
core[1] = g_slist_nth_data(zmat->zcores, n-zval->connect[1]);
core[2] = g_slist_nth_data(zmat->zcores, n-zval->connect[2]);
g_assert(core[0] != NULL);
g_assert(core[1] != NULL);
g_assert(core[2] != NULL);
r = zmat->distance_scale * zval->value[0];
a = zmat->angle_scale * zval->value[1];
d = zmat->angle_scale * zval->value[2];
/* setup vectors */
ARR3SET(v2, core[1]->x);
ARR3SUB(v2, core[0]->x);
ARR3SET(v3, core[2]->x);
ARR3SUB(v3, core[1]->x);
/* rotate v3 about v2 to give dihedral */
matrix_v_rotation(m1, v2, d);
vecmat(m1, v3);
/* get rotation axis and matrix for bond angle */
crossprod(v1, v3, v2);
matrix_v_rotation(m2, v1, a);
normalize(v2, 3);
VEC3MUL(v2, r);
vecmat(m2, v2);
/* generate the atom position */
core[3] = new_core(zval->elem, model);
model->cores = g_slist_prepend(model->cores, core[3]);
zmat->zcores = g_slist_prepend(zmat->zcores, core[3]);
ARR3SET(core[3]->x, core[0]->x);
ARR3ADD(core[3]->x, v2);
/* TODO (maybe) - some zmatrix constructions implicitly assume */
/* some checking for duplicate atoms & reversing the torsional */
/* angle sense to accomodate this. */
break;
}
n++;
}
/* zmatrix cores are created in cartesians - revert to fractional if required */
if (model->fractional)
{
for (list=zmat->zcores ; list ; list=g_slist_next(list))
{
core[0] = list->data;
vecmat(model->ilatmat, core[0]->x);
}
}
}
