/* Name: insert_core
* Notes: See the insert_[socket|core|thread] description above
*/
int insert_core(struct cpu_socket *s, struct rawsyscpu *r)
{
struct cpu_socket *slist; /* for walking through list */
struct cpu_socket *thiss; /* The socket we belong on */
struct cpu_core *thisc; /* The item we are working with */
struct cpu_core *clist;
struct cpu_core *clast;
/* Find the right socket */
slist = s;
thiss = NULL;
while ( slist )
{
if ( slist->id == r->physical_package_id )
thiss = slist;
slist = slist->next;
}
if ( NULL == thiss )
return(1);
/* There are lots of implications of exiting here - leaving lots of
haning memory locations, but basically we gotta cut and run...
If you can't malloc() then it is over. */
if ( NULL == (thisc = new_core(r->core_id)) )
return(1);
/*** ordered insert ***/
/* Top of the list (no other items) */
if ( thiss->clist == NULL )
{
thiss->clist = thisc;
return(0);
}
/* Top of the list (sorted first) */
if ( thiss->clist->id > thisc->id )
{
thisc->next = thiss->clist;
thiss->clist = thisc;
return(0);
}
if ( thiss->clist->id == thisc->id )
{
/* A bit wasteful - but we only do it once */
free(thisc);
return(0);
}
/* into the middle */
clast = thiss->clist;
clist = clast->next;
while ( clist )
{
if ( clist->id > thisc->id )
{
thisc->next = clast->next;
clast->next = thisc;
return(0);
}
if ( clist->id == thisc->id )
{
free(thisc);
return(0);
}
clast = clist;
clist = clist->next;
}
/* Now at the end */
clast->next = thisc;
return(0);
}
gint read_aims(gchar *filename, struct model_pak *model)
{
gint i, num_tokens;
gchar **buff;
gpointer scan;
struct core_pak *core;
g_assert(model != NULL);
scan = scan_new(filename);
if (!scan) return(1);
while (!scan_complete(scan)) {
buff = scan_get_tokens(scan, &num_tokens);
/*
for debugging purposes
produces a compiler warning about an
implicit declaration of function 'g_printf'
though this is a valid glib function since 2.2
http://library.gnome.org/devel/glib/2.18/glib-String-Utility-Functions.html#g-printf
*/
/*
for (i=0; i<num_tokens; i++) {
g_printf(" %s ", buff[i]);
}
printf("\n");
*/
if (!buff) break;
/* read cell vectors */
if ( g_strrstr(*buff, "lattice_vector") != NULL ) {
for (i=0 ; i<3 ; i++) {
if (num_tokens >= 3) {
model->latmat[i] = str_to_float(*(buff+1));
model->latmat[i+3] = str_to_float(*(buff+2));
model->latmat[i+6] = str_to_float(*(buff+3));
}
else {
gui_text_show(ERROR, "error reading AIMS lattice vectors \n");
return(2);
}
g_strfreev(buff);
buff = scan_get_tokens(scan, &num_tokens);
}
model->periodic = 3;
model->construct_pbc = TRUE;
}
/* read coordinates */
if ( g_strrstr(*buff, "atom") != NULL ) {
if ( ( num_tokens >= 4 ) && ( elem_symbol_test(*(buff+4)) ) ) {
core = new_core(*(buff+4), model);
core->x[0] = str_to_float(*(buff+1));
core->x[1] = str_to_float(*(buff+2));
core->x[2] = str_to_float(*(buff+3));
model->cores = g_slist_prepend(model->cores, core);
}
else {
gui_text_show(ERROR, "error reading AIMS lattice vectors \n");
return(2);
}
}
g_strfreev(buff);
}
/* done reading */
scan_free(scan);
/* model setup */
g_free(model->filename);
model->filename = g_strdup(filename);
g_free(model->basename);
model->basename = g_path_get_basename(filename);
model->fractional = FALSE;
model_prep(model);
return(0);
}
gint get_data(FILE *fp, struct model_pak *model, gint have_basis)
{
gchar **buff, *line;
gint num_tokens;
struct core_pak *core;
/* process title line */
line = file_read_line(fp);
if (!line)
{
gui_text_show(ERROR, "unexpected end of file reading title\n");
return(2);
}
model->gamess.title = g_strstrip(line);
/* process symmetry line */
line = file_read_line(fp);
if (!line)
{
gui_text_show(ERROR, "unexpected end of file reading symmetry\n");
return(2);
}
if (g_ascii_strncasecmp(line, "c1", 2) != 0)
{
/* TODO handle symmetry! */
gui_text_show(WARNING, "only C1 symmetry understood at present\n");
}
g_free(line);
/* process coordinates */
line = file_read_line(fp);
if (!line)
{
gui_text_show(ERROR, "unexpected end of file reading coordinates\n");
return(2);
}
while (g_ascii_strncasecmp(line, " $end", 5) != 0)
{
buff = tokenize(line, &num_tokens);
/* TODO Store GAMESS label and use in .inp files */
if (num_tokens > 4)
{
core = new_core(elements[(int) str_to_float(*(buff+1))].symbol, model);
if (model->gamess.units == GMS_ANGS)
{
core->x[0] = str_to_float(*(buff+2));
core->x[1] = str_to_float(*(buff+3));
core->x[2] = str_to_float(*(buff+4));
}
else
{
core->x[0] = str_to_float(*(buff+2)) * BOHR_TO_ANGS;
core->x[1] = str_to_float(*(buff+3)) * BOHR_TO_ANGS;
core->x[2] = str_to_float(*(buff+4)) * BOHR_TO_ANGS;
}
model->cores = g_slist_append(model->cores, core);
g_strfreev(buff);
if (!have_basis)
{
model->gamess.basis = GMS_USER;
/* TODO - read instead of skipping */
for(;;)
{
line = file_read_line(fp);
if (!line)
break;
buff = tokenize(line, &num_tokens);
g_strfreev(buff);
if (!num_tokens)
break;
}
}
}
/* get the next line */
g_free(line);
line = file_read_line(fp);
if (!line)
{
gui_text_show(ERROR, "unexpected end of file reading coordinates\n");
return(2);
}
}
g_free(line);
return(0);
}
gint read_gms_out_block(FILE *fp, struct model_pak *model, gint num_skip, gint bohr)
{
gint i, num_tokens;
gchar **buff, line[LINELEN];
GString *title, *energy_string, *grad_string;
GSList *clist;
struct core_pak *core;
clist = model->cores;
/* ignore first num_skip lines */
for (i=0 ; i<num_skip; i++)
if (fgetline(fp, line))
{
gui_text_show(ERROR, "unexpected end of file reading coordinates\n");
return(11);
}
model->construct_pbc = FALSE;
model->fractional = FALSE;
/* get 1st line of coords */
if (fgetline(fp, line))
{
gui_text_show(ERROR, "unexpected end of file reading coordinates\n");
return(11);
}
buff = tokenize(line, &num_tokens);
while (num_tokens > 4)
{
if (clist)
{
core = clist->data;
clist = g_slist_next(clist);
}
else
{
core = new_core(elements[(int) str_to_float(*(buff+1))].symbol, model);
model->cores = g_slist_append(model->cores, core);
}
if (bohr)
{
core->x[0] = BOHR_TO_ANGS*str_to_float(*(buff+2));
core->x[1] = BOHR_TO_ANGS*str_to_float(*(buff+3));
core->x[2] = BOHR_TO_ANGS*str_to_float(*(buff+4));
}
else
{
core->x[0] = str_to_float(*(buff+2));
core->x[1] = str_to_float(*(buff+3));
core->x[2] = str_to_float(*(buff+4));
}
/* get next line */
g_strfreev(buff);
if (fgetline(fp, line))
{
gui_text_show(ERROR, "unexpected end of file reading coordinates\n");
return(11);
}
buff = tokenize(line, &num_tokens);
}
g_strfreev(buff);
/* search for energy */
while (!fgetline(fp, line))
{
if (g_ascii_strncasecmp(line, " FINAL", 6) == 0)
{
buff = tokenize(line, &num_tokens);
if (g_ascii_strncasecmp(*(buff+1), "ENERGY", 6) == 0)
model->gamess.energy = str_to_float(*(buff+3));
else
model->gamess.energy = str_to_float(*(buff+4));
model->gamess.have_energy = TRUE;
g_strfreev(buff);
break;
}
}
/* update for MP? */
if (model->gamess.MP_level > 0)
{
while (!fgetline(fp, line))
{
if (g_strrstr(line ,"E(MP2)") != NULL)
{
buff = tokenize(line, &num_tokens);
model->gamess.energy = str_to_float(*(buff+1));
model->gamess.have_energy = TRUE;
g_strfreev(buff);
break;
}
}
}
/* search for gradient and read any properties */
while (!fgetline(fp, line))
{
if (g_ascii_strncasecmp(line, " NET CHARGES:", 13) == 0)
{
clist = model->cores;
/* skip forward four lines */
for (i=0 ; i<4; i++)
if (fgetline(fp, line))
{
gui_text_show(ERROR, "unexpected end of file reading fitted charges\n");
return(11);
}
while (clist != NULL)
{
buff = tokenize(line, &num_tokens);
core = clist->data;
core->lookup_charge = FALSE;
core->charge = str_to_float(*(buff+1));
g_strfreev(buff);
clist = g_slist_next(clist);
if (fgetline(fp, line))
{
gui_text_show(ERROR, "unexpected end of file reading fitted charges\n");
return(11);
}
}
}
if (g_ascii_strncasecmp(line, " MAXIMUM GRADIENT", 26) == 0)
{
buff = tokenize(line, &num_tokens);
model->gamess.max_grad = str_to_float(*(buff+3));
model->gamess.have_max_grad = TRUE;
model->gamess.rms_grad = str_to_float(*(buff+7));
model->gamess.have_rms_grad = TRUE;
g_strfreev(buff);
/* check next line to see if converged */
if (fgetline(fp, line))
{
gui_text_show(ERROR, "unexpected end of file reading equilibrium status\n");
return(11);
}
if (g_ascii_strncasecmp(line, "1 ***** EQUILIBRIUM GEOMETRY LOCATED *****", 46) == 0)
model->gamess.converged = TRUE;
break;
}
}
g_free(model->title);
title = g_string_new("");
if (model->gamess.have_energy)
{
energy_string = g_string_new("");
g_string_append_printf(energy_string, "%.5f H", model->gamess.energy);
property_add_ranked(3, "Energy", energy_string->str, model);
g_string_free(energy_string, TRUE);
g_string_append_printf(title, "E");
if (model->gamess.MP_level > 0)
g_string_append_printf(title, "(MP%d)", model->gamess.MP_level);
g_string_append_printf(title, " = %.5f H", model->gamess.energy);
}
if (model->gamess.have_rms_grad)
{
grad_string = g_string_new("");
g_string_append_printf(grad_string, "%.4f H/B", model->gamess.rms_grad);
property_add_ranked(4, "RMS Gradient", grad_string->str, model);
g_string_free(grad_string, TRUE);
g_string_append_printf(title, ", grad = %.5f", model->gamess.rms_grad);
}
if (model->gamess.have_max_grad)
{
grad_string = g_string_new("");
g_string_append_printf(grad_string, "%.4f H/B", model->gamess.max_grad);
property_add_ranked(4, "Maximum Gradient", grad_string->str, model);
g_string_free(grad_string, TRUE);
}
model->title = g_strdup(title->str);
g_string_free(title, TRUE);
return(0);
}
gint read_about_block(FILE *fp, struct model_pak *model)
{
gint i, num_tokens;
gchar **buff, line[LINELEN];
gdouble acell[3];
GString *title;
GSList *clist;
struct core_pak *core;
clist = model->cores;
if (optcell > 0)
{
/* go to acell line and read it */
if (fgetline(fp, line))
{
gui_text_show(ERROR, "unexpected end of file reading cell dimensions in animation\n");
return(2);
}
buff = tokenize(line, &num_tokens);
acell[0] = str_to_float(*(buff+1)) * AU2ANG;
acell[1] = str_to_float(*(buff+2)) * AU2ANG;
acell[2] = str_to_float(*(buff+3)) * AU2ANG;
g_strfreev(buff);
/* get the cell vectors i.e. rprim.acell */
/* NB: gdis wants transposed ABINIT matrix */
for (i=0; i<3; i++)
{
if (fgetline(fp, line))
{
gui_text_show(ERROR, "unexpected end of file reading cell dimensions\n");
return(2);
}
buff = tokenize(line + 8, &num_tokens);
model->latmat[0+i] = acell[i] * str_to_float(*(buff+0));
model->latmat[3+i] = acell[i] * str_to_float(*(buff+1));
model->latmat[6+i] = acell[i] * str_to_float(*(buff+2));
g_strfreev(buff);
}
for (i=0; i<4; i++)
{
if (fgetline(fp, line))
{
gui_text_show(ERROR, "unexpected end of file skipping to coordinates in animation\n");
return(2);
}
}
}
/* get 1st line of coords */
if (fgetline(fp, line))
return(1);
buff = tokenize(line, &num_tokens);
while (g_ascii_strncasecmp(line, " Cartesian forces", 17) != 0)
{
if (clist)
{
core = (struct core_pak *) clist->data;
clist = g_slist_next(clist);
}
else
{
core = new_core(*(buff+4), model);
model->cores = g_slist_append(model->cores, core);
}
core->x[0] = AU2ANG*str_to_float(*(buff+0));
core->x[1] = AU2ANG*str_to_float(*(buff+1));
core->x[2] = AU2ANG*str_to_float(*(buff+2));
#if DEBUG_READ_ABOUT
printf("new coords %f %f %f\n", core->x[0], core->x[1], core->x[2]);
#endif
/* get next line */
g_strfreev(buff);
if (fgetline(fp, line))
return(2);
buff = tokenize(line, &num_tokens);
}
/* get gradients */
model->abinit.max_grad = str_to_float(*(buff+4));
model->abinit.rms_grad = str_to_float(*(buff+5));
g_strfreev(buff);
/* get energy */
if (fgetline(fp, line))
return(2);
while (g_ascii_strncasecmp(line, " At the end of Broyden", 22) != 0)
{
if (fgetline(fp, line))
return(2);
}
buff = tokenize(line, &num_tokens);
model->abinit.energy = str_to_float(*(buff+9));
title = g_string_new("");
g_string_append_printf(title, "E");
g_string_append_printf(title, " = %.4f Ha, ", model->abinit.energy);
g_string_append_printf(title, "max grad = %.5f", model->abinit.max_grad);
model->title = g_strdup(title->str);
g_string_free(title, TRUE);
return(0);
}
gint read_cel(gchar *filename, struct model_pak *model)
{
gchar *line;
FILE *fp;
int i;
gint num_tokens, natom=0;
gchar **buff;
struct core_pak *core;
/* checks */
g_return_val_if_fail(model != NULL, 1);
g_return_val_if_fail(filename != NULL, 2);
fp = fopen(filename, "rt");
if (!fp)
return 3;
/* 1st line - cell parameters */
line = file_read_line(fp);
if (!line || strlen(line) < 5 || g_ascii_strncasecmp("cell", line, 4) != 0)
{
printf("The first line should start with the keyword CELL.\n");
return 4;
}
buff = tokenize(line+4, &num_tokens);
g_free(line);
if (num_tokens < 6)
{
g_strfreev(buff);
printf("Keyword CELL should be followed by six numbers.\n");
return 5;
}
for (i=0; i<3; ++i)
model->pbc[i] = str_to_float(buff[i]);
for (i=3; i<6; ++i)
model->pbc[i] = str_to_float(buff[i]) * D2R;
g_strfreev(buff);
/* next lines - atomic positions */
for (;;)
{
line = file_read_line(fp);
if (!line) /*the end of file*/
{
printf("No 'rgnr' symmetry line found.\n");
return 6;
}
else if (g_ascii_strncasecmp("rgnr", line, 4) == 0) /*no more atomic pos.*/
{
break;
}
else if (g_ascii_strncasecmp("natom", line, 5) == 0)/*number of atoms */
/*some old .cel files have second line with number of atoms eg. "natom 6"*/
{
buff = tokenize(line, &num_tokens);
if (num_tokens > 1)
natom = str_to_float(buff[1]);
else
printf("Warning: ignoring `natom' line:\n%s\n", line);
g_free(line);
g_strfreev(buff);
}
else if (strncmp(" ", line, 4) != 0) /* atomic position */
{
buff = tokenize(line, &num_tokens);
g_free(line);
if (num_tokens < 5)
{
g_strfreev(buff);
continue;
}
core = new_core(*buff, model);
core->atom_label = g_strdup(buff[0]);
/* in second column there is either atomic number
* or something like "Mg2+" or "K+". The second form is for
* " the use of different bonding states of one and the same
* element (e.g. Fe2+ and Fe3+ in Fe3O4)"
* FIXME how these bonding states can be interpreted in GDIS */
if (g_ascii_isdigit(buff[1][0]))
core->atom_code = str_to_float(buff[1]);
else
{
core->atom_code = elem_symbol_test(buff[1]);
}
for (i=0; i<3; ++i)
core->x[i] = str_to_float(buff[2+i]);
/* TODO interpret 2 next optional numbers:
* so-called multiplied substitution and replacement factor (SOF)
* and isotropic Debye-Waller factor
* FIXME can they be interpreted by GDIS? -MW */
model->cores = g_slist_prepend(model->cores, core);
g_strfreev(buff);
}
else /* replacement atom */
{
/*FIXME replacement atoms are now silently ignored
* how can I use this information in GDIS? - MW*/
g_free(line);
}
}
/* last line - symmetry */
buff = tokenize(line, &num_tokens);
model->sginfo.spacenum = str_to_float(buff[1]);
/* FIXME/TODO how to interpret the second (optional) number?
* From fileformat docs:
* "sometimes there exists more than one setting of a space-group type.
* Thus, a further number must be given if the structure hasn't been described
* using a conventional setting (standard setting)."
* http://users.omskreg.ru/~kolosov/bam/a_v/v_1/powder/details/strucdat.htm
* http://users.omskreg.ru/~kolosov/bam/a_v/v_1/powder/details/setting.htm
* Unfortunatelly I'm ignorant about space-groups - MW
*/
g_free(line);
g_strfreev(buff);
if (natom>0 && natom != g_slist_length(model->cores))
printf("Warning: expected %i atoms, have %i.", natom,
g_slist_length(model->cores));
/* model setup */
model->fractional = TRUE;
model->periodic = 3;
strcpy(model->filename, filename);
g_free(model->basename);
model->basename = parse_strip(filename);
model_prep(model);
return 0;
}
void xml_parse_atom(const gchar **names, const gchar **values)
{
gint i, n;
gchar **buff;
g_assert(xml_model != NULL);
/* init structure */
if (!xml_core)
{
xml_core = new_core("X", xml_model);
xml_model->cores = g_slist_prepend(xml_model->cores, xml_core);
}
/* process attributes (if any) */
i=0;
while (*(names+i))
{
if (g_ascii_strncasecmp(*(names+i), "elementType\0", 12) == 0)
{
/* FIXME - potential overflow bug here, since label is an array */
g_free(xml_core->atom_label);
xml_core->atom_label = g_strdup(*(values+i));
core_init(xml_core->atom_label, xml_core, xml_model);
}
if (g_ascii_strncasecmp(*(names+i), "xyzf", 4) == 0)
{
buff = tokenize(*(values+i), &n);
if (n > 2)
{
xml_core->x[0] = str_to_float(*(buff+0));
xml_core->x[1] = str_to_float(*(buff+1));
xml_core->x[2] = str_to_float(*(buff+2));
xml_model->fractional = TRUE;
}
}
if (g_ascii_strncasecmp(*(names+i), "xf", 2) == 0)
{
xml_core->x[0] = str_to_float(*(values+i));
/* FIXME - inefficient to repeat this for all atoms */
/* but may be necessary if every atom is allowed to be cart or fract */
xml_model->fractional = TRUE;
}
if (g_ascii_strncasecmp(*(names+i), "x3", 2) == 0)
{
xml_core->x[0] = str_to_float(*(values+i));
/* FIXME - inefficient to repeat this for all atoms */
/* but may be necessary if every atom is allowed to be cart or fract */
xml_model->fractional = FALSE;
}
if (g_ascii_strncasecmp(*(names+i), "yf", 2) == 0 ||
g_ascii_strncasecmp(*(names+i), "y3", 2) == 0)
{
xml_core->x[1] = str_to_float(*(values+i));
}
if (g_ascii_strncasecmp(*(names+i), "zf", 2) == 0 ||
g_ascii_strncasecmp(*(names+i), "z3", 2) == 0)
{
xml_core->x[2] = str_to_float(*(values+i));
}
i++;
}
}
static void handle_one_cpu(unsigned int number, char *vendor, int family, int model)
{
char filename[1024];
ifstream file;
unsigned int package_number = 0;
unsigned int core_number = 0;
class abstract_cpu *package, *core, *cpu;
sprintf(filename, "/sys/devices/system/cpu/cpu%i/topology/core_id", number);
file.open(filename, ios::in);
if (file) {
file >> core_number;
file.close();
}
sprintf(filename, "/sys/devices/system/cpu/cpu%i/topology/physical_package_id", number);
file.open(filename, ios::in);
if (file) {
file >> package_number;
if (package_number == (unsigned int) -1)
package_number = 0;
file.close();
}
if (system_level.children.size() <= package_number)
system_level.children.resize(package_number + 1, NULL);
if (!system_level.children[package_number]) {
system_level.children[package_number] = new_package(package_number, number, vendor, family, model);
system_level.childcount++;
}
package = system_level.children[package_number];
package->parent = &system_level;
if (package->children.size() <= core_number)
package->children.resize(core_number + 1, NULL);
if (!package->children[core_number]) {
package->children[core_number] = new_core(core_number, number, vendor, family, model);
package->childcount++;
}
core = package->children[core_number];
core->parent = package;
if (core->children.size() <= number)
core->children.resize(number + 1, NULL);
if (!core->children[number]) {
core->children[number] = new_cpu(number, vendor, family, model);
core->childcount++;
}
cpu = core->children[number];
cpu->parent = core;
if (number >= all_cpus.size())
all_cpus.resize(number + 1, NULL);
all_cpus[number] = cpu;
}
gint read_dmol_frame(FILE *fp, struct model_pak *model)
{
gint i, num_tokens;
gchar *line, **buff;
struct core_pak *core;
g_assert(fp != NULL);
line = file_read_line(fp);
while (line)
{
/* read cell vectors */
if (g_ascii_strncasecmp(line, "$cell", 5) == 0 && model)
{
for (i=0 ; i<3 ; i++)
{
g_free(line);
line = file_read_line(fp);
buff = tokenize(line, &num_tokens);
if (num_tokens > 2)
{
model->latmat[i] = AU2ANG*str_to_float(*(buff));
model->latmat[i+3] = AU2ANG*str_to_float(*(buff+1));
model->latmat[i+6] = AU2ANG*str_to_float(*(buff+2));
}
g_strfreev(buff);
}
model->periodic = 3;
model->construct_pbc = TRUE;
}
/* read coordinates */
if (g_ascii_strncasecmp(line, "$coord", 5) == 0 && model)
{
g_free(line);
line = file_read_line(fp);
buff = tokenize(line, &num_tokens);
while (num_tokens > 3)
{
if (elem_symbol_test(*buff))
{
core = new_core(*buff, model);
model->cores = g_slist_prepend(model->cores, core);
core->x[0] = AU2ANG*str_to_float(*(buff+1));
core->x[1] = AU2ANG*str_to_float(*(buff+2));
core->x[2] = AU2ANG*str_to_float(*(buff+3));
}
g_free(line);
line = file_read_line(fp);
g_strfreev(buff);
buff = tokenize(line, &num_tokens);
}
g_strfreev(buff);
model->fractional = FALSE;
}
/* terminate frame read */
if (g_ascii_strncasecmp(line, "$end", 4) == 0)
return(0);
g_free(line);
line = file_read_line(fp);
}
return(1);
}
/* ---- example xml handler */
void* handler (SimpleXmlParser parser, SimpleXmlEvent event,
const char* szName, const char* szAttribute, const char* szValue)
{
static int nDepth= 0;
char *tmp;
char szHandlerName[32];
char szHandlerAttribute[32];
char *szHandlerValue;
//struct socket_data *news;
//struct core_data *newc;
//struct thread_data *newt;
int last_cid=0;
szHandlerValue=malloc(32);
memset(szHandlerValue,0,32);
if (szName != NULL) {
trim(szName, szHandlerName);
}
if (szAttribute != NULL) {
trim(szAttribute, szHandlerAttribute);
}
if (szValue != NULL) {
trim(szValue, szHandlerValue);
}
if (event == ADD_SUBTAG) {
fprintf(stderr,"depth: %d, val: %s\n",nDepth,szHandlerName);
fprintf(stderr, "%6li: %s add subtag (%s)\n",
simpleXmlGetLineNumber(parser), getIndent(nDepth), szHandlerName);
nDepth++;
} else if (event == ADD_ATTRIBUTE) {
// printf("attribute tag:%s %s=%s\n",szHandlerName, szHandlerAttribute, szHandlerValue);
fprintf(stderr, "%6li: %s ///add attribute to tag %s ([%s]=[%s])\n",
simpleXmlGetLineNumber(parser), getIndent(nDepth), szHandlerName, szHandlerAttribute, szHandlerValue);
if ( (!strcmp(szHandlerAttribute,"cache-level")) && (!strcmp(szHandlerValue,"3")) ) {
//attribute cache-level=3 detected: new L3 domain
fprintf(stderr,"\n* NEW SOCKET *\n");
new_socket(last_sid,last_sid);
push_socket_id(last_sid);
last_sid++;
level=3;
}
if ( (!strcmp(szHandlerAttribute,"name")) && (!strcmp(szHandlerValue,"SMT")) ) {
//attribute cache-level=2 detected: new L2 domain
fprintf(stderr,"\n * NEW CORE, Sock %d * \n", last_sid - 1);
//uncomment for noSMP:
//level=10;
//ucomment for SMP:
last_cid=pop_core_id();
new_core(0,last_cid,last_sid - 1);
} else if ( (!strcmp(szHandlerAttribute,"name")) && (!strcmp(szHandlerValue,"THREAD")) ) {
//attribute cache-level=2 detected: new L2 domain
fprintf(stderr,"\n* NEW THREAD, Sock %d *\n", last_sid - 1);
last_cid=pop_core_id();
new_thread(0,last_cid,last_sid - 1);
}
if ( (!strcmp(szHandlerAttribute,"level")) && (!strcmp(szHandlerValue,"3")) ) {
//no cpu count="2"/SMT/THREAD Routing!
level=300;
} else if ( (!strcmp(szHandlerAttribute,"level")) && (!strcmp(szHandlerValue,"2")) ) {
//attribute cache-level=2 detected: new L2 domain
fprintf(stderr,"\n* !NEW LOGICAL CORE %d!, Sock: %d*\n", last_cid,last_sid - 1);
//We have "cpu count="2" and SMT/THREAD flag name
level=200;
}
} else if (event == ADD_CONTENT) {
fprintf(stderr,"depth: %d, LEVEL %d, context for:[%s] [%s]\n",nDepth,level,szHandlerName, szHandlerValue);
if (level==200) {
if (!strcmp(szHandlerName,"cpu")) {
fprintf(stderr," !ROUTE LEVEL 10: Cores ID processed: %s, SOCKET: %d\n",szHandlerValue, last_sid - 1 );
while ((tmp = strsep(&szHandlerValue, ",")) != NULL) {
if (tmp[0] == '\0')
break; /* XXX */
trim_spaces(tmp);
// comment for no SMP?
push_core_id(atoi(tmp));
fprintf(stderr,"\n\n\nHA: [%d]\n\n\n",atoi(tmp));
// uncomment for no SMP:
// last_cid=pop_core_id();
// new_core(0,atoi(tmp),last_sid - 1);
}
// drop level
// level=9;
}
} else if (level==300) {
//no cpu count="2"/SMT/THREAD Routing!
if (!strcmp(szHandlerName,"cpu")) {
fprintf(stderr," !ROUTE LEVEL 10: Cores ID processed: %s, SOCKET: %d\n",szHandlerValue, last_sid - 1 );
while ((tmp = strsep(&szHandlerValue, ",")) != NULL) {
if (tmp[0] == '\0')
break; /* XXX */
trim_spaces(tmp);
// comment for no SMP?
push_core_id(atoi(tmp));
fprintf(stderr,"\n\n\nHA: [%d]\n\n\n",atoi(tmp));
// uncomment for no SMP:
last_cid=pop_core_id();
new_core(0,atoi(tmp),last_sid - 1);
}
// drop level
// level=9;
}
}
fprintf(stderr, "%6li: %s add content to tag %s (%s)\n",
simpleXmlGetLineNumber(parser), getIndent(nDepth), szHandlerName, szHandlerValue);
} else if (event == FINISH_ATTRIBUTES) {
fprintf(stderr,"finish for:%s\n",szHandlerName);
fprintf(stderr, "%6li: %s finish attributes (%s)\n",
simpleXmlGetLineNumber(parser), getIndent(nDepth), szHandlerName);
} else if (event == FINISH_TAG) {
fprintf(stderr,"finish for:%s\n",szHandlerName);
fprintf(stderr, "%6li: %s finish tag (%s)\n",
simpleXmlGetLineNumber(parser), getIndent(nDepth), szHandlerName);
nDepth--;
if (level==10) {
if (!strcmp(szHandlerName,"cpu"))
level=0;
}
}
//list_sockets();
return handler;
}
gint read_diffax(gchar *filename, struct model_pak *model)
{
gint num_tokens, num_layer, tot_layer;
gdouble offset;
gchar **buff;
GSList *list1, *list2;
struct core_pak *core;
struct layer_pak *layer;
FILE *fp;
/* checks */
g_return_val_if_fail(model != NULL, 1);
g_return_val_if_fail(filename != NULL, 2);
fp = fopen(filename, "rt");
if (!fp)
return(3);
/* setup */
model->id = DIFFAX_INP;
model->fractional = TRUE;
model->periodic = 3;
model->colour_scheme = REGION;
strcpy(model->filename, filename);
g_free(model->basename);
model->basename = parse_strip(filename);
/* scan the file */
while ((buff = get_tokenized_line(fp, &num_tokens)))
{
diffax_keyword_search:;
/* restricted unit cell */
if (g_ascii_strncasecmp("structural", *buff, 10) == 0)
{
g_strfreev(buff);
buff = get_tokenized_line(fp, &num_tokens);
if (num_tokens > 3)
{
model->pbc[0] = str_to_float(*(buff+0));
model->pbc[1] = str_to_float(*(buff+1));
model->pbc[2] = str_to_float(*(buff+2));
model->pbc[3] = PI/2.0;
model->pbc[4] = PI/2.0;
model->pbc[5] = D2R*str_to_float(*(buff+3));
}
}
/* layer testing */
if (g_ascii_strncasecmp("layer", *buff, 5) == 0)
{
layer = g_malloc(sizeof(struct model_pak));
layer->width = 1.0;
VEC3SET(layer->centroid, 0.5, 0.5, 0.5);
layer->cores = NULL;
model->layer_list = g_slist_prepend(model->layer_list, layer);
g_strfreev(buff);
buff = get_tokenized_line(fp, &num_tokens);
if (buff)
{
/* TODO - if centrosymmetric : add a -1 operation */
}
/* get layer data */
g_strfreev(buff);
buff = get_tokenized_line(fp, &num_tokens);
while (buff)
{
if (elem_symbol_test(*buff))
{
if (num_tokens > 6)
{
/*
printf("[%s] [%s %s %s]\n", *buff, *(buff+2), *(buff+3), *(buff+4));
*/
core = new_core(*buff, model);
model->cores = g_slist_prepend(model->cores, core);
layer->cores = g_slist_prepend(layer->cores, core);
core->x[0] = str_to_float(*(buff+2));
core->x[1] = str_to_float(*(buff+3));
core->x[2] = str_to_float(*(buff+4));
core->sof = str_to_float(*(buff+5));
}
}
else
goto diffax_keyword_search;
/* get next line of tokens */
g_strfreev(buff);
buff = get_tokenized_line(fp, &num_tokens);
}
}
g_strfreev(buff);
}
/* TODO - enumerate layers and scale, so they are stacked 1..n in a single cell */
/* also label the layers as different region types */
model->layer_list = g_slist_reverse(model->layer_list);
num_layer = 0;
tot_layer = g_slist_length(model->layer_list);
model->pbc[2] *= tot_layer;
#if DEBUG_READ_DIFFAX
printf("Read in %d layers.\n", tot_layer);
#endif
for (list1=model->layer_list ; list1 ; list1=g_slist_next(list1))
{
layer = (struct layer_pak *) list1->data;
layer->width = 1.0 / (gdouble) tot_layer;
offset = (gdouble) num_layer * layer->width;
VEC3SET(layer->centroid, 0.0, 0.0, offset);
for (list2=layer->cores ; list2 ; list2=g_slist_next(list2))
{
core = (struct core_pak *) list2->data;
/* scale to within the big cell (encloses all DIFFAX layers) */
core->x[2] *= layer->width;
/* offset each particular layer */
core->x[2] += offset;
core->region = num_layer;
}
num_layer++;
}
/* end of read */
fclose(fp);
/* post read setup */
model->cores = g_slist_reverse(model->cores);
model_prep(model);
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);
}
}
}
gint read_gromacs_gro(gchar *filename, struct model_pak *model)
{
gint num_tokens;
gchar *line, **buff;
FILE *fp;
g_assert(model != NULL);
fp = fopen(filename,"rt");
if (!fp)
return(1);
/* skip title */
line = file_read_line(fp);
g_free(line);
line = file_read_line(fp);
while (line)
{
/* FIXME - properly should do formatted read, since things can be */
/* adjacent with no spaces in between -> tokenize() will fail */
/*
fprintf(fp, "%5i%5s%5s%5i%8.3f%8.3f%8.3f%8.4f%8.4f%8.4f\n",
n, "UNK", core->atom_label, 1,
x[0], x[1], x[2], 0.1*core->v[0], 0.1*core->v[1], 0.1*core->v[2]);
*/
if (strlen(line) > 10)
{
/* tokenize from atom label (avoids some problems with no space separation) */
buff = tokenize(&line[10], &num_tokens);
if (num_tokens > 4)
{
/* TODO - deal with water properly (ie set atom_types) */
if (g_ascii_strncasecmp(*(buff+0), "HW", 2) == 0)
{
g_free(*(buff+0));
*(buff+0) = g_strdup("H");
}
if (g_ascii_strncasecmp(*(buff+0), "OW", 2) == 0)
{
g_free(*(buff+0));
*(buff+0) = g_strdup("O");
}
if (elem_test(*(buff+0)))
{
struct core_pak *core = new_core(*(buff+0), model);
core->x[0] = 10.0*str_to_float(*(buff+2));
core->x[1] = 10.0*str_to_float(*(buff+3));
core->x[2] = 10.0*str_to_float(*(buff+4));
model->cores = g_slist_prepend(model->cores, core);
}
}
g_strfreev(buff);
}
g_free(line);
line = file_read_line(fp);
}
model->cores = g_slist_reverse(model->cores);
model_prep(model);
fclose(fp);
return(0);
}
gint read_nwout_block(FILE *fp, struct model_pak *model)
{
gint num_tokens;
gchar **buff, line[LINELEN], *text;
GString *gstring;
GSList *clist;
struct core_pak *core;
clist = model->cores;
/* skip until get a 1 in first column for first coordinate */
if (fgetline(fp, line))
return(1);
while (g_ascii_strncasecmp(line, " 1", 5) != 0)
{
if (fgetline(fp, line))
return(1);
}
buff = tokenize(line, &num_tokens);
while (num_tokens > 0)
{
if (clist)
{
core = clist->data;
clist = g_slist_next(clist);
}
else
{
core = new_core(*(buff+1), model);
model->cores = g_slist_append(model->cores, core);
}
core->x[0] = str_to_float(*(buff+3));
core->x[1] = str_to_float(*(buff+4));
core->x[2] = str_to_float(*(buff+5));
#if DEBUG_READ_NWOUT
P3VEC("coords: ", core->x);
#endif
/* get next line */
g_strfreev(buff);
if (fgetline(fp, line))
return(2);
buff = tokenize(line, &num_tokens);
}
g_strfreev(buff);
/* read until get the details of the current optimisation step */
while (g_ascii_strncasecmp(line, "@", 1) != 0)
{
if (fgetline(fp, line))
return(0);
}
buff = tokenize(line, &num_tokens);
while (g_ascii_strncasecmp(line, "@", 1) == 0)
{
if (g_ascii_isdigit(buff[1][0]))
{
text = format_value_and_units(*(buff+2), 5);
gstring = g_string_new(text);
g_free(text);
g_string_append(gstring, " a.u.");
property_add_ranked(3, "Energy", gstring->str, model);
g_string_free(gstring, TRUE);
text = format_value_and_units(*(buff+5), 5);
gstring = g_string_new(text);
g_free(text);
g_string_append(gstring, " a.u./A");
property_add_ranked(4, "RMS Gradient", gstring->str, model);
g_string_free(gstring, TRUE);
}
/* get next line */
g_strfreev(buff);
if (fgetline(fp, line))
return(2);
buff = tokenize(line, &num_tokens);
}
return(0);
}
gint read_rietica(gchar *filename, struct model_pak *model)
{
gint i, phases=0, skip, num_tokens;
gchar **buff, *line;
float x, y, z;
gpointer scan;
GSList *list;
struct core_pak *core;
/* checks */
g_assert(model != NULL);
scan = scan_new(filename);
if (!scan)
return(1);
/* FIXME - stop the previous file routines setting this */
model->id = -1;
while (!scan_complete(scan))
{
buff = scan_get_tokens(scan, &num_tokens);
/* search for structure start */
if (num_tokens)
{
if (g_ascii_strncasecmp(*buff, "***", 3) == 0)
{
if (phases)
model = model_new();
phases++;
/* structure name - omit the 1st and last tokens (ie "***") */
if (num_tokens > 1)
{
g_free(*(buff+num_tokens-1));
*(buff+num_tokens-1) = NULL;
g_free(model->basename);
model->basename = g_strjoinv(" ", buff+1);
}
/* parse spacegroup */
line = scan_get_line(scan);
line = scan_get_line(scan);
model->sginfo.spacename = g_strstrip(g_strdup(line));
model->sginfo.spacenum = -1;
/* parse a structure */
skip = 0;
while (!scan_complete(scan))
{
g_strfreev(buff);
buff = scan_get_tokens(scan, &num_tokens);
if (num_tokens)
{
if (elem_symbol_test(*buff))
{
/* new core */
/*
if (num_tokens > 6)
*/
{
core = new_core(*buff, model);
model->cores = g_slist_prepend(model->cores, core);
/* formatted output can result in -ve signs "joining" tokens */
line = scan_cur_line(scan);
/* no doubt some fortran programmer thought this was a clever format */
sscanf(line, "%*16c%8f%8f%8f", &x, &y, &z);
VEC3SET(core->x, x, y, z);
/*
printf("> %s", line);
P3VEC(" - ", core->x);
core->x[0] = str_to_float(*(buff+2));
core->x[1] = str_to_float(*(buff+3));
core->x[2] = str_to_float(*(buff+4));
core->sof = str_to_float(*(buff+6));
*/
skip = 0;
}
}
else
skip++;
}
/* 4 lines after the last core - parse cell info and terminate structure */
if (skip == 4)
{
if (num_tokens > 5)
{
for (i=6 ; i-- ; )
model->pbc[i] = str_to_float(*(buff+i));
model->pbc[3] *= D2R;
model->pbc[4] *= D2R;
model->pbc[5] *= D2R;
}
break;
}
}
}
}
g_strfreev(buff);
}
/* setup all new structures */
for (list=sysenv.mal ; list ; list=g_slist_next(list))
{
model = list->data;
if (model->id == -1)
{
model->id = RIETICA;
model->periodic = 3;
model->fractional = TRUE;
strcpy(model->filename, filename);
model->cores = g_slist_reverse(model->cores);
model_prep(model);
}
}
scan_free(scan);
return(0);
}
