static tsi_peer peer_from_cert_name_test_entry(
const cert_name_test_entry *entry) {
size_t i;
tsi_peer peer;
name_list *nl;
parsed_names dns_entries = parse_names(entry->dns_names);
parsed_names ip_entries = parse_names(entry->ip_names);
nl = dns_entries.names;
GPR_ASSERT(tsi_construct_peer(
1 + dns_entries.name_count + ip_entries.name_count, &peer) ==
TSI_OK);
GPR_ASSERT(tsi_construct_string_peer_property_from_cstring(
TSI_X509_SUBJECT_COMMON_NAME_PEER_PROPERTY, entry->common_name,
&peer.properties[0]) == TSI_OK);
i = 1;
while (nl != NULL) {
char *processed = processed_name(nl->name);
GPR_ASSERT(tsi_construct_string_peer_property(
TSI_X509_SUBJECT_ALTERNATIVE_NAME_PEER_PROPERTY, processed,
strlen(nl->name), &peer.properties[i++]) == TSI_OK);
nl = nl->next;
gpr_free(processed);
}
nl = ip_entries.names;
while (nl != NULL) {
char *processed = processed_name(nl->name);
GPR_ASSERT(tsi_construct_string_peer_property(
TSI_X509_SUBJECT_ALTERNATIVE_NAME_PEER_PROPERTY, processed,
strlen(nl->name), &peer.properties[i++]) == TSI_OK);
nl = nl->next;
gpr_free(processed);
}
destruct_parsed_names(&dns_entries);
destruct_parsed_names(&ip_entries);
return peer;
}
static gmx_bool parse_entry(char **string, int natoms, t_atoms *atoms,
t_blocka *block, char ***gn,
atom_id *nr, atom_id *index, char *gname)
{
static char **names, *ostring;
static gmx_bool bFirst = TRUE;
int j, n_names, sel_nr1;
atom_id i, nr1, *index1;
char c;
gmx_bool bRet, bCompl;
if (bFirst)
{
bFirst = FALSE;
snew(names, MAXNAMES);
for (i = 0; i < MAXNAMES; i++)
{
snew(names[i], NAME_LEN+1);
}
}
bRet = FALSE;
sel_nr1 = NOTSET;
while (*string[0] == ' ')
{
(*string)++;
}
if ((*string)[0] == '!')
{
bCompl = TRUE;
(*string)++;
while (*string[0] == ' ')
{
(*string)++;
}
}
else
{
bCompl = FALSE;
}
ostring = *string;
if (parse_int(string, &sel_nr1) ||
parse_string(string, &sel_nr1, block->nr, *gn))
{
if ((sel_nr1 >= 0) && (sel_nr1 < block->nr))
{
copy_group(sel_nr1, block, nr, index);
strcpy(gname, (*gn)[sel_nr1]);
printf("Copied index group %d '%s'\n", sel_nr1, (*gn)[sel_nr1]);
bRet = TRUE;
}
else
{
printf("Group %d does not exist\n", sel_nr1);
}
}
else if ((*string)[0] == 'a')
{
(*string)++;
if (check_have_atoms(atoms, ostring))
{
if (parse_int(string, &sel_nr1))
{
bRet = select_atomnumbers(string, atoms, sel_nr1, nr, index, gname);
}
else if (parse_names(string, &n_names, names))
{
bRet = select_atomnames(atoms, n_names, names, nr, index, FALSE);
make_gname(n_names, names, gname);
}
}
}
else if ((*string)[0] == 't')
{
(*string)++;
if (check_have_atoms(atoms, ostring) &&
parse_names(string, &n_names, names))
{
if (atoms->atomtype == NULL)
{
printf("Need a run input file to select atom types\n");
}
else
{
bRet = select_atomnames(atoms, n_names, names, nr, index, TRUE);
make_gname(n_names, names, gname);
}
}
}
else if (strncmp(*string, "res", 3) == 0)
{
(*string) += 3;
if (check_have_atoms(atoms, ostring) &&
parse_int(string, &sel_nr1) &&
(sel_nr1 >= 0) && (sel_nr1 < block->nr) )
{
bRet = atoms_from_residuenumbers(atoms,
sel_nr1, block, nr, index, (*gn)[sel_nr1]);
sprintf(gname, "atom_%s", (*gn)[sel_nr1]);
}
}
else if (strncmp(*string, "ri", 2) == 0)
{
(*string) += 2;
if (check_have_atoms(atoms, ostring) &&
parse_int_char(string, &sel_nr1, &c))
{
bRet = select_residueindices(string, atoms, sel_nr1, c, nr, index, gname);
}
}
else if ((*string)[0] == 'r')
{
(*string)++;
if (check_have_atoms(atoms, ostring))
{
if (parse_int_char(string, &sel_nr1, &c))
{
bRet = select_residuenumbers(string, atoms, sel_nr1, c, nr, index, gname);
}
else if (parse_names(string, &n_names, names))
{
bRet = select_residuenames(atoms, n_names, names, nr, index);
make_gname(n_names, names, gname);
}
}
}
else if (strncmp(*string, "chain", 5) == 0)
{
(*string) += 5;
if (check_have_atoms(atoms, ostring) &&
parse_names(string, &n_names, names))
{
bRet = select_chainnames(atoms, n_names, names, nr, index);
sprintf(gname, "ch%s", names[0]);
for (i = 1; i < n_names; i++)
{
strcat(gname, names[i]);
}
}
}
if (bRet && bCompl)
{
snew(index1, natoms-*nr);
nr1 = 0;
for (i = 0; i < natoms; i++)
{
j = 0;
while ((j < *nr) && (index[j] != i))
{
j++;
}
if (j == *nr)
{
if (nr1 >= natoms-*nr)
{
printf("There are double atoms in your index group\n");
break;
}
index1[nr1] = i;
nr1++;
}
}
*nr = nr1;
for (i = 0; i < nr1; i++)
{
index[i] = index1[i];
}
sfree(index1);
for (i = strlen(gname)+1; i > 0; i--)
{
gname[i] = gname[i-1];
}
gname[0] = '!';
printf("Complemented group: %d atoms\n", *nr);
}
return bRet;
}
void create_nullspace_system(boost::filesystem::path output_name,
boost::filesystem::path input_name,
BertiniRealConfig & program_options,
NullspaceConfiguration *ns_config)
/***************************************************************\
* USAGE: setup input file for one deflation iteration *
* ARGUMENTS: number of declaration statments, name of file, *
* command to run Matlab, and dimension of nullspace *
* RETURN VALUES: creates new file *
* NOTES: *
\***************************************************************/
{
int *declarations = NULL;
partition_parse(&declarations, input_name, "func_input_real" , "config_real" ,0); // the 0 means not self conjugate mode
int ii, numVars = 0, numFuncs = 0, numConstants = 0;
int *lineVars = NULL, *lineFuncs = NULL, *lineConstants = NULL;
char ch, *str = NULL, **vars = NULL, **funcs = NULL, **consts = NULL;
FILE *IN = NULL, *OUT = NULL;
// move the file & open it
IN = safe_fopen_read("func_input_real");
// setup variables
if (declarations[0] > 0)
{ // using variable_group
parse_names(&numVars, &vars, &lineVars, IN,const_cast< char *>("variable_group"), declarations[0]);
}
else
{ // using hom_variable_group
parse_names(&numVars, &vars, &lineVars, IN,const_cast< char *>("hom_variable_group"), declarations[1]);
}
// setup constants
rewind(IN);
parse_names(&numConstants, &consts, &lineConstants, IN,const_cast< char *>("constant"), declarations[8]);
// setup functions
rewind(IN);
parse_names(&numFuncs, &funcs, &lineFuncs, IN, const_cast< char *>("function"), declarations[9]);
fclose(IN);
// setup Matlab script
create_matlab_determinantal_system("matlab_nullspace_system.m", "func_input_real",
ns_config,
numVars, vars, lineVars, numConstants, consts, lineConstants, numFuncs, funcs, lineFuncs);
// run Matlab script
std::stringstream converter;
converter << program_options.matlab_command() << " matlab_nullspace_system";
system(converter.str().c_str());
converter.clear(); converter.str("");
// setup new file
OUT = safe_fopen_write(output_name.c_str());
fprintf(OUT, "\n\nINPUT\n");
std::string constants = just_constants("func_input_real",numConstants,consts,lineConstants);
fprintf(OUT, "%s\n\n",constants.c_str());
fprintf(OUT,"variable_group ");
for (ii=0;ii<numVars; ii++){
fprintf(OUT,"%s",vars[ii]);
(ii==numVars-1) ? fprintf(OUT,";\n") : fprintf(OUT,", ");
}
for (ii=0; ii<ns_config->num_projections; ii++) {
std::stringstream projname;
projname << "pi_" << ii+1;
write_vector_as_constants(ns_config->target_projection[ii], projname.str(), OUT);
}
if (!ns_config->randomizer()->is_square()) {
write_matrix_as_constants( *(ns_config->randomizer()->get_mat_full_prec()), "r", OUT);
}
WaitOnGeneratedFile("derivative_polynomials_declaration");
IN = safe_fopen_read("derivative_polynomials_declaration");
while ((ch = fgetc(IN)) != EOF)
fprintf(OUT, "%c", ch);
fclose(IN);
// END; written in the above transciption
fprintf(OUT,"END;\n\n\n");
write_vector_as_constants(ns_config->v_patch, "synthetic_var_patch", OUT);
fprintf(OUT,"function synth_var_patch;\n");
fprintf(OUT,"synth_var_patch = ");
for (ii=0; ii<(ns_config->num_v_vars); ii++) {
fprintf(OUT,"synthetic_var_patch_%d * synth%d",ii+1,ii+1);
(ii==ns_config->num_v_vars-1) ? fprintf(OUT,";\n") : fprintf(OUT," + ");
}
fprintf(OUT,"\n\nTODO: add natural variable patch");
fclose(OUT);
// clear memory
free(str);
for (ii = 0; ii < numVars; ii++)
free(vars[ii]);
free(vars);
free(lineVars);
for (ii = 0; ii < numConstants; ii++)
free(consts[ii]);
free(consts);
free(lineConstants);
for (ii = 0; ii < numFuncs; ii++)
free(funcs[ii]);
free(funcs);
free(lineFuncs);
return;
}