static int parse_names(char **string,int *n_names,char **names)
{
int i;
*n_names=0;
while ((isalnum_star((*string)[0]) || ((*string)[0]==' '))) {
if (isalnum_star((*string)[0])) {
if (*n_names >= MAXNAMES)
gmx_fatal(FARGS,"To many names: %d\n",*n_names+1);
i=0;
while (isalnum_star((*string)[i])) {
names[*n_names][i]=(*string)[i];
i++;
if (i > NAME_LEN) {
printf("Name is too long, the maximum is %d characters\n",NAME_LEN);
return 0;
}
}
names[*n_names][i]='\0';
if (!bCase)
upstring(names[*n_names]);
*string += i;
(*n_names)++;
}
else
(*string)++;
}
return *n_names;
}
int find_group(char s[], int ngrps, char **grpname)
{
int aa, i, n;
char string[STRLEN];
gmx_bool bMultiple;
bMultiple = FALSE;
n = strlen(s);
aa=NOTSET;
/* first look for whole name match */
if (aa==NOTSET)
for(i=0; i<ngrps; i++)
if (gmx_strcasecmp_min(s,grpname[i])==0) {
if(aa!=NOTSET)
bMultiple = TRUE;
aa=i;
}
/* second look for first string match */
if (aa==NOTSET)
for(i=0; i<ngrps; i++)
if (gmx_strncasecmp_min(s,grpname[i],n)==0) {
if(aa!=NOTSET)
bMultiple = TRUE;
aa=i;
}
/* last look for arbitrary substring match */
if (aa==NOTSET) {
upstring(s);
minstring(s);
for(i=0; i<ngrps; i++) {
strcpy(string, grpname[i]);
upstring(string);
minstring(string);
if (strstr(string,s)!=NULL) {
if(aa!=NOTSET)
bMultiple = TRUE;
aa=i;
}
}
}
if (bMultiple) {
printf("Error: Multiple groups '%s' selected\n", s);
aa=NOTSET;
}
return aa;
}
static void add_prop(aprop_t *ap,gmx_residuetype_t restype,
char *resnm,char *atomnm,
real p,int line)
{
int i,j;
gmx_bool bExact;
j = get_prop_index(ap,restype,resnm,atomnm,&bExact);
if (!bExact) {
if (ap->nprop >= ap->maxprop) {
ap->maxprop += 10;
srenew(ap->resnm,ap->maxprop);
srenew(ap->atomnm,ap->maxprop);
srenew(ap->value,ap->maxprop);
srenew(ap->bAvail,ap->maxprop);
for(i=ap->nprop; (i<ap->maxprop); i++) {
ap->atomnm[i] = NULL;
ap->resnm[i] = NULL;
ap->value[i] = 0;
ap->bAvail[i] = FALSE;
}
}
upstring(atomnm);
upstring(resnm);
ap->atomnm[ap->nprop] = strdup(atomnm);
ap->resnm[ap->nprop] = strdup(resnm);
j = ap->nprop;
ap->nprop++;
}
if (ap->bAvail[j]) {
if (ap->value[j] == p)
fprintf(stderr,"Warning double identical entries for %s %s %g on line %d in file %s\n",
resnm,atomnm,p,line,ap->db);
else {
fprintf(stderr,"Warning double different entries %s %s %g and %g on line %d in file %s\n"
"Using last entry (%g)\n",
resnm,atomnm,p,ap->value[j],line,ap->db,p);
ap->value[j] = p;
}
}
else {
ap->bAvail[j] = TRUE;
ap->value[j] = p;
}
}
void do_view(const output_env_t oenv, const char *fn, const char *opts)
{
char buf[STRLEN], env[STRLEN];
const char *cmd;
int ftp, n;
if (output_env_get_view(oenv) && fn)
{
if (getenv("DISPLAY") == NULL)
{
fprintf(stderr, "Can not view %s, no DISPLAY environment variable.\n", fn);
}
else
{
ftp = fn2ftp(fn);
sprintf(env, "GMX_VIEW_%s", ftp2ext(ftp));
upstring(env);
switch (ftp)
{
case efXVG:
if (!(cmd = getenv(env)) )
{
if (getenv("GMX_USE_XMGR") )
{
cmd = "xmgr";
}
else
{
cmd = "xmgrace";
}
}
break;
default:
if ( (n = can_view(ftp)) )
{
if (!(cmd = getenv(env)) )
{
cmd = view_program[n];
}
}
else
{
fprintf(stderr, "Don't know how to view file %s", fn);
return;
}
}
if (strlen(cmd) )
{
sprintf(buf, "%s %s %s &", cmd, opts ? opts : "", fn);
fprintf(stderr, "Executing '%s'\n", buf);
if (0 != system(buf) )
{
gmx_fatal(FARGS, "Failed executing command: %s", buf);
}
}
}
}
}
gmx_bool gmx_atomprop_query(gmx_atomprop_t aps,
int eprop,const char *resnm,const char *atomnm,
real *value)
{
gmx_atomprop *ap = (gmx_atomprop*) aps;
size_t i;
int j;
#define MAXQ 32
char atomname[MAXQ],resname[MAXQ];
gmx_bool bExact;
set_prop(aps,eprop);
if ((strlen(atomnm) > MAXQ-1) || (strlen(resnm) > MAXQ-1)) {
if (debug)
fprintf(debug,"WARNING: will only compare first %d characters\n",
MAXQ-1);
}
if (isdigit(atomnm[0])) {
/* put digit after atomname */
for (i=1; (i<min(MAXQ-1,strlen(atomnm))); i++)
atomname[i-1] = atomnm[i];
atomname[i-1] = atomnm[0];
atomname[i] = '\0';
}
else {
strncpy(atomname,atomnm,MAXQ-1);
}
upstring(atomname);
strncpy(resname,resnm,MAXQ-1);
upstring(resname);
j = get_prop_index(&(ap->prop[eprop]),ap->restype,resname,
atomname,&bExact);
if (j >= 0) {
*value = ap->prop[eprop].value[j];
return TRUE;
}
else {
*value = ap->prop[eprop].def;
return FALSE;
}
}
/* Print CPU information */
int print_cpuinfo(void)
{
char soc_name[10];
strncpy(soc_name, CONFIG_SYS_SOC, 10);
upstring(soc_name);
puts(soc_name);
puts("\n");
/* TBD: Add printf of major/minor rev info, stepping, etc. */
return 0;
}
void do_view(char *fn, char *opts)
{
#define N_EXT 3
char buf[STRLEN], env[20], ext[N_EXT], *cmd, *defopts=NULL;
int ftp, n;
char *disp;
if (bDoView() && fn) {
#ifdef SPEC_CPU
disp = NULL;
#else
disp = getenv("DISPLAY");
#endif
if (disp == NULL) {
fprintf(stderr,"Can not view %s, no DISPLAY environment variable.\n",fn);
} else {
ftp=fn2ftp(fn);
strncpy(ext, ftp2ext(ftp), N_EXT);
upstring(ext);
sprintf(env, "GMX_VIEW_%s", ext);
if ( (n=can_view(ftp)) ) {
#ifdef SPEC_CPU
cmd = NULL;
#else
cmd = getenv(env);
#endif
if ( ! cmd )
cmd=view_program[n];
} else {
fprintf(stderr,"Don't know how to view file %s",fn);
return;
}
/* Add command line option -nxy for xmgrace */
if (ftp == efXVG && strcmp(cmd,"xmgrace") == 0)
defopts = "-nxy";
if ( strlen(cmd) ) {
sprintf(buf,"%s %s%s%s%s%s &",
cmd,
opts ? opts : "",opts ? " " : "",
defopts ? defopts : "",defopts ? " " : "",
fn);
fprintf(stderr,"Executing '%s'\n",buf);
system(buf);
}
}
}
}
/* {{{ MySQL_ArtResultSet::findColumn() -I- */
uint32_t
MySQL_ArtResultSet::findColumn(const sql::SQLString& columnLabel) const
{
CPP_ENTER("MySQL_ArtResultSet::columnLabel");
checkValid();
boost::scoped_array< char > upstring(sql::mysql::util::utf8_strup(columnLabel.c_str(), 0));
FieldNameIndexMap::const_iterator iter = field_name_to_index_map.find(upstring.get());
if (iter == field_name_to_index_map.end()) {
return 0;
}
/* findColumn returns 1-based indexes */
return iter->second + 1;
}
void do_view(const output_env_t oenv,const char *fn, const char *opts)
{
char buf[STRLEN], env[STRLEN];
const char *cmd;
int ftp, n;
if (output_env_get_view(oenv) && fn) {
if (getenv("DISPLAY") == NULL) {
fprintf(stderr,"Can not view %s, no DISPLAY environment variable.\n",fn);
} else {
ftp=fn2ftp(fn);
sprintf(env, "GMX_VIEW_%s", ftp2ext(ftp));
upstring(env);
switch(ftp) {
case efXVG:
if ( ! (cmd=getenv(env)) ) {
if ( getenv("XMGR") )
cmd="xmgr";
else
cmd="xmgrace";
}
break;
default:
if ( (n=can_view(ftp)) ) {
if ( ! (cmd=getenv(env)) )
cmd=view_program[n];
} else {
fprintf(stderr,"Don't know how to view file %s",fn);
return;
}
}
if ( strlen(cmd) ) {
sprintf(buf,"%s %s %s &",cmd,opts ? opts : "",fn);
fprintf(stderr,"Executing '%s'\n",buf);
#ifdef GMX_NO_SYSTEM
printf("Warning-- No calls to system(3) supported on this platform.");
printf("Warning-- Skipping execution of 'system(\"%s\")'.", buf);
#else
if( 0 != system(buf) )
{
gmx_fatal(FARGS,"Failed executing command: %s",buf);
}
#endif
}
}
}
}
/* {{{ MySQL_ArtResultSet::MySQL_ArtResultSet() -I- */
MySQL_ArtResultSet::MySQL_ArtResultSet(const StringList& fn, rset_t* const rs, boost::shared_ptr< MySQL_DebugLogger > & l)
: num_fields(static_cast<int>(fn.size())), rset(rs), current_record(rset->begin()),
started(false), field_index_to_name_map(new sql::SQLString[num_fields]),
num_rows(rset->size()), row_position(0), is_closed(false), logger(l)
{
CPP_ENTER("MySQL_ArtResultSet::MySQL_ArtResultSet");
CPP_INFO_FMT("metadata.size=%d resultset.size=%d", fn.size(), rset->size());
// field_index_to_name_map = new sql::SQLString[num_fields];
unsigned int idx = 0;
for (StringList::const_iterator it = fn.begin(), e = fn.end(); it != e; ++it, ++idx) {
boost::scoped_array< char > upstring(sql::mysql::util::utf8_strup(it->c_str(), 0));
field_name_to_index_map[sql::SQLString(upstring.get())] = idx;
field_index_to_name_map[idx] = upstring.get();
}
meta.reset(new MySQL_ArtResultSetMetaData(this, logger));
}
void do_addhelp(CHAR_DATA *ch, char *argument)
{
MYSQL *conn;
char buf[MSL*3], title[MSL], skill[MSL], arg[MSL], *ttitle;
char *escape, *escape2;
int minlevel;
if(!str_cmp(argument,""))
{
send_to_char("Syntax: addhelp edit\n\r",ch);
send_to_char("Syntax: addhelp 'help title' 'skill required' minimumlevel\n\r",ch);
send_to_char("Example: addhelp 'HELP NEW FORMAT' 'none' 0\n\r",ch);
send_to_char("Any words in the title will be keywords, case insensitive, that the help command searches for.\n\r",ch);
send_to_char("The skill required is the name of a skill you must have at 1% or greater to view the help.\n\r",ch);
send_to_char("It should only be used for cabal power helpfiles and other semi-secret helpfiles and should be 'none' otherwise.\n\r",ch);
send_to_char("Minimum level is the minimum level required to view this helpfile, and should have a 0 if it's not\n\r",ch);
send_to_char("an immortal or level dependant helpfile.\n\r",ch);
send_to_char("Addhelp edit will allow you to change and add the actual text of your helpfile, and must be done first.\n\r",ch);
return;
}
if(!str_cmp(argument, "edit"))
return enter_text(ch, addhelp_end_fun);
if(!ch->pcdata->entered_text || ch->pcdata->entered_text[0] == '\0' || !str_cmp(ch->pcdata->entered_text, ""))
return send_to_char("You haven't specified the contents of your helpfile.\n\r",ch);
conn = open_conn();
if(!conn)
return send_to_char("Error opening help database.\n\r",ch);
argument = one_argument(argument,title);
argument = one_argument(argument,skill);
argument = one_argument(argument,arg);
ttitle = palloc_string(upstring(title));
minlevel = atoi(arg);
escape = (char *)escape_string(ttitle);
escape2 = (char *)escape_string(ch->pcdata->entered_text);
sprintf(buf,"INSERT INTO helpfiles VALUES(NULL, \"%s\", \"%s\", %d, \"%s\")",
escape, skill, minlevel, escape2);
mysql_query(conn, buf);
sprintf(buf,"Help file added:\n\rTitle: %s\n\rSkill Required: %s\n\rMinimum Level: %d\n\rHelp Text: %s\n\r",
ttitle, skill, minlevel, ch->pcdata->entered_text);
send_to_char(buf,ch);
do_disc(conn);
}
/*! \brief Support handling restarts
*
* \todo Clean this up (next patch)
*
* Read just the simulation 'generation' and with bTryToAppendFiles check files.
* This is is needed at the beginning of mdrun,
* to be able to rename the logfile correctly.
* When file appending is requested, checks which output files are present,
* and returns TRUE/FALSE in bDoAppendFiles if all or none are present.
* If only some output files are present, give a fatal error.
* When bDoAppendFiles is TRUE upon return, bAddPart will tell whether the simulation part
* needs to be added to the output file name.
*
* This routine cannot print tons of data, since it is called before
* the log file is opened. */
static void
read_checkpoint_data(const char *filename, int *simulation_part,
t_commrec *cr,
gmx_bool bTryToAppendFiles,
int nfile, const t_filenm fnm[],
const char *part_suffix,
gmx_bool *bAddPart,
gmx_bool *bDoAppendFiles)
{
t_fileio *fp;
int nfiles;
gmx_file_position_t *outputfiles;
int nexist, f;
char *fn, suf_up[STRLEN];
*bDoAppendFiles = FALSE;
if (SIMMASTER(cr))
{
if (!gmx_fexist(filename) || (!(fp = gmx_fio_open(filename, "r")) ))
{
*simulation_part = 0;
}
else
{
read_checkpoint_simulation_part_and_filenames(fp,
simulation_part,
&nfiles,
&outputfiles);
if (bTryToAppendFiles)
{
nexist = 0;
for (f = 0; f < nfiles; f++)
{
if (exist_output_file(outputfiles[f].filename, nfile, fnm))
{
nexist++;
}
}
if (nexist == nfiles)
{
*bDoAppendFiles = bTryToAppendFiles;
}
else if (nexist > 0)
{
fprintf(stderr,
"Output file appending has been requested,\n"
"but some output files listed in the checkpoint file %s\n"
"are not present or are named differently by the current program:\n",
filename);
fprintf(stderr, "output files present:");
for (f = 0; f < nfiles; f++)
{
if (exist_output_file(outputfiles[f].filename,
nfile, fnm))
{
fprintf(stderr, " %s", outputfiles[f].filename);
}
}
fprintf(stderr, "\n");
fprintf(stderr, "output files not present or named differently:");
for (f = 0; f < nfiles; f++)
{
if (!exist_output_file(outputfiles[f].filename,
nfile, fnm))
{
fprintf(stderr, " %s", outputfiles[f].filename);
}
}
fprintf(stderr, "\n");
gmx_fatal(FARGS, "File appending requested, but %d of the %d output files are not present or are named differently", nfiles-nexist, nfiles);
}
}
if (*bDoAppendFiles)
{
if (nfiles == 0)
{
gmx_fatal(FARGS, "File appending requested, but no output file information is stored in the checkpoint file");
}
fn = outputfiles[0].filename;
if (strlen(fn) < 4 ||
gmx_strcasecmp(fn+strlen(fn)-4, ftp2ext(efLOG)) == 0)
{
gmx_fatal(FARGS, "File appending requested, but the log file is not the first file listed in the checkpoint file");
}
/* Set bAddPart to whether the suffix string '.part' is present
* in the log file name.
*/
strcpy(suf_up, part_suffix);
upstring(suf_up);
*bAddPart = (strstr(fn, part_suffix) != NULL ||
strstr(fn, suf_up) != NULL);
}
sfree(outputfiles);
}
}
if (PAR(cr))
{
gmx_bcast(sizeof(*simulation_part), simulation_part, cr);
if (*simulation_part > 0 && bTryToAppendFiles)
{
gmx_bcast(sizeof(*bDoAppendFiles), bDoAppendFiles, cr);
gmx_bcast(sizeof(*bAddPart), bAddPart, cr);
}
}
}