void show_editor()
{
parse_from_file();
editor_initialize();
flush_on_screen();
show_cursor();
}
GridMapData::GridMapData (SCM desc)
{
grid_width = -1;
grid_height = -1;
while (!gh_null_p (desc))
{
SCM symbol = gh_caar(desc);
SCM data = gh_cdar(desc);
if (gh_equal_p (gh_symbol2scm ("file"), symbol))
{
parse_from_file (data);
}
else
{
std::cout << "GridMapData: Unknown data type: '" << std::flush;
gh_display (symbol);
std::cout << "' with data: " << std::flush;
gh_display (data);
std::cout << std::endl;
return;
}
desc = gh_cdr (desc);
}
}
int vbucket_config_parse(VBUCKET_CONFIG_HANDLE handle,
vbucket_source_t data_source,
const char *data)
{
if (data_source == LIBVBUCKET_SOURCE_FILE) {
return parse_from_file(handle, data);
} else {
return parse_from_memory(handle, data);
}
}
int vbucket_config_parse2(VBUCKET_CONFIG_HANDLE handle,
vbucket_source_t data_source,
const char *data,
const char *peername)
{
handle->localhost = peername;
handle->nlocalhost = peername ? strlen(peername) : 0;
if (data_source == LIBVBUCKET_SOURCE_FILE) {
return parse_from_file(handle, data);
} else {
return parse_from_memory(handle, data);
}
}
int main(int an, char **ac) {
struct xmlnode *scene, *hypervisor, *mmu, *map, *guest;
char fn[128];
uint64_t i, j;
if (an != 2) {
fprintf(stderr, "ERROR: need build directory argument.\n");
return 1;
}
sprintf(fn, "%s/scenario_p_laidout.xml", ac[1]);
scene = parse_from_file(fn, STRUCT_SCENARIO);
if (!scene) {
fprintf(stderr, "ERROR: could not load scenario: %s.\n", xml_errormsg);
return 1;
}
// ---------------------------------------------------------------------------
hypervisor = get_child(scene, STRUCT_HYPERVISOR);
mmu = get_child(hypervisor, STRUCT_MMU);
iterate_over_children(i, mmu, STRUCT_MAP, map) {
if (strcmp(map->attrs[MAP_ATTR_XREF].value.string, "core_rx") == 0) {
globals_window[0] = get_dict_hex(map->attrs + MAP_ATTR_BASE, 0);
break;
}
}
globals_window[1] = ~0UL;
prepare_map(scene, mmu);
layout_map_fixmaps(scene, mmu);
layout_map(scene, mmu, -1);
for (i = 0; i < hypervisor->attrs[HYPERVISOR_ATTR_NCPUS].value.number; i++) {
struct range *Rclone = clone_range(map_range);
layout_map(scene, mmu, i);
map_range = Rclone;
}
map_range = NULL;
iterate_over_children(i, scene, STRUCT_GUEST, guest) {
mmu = get_child(guest, STRUCT_MMU);
iterate_over_children(j, mmu, STRUCT_MAP, map) {
if (!attr_exists(map->attrs + MAP_ATTR_BASE)) {
fprintf(stderr, "ERROR: no dynamic placement for guests.\n");
return 1;
}
}
}
/**
* \brief Main entry of the program
* \details The 2 variables \b argc and \b argv are used for extracting
* command line parameters.
* \param argc Number of arguments, at least one as \b argv contains at least the program's name.
* \param argv[] Array of character strings containing the arguments.
* \return On exit returns EXIT_SUCCESS, EXIT_FAILURE otherwise.
*/
int main(int argc, char** argv)
{
/* arguments parsing, we need at least "prog_name -i an_input_file"
* prints some more instructions if needed
*/
if (argc < 3)
{
fprintf(stdout,"[Info] No input file ! \n");
help(argv);
return EXIT_SUCCESS;
}
uint32_t i;
char seed[128] = "";
char inpf[FILENAME_MAX] = "";
DATA dat ;
SPDAT spdat = {5,5,0.5,NULL,0};
ATOM *at = NULL;
// function pointers for energy and gradient, and trajectory
get_ENER = NULL;
get_DV = NULL;
write_traj= &(write_dcd);
// arguments parsing
for (i=1; i<(uint32_t)argc; i++)
{
// get name of input file
if (!strcasecmp(argv[i],"-i"))
{
sprintf(inpf,"%s",argv[++i]);
}
// get user specified seed, 128 characters max, keep it as a string for the moment
else if (!strcasecmp(argv[i],"-seed"))
{
sprintf(seed,"%s",argv[++i]);
}
// reopen stdout to user specified file
else if (!strcasecmp(argv[i],"-o"))
{
freopen(argv[++i],"w",stdout);
is_stdout_redirected = 1 ;
}
// specify the logging level
else if (!strcasecmp(argv[i],"-log"))
{
if (!strcasecmp(argv[++i],"no"))
{
LOG_SEVERITY = LOG_NOTHING;
}
else if (!strcasecmp(argv[i],"err"))
{
LOG_SEVERITY = LOG_ERROR;
}
else if (!strcasecmp(argv[i],"warn"))
{
LOG_SEVERITY = LOG_WARNING;
}
else if (!strcasecmp(argv[i],"info"))
{
LOG_SEVERITY = LOG_INFO;
}
else if (!strcasecmp(argv[i],"dbg"))
{
LOG_SEVERITY = LOG_DEBUG;
}
else
fprintf(stdout,"[Warning] Unknown log level '%s' : default value used.\n\n",argv[i]);
}
#ifdef _OPENMP
// if compiled with openMP the user can specify a maximum number of cpus to use
// check if it is not higher than the real amount of cpus
else if (!strcasecmp(argv[i],"-np"))
{
nthreads=atoi(argv[++i]);
ncpus=omp_get_num_procs();
(nthreads < ncpus) ? omp_set_num_threads(nthreads) : omp_set_num_threads(ncpus);
//omp_set_num_threads(nthreads);
}
#endif
// print help and proper exit
else if ( !strcasecmp(argv[i],"-h") || !strcasecmp(argv[i],"-help") || !strcasecmp(argv[i],"--help") )
{
help(argv);
return EXIT_SUCCESS;
}
// error if unknown command line option
else
{
fprintf(stdout,"[Error] Argument '%s' is unknown.\n",argv[i]);
help(argv);
exit(-2);
}
}
//prepare log files if necessary
init_logfiles();
// Print date and some env. variables
fprintf(stdout,"Welcome to %s ! Command line arguments succesfully parsed, now intialising parameters...\n\n",argv[0]);
fprintf(stdout,"Logging level is : %s : see the documentation to see which .log files are generated, and what they contain.\n\n",get_loglevel_string());
fprintf(stdout,"Now printing some local informations : \n");
fprintf(stdout,"DATE : %s\n",get_time());
fprintf(stdout,"HOSTNAME : %s\n",getenv("HOSTNAME"));
fprintf(stdout,"USER : %s\n",getenv("USER"));
fprintf(stdout,"PWD : %s\n",getenv("PWD"));
/*
* Random numbers can be generated by using the standard functions from the C library (no guarantee on the quality)
* or by using the dSFMT generator (default, extremely stable, no redudancy )
* if STDRAND is defined we use the C library.
*
* Random numbers are stored in a double array dat.rn, of size dat.nrn
*
* If no string seed was passed by command line we generate one by using the unix timestamp
* -For STDRAND, this is directly used for srand()
* -For dSFMT, an array of integers generated by using the string seed is sent to dsfmt_init_by_array
*
*/
if (!strlen(seed))
sprintf(seed,"%d",(uint32_t)time(NULL)) ;
LOG_PRINT(LOG_INFO,"seed = %s \n",seed);
dat.nrn = 2048 ;
dat.rn = calloc(dat.nrn,sizeof dat.rn);
#ifdef STDRAND
srand( (uint32_t)labs(atol(seed)) );
#else
dat.seeds = calloc(strlen(seed),sizeof dat.seeds);
for (i=0; i<(uint32_t)strlen(seed); i++)
dat.seeds[i] = (uint32_t) seed[i] << 8;
for (i=0; i<(uint32_t)strlen(seed); i++)
dat.seeds[i] *= (dat.seeds[strlen(seed)-1]+i+1);
dsfmt_init_by_array(&(dat.dsfmt),dat.seeds,(int32_t)strlen(seed));
for (i=0; i<(uint32_t)strlen(seed); i++)
{
LOG_PRINT(LOG_INFO,"dat.seeds[%d] = %d \n",strlen(seed)-1-i,dat.seeds[strlen(seed)-1-i]);
}
#endif
// parse input file, initialise atom list
parse_from_file(inpf,&dat,&spdat,&at);
// set the pointer to the default V and dV functions
if(get_ENER==NULL)
get_ENER = &(get_LJ_V);
if(get_DV==NULL)
get_DV = &(get_LJ_DV);
// allocate arrays used by energy minimisation function
alloc_minim(&dat);
// sum up parameters to output file
#ifdef _OPENMP
fprintf(stdout,"\nStarting program with %d threads (%d cpus available)\n\n",nthreads,ncpus);
#else
fprintf(stdout,"\nStarting program in sequential mode\n\n");
#endif
fprintf(stdout,"Seed = %s \n\n",seed);
if (get_ENER==&(get_LJ_V))
fprintf(stdout,"Using L-J potential\n");
else if (get_ENER==&(get_AZIZ_V))
fprintf(stdout,"Using Aziz potential\n");
#ifdef LUA_PLUGINS
else if (get_ENER==&(get_lua_V))
fprintf(stdout,"Using plugin pair potential\n");
else if (get_ENER==&(get_lua_V_ffi))
fprintf(stdout,"Using plugin ffi potential\n");
#endif
if (charmm_units)
fprintf(stdout,"Using CHARMM units.\n\n");
else
fprintf(stdout,"Using REDUCED units.\n\n");
fprintf(stdout,"Energy saved each %d steps in file %s\n",io.esave,io.etitle);
fprintf(stdout,"Trajectory saved each %d steps in file %s\n",io.trsave,io.trajtitle);
fprintf(stdout,"Initial configuration saved in file %s\n",io.crdtitle_first);
fprintf(stdout,"Final configuration saved in file %s\n\n",io.crdtitle_last);
// get values of best minima for several well known LJ clusters
getValuesFromDB(&dat);
// set the inverse temperature depending of the type of units used
if (charmm_units)
dat.beta = 1.0/(KBCH*dat.T);
else
dat.beta = 1.0/(dat.T);
// again print parameters
fprintf(stdout,"method = %s\n",dat.method);
fprintf(stdout,"natom = %d\n",dat.natom);
fprintf(stdout,"nsteps = %"PRIu64"\n",dat.nsteps);
fprintf(stdout,"T = %lf \n",dat.T);
fprintf(stdout,"beta = %lf\n",dat.beta);
if(dat.d_max_when==0)
fprintf(stdout,"dmax = %lf (fixed) \n\n",dat.d_max);
else
fprintf(stdout,"dmax = %4.2lf updated each %d steps for "
"targeting %4.2lf %% of acceptance \n\n",dat.d_max,dat.d_max_when,dat.d_max_tgt);
// then depending of the type of simulation run calculation
if (strcasecmp(dat.method,"metrop")==0)
{
start_classic(&dat,at);
}
else if (strcasecmp(dat.method,"spav")==0)
{
start_spav(&dat,&spdat,at);
}
else
{
LOG_PRINT(LOG_ERROR,"Method [%s] unknowm.\n",dat.method);
free(dat.rn);
#ifndef STDRAND
free(dat.seeds);
#endif
exit(-3);
}
#ifdef __unix__
// compatible with some unixes-like OS: the struct rusage communicates with the kernel directly.
struct rusage infos_usage;
getrusage(RUSAGE_SELF,&infos_usage);
fprintf(stdout,"Maximum amount of memory used in kBytes is : %ld\n",infos_usage.ru_maxrss);
fprintf(stdout,"Execution time in Seconds : %lf\n",
(double)infos_usage.ru_utime.tv_sec+(double)infos_usage.ru_utime.tv_usec/1000000.0 +
(double)infos_usage.ru_stime.tv_sec+(double)infos_usage.ru_stime.tv_usec/1000000.0
);
#endif
fprintf(stdout,"End of program\n");
// free memory and exit properly
free(dat.rn);
#ifndef STDRAND
free(dat.seeds);
#endif
free(at);
dealloc_minim();
#ifdef LUA_PLUGINS
end_lua();
#endif //LUA_PLUGINS
// closing log files is the last thing to do as errors may occur at the end
close_logfiles();
return EXIT_SUCCESS;
}
