void PammObject::setup( const std::string& filename, const double& reg, const std::vector<std::string>& valnames,
const std::vector<bool>& pbcin, const std::vector<std::string>& imin, const std::vector<std::string>& imax,
std::string& errorstr ) {
IFile ifile; regulariser=reg;
if( !ifile.FileExist(filename) ) {
errorstr = "could not find file named " + filename;
return;
}
std::vector<std::unique_ptr<Value>> pos;
pbc.resize( valnames.size() );
min.resize( valnames.size() );
max.resize( valnames.size() );
for(unsigned i=0; i<valnames.size(); ++i) {
pbc[i]=pbcin[i]; min[i]=imin[i]; max[i]=imax[i];
pos.emplace_back( new Value() );
if( !pbc[i] ) pos[i]->setNotPeriodic();
else pos[i]->setDomain( min[i], max[i] );
}
ifile.open(filename); ifile.allowIgnoredFields(); kernels.resize(0);
for(unsigned k=0;; ++k) {
std::unique_ptr<KernelFunctions> kk = KernelFunctions::read( &ifile, false, valnames );
if( !kk ) break ;
kk->normalize( Tools::unique2raw( pos ) );
kernels.emplace_back( std::move(kk) );
ifile.scanField();
}
ifile.close();
}
void PlumedMain::readInputFile(std::string str) {
plumed_assert(initialized);
log.printf("FILE: %s\n",str.c_str());
IFile ifile;
ifile.link(*this);
ifile.open(str);
ifile.allowNoEOL();
std::vector<std::string> words;
while(Tools::getParsedLine(ifile,words) && words[0]!="ENDPLUMED") readInputWords(words);
log.printf("END FILE: %s\n",str.c_str());
log.flush();
pilots=actionSet.select<ActionPilot*>();
}
IFile* open(const DeviceList& device_list, const Path& file, Mode mode) override
{
IFile* prev = createFile(device_list);
if (prev)
{
if (prev->open(file, mode))
{
return prev;
}
else
{
prev->release();
return nullptr;
}
}
return nullptr;
}
void testIO(unsigned nr, SocketEndpoint *ep)
{
IFile *ifile;
IFileIO *ifileio;
unsigned fsize = (unsigned)(((double)nr * (double)rs) / (1024.0 * 1024.0));
fflush(NULL);
fprintf(stdout,"\n");
fflush(NULL);
for(int j=0; j<2; j++)
{
if (j==0)
fprintf(stdout, "File size: %d (MB) Cache, ", fsize);
else
fprintf(stdout, "\nFile size: %d (MB) Nocache, ", fsize);
if (ep != NULL)
{
ifile = createRemoteFile(*ep, tmpfile);
fprintf(stdout, "Remote: (%s)\n", server.toCharArray());
}
else
{
ifile = createIFile(tmpfile);
fprintf(stdout, "Local:\n");
}
ifile->remove();
unsigned st = msTick();
IFEflags extraFlags = IFEcache;
if (j==1)
extraFlags = IFEnocache;
ifileio = ifile->open(IFOcreate, extraFlags);
unsigned iter = nr / 40;
__int64 pos = 0;
for (int i=0;i<nr;i++)
{
ifileio->write(pos, rs, record);
pos += rs;
if ((i % iter) == 0)
{
fprintf(stdout,".");
fflush(NULL);
}
}
ifileio->close();
double rsec = (double)(msTick() - st)/1000.0;
unsigned iorate = (unsigned)((double)fsize / rsec);
fprintf(stdout, "\nwrite - elapsed time = %6.2f (s) iorate = %4d (MB/s)\n", rsec, iorate);
st = msTick();
extraFlags = IFEcache;
if (j==1)
extraFlags = IFEnocache;
ifileio = ifile->open(IFOread, extraFlags);
pos = 0;
for (int i=0;i<nr;i++)
{
ifileio->read(pos, rs, record);
pos += rs;
if ((i % iter) == 0)
{
fprintf(stdout,".");
fflush(NULL);
}
}
ifileio->close();
rsec = (double)(msTick() - st)/1000.0;
iorate = (unsigned)((double)fsize / rsec);
fprintf(stdout, "\nread -- elapsed time = %6.2f (s) iorate = %4d (MB/s)\n", rsec, iorate);
ifileio->Release();
ifile->remove();
ifile->Release();
}
}
