/* * Open the netcdf file, read all dimension and variable IDs, close.
* Return the number of frames in the file.
*/
int Traj_AmberNetcdf::setupTrajin(std::string const& fname, Topology* trajParm)
{
filename_.SetFileNameWithExpansion( fname );
if (openTrajin()) return TRAJIN_ERR;
// Sanity check - Make sure this is a Netcdf trajectory
if ( GetNetcdfConventions() != NC_AMBERTRAJ ) {
mprinterr("Error: Netcdf file %s conventions do not include \"AMBER\"\n",filename_.base());
return TRAJIN_ERR;
}
// Get global attributes
std::string attrText = GetAttrText("ConventionVersion");
if ( attrText != "1.0")
mprintf("Warning: Netcdf file %s has ConventionVersion that is not 1.0 (%s)\n",
filename_.base(), attrText.c_str());
// Get title
SetTitle( GetAttrText("title") );
// Get Frame info
if ( SetupFrame()!=0 ) return TRAJIN_ERR;
// Setup Coordinates/Velocities
if ( SetupCoordsVelo()!=0 ) return TRAJIN_ERR;
SetVelocity( HasVelocities() );
// Check that specified number of atoms matches expected number.
if (Ncatom() != trajParm->Natom()) {
mprinterr("Error: Number of atoms in NetCDF file %s (%i) does not\n",
filename_.base(),Ncatom());
mprinterr(" match number in associated parmtop (%i)!\n",trajParm->Natom());
return TRAJIN_ERR;
}
// Setup Time
if ( SetupTime()!=0 ) return TRAJIN_ERR;
// Box info
double boxcrd[6];
if (SetupBox(boxcrd, NC_AMBERTRAJ) == 1) // 1 indicates an error
return TRAJIN_ERR;
SetBox( boxcrd );
// Replica Temperatures - Allowed to fail silently
if (SetupTemperature() == 0)
SetTemperature( true );
// Replica Dimensions
if ( SetupMultiD() == -1 ) return TRAJIN_ERR;
// NOTE: TO BE ADDED
// labelDID;
//int cell_spatialDID, cell_angularDID;
//int spatialVID, cell_spatialVID, cell_angularVID;
// Amber Netcdf coords are float. Allocate a float array for converting
// float to/from double.
if (Coord_ != 0) delete[] Coord_;
Coord_ = new float[ Ncatom3() ];
if (Veloc_ != 0) delete[] Veloc_;
if (velocityVID_ != -1)
Veloc_ = new float[ Ncatom3() ];
else
Veloc_ = 0;
if (debug_>1) NetcdfDebug();
closeTraj();
// NetCDF files are always seekable
SetSeekable( true );
return Ncframe();
}
/* * Open the netcdf file, read all dimension and variable IDs, close.
* Return the number of frames in the file.
*/
int Traj_AmberNetcdf::setupTrajin(FileName const& fname, Topology* trajParm)
{
filename_ = fname;
if (openTrajin()) return TRAJIN_ERR;
readAccess_ = true;
// Sanity check - Make sure this is a Netcdf trajectory
if ( GetNetcdfConventions() != NC_AMBERTRAJ ) {
mprinterr("Error: Netcdf file %s conventions do not include \"AMBER\"\n",filename_.base());
return TRAJIN_ERR;
}
// Get global attributes
std::string attrText = GetAttrText("ConventionVersion");
if ( attrText != "1.0")
mprintf("Warning: Netcdf file %s has ConventionVersion that is not 1.0 (%s)\n",
filename_.base(), attrText.c_str());
// Get title
SetTitle( GetAttrText("title") );
// Get Frame info
if ( SetupFrameDim()!=0 ) return TRAJIN_ERR;
if ( Ncframe() < 1 ) {
mprinterr("Error: Netcdf file is empty.\n");
return TRAJIN_ERR;
}
// Setup Coordinates/Velocities
if ( SetupCoordsVelo( useVelAsCoords_ )!=0 ) return TRAJIN_ERR;
// Check that specified number of atoms matches expected number.
if (Ncatom() != trajParm->Natom()) {
mprinterr("Error: Number of atoms in NetCDF file %s (%i) does not\n"
"Error: match number in associated parmtop (%i)!\n",
filename_.base(), Ncatom(), trajParm->Natom());
return TRAJIN_ERR;
}
// Setup Time - FIXME: Allowed to fail silently
SetupTime();
// Box info
double boxcrd[6];
if (SetupBox(boxcrd, NC_AMBERTRAJ) == 1) // 1 indicates an error
return TRAJIN_ERR;
// Replica Temperatures - FIXME: Allowed to fail silently
SetupTemperature();
// Replica Dimensions
ReplicaDimArray remdDim;
if ( SetupMultiD(remdDim) == -1 ) return TRAJIN_ERR;
// Set traj info: FIXME - no forces yet
SetCoordInfo( CoordinateInfo(remdDim, Box(boxcrd), HasVelocities(),
HasTemperatures(), HasTimes(), false) );
// NOTE: TO BE ADDED
// labelDID;
//int cell_spatialDID, cell_angularDID;
//int spatialVID, cell_spatialVID, cell_angularVID;
// Amber Netcdf coords are float. Allocate a float array for converting
// float to/from double.
if (Coord_ != 0) delete[] Coord_;
Coord_ = new float[ Ncatom3() ];
if (debug_>1) NetcdfDebug();
closeTraj();
return Ncframe();
}
void main(void) //------------ Main Program ---------------------------------------------------------------
{
ADCON1 = 0x0F;
CMCON = 0x07;
lcd_init();
TRISA = 0b00110000; //Set PORTAs as outputs and inputs
version();//Show version number
Startup();//Startup
SetupTime(); //Get Time
SetupAlarmTimeA(); //Get Alarm Time for Subject A
SetupAlarmTimeB(); //Get Alarm Time for Subject B
SetupAlarmTimeC(); //Get Alarm Time for Subject C
SetupTimerInterruptRegisters();
while(1)
{
if(hour==hourA && minute==minuteA && AlarmAOff == 0)
{
//On Buzzer RA0 and LED RA1
PORTAbits.RA0 = 1;
PORTAbits.RA1 = 1;
while (PORTAbits.RA5 == 1); //when mute is pressed
AlarmAOff = 1;
}
else if(hour==hourB && minute==minuteB && AlarmBOff == 0)
{
//On Buzzer RA0 and LED RA2
PORTAbits.RA0 = 1;
PORTAbits.RA2 = 1;
while (PORTAbits.RA5 == 1); //when mute is pressed
AlarmBOff = 1;
}
else if(hour==hourC && minute==minuteC && AlarmC2Off == 0)
{
//On Buzzer RA0 and LED RA3
PORTAbits.RA0 = 1;
PORTAbits.RA3 = 1;
while (PORTAbits.RA5 == 1); //when mute is pressed
AlarmC2Off = 1;
}
else
{
PORTA = 0b00000000; //Off Buzzer and All LEDS at start
}
}
}
/** Set up netcdf restart file for reading, get all variable and dimension IDs.
* Also check number of atoms against associated parmtop.
*/
int Traj_AmberRestartNC::setupTrajin(std::string const& fname, Topology* trajParm)
{
filename_.SetFileNameWithExpansion( fname );
if (openTrajin()) return TRAJIN_ERR;
// Sanity check - Make sure this is a Netcdf restart
if ( GetNetcdfConventions() != NC_AMBERRESTART ) {
mprinterr("Error: Netcdf restart file %s conventions do not include \"AMBERRESTART\"\n",
filename_.base());
return TRAJIN_ERR;
}
// Get global attributes
std::string attrText = GetAttrText("ConventionVersion");
if (attrText!="1.0")
mprintf("Warning: Netcdf restart file %s has ConventionVersion that is not 1.0 (%s)\n",
filename_.base(), attrText.c_str());
// Get title
SetTitle( GetAttrText("title") );
// Setup Coordinates/Velocities
if ( SetupCoordsVelo()!=0 ) return TRAJIN_ERR;
SetVelocity( HasVelocities() );
// Check that specified number of atoms matches expected number.
if (Ncatom() != trajParm->Natom()) {
mprinterr("Error: Number of atoms in NetCDF restart file %s (%i) does not\n",
filename_.base(), Ncatom());
mprinterr(" match number in associated parmtop (%i)!\n",trajParm->Natom());
return TRAJIN_ERR;
}
// Setup Time
if ( SetupTime()!=0 ) return TRAJIN_ERR;
// Box info
double boxcrd[6];
if (SetupBox(boxcrd, NC_AMBERRESTART) == 1) // 1 indicates an error
return TRAJIN_ERR;
SetBox( boxcrd );
// Replica Temperatures - allowed to fail silently
if (SetupTemperature() == 0)
SetTemperature( true );
if ( SetupMultiD() == -1 ) return TRAJIN_ERR;
// NOTE: TO BE ADDED
// labelDID;
//int cell_spatialDID, cell_angularDID;
//int spatialVID, cell_spatialVID, cell_angularVID;
closeTraj();
// Only 1 frame for NC restarts
return 1;
}
// Traj_NcEnsemble::setupTrajin()
int Traj_NcEnsemble::setupTrajin(FileName const& fname, Topology* trajParm)
{
# ifdef MPI
if (NoPnetcdf()) return TRAJIN_ERR;
# endif
readAccess_ = true;
filename_ = fname;
//if (openTrajin()) return TRAJIN_ERR;
// Open single thread for now
if (NC_openRead( filename_.Full() )) return TRAJIN_ERR;
// Sanity check - Make sure this is a Netcdf ensemble trajectory
if ( GetNetcdfConventions() != NC_AMBERENSEMBLE ) {
mprinterr("Error: Netcdf file %s conventions do not include \"AMBERENSEMBLE\"\n",
filename_.base());
return TRAJIN_ERR;
}
// This will warn if conventions are not 1.0
CheckConventionsVersion();
// Get title
SetTitle( GetNcTitle() );
// Get Frame info
if ( SetupFrameDim()!=0 ) return TRAJIN_ERR;
if ( Ncframe() < 1 ) {
mprinterr("Error: Netcdf file is empty.\n");
return TRAJIN_ERR;
}
// Get ensemble info
int ensembleSize = SetupEnsembleDim();
if (ensembleSize < 1) {
mprinterr("Error: Could not get ensemble dimension info.\n");
return TRAJIN_ERR;
}
// Setup Coordinates/Velocities
if ( SetupCoordsVelo( useVelAsCoords_, useFrcAsCoords_ )!=0 ) return TRAJIN_ERR;
// Check that specified number of atoms matches expected number.
if (Ncatom() != trajParm->Natom()) {
mprinterr("Error: Number of atoms in NetCDF file %s (%i) does not\n"
"Error: match number in associated parmtop (%i)!\n",
filename_.base(), Ncatom(), trajParm->Natom());
return TRAJIN_ERR;
}
// Setup Time - FIXME: Allowed to fail silently
SetupTime();
// Box info
Box nc_box;
if (SetupBox(nc_box, NC_AMBERENSEMBLE) == 1) // 1 indicates an error
return TRAJIN_ERR;
// Replica Temperatures - FIXME: Allowed to fail silently
SetupTemperature();
// Replica Dimensions
ReplicaDimArray remdDim;
if ( SetupMultiD(remdDim) == -1 ) return TRAJIN_ERR;
// Set traj info: FIXME - no forces yet
SetCoordInfo( CoordinateInfo(ensembleSize, remdDim, nc_box, HasVelocities(),
HasTemperatures(), HasTimes(), false) );
if (debug_>1) NetcdfDebug();
//closeTraj();
// Close single thread for now
NC_close();
// Set up local ensemble parameters
# ifdef MPI
ensembleStart_ = Parallel::World().Rank();
ensembleEnd_ = Parallel::World().Rank() + 1;
# else
ensembleStart_ = 0;
ensembleEnd_ = ensembleSize;
# endif
// DEBUG: Print info for all ranks
WriteVIDs();
// Allocate float array
if (Coord_ != 0) delete[] Coord_;
Coord_ = new float[ Ncatom3() ];
return Ncframe();
}
void main(void)
{
#ifdef CAN_OPEN_ENABLE
BYTE i;
#endif
//===================================
//#if ((BUFFER_LEN_UART>1000)||(COUNT_UART_BUF>4))
InitWatchDog();
//#endif
I2C_Init(0);
I2C_Init(1);
InitUART(0);
SetupTime();
InitReloadTimer0();
InitServiceUart0();
InitIrqLevels();
__set_il(7); /* allow all levels */
__EI(); /* globally enable interrupts */
//===================================
InitProgrammVar();
//===================================
if(INIT_BLOK!=NULL)
INIT_BLOK();
//===================================
#ifdef CAN_OPEN_ENABLE
setState(Initialisation);
#else
SetupCAN(SPEED_CAN_0, SPEED_CAN_1, SPEED_CAN_2);
#endif
//===================================
#ifdef EN_SR_ZN_CYKL
add_timer(&TimerSrZnC);
#endif
#ifdef CASH_PDO_DATA
add_timer(&TimerCashCan);
#endif
puts((BYTE *)"===============================================================================\r\n");
puts((BYTE *)" Terminal Fujitsu MB96F338 \r\n");
puts((BYTE *)"===============================================================================\r\n$>");
while(1)
{
//========================================
clrwdt; // обнуление WatchDog таймера
//========================================
CyclicModules(); // цикличные операции выполняемые в каждом блоке
//========================================
if(DRIVER_BLOK!=NULL) // Функционал конкретного блока
DRIVER_BLOK();
//========================================
#ifdef CAN_OPEN_ENABLE
receiveMsgHandler(0);
receiveMsgHandler(1);
receiveMsgHandler(2);
DriverCanOpen();
#ifdef CASH_PDO_DATA
if(getTimer(&TimerCashCan)==0)
{
setTimer(&TimerCashCan, 30); // обновляем данные в объектном словаре 1 раз в 30 мс
for(i=0;i<30;i++) buildPDO_CASH(0x1800+i);
if(program.Cnt1WareDev == 0)
GetDataWare(0);
}
#endif
#endif
//========================================
#ifdef TERMINAL_EN
Terminal();
#endif
//========================================
// подсчёт среднего времени цикла в мкс
#ifdef EN_SR_ZN_CYKL
program.CountCikl_1s++;
if(getTimer(&TimerSrZnC)==0)
{
program.SrCikl_mks = 1000000/program.CountCikl_1s; // среднее значение цикла в мкс
program.CountCikl_1s = 0;
setTimer(&TimerSrZnC, 1000);
}
#endif
//========================================
}
}
