bool CNSVariable::SetPrimVar_Compressible(double eddy_visc, double turb_ke, CFluidModel *FluidModel) {
unsigned short iVar;
bool check_dens = false, check_press = false, check_sos = false, check_temp = false, RightVol = true;
SetVelocity(); // Computes velocity and velocity^2
double density = GetDensity();
double staticEnergy = GetEnergy()-0.5*Velocity2 - turb_ke;
/* check will be moved inside fluid model plus error description strings*/
FluidModel->SetTDState_rhoe(density, staticEnergy);
check_dens = SetDensity();
check_press = SetPressure(FluidModel->GetPressure());
check_sos = SetSoundSpeed(FluidModel->GetSoundSpeed2());
check_temp = SetTemperature(FluidModel->GetTemperature());
/*--- Check that the solution has a physical meaning ---*/
if (check_dens || check_press || check_sos || check_temp) {
/*--- Copy the old solution ---*/
for (iVar = 0; iVar < nVar; iVar++)
Solution[iVar] = Solution_Old[iVar];
/*--- Recompute the primitive variables ---*/
SetVelocity(); // Computes velocity and velocity^2
double density = GetDensity();
double staticEnergy = GetEnergy()-0.5*Velocity2 - turb_ke;
/* check will be moved inside fluid model plus error description strings*/
FluidModel->SetTDState_rhoe(density, staticEnergy);
check_dens = SetDensity();
check_press = SetPressure(FluidModel->GetPressure());
check_sos = SetSoundSpeed(FluidModel->GetSoundSpeed2());
check_temp = SetTemperature(FluidModel->GetTemperature());
RightVol = false;
}
/*--- Set enthalpy ---*/
SetEnthalpy(); // Requires pressure computation.
/*--- Set laminar viscosity ---*/
SetLaminarViscosity(FluidModel->GetLaminarViscosity(FluidModel->GetTemperature(), GetDensity()));
/*--- Set eddy viscosity ---*/
SetEddyViscosity(eddy_visc);
return RightVol;
}
bool CNSVariable::SetPrimVar_Compressible(double eddy_visc, double turb_ke, CConfig *config) {
unsigned short iVar;
bool check_dens = false, check_press = false, check_sos = false, check_temp = false, RightVol = true;
double Gas_Constant = config->GetGas_ConstantND();
double Gamma = config->GetGamma();
SetVelocity(); // Computes velocity and velocity^2
check_dens = SetDensity(); // Check the density
check_press = SetPressure(Gamma, turb_ke); // Requires velocity2 computation.
check_sos = SetSoundSpeed(Gamma); // Requires pressure computation.
check_temp = SetTemperature(Gas_Constant); // Requires pressure computation.
/*--- Check that the solution has a physical meaning ---*/
if (check_dens || check_press || check_sos || check_temp) {
/*--- Copy the old solution ---*/
for (iVar = 0; iVar < nVar; iVar++)
Solution[iVar] = Solution_Old[iVar];
/*--- Recompute the primitive variables ---*/
SetVelocity();
check_dens = SetDensity();
check_press = SetPressure(Gamma, turb_ke);
check_sos = SetSoundSpeed(Gamma);
check_temp = SetTemperature(Gas_Constant);
RightVol = false;
}
/*--- Set enthalpy ---*/
SetEnthalpy(); // Requires pressure computation.
/*--- Set laminar viscosity ---*/
SetLaminarViscosity(config); // Requires temperature computation.
/*--- Set eddy viscosity ---*/
SetEddyViscosity(eddy_visc);
return RightVol;
}
/* * 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();
}
MPMBase::MPMBase(int elem,int theMatl,double angin)
{
int i;
inElem=elem;
mp=-1.; // calculated in PreliminaryCalcs, unless set in input file
matnum=theMatl;
SetAnglez0InDegrees(angin);
SetAngley0InDegrees(0.0);
SetAnglex0InDegrees(0.0);
// space to hold velocity fields
// these only change if there are cracks
vfld = (char *)malloc(maxShapeNodes*sizeof(char));
for(i=1; i<maxShapeNodes; i++)
vfld[i]=NO_CRACK;
// zero stresses and strains
ZeroTensor(&sp);
pressure = 0.;
ZeroTensor(&ep);
ZeroTensor(&eplast);
ZeroTensorAntisym(&wrot);
ZeroVector(&acc);
// zero energies
plastEnergy=0.;
dispEnergy=0.;
workEnergy=0.;
resEnergy=0.;
heatEnergy=0.;
entropy=0;
// for J integral if needed (on non-rigid only)
velGrad=NULL;
// material data is needed
matData=NULL;
// concentration (c units) and gradient (c units/mm)
pConcentration=0.;
pDiffusion=NULL;
// temperature (degrees) and gradient (degrees/mm)
SetTemperature(0.,0.);
pTemp=NULL;
// CPDI data
cpdi = NULL;
faceArea = NULL;
// PS - when point created, velocity and position and ext force should be set too
ZeroVector(&vel);
// counts crossing and sign is whether or not left the grid
elementCrossings=0;
// rotation matrix (when tracked)
Rtot = NULL;
}
void
init_clara()
{
at_32 n,handle;
C(GetAvailableCameras(&n));
C(GetCameraHandle(n-1,&handle));
C(SetCurrentCamera(handle));
C(Initialize("/usr/local/etc/andor"));
// C(SetTriggerMode(1 /*external*/));
C(SetTriggerMode(0 /*internal*/));
C(SetExposureTime(.001));
C(SetReadMode(4 /*image*/));
C(SetAcquisitionMode(1 /*single scan*/));
C(CoolerON());
C(SetADChannel(1 /*fast*/));
C(SetFastExtTrigger(1));
C(SetFrameTransferMode(1));
int h=512, w=512;
clara_h=h;
clara_w=w;
//C(SetIsolatedCropMode(1,h,w,1,1));
C(SetImage(1,1,1,w,1,h));
C(GetSizeOfCircularBuffer(&clara_circ_buf_size));
clara_buf=malloc(sizeof(*clara_buf)*
h*w*clara_circ_buf_size);
if(!clara_buf)
printf("can't allocate memory for pictures\n");
//C(SetAcquisitionMode(5 /*run till abort*/));
C(SetTemperature(-15));
}
void ANDOR885_Camera::setCoolerStat(int stat) throw(std::exception)
{
int errorValue;
if (stat == ANDOR_ON) {
if (coolerStat != ANDOR_ON) {
errorValue = SetTemperature(coolerSetpt);
throwError(errorValue, "Error setting cooler temperature");
errorValue = CoolerON();
throwError(errorValue, "Error turning on cooler");
coolerStat = ANDOR_ON;
}
}
else if (stat == ANDOR_OFF) {
if (coolerStat != ANDOR_OFF) {
errorValue = CoolerOFF();
throwError(errorValue, "Error turning off cooler");
coolerStat = ANDOR_OFF;
}
}
else {
throw ANDOR885_Exception("Unrecognized Cooler Status requested");
}
}
// Traj_AmberCoord::processWriteArgs()
int Traj_AmberCoord::processWriteArgs(ArgList& argIn) {
SetTemperature( argIn.hasKey("remdtraj") );
if (argIn.hasKey("highprecision")) {
outfmt_ = "%8.6lf";
highPrecision_ = true;
}
return 0;
}
// Traj_AmberRestartNC::processWriteArgs()
int Traj_AmberRestartNC::processWriteArgs(ArgList& argIn) {
// For write, assume we want velocities unless specified
SetVelocity(!argIn.hasKey("novelocity"));
SetTemperature(argIn.hasKey("remdtraj"));
time0_ = argIn.getKeyDouble("time0", 1.0);
dt_ = argIn.getKeyDouble("dt",1.0);
return 0;
}
void FGTank::ResetToIC(void)
{
SetTemperature( InitialTemperature );
SetStandpipe ( InitialStandpipe );
SetContents ( InitialContents );
PctFull = 100.0*Contents/Capacity;
SetPriority( InitialPriority );
CalculateInertias();
}
void FGTank::ResetToIC(void)
{
SetTemperature( InitialTemperature );
SetStandpipe ( InitialStandpipe );
SetContents ( InitialContents );
PctFull = 100.0*Contents/Capacity;
SetPriority( InitialPriority );
PreviousUsed = 0.0;
}
bool ANDOR885_Camera::deviceExit()
{
int errorValue;
bool error = false;
int temp;
//Stop Acquisition; ignore errors
AbortIfAcquiring();
//CloseShutter
shutterMode = SHUTTERMODE_CLOSE;
errorValue = SetShutter(ttl,shutterMode,closeTime,openTime);
printError(errorValue, "Shutter error", &error, ANDOR_ERROR);
int i = -1;
errorValue = IsCoolerOn(&i);
printError(errorValue, "Error determing cooler status", &error, ANDOR_ERROR);
if (!error) {
if (i == 1) {
GetTemperature(&temp);
if(temp < 5) {
coolerSetpt = 10;
}
errorValue = SetTemperature(coolerSetpt);
printError(errorValue, "Error setting cooler temperature", &error, ANDOR_ERROR);
}
if (!error) {
GetTemperature(&temp);
while(temp < 5) {
std::cerr << "Camera temperature rising...: " << temp << " deg C" << std::endl;
Sleep(2000);
GetTemperature(&temp);
}
}
if (i == 1){
errorValue=CoolerOFF(); // Switch off cooler (if used)
printError(errorValue, "Error switching cooler off", &error, ANDOR_ERROR);
if (!error) {
coolerStat = ANDOR_OFF;
}
}
}
errorValue = ShutDown();
printError(errorValue, "Error shutting down", &error, ANDOR_ERROR);
std::cerr << "Shutting down..." << std::endl;
initialized = false;
return error;
}
void ANDOR885_Camera::setCoolerSetpt(int setpt) throw(std::exception)
{
int errorValue;
if (setpt > maxTemp || setpt < minTemp) {
throw ANDOR885_Exception("Chosen temperature out of range.\n Temperature must be between "
+ STI::Utils::valueToString(minTemp) + " and " + STI::Utils::valueToString(maxTemp));
}
errorValue = SetTemperature(coolerSetpt);
throwError(errorValue, "Error setting cooler temperature");
coolerSetpt = setpt;
}
void
uninit_clara()
{
C(SetTemperature(temp_shutoff));
float t;
GetTemperatureF(&t);
while(fabsf(temp_shutoff-t)>5){
printf("temperature is %f should be %d\n",
t,temp_shutoff);
GetTemperatureF(&t);
sleep(5);
}
C(ShutDown());
}
vector<double> const& tWeightUpdateGradient::UpdateWeights(double newtemp,vector<double> const& gradient)
{
// cerr << "Updating weight for gradient\n";
// make sure we got all the gradients
assert(gradient.size()==OrigWeights().size());
cerr << "new temp = "<<newtemp<<endl;
SetTemperature(newtemp);
if ( newtemp == 0.0 )
return CurrentWeights();
vector<double>& prevWeights = PrevWeights();
vector<double> const& origWeights = OrigWeights();
double beta = _origDamping/newtemp;
double gamma = _prevDamping/newtemp;
double sfact = 1.0/(beta+gamma);
double bfact = beta*sfact;
double gfact = gamma*sfact;
double origsum = 0.0;
double maxw = -HUGE_VAL;
// go over the instances and update new weights
int i;
for ( i=0 ; i<prevWeights.size() ; i++ ) {
origsum += origWeights[i];
double weight = bfact*log(origWeights[i]) + gfact*log(prevWeights[i]) - sfact*_lRate*gradient[i];
prevWeights[i] = weight;
if ( weight > maxw )
maxw = weight;
}
// normalize
double wsum = 0.0;
for ( i=0 ; i<prevWeights.size() ; i++ ) {
prevWeights[i] -= maxw;
prevWeights[i] = exp(prevWeights[i]);
if ( prevWeights[i] < TINY )
prevWeights[i] = TINY;
wsum += prevWeights[i];
}
double f = origsum / wsum;
for ( i=0 ; i<prevWeights.size() ; i++ ) {
prevWeights[i] *= f;
cerr << "Weight " << i << "=" << prevWeights[i] << "("<<gradient[i]<<")"<<endl;
}
return CurrentWeights();
}
/** 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;
}
vector<double> const& tWeightUpdateRandom::UpdateWeights(double newtemp,vector<double> const& gradient)
{
// cerr << "Updating weight for random\n";
SetTemperature(newtemp);
if ( newtemp == 0.0 )
return CurrentWeights();
vector<double>& prevWeights = PrevWeights();
vector<double> const& origWeights = OrigWeights();
//mn130103 double scale = sqrt(newtemp);
double var = 1.0/newtemp;
double wsum = 0.0;
double origsum = 0.0;
int i;
// go over the instances and update new weights
for ( i=0 ; i<prevWeights.size() ; i++ ) {
//mn130103 double noise = 0.0;
double weight = 0.0;
// sampling is according to original weight
// This assumes original weights are whole numbers!!!
for ( int w=1 ; w <= origWeights[i] ; w++ )
weight += _RandomProbGenerator.SampleGamma(var) * newtemp;
if ( weight < TINY )
weight = TINY;
prevWeights[i] = weight;
origsum += origWeights[i];
wsum += weight;
}
// normalize
double fact = origsum / wsum;
for ( i=0 ; i<prevWeights.size() ; i++ ) {
prevWeights[i] *= fact;
// cerr << "Weight " << i << "=" << prevWeights[i] << endl;
}
return CurrentWeights();
}
bool ATIKCCD::ISNewSwitch(const char *dev, const char *name, ISState *states, char *names[], int n)
{
if (dev != nullptr && !strcmp(dev, getDeviceName()))
{
// Gain/Offset Presets
if (!strcmp(name, ControlPresetsSP.name))
{
int prevIndex = IUFindOnSwitchIndex(&ControlPresetsSP);
IUUpdateSwitch(&ControlPresetsSP, states, names, n);
int targetIndex = IUFindOnSwitchIndex(&ControlPresetsSP);
uint16_t value = static_cast<uint16_t>(targetIndex + 2);
uint8_t *data = reinterpret_cast<uint8_t*>(&value);
int rc = ArtemisCameraSpecificOptionSetData(hCam, ID_AtikHorizonGOPresetMode, data, 2);
if (rc != ARTEMIS_OK)
{
ControlPresetsSP.s = IPS_ALERT;
IUResetSwitch(&ControlPresetsSP);
ControlPresetsS[prevIndex].s = ISS_ON;
}
else
ControlPresetsSP.s = IPS_OK;
IDSetSwitch(&ControlPresetsSP, nullptr);
return true;
}
// Cooler controler
if (!strcmp(name, CoolerSP.name))
{
if (IUUpdateSwitch(&CoolerSP, states, names, n) < 0)
{
CoolerSP.s = IPS_ALERT;
IDSetSwitch(&CoolerSP, nullptr);
return true;
}
bool enabled = (CoolerS[COOLER_ON].s == ISS_ON);
// If user turns on cooler, but the requested temperature is higher than current temperature
// then we set temperature to zero degrees. If that was still higher than current temperature
// we return an error
if (enabled && TemperatureRequest > TemperatureN[0].value)
{
TemperatureRequest = 0;
// If current temperature is still lower than zero, then we shouldn't risk
// setting temperature to any arbitrary value. Instead, we report an error and ask
// user to explicitly set the requested temperature.
if (TemperatureRequest > TemperatureN[0].value)
{
CoolerS[COOLER_ON].s = ISS_OFF;
CoolerS[COOLER_OFF].s = ISS_OFF;
CoolerSP.s = IPS_ALERT;
LOGF_WARN("Cannot manually activate cooler since current temperature is %.2f. To activate cooler, request a lower temperature.", TemperatureN[0].value);
IDSetSwitch(&CoolerSP, nullptr);
return true;
}
SetTemperature(0);
return true;
}
return activateCooler(enabled);
}
}
return INDI::CCD::ISNewSwitch(dev, name, states, names, n);
}
// Traj_AmberNetcdf::processWriteArgs()
int Traj_AmberNetcdf::processWriteArgs(ArgList& argIn) {
SetTemperature(argIn.hasKey("remdtraj"));
SetVelocity(argIn.hasKey("velo"));
return 0;
}
KVHarpeeIC::KVHarpeeIC(UInt_t number, Float_t pressure, Float_t temp, Float_t thick) : KVVAMOSDetector(number, "C4H10")
{
// Make the ionisation chamber of Harpee composed by:
// - one 1.5 mylar window;
// - 3 volumes of C4H10 with thicknesses (2*dz): 2.068 cm, thick, 1.278 cm.
// By default thick=10.457 cm;
// Only the 2nd gaz volume is "active".
//
// The width (2*dx) of this detector is ??? and the height (2*dy) is ???.
// The ionisation chamber is closed with the silicon wall in Harpee.
//
// Input: pressure - pressure of the gaz in mbar
// temp - temperature of the gaz in degrees celsius.
// Default temperature = 19°C
// thick - the thickness in cm of the 2nd volume of gaz.
Warning("KVHarpeeIC", "Check if the width, the height and the thickness are correct in this constructor");
init();
SetType("CHI");
SetLabel("CHI");
SetName(GetArrayName());
// number of absorber
Int_t Nabs = 4;
// material of each absorber
const Char_t* mat[] = {"Myl", "C4H10", "C4H10", "C4H10"};
// thickness of each absorber
Float_t th[] = {
static_cast<Float_t>(1.5 * KVUnits::um),
static_cast<Float_t>(2.068 * KVUnits::cm),
static_cast<Float_t>(thick * KVUnits::cm),
static_cast<Float_t>(1.278 * KVUnits::cm)
};
// active absorber flag
Bool_t active[] = { kFALSE, kFALSE, kTRUE, kFALSE};
// width and height of the detector. TO BE VERIFIED
Float_t w = 40 * KVUnits::cm;
Float_t h = 12 * KVUnits::cm;
// total thickness of the detector
Float_t wtot = 0;
for (Int_t i = 0; i < Nabs; i++) wtot += th[i];
// pressure and temperature of the detector
SetPressure(pressure * KVUnits::mbar);
SetTemperature(temp);
// Adding the absorbers
TGeoShape* shape = NULL;
for (Int_t i = 0; i < Nabs; i++) {
Double_t dx = w / 2;
Double_t dy = h / 2;
Double_t dz = th[i] / 2;
fTotThick += th[i];
// box shape of the absorber
shape = new TGeoBBox(dx, dy, dz);
// build and position absorber in mother volume.
// Reference is the center of absorber
Double_t ztrans = dz - wtot / 2;
for (Int_t j = 0; j < Nabs - 1; j++) ztrans += (j < i) * th[j];
TGeoTranslation* tr = new TGeoTranslation(0., 0., ztrans);
AddAbsorber(mat[i], shape, tr, active[i]);
}
}
void FGStandardAtmosphere::SetTemperatureSL(double t, eTemperature unit)
{
SetTemperature(t, 0.0, unit);
}
// Traj_AmberCoord::setupTrajin()
int Traj_AmberCoord::setupTrajin(std::string const& fname, Topology* trajParm)
{
// Set up file for reading
if (file_.SetupRead( fname, debug_ )) return TRAJIN_ERR;
// Attempt to open the file. Read and set the title and titleSize
if ( file_.OpenFile() ) return TRAJIN_ERR;
std::string title = file_.GetLine();
// Allocate mem to read in frame (plus REMD header if present). REMD
// header is checked for when file is IDd. Title size is used in seeking.
natom3_ = trajParm->Natom() * 3;
file_.SetupFrameBuffer( natom3_, 8, 10, hasREMD_, title.size() );
if (debug_ > 0) {
mprintf("Each frame is %u bytes", file_.FrameSize());
if (hasREMD_ != 0) mprintf(" (including REMD header)");
mprintf(".\n");
}
// Read the first frame of coordinates
if ( file_.ReadFrame() == -1 ) {
mprinterr("Error in read of Coords frame 1 of trajectory %s.\n", file_.Filename().base());
return TRAJIN_ERR;
}
// Check for box coordinates. If present, update the frame size and
// reallocate the frame buffer.
Box boxInfo;
std::string nextLine = file_.GetLine();
if ( !nextLine.empty() ) {
if (debug_>0) rprintf("DEBUG: Line after first frame: (%s)\n", nextLine.c_str());
if ( IsRemdHeader(nextLine.c_str()) ) {
// REMD header - no box coords
numBoxCoords_ = 0;
} else {
double box[8];
numBoxCoords_ = sscanf(nextLine.c_str(), "%8lf%8lf%8lf%8lf%8lf%8lf%8lf%8lf",
box, box+1, box+2, box+3, box+4, box+5, box+6, box+7);
if (numBoxCoords_ == -1) {
mprinterr("Error: Could not read Box coord line of trajectory %s.",file_.Filename().base());
return TRAJIN_ERR;
} else if (numBoxCoords_ == 8) {
// Full line of coords was read, no box coords.
numBoxCoords_ = 0;
} else if (numBoxCoords_ == 3) {
// Box lengths only, ortho. or truncated oct. Use default parm angles.
box[3] = boxAngle_[0] = trajParm->ParmBox().Alpha();
box[4] = boxAngle_[1] = trajParm->ParmBox().Beta();
box[5] = boxAngle_[2] = trajParm->ParmBox().Gamma();
boxInfo.SetBox( box );
} else if (numBoxCoords_ == 6) {
// General triclinic. Set lengths and angles.
boxInfo.SetBox( box );
} else {
mprinterr("Error: Expect only 3 or 6 box coords, got %i\n", numBoxCoords_);
mprinterr("Error: Box line=[%s]\n", nextLine.c_str());
return TRAJIN_ERR;
}
}
// Reallocate frame buffer accordingly
file_.ResizeBuffer( numBoxCoords_ );
}
// Calculate Frames and determine seekable. If not possible and this is not a
// compressed file the trajectory is probably corrupted. Frames will
// be read until EOF.
int Frames = 0;
if (debug_>0)
rprintf("Title offset=%lu FrameSize=%lu UncompressedFileSize=%lu\n",
title.size(), file_.FrameSize(), file_.UncompressedSize());
off_t title_size = (off_t) title.size();
off_t frame_size = (off_t) file_.FrameSize();
off_t uncompressed_size = file_.UncompressedSize();
off_t file_size = uncompressed_size - title_size;
bool seekable = false;
if (file_.Compression() != CpptrajFile::NO_COMPRESSION) {
// -----==== AMBER TRAJ COMPRESSED ====------
// If the uncompressed size of compressed file is reported as <= 0,
// uncompressed size cannot be determined. Read coordinates until
// EOF.
if (uncompressed_size <= 0) {
mprintf("Warning: %s: Uncompressed size of trajectory could not be determined.\n",
file_.Filename().base());
if (file_.Compression() == CpptrajFile::BZIP2)
mprintf(" (This is normal for bzipped files)\n");
mprintf(" Number of frames could not be calculated.\n");
mprintf(" Frames will be read until EOF.\n");
Frames = TRAJIN_UNK;
seekable = false;
} else {
// Frame calculation for large gzip files
if (file_.Compression() == CpptrajFile::GZIP) {
// Since this is gzip compressed, if the file_size % frame size != 0,
// it could be that the uncompressed filesize > 4GB. Since
// ISIZE = uncompressed % 2^32,
// try ((file_size + (2^32 * i)) % frame_size) and see if any are 0.
if ( (file_size % frame_size) != 0) {
// Determine the maximum number of iterations to try based on the
// fact that Amber trajectories typically compress about 3x with
// gzip.
off_t tmpfsize = ((file_size * 4) - uncompressed_size) / 4294967296LL;
int maxi = (int) tmpfsize;
++maxi;
if (debug_>1)
mprintf("\tLooking for uncompressed gzip size > 4GB, %i iterations.\n",maxi);
tmpfsize = 0;
bool sizeFound = false;
for (int i = 0; i < maxi; i++ ) {
tmpfsize = (4294967296LL * i) + file_size;
if ( (tmpfsize % frame_size) == 0) {sizeFound=true; break;}
}
if (sizeFound) file_size = tmpfsize;
}
}
if ((file_size % frame_size) == 0) {
Frames = (int) (file_size / frame_size);
seekable = true;
} else {
mprintf("Warning: %s: Number of frames in compressed traj could not be determined.\n",
file_.Filename().base());
mprintf(" Frames will be read until EOF.\n");
Frames = TRAJIN_UNK;
seekable=false;
}
}
} else {
// ----==== AMBER TRAJ NOT COMPRESSED ====----
Frames = (int) (file_size / frame_size);
if ( (file_size % frame_size) == 0 ) {
seekable = true;
} else {
mprintf("Warning: %s: Could not accurately predict # frames. This usually \n",
file_.Filename().base());
mprintf(" indicates a corrupted trajectory. Will attempt to read %i frames.\n",
Frames);
seekable=false;
}
}
if (debug_>0)
rprintf("Atoms: %i FrameSize: %lu TitleSize: %lu NumBox: %i Seekable: %i Frames: %i\n\n",
trajParm->Natom(), frame_size, title_size, numBoxCoords_, (int)seekable, Frames);
// Close the file
file_.CloseFile();
// Set trajectory info
SetBox( boxInfo );
SetTemperature( hasREMD_ != 0 );
SetTitle( title );
SetSeekable( seekable );
return Frames;
}
//------------------------------------------------------------------------------
// FUNCTION NAME: InitializeCamera()
//
// RETURNS: If the function terminates before entering the message loop,
// return FALSE.
// Otherwise, return the WPARAM value sent by the WM_QUIT
// message.
//
// LAST MODIFIED: PMcK 11/11/98
//
// DESCRIPTION: calls initialization function, processes message loop
//
// Windows recognizes this function by name as the initial
// entry point for the program. This function calls the
// application initialization routine, if no other instance of
// the program is running, and always calls the instance
// initialization routine. It then executes a message
// retrieval and dispatch loop that is the top-level control
// structure for the remainder of execution. The loop is
// terminated when a WM_QUIT message is received, at which
// time this function exits the application instance by
// returning the value passed by PostQuitMessage().
//
// If the function must abort before entering the message loop,
// it returns the conventional value NULL.
//
//
// ARGUMENTS: hInstance - The handle to the instance of this application
// that is currently being executed.
//
// hPrevInstance - The handle to the instance of this
// application that was last executed. If this is the only
// instance of this application executing, hPrevInstance is
// NULL. In Win32 applications, this parameter is always NULL.
//
// lpCmdLine - A pointer to a null terminated string specifying
// the command line of the application.
//
// nCmdShow - Specifies how the main window is to be diplayed.
//------------------------------------------------------------------------------
bool ANDOR885_Camera::InitializeCamera()
{
AndorCapabilities caps;
char aBuffer[256];
int errorValue;
bool errorFlag = false;
// int test,test2; //need to pause while camera initializes
float speed, STemp, gain;
int iSpeed, nAD, nAmp, nPreAmp, index, IsPreAmpAvailable;
int i;
caps.ulSize = sizeof(AndorCapabilities);
long numCameras;
GetAvailableCameras(&numCameras);
GetCurrentDirectoryA(256,aBuffer);// Look in current working directory
// for driver files. Note: had to override usual mapping of GetCurrentDirectory to
// GetCurrentDirectoryW because of mismatch of argument types.
errorValue=Initialize(aBuffer); // Initialize driver in current directory
printError(errorValue, "Initialize error", &errorFlag, ANDOR_ERROR);
if (errorFlag)
return true;
// Get camera capabilities
errorValue=GetCapabilities(&caps);
printError(errorValue, "Get Andor Capabilities information Error", &errorFlag, ANDOR_ERROR);
// Get Head Model
errorValue=GetHeadModel(model);
printError(errorValue, "Get Head Model information Error", &errorFlag, ANDOR_ERROR);
// Get detector information
errorValue=GetDetector(&imageWidth,&imageHeight);
printError(errorValue, "Get Detector information Error", &errorFlag, ANDOR_ERROR);
// Set frame transfer mode
errorValue=SetFrameTransferMode((frameTransfer == ANDOR_ON) ? 1 : 0);
printError(errorValue, "Set Frame Transfer Mode Error", &errorFlag, ANDOR_ERROR);
// Set acquisition mode to required setting specified in xxxxWndw.c
errorValue=SetAcquisitionMode(acquisitionMode);
printError(errorValue, "Set Acquisition Mode Error", &errorFlag, ANDOR_ERROR);
if(caps.ulGetFunctions > 32)
{
GetEMCCDGain(&EMCCDGain);
}
if(readMode == READMODE_IMAGE) {
// This function only needs to be called when acquiring an image. It sets
// the horizontal and vertical binning and the area of the image to be
// captured. In this example it is set to 1x1 binning and is acquiring the
// whole image
SetImage(1,1,1,imageWidth,1,imageHeight);
}
// Set read mode to required setting specified in xxxxWndw.c
errorValue=SetReadMode(readMode);
printError(errorValue, "Set Read Mode Error", &errorFlag, ANDOR_ERROR);
// Set Vertical speed to max
/* STemp = 0;
VSnumber = 0;
GetNumberVSSpeeds(&index);
for(iSpeed=0; iSpeed<index; iSpeed++){
GetVSSpeed(iSpeed, &speed);
if(speed > STemp){
STemp = speed;
VSnumber = iSpeed;
}
}
errorValue=SetVSSpeed(VSnumber);
printError(errorValue, "Set Vertical Speed Error", &errorFlag, ANDOR_ERROR);
*/
if (!notDestructed){
STemp = 0;
GetNumberVSSpeeds(&index);
for(iSpeed=0; iSpeed < index; iSpeed++){
GetVSSpeed(iSpeed, &speed);
verticalShiftSpeed_t.choices[iSpeed] = STI::Utils::valueToString(speed);
if(speed > STemp){
STemp = speed;
verticalShiftSpeed = iSpeed;
}
}
verticalShiftSpeed_t.initial = (--verticalShiftSpeed_t.choices.end())->second;
}
errorValue = SetVSSpeed(verticalShiftSpeed);
printError(errorValue, "Set Vertical Speed Error", &errorFlag, ANDOR_ERROR);
/* Set Vertical Clock Voltage;
note: only the fastest vertical shift speeds will benefit from the higher clock voltage;
increasing clock voltage adds noise.
*/
if (!notDestructed) {
index = 0;
errorValue = GetNumberVSAmplitudes(&index);
if (errorValue == DRV_SUCCESS) {
for (i = 0; i < index; i++){
if (i == 0){
verticalClockVoltage_t.choices[i] = "Normal";
} else {
verticalClockVoltage_t.choices[i] = STI::Utils::valueToString(i);
}
}
verticalClockVoltage_t.initial = (verticalClockVoltage_t.choices.begin())->second;
}
}
errorValue = SetVSAmplitude(0);
printError(errorValue, "Set Vertical Clock Voltage Error", &errorFlag, ANDOR_ERROR);
// Set Horizontal Speed to max and check bit depth
//(scan over all possible AD channels; although, the 885 has only one 14-bit channel)
STemp = 0;
// HSnumber = 0;
ADnumber = 0;
if (!notDestructed) {
errorValue = GetNumberADChannels(&nAD);
if (errorValue != DRV_SUCCESS){
std::cerr << "Get number AD Channel Error\n";
errorFlag = true;
}
else if (nAD != 1) {
std::cerr << "Expect 1 AD channel for this camera. The following code will miss channels\n";
errorFlag = true;
}
else {
errorValue = GetNumberHSSpeeds(0, 0, &index);
if(errorValue == DRV_SUCCESS){
for (iSpeed = 0; iSpeed < index; iSpeed++) {
GetHSSpeed(0, 0, iSpeed, &speed);
horizontalShiftSpeed_t.choices[iSpeed] = STI::Utils::valueToString(speed);
if(speed < STemp){
STemp = speed;
horizontalShiftSpeed = iSpeed;
}
}
horizontalShiftSpeed_t.initial = horizontalShiftSpeed_t.choices.find(horizontalShiftSpeed)->second;
}
//getBitDepth
if (DRV_SUCCESS != GetBitDepth(0, &bitDepth))
return true;
}
errorValue = GetNumberAmp(&nAmp);
printError(errorValue, "Get Number Amplifiers Error", &errorFlag, ANDOR_ERROR);
errorValue = GetNumberPreAmpGains(&nPreAmp);
printError(errorValue, "Get Number Preamplifiers Error", &errorFlag, ANDOR_ERROR);
if (nAmp == 1 && nAD == 1) {
for (i = 0; i < nPreAmp; i++) {
errorValue = GetPreAmpGain(i, &gain);
errorValue = IsPreAmpGainAvailable(0,0,horizontalShiftSpeed,i,&IsPreAmpAvailable);
if (IsPreAmpAvailable == 1) {
preAmpGain_t.choices[i] = STI::Utils::valueToString(gain);
}
}
if (!preAmpGain_t.choices.empty()) {
preAmpGain = preAmpGain_t.choices.begin()->first;
//preAmpGainPos = 0;
preAmpGain_t.initial = (preAmpGain_t.choices.begin())->second; // set the initial condition for the preamplifier gain
errorValue = SetPreAmpGain(preAmpGain);
printError(errorValue, "Set AD Channel Error", &errorFlag, ANDOR_ERROR);
} else {
std::cerr << "No gains available at this speed. Weird.";
errorFlag = true;
}
} else {
std::cerr << "Unexpected number of A/D's or output amps" << std::endl;
std::cerr << "Expected A/D's: 1 \t Measured: " << nAD << std::endl;
std::cerr << "Expected output Amps: 1 \t Measured: " << nAmp << std::endl;
errorFlag = true;
}
}
else {
errorValue = SetPreAmpGain(preAmpGain);
printError(errorValue, "Set AD Channel Error", &errorFlag, ANDOR_ERROR);
}
errorValue=SetADChannel(ADnumber);
printError(errorValue, "Set AD Channel Error", &errorFlag, ANDOR_ERROR);
errorValue=SetHSSpeed(0,horizontalShiftSpeed);
printError(errorValue, "Set Horizontal Speed Error", &errorFlag, ANDOR_ERROR);
if(errorFlag)
//MessageBox(GetActiveWindow(),aBuffer,"Error!",MB_OK); SMD
std::cerr<<aBuffer<<std::endl;
// Wait for 2 seconds to allow MCD to calibrate fully before allowing an
// acquisition to begin
// test=GetTickCount();
// do{
// test2=GetTickCount()-test;
// }while(test2<2000);
Sleep(2000);
errorValue = SetExposureTime(exposureTime);
printError(errorValue, "Exposure time error", &errorFlag, ANDOR_ERROR);
// It is necessary to get the actual times as the system will calculate the
// nearest possible time. eg if you set exposure time to be 0, the system
// will use the closest value (around 0.01s)
GetAcquisitionTimings(&exposureTime,&accumulateTime,&kineticTime);
std::cerr << "Actual Exposure Time is " << exposureTime << " s.\n";
// Set Shutter is made up of ttl level, shutter and open close time
//Check Get open close time
if(openTime==0)
openTime=1;
if(closeTime==0)
closeTime=1;
// Set shutter
errorValue=SetShutter(ttl,shutterMode,closeTime,openTime);
if(errorValue!=DRV_SUCCESS){
std::cerr << "Shutter error\n";
errorFlag = true;
}
else
std::cerr << "Shutter set to specifications\n";
/*// Determine availability of trigger option and set trigger selection
std::map<int,std::string>::iterator it;
std::vector<int> triggerKeys;
for (it = triggerMode_t.choices.begin(); it != triggerMode_t.choices.end(); it++)
{
errorValue = SetTriggerMode(it->first);
if (errorValue != DRV_SUCCESS)
triggerKeys.push_back(it->first);
}
for (int i = 0; i < triggerKeys.size(); i++)
triggerMode_t.choices.erase(triggerKeys.at(i));
if (triggerMode_t.choices.empty()) {
std::cerr << "No triggerModes found" << std::endl;
return true;
}
else if (triggerMode_t.choices.find(TRIGGERMODE_EXTERNAL_EXPOSURE) !=
triggerMode_t.choices.end())
triggerMode = TRIGGERMODE_EXTERNAL_EXPOSURE;
else if (triggerMode_t.choices.find(TRIGGERMODE_EXTERNAL) !=
triggerMode_t.choices.end())
triggerMode = TRIGGERMODE_EXTERNAL;
else
triggerMode = triggerMode_t.choices.begin()->first;
errorValue=SetTriggerMode(triggerMode);
printError(errorValue, "Set Trigger Mode Error", &errorFlag, ANDOR_ERROR);
triggerMode_t.initial = triggerMode_t.choices.find(triggerMode)->second;
*/
// Determine availability of trigger option and set trigger selection
std::map<int,std::string>::iterator it;
std::vector<int> triggerKeys;
for (it = triggerMode_t.choices.begin(); it != triggerMode_t.choices.end(); it++)
{
errorValue = SetTriggerMode(it->first);
if (errorValue != DRV_SUCCESS)
triggerKeys.push_back(it->first);
}
for (int i = 0; i < triggerKeys.size(); i++)
triggerMode_t.choices.erase(triggerKeys.at(i));
if (triggerMode_t.choices.empty()) {
std::cerr << "No triggerModes found" << std::endl;
return true;
}
else if (triggerMode_t.choices.find(TRIGGERMODE_EXTERNAL_EXPOSURE) !=
triggerMode_t.choices.end())
triggerMode = TRIGGERMODE_EXTERNAL_EXPOSURE;
else if (triggerMode_t.choices.find(TRIGGERMODE_EXTERNAL) !=
triggerMode_t.choices.end())
triggerMode = TRIGGERMODE_EXTERNAL;
else
triggerMode = triggerMode_t.choices.begin()->first;
errorValue=SetTriggerMode(triggerMode);
printError(errorValue, "Set Trigger Mode Error", &errorFlag, ANDOR_ERROR);
triggerMode_t.initial = triggerMode_t.choices.find(triggerMode)->second;
errorValue = GetTemperatureRange(&minTemp, &maxTemp);
if (errorValue != DRV_SUCCESS){
std::cerr << "Error finding temperature range or camera is not on" << std::endl;
errorFlag = true;
}
else {
std::cerr << "Temperature must be between " << minTemp << " and " << maxTemp << std::endl;
std::cerr << "Warning: Water cooling is required for temperatures < -58 deg C" << std::endl;
//Set temperature
if (coolerSetpt > maxTemp || coolerSetpt < minTemp) {
std::cerr << "Chosen temperature out of range." << std::endl;
if (coolerSetpt > maxTemp)
coolerSetpt = maxTemp;
else
coolerSetpt = minTemp;
std::cerr << "Resetting temp to nearest acceptable value " << std::endl;
}
errorValue = SetTemperature(coolerSetpt);
printError(errorValue, "Error setting cooler temperature", &errorFlag, ANDOR_ERROR);
int i;
errorValue = IsCoolerOn(&i);
if (i == 0) {
// if it's off and it's supposed to be on, turn it on
if (coolerStat == ANDOR_ON) {
std::cerr << "Turning on cooler." << std::endl;
errorValue = CoolerON();
printError(errorValue, "Error turning on cooler", &errorFlag, ANDOR_ERROR);
}
} else if (i == 1) {
std::cerr << "Cooler is on." << std::endl;
//if it's on and it's supposed to be off, turn it off
if (coolerStat == ANDOR_OFF)
{
errorValue = CoolerOFF();
printError(errorValue, "Error turning off cooler", &errorFlag, ANDOR_ERROR);
} else {
errorValue = GetTemperature(&i);
switch(errorValue){
case DRV_TEMP_STABILIZED:
std::cerr << "Cooler temp has stabilized at " << i << " deg C" << std::endl;
break;
case DRV_TEMP_NOT_REACHED:
std::cerr << "Cooler temp is " << i << " deg C" << std::endl;
std::cerr << "Cooler setpoint has not been reached." << std::endl;
std::cerr << "This may be because water cooling is required for setpoints < -58 deg C" << std::endl;
std::cerr << "Either wait or try resetting cooler setpoint" << std::endl;
break;
case DRV_TEMP_DRIFT:
std::cerr << "Cooler temp is " << i << " deg C" << std::endl;
std::cerr << "Cooler temperature has drifted. Try resetting setpoint" << std::endl;
break;
case DRV_TEMP_NOT_STABILIZED:
std::cerr << "Cooler temp is " << i << " deg C" << std::endl;
std::cerr << "Temperature has been reached, but cooler has not stabilized" << std::endl;
std::cerr << "Either wait or try resetting cooler setpoint" << std::endl;
break;
default:
std::cerr << "Unrecognized error sequence. Camera may be off or acquiring" << std::endl;
break;
}
}
}
if(!errorFlag){
std::cerr << "Cooler temperature set to: " << coolerSetpt << std::endl;
}
}
errorValue = SetSpool(0,0,NULL,10); //Disable spooling
printError(errorValue, "Spool mode error", &errorFlag, ANDOR_ERROR);
// Returns the value from PostQuitMessage
return errorFlag;
}
