void MuscleOutput(MSA &msa)
{
MHackEnd(msa);
if (g_bStable)
{
MSA msaStable;
Stabilize(msa, msaStable);
msa.Clear(); // save memory
DoOutput(msaStable);
}
else
DoOutput(msa);
}
// Buffer a single byte
int
LineBuffer::
Buffer( char c )
{
if ( ( '\n' == c ) || ( '\0' == c ) || ( bufcount >= bufsize ) ) {
return DoOutput( false );
} else {
*bufptr = c;
bufptr++;
bufcount++;
return 0;
}
}
bool TSimpleTextMiner::Run()
{
if (Input == NULL || Output == NULL)
return false;
Wtroka text;
SDocumentAttribtes docAttr;
ETypeOfDocument type;
while (DoInput(text, docAttr, type)) {
bool res = DoProcess(text, docAttr, type);
if (res)
res = DoOutput(docAttr);
if (!res && Errors != NULL && dynamic_cast<TStringStream*>(ErrorStream) != NULL) {
TStringStream* str = static_cast<TStringStream*>(ErrorStream);
Errors->OutputError(str->Str());
str->clear();
}
}
return true;
}
//______________________________________________________________________________
void MainWindow::init()
{ //initialisation of the gui
//recall objects from .ui file and connect them with user functions
ui_ConvertButton = this->findChild<QCommandLinkButton*>("ConvertButton");
ui_ExitButton = this->findChild<QCommandLinkButton*>("ExitButton");
ui_OutputButton = this->findChild<QCommandLinkButton*>("OutputButton");
connect(ui_ConvertButton, SIGNAL(clicked()), this, SLOT(DoConvert()));
connect(ui_ExitButton, SIGNAL(clicked()), this, SLOT(DoExit()));
connect(ui_OutputButton, SIGNAL(clicked()), this, SLOT(DoOutput()));
ui_actionExit = this->findChild<QAction*>("actionExit");
ui_actionLoad = this->findChild<QAction*>("actionLoad");
ui_actionSave = this->findChild<QAction*>("actionSave");
connect(ui_actionExit, SIGNAL(triggered()), this, SLOT(DoExit()));
connect(ui_actionSave, SIGNAL(triggered()), this, SLOT(DoSave()));
connect(ui_actionLoad, SIGNAL(triggered()), this, SLOT(DoLoad()));
ui_EmaxSpinBox = this->findChild<QSpinBox*>("EmaxSpinBox");
ui_BinSizeSpinBox = this->findChild<QSpinBox*>("BinSizeSpinBox");
ui_ASpinBox = this->findChild<QSpinBox*>("ASpinBox");
ui_ZSpinBox = this->findChild<QSpinBox*>("ZSpinBox");
ui_SpinParitySpinBox = this->findChild<QDoubleSpinBox*>("SpinParitySpinBox");
ui_SpinParitySpinBox_2 = this->findChild<QDoubleSpinBox*>("SpinParitySpinBox_2");
ui_SpinParitySpinBox_n1 = this->findChild<QDoubleSpinBox*>("SpinParitySpinBox_n1");
ui_SpinParitySpinBox_n2 = this->findChild<QDoubleSpinBox*>("SpinParitySpinBox_n2");
ui_TorASpinBox_1 = this->findChild<QDoubleSpinBox*>("TorASpinBox_1");
ui_TorASpinBox_2 = this->findChild<QDoubleSpinBox*>("TorASpinBox_2");
ui_PairSpinBox = this->findChild<QDoubleSpinBox*>("PairSpinBox");
ui_ParityBox = this->findChild<QDoubleSpinBox*>("ParityBox");
ui_E1doubleSpinBox_1 = this->findChild<QDoubleSpinBox*>("E1doubleSpinBox_1");
ui_E1doubleSpinBox_2 = this->findChild<QDoubleSpinBox*>("E1doubleSpinBox_2");
ui_E1doubleSpinBox_3 = this->findChild<QDoubleSpinBox*>("E1doubleSpinBox_3");
ui_E1doubleSpinBox_4 = this->findChild<QDoubleSpinBox*>("E1doubleSpinBox_4");
ui_E1doubleSpinBox_5 = this->findChild<QDoubleSpinBox*>("E1doubleSpinBox_5");
ui_E1doubleSpinBox_6 = this->findChild<QDoubleSpinBox*>("E1doubleSpinBox_6");
ui_M1doubleSpinBox_1 = this->findChild<QDoubleSpinBox*>("M1doubleSpinBox_1");
ui_OutputLabel = this->findChild<QLabel*>("OutputLabel");
ui_TorALabel_1 = this->findChild<QLabel*>("TorALabel_1");
ui_TorALabel_2 = this->findChild<QLabel*>("TorALabel_2");
ui_EmaxLabel = this->findChild<QLabel*>("EmaxLabel");
ui_E1label_1 = this->findChild<QLabel*>("E1Label_1");
ui_E1label_2 = this->findChild<QLabel*>("E1Label_2");
ui_E1label_3 = this->findChild<QLabel*>("E1Label_3");
ui_E1label_4 = this->findChild<QLabel*>("E1Label_4");
ui_E1label_5 = this->findChild<QLabel*>("E1Label_5");
ui_E1label_6 = this->findChild<QLabel*>("E1Label_6");
ui_M1label_1 = this->findChild<QLabel*>("M1Label_1");
ui_M1label_2 = this->findChild<QLabel*>("M1Label_2");
ui_Levellabel = this->findChild<QLabel*>("Levellabel");
ui_Spectrumlabel = this->findChild<QLabel*>("SpectrumLabel");
ui_progressbar = this->findChild<QProgressBar*>("progressBar");
ui_E1pushButton = this->findChild<QPushButton*>("E1pushButton");
connect(ui_E1pushButton, SIGNAL(clicked()),this,SLOT(DoSelectfile1()));
ui_M1pushButton = this->findChild<QPushButton*>("M1pushButton");
connect(ui_M1pushButton, SIGNAL(clicked()),this,SLOT(DoSelectfile2()));
ui_LevelpushButton = this->findChild<QPushButton*>("LevelpushButton");
connect(ui_LevelpushButton, SIGNAL(clicked()),this,SLOT(DoSelectfile3()));
ui_LevelpushButton_2 = this->findChild<QPushButton*>("LevelpushButton_2");
connect(ui_LevelpushButton_2, SIGNAL(clicked()),this,SLOT(Clear()));
ui_SpectrumButton = this->findChild<QPushButton*>("SpectrumButton");
connect(ui_SpectrumButton, SIGNAL(clicked()),this,SLOT(DoSelectfile4()));
ui_DensityEnergyComboBox = this->findChild<QComboBox*>("DensityEnergyComboBox");
connect(ui_DensityEnergyComboBox,SIGNAL(currentIndexChanged(int)) ,this,SLOT(DoModel()));
ui_ReactionComboBox = this->findChild<QComboBox*>("ReactionComboBox");
connect(ui_ReactionComboBox,SIGNAL(currentIndexChanged(int)) ,this,SLOT(DoEmax()));
ui_E1StrengthComboBox = this->findChild<QComboBox*>("E1StrengthComboBox");
connect(ui_E1StrengthComboBox,SIGNAL(currentIndexChanged(int)) ,this,SLOT(DoE1()));
ui_M1StrengthComboBox = this->findChild<QComboBox*>("M1StrengthComboBox");
connect(ui_M1StrengthComboBox,SIGNAL(currentIndexChanged(int)) ,this,SLOT(DoM1()));
ui_E1pushButton->hide();
ui_E1label_6->hide();
ui_E1doubleSpinBox_3->hide();
ui_E1doubleSpinBox_4->hide();
ui_E1doubleSpinBox_5->hide();
ui_E1doubleSpinBox_6->hide();
ui_M1label_1->hide();
ui_M1label_2->hide();
ui_M1doubleSpinBox_1->hide();
ui_M1pushButton->hide();
ui_Spectrumlabel->hide();
ui_SpectrumButton->hide();
}
// Flush the input buffer
int
LineBuffer::
Flush( void )
{
return DoOutput( false );
}
int DoSolve(DMMG *dmmg)
/* ------------------------------------------------------------------- */
{
AppCtx *user = (AppCtx*)dmmg[0]->user;
Parameter *param;
PetscReal t_output = 0.0;
int ierr, n_plot = 0, Ncomponents, components[3];
DA da = DMMGGetDA(dmmg);
Vec Xstar;
Characteristic c;
ierr = PetscBagGetData(user->bag,(void**)¶m);
CHKERRQ(ierr);
ierr = DAGetGlobalVector(da, &Xstar);
CHKERRQ(ierr);
/*------------ BEGIN CHARACTERISTIC SETUP ---------------*/
ierr = CharacteristicCreate(PETSC_COMM_WORLD, &c);
CHKERRQ(ierr);
/* set up the velocity interpolation system */
Ncomponents = 2;
components[0] = 0;
components[1] = 1;
ierr = CharacteristicSetVelocityInterpolationLocal(c, da, DMMGGetx(dmmg), user->Xold, Ncomponents, components, InterpVelocity2D, user);
CHKERRQ(ierr);
/* set up the fields interpolation system */
Ncomponents = 1;
components[0] = 2;
ierr = CharacteristicSetFieldInterpolationLocal(c, da, user->Xold, Ncomponents, components, InterpFields2D, user);
CHKERRQ(ierr);
/*------------ END CHARACTERISTIC SETUP ----------------*/
/* output initial data */
PetscPrintf(PETSC_COMM_WORLD," Initialization, Time: %5.4g\n", param->t);
if (param->verify) {
ierr = DoVerification(dmmg,user);
CHKERRQ(ierr);
}
ierr = DoOutput(dmmg,n_plot);
CHKERRQ(ierr);
t_output += param->t_output_interval;
n_plot++;
/* timestep loop */
for (param->t=param->dt; param->t<=param->t_max; param->t+=param->dt) {
if (param->n > param->N_steps) {
PetscPrintf(PETSC_COMM_WORLD,"EXCEEDED MAX NUMBER OF TIMESTEPS! EXITING SOLVE!\n");
return 0;
}
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Solve at time t & copy solution into solution vector.
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/* Copy in the velocities to Xstar */
ierr = VecCopy(DMMGGetx(dmmg), Xstar);
CHKERRQ(ierr);
/* Put \phi_* into Xstar */
ierr = CharacteristicSolve(c, param->dt, Xstar);
CHKERRQ(ierr);
/* Copy the advected field into the solution \phi_t = \phi_* */
ierr = VecCopy(Xstar, DMMGGetx(dmmg));
CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Copy new solution to old solution in prep for the next timestep.
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = VecCopy(DMMGGetx(dmmg), user->Xold);
CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Timestep complete, report and update counter.
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
PetscPrintf(PETSC_COMM_WORLD," Step: %d, Time: %5.4g\n", param->n, param->t);
param->n++;
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Verify and make output.
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
if (param->verify) {
ierr = DoVerification(dmmg,user);
CHKERRQ(ierr);
}
if (param->t >= t_output) {
ierr = DoOutput(dmmg,n_plot);
CHKERRQ(ierr);
t_output += param->t_output_interval;
n_plot++;
}
}
ierr = DARestoreGlobalVector(da, &Xstar);
CHKERRQ(ierr);
ierr = CharacteristicDestroy(c);
CHKERRQ(ierr);
return 0;
}
