kspaceFirstOrder3D-OMP 1.0
The C++ implementation of the k-wave toolbox for the time-domain simulation of acoustic wave fields in 3D
Public Member Functions | Protected Member Functions | Protected Attributes | Private Attributes
TKSpaceFirstOrder3DSolver Class Reference

Class responsible for running the k-space first order 3D method.

#include <KSpaceFirstOrder3DSolver.h>

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List of all members.

Public Member Functions

 TKSpaceFirstOrder3DSolver ()
 Constructor.
virtual ~TKSpaceFirstOrder3DSolver ()
 Destructor.
virtual void AllocateMemory ()
 Memory allocation.
virtual void FreeMemory ()
 Memory deallocation.
virtual void LoadInputData ()
 Load simulation data from the input file.
virtual void Compute ()
 Compute the 3D kspace first order simulation.
virtual void PrintParametersOfSimulation (FILE *file)
 Print parameters of the simulation.
virtual size_t ShowMemoryUsageInMB ()
 Get memory usage in MB.
string GetCodeName ()
 Get code name.
void PrintFullNameCodeAndLicense (FILE *file)
 Print the code name and license.
double GetTotalTime () const
 Get total simulation time.
double GetPreProcessingTime () const
 Get pre-processing time.
double GetDataLoadTime () const
 Get data load time.
double GetSimulationTime () const
 Get simulation time (time loop)
double GetPostProcessingTime () const
 Get post-processing time.

Protected Member Functions

 TKSpaceFirstOrder3DSolver (const TKSpaceFirstOrder3DSolver &src)
 Copy constructor not allowed for public.
TKSpaceFirstOrder3DSolveroperator= (const TKSpaceFirstOrder3DSolver &src)
 operator = not allowed for public
void InitializeFFTWPlans ()
 Initialize FFT plans.
void PreProcessingPhase ()
 Compute pre-processing phase.
void Compute_MainLoop ()
 Compute the main time loop of the kspaceFirstOrder3D.
void PostPorcessing ()
 Post processing, and closing the output streams.
void StoreSensorData ()
 Store sensor data.
void StoreIntensityData ()
 Store intensity data.
void WriteOutputDataInfo ()
 Write statistics and header into the output file.
void Compute_uxyz ()
 compute new values of for ux_sgx, uy_sgy, uz_sgz
void Compute_duxyz ()
 Compute new values of for duxdx, duydy, dzdz.
void Compute_rhoxyz_nonlinear ()
 Compute new values of rhox, rhoy, rhoz for non-linear case.
void Compute_rhoxyz_linear ()
 Compute new values of rhox, rhoy, rhoz for linear case.
void Add_u_source ()
 Add u source to the particle velocity.
void Add_p_source ()
 Add in pressure source.
void Generate_kappa ()
 Generate kappa matrix for non-absorbing media.
void Generate_kappa_absorb_nabla1_absorb_nabla2 ()
 Generate kappa matrix, absorb_nabla1, absorb_nabla2 for absorbing media.
void Generate_absorb_tau_absorb_eta_matrix ()
 Generate absorb_tau, absorb_eta for heterogenous media.
void Caclucalte_dt_rho0_non_uniform ()
 Calculate dt ./ rho0 for non-uniform grids.
void Calculate_p0_source ()
 Calculate p0_source.
void Compute_c2 ()
 Calculate c^2.
void Compute_ddx_kappa_fft_p (TRealMatrix &X_Matrix, TFFTWComplexMatrix &FFT_X, TFFTWComplexMatrix &FFT_Y, TFFTWComplexMatrix &FFT_Z, TRealMatrix &kappa, TComplexMatrix &ddx, TComplexMatrix &ddy, TComplexMatrix &ddz)
 Compute part of the new velocity - gradient in p.
void Compute_new_p_nonlinear ()
 Calculate new p, non-linear case.
void Compute_new_p_linear ()
 Calculate new p linear-case, absorbing.
void Calculate_SumRho_BonA_SumDu_SSE2 (TRealMatrix &RHO_Temp, TRealMatrix &BonA_Temp, TRealMatrix &Sum_du)
 Calculate three temporary sums in the new pressure formula, non-linear absorbing case, SSE2 version.
void Calculate_SumRho_SumRhoDu (TRealMatrix &Sum_rhoxyz, TRealMatrix &Sum_rho0_du)
 Calculate two temporary sums in the new pressure formula, linear absorbing case.
void Compute_Absorb_nabla1_2_SSE2 (TFFTWComplexMatrix &FFT_1, TFFTWComplexMatrix &FFT_2)
 Compute absorbing term with abosrb_nabla1 and absorb_nabla2, SSE2 version.
void Sum_Subterms_nonlinear (TRealMatrix &Absorb_tau_temp, TRealMatrix &Absorb_eta_temp, TRealMatrix &BonA_temp)
 Sum sub-terms to calculate new pressure, non-linear case.
void Sum_Subterms_linear (TRealMatrix &Absorb_tau_temp, TRealMatrix &Absorb_eta_temp, TRealMatrix &Sum_rhoxyz)
 Sum sub-terms to calculate new pressure, linear case.
void Sum_new_p_nonlinear_lossless ()
 Sum sub-terms for new p, linear lossless case.
void Sum_new_p_linear_lossless ()
 Sum sub-terms for new p, linear lossless case.
void PrintStatisitcs ()
 Print progress statistics.
void PrintOtputHeader ()
 Print the header of the progress statistics.
TRealMatrixGet_kappa ()
 Get the kappa matrix from the container.
TRealMatrixGet_c2 ()
 Get the c^2 matrix from the container.
TRealMatrixGet_p ()
 Get the p matrix from the container.
Tuxyz_sgxyzMatrixGet_ux_sgx ()
 Get the ux_sgx matrix from the container.
Tuxyz_sgxyzMatrixGet_uy_sgy ()
 Get the uy_sgy matrix from the container.
Tuxyz_sgxyzMatrixGet_uz_sgz ()
 Get the uz_sgz matrix from the container.
TRealMatrixGet_duxdx ()
 Get the duxdx matrix from the container.
TRealMatrixGet_duydy ()
 Get the duydy matrix from the container.
TRealMatrixGet_duzdz ()
 Get the duzdz matrix from the container.
TRealMatrixGet_dt_rho0_sgx ()
 Get the dt.*rho0_sgx matrix from the container.
TRealMatrixGet_dt_rho0_sgy ()
 Get the dt.*rho0_sgy matrix from the container.
TRealMatrixGet_dt_rho0_sgz ()
 Get the dt.*rho0_sgz matrix from the container.
TRealMatrixGet_rhox ()
 Get the rhox matrix from the container.
TRealMatrixGet_rhoy ()
 Get the rhoy matrix from the container.
TRealMatrixGet_rhoz ()
 Get the rhoz matrix from the container.
TRealMatrixGet_rho0 ()
 Get the rho0 matrix from the container.
TComplexMatrixGet_ddx_k_shift_pos ()
 Get the ddx_k_shift_pos matrix from the container.
TComplexMatrixGet_ddy_k_shift_pos ()
 Get the ddy_k_shift_pos matrix from the container.
TComplexMatrixGet_ddz_k_shift_pos ()
 Get the ddz_k_shift_pos matrix from the container.
TComplexMatrixGet_ddx_k_shift_neg ()
 Get the ddx_k_shift_neg matrix from the container.
TComplexMatrixGet_ddy_k_shift_neg ()
 Get the ddy_k_shift_neg matrix from the container.
TComplexMatrixGet_ddz_k_shift_neg ()
 Get the ddz_k_shift_neg matrix from the container.
TRealMatrixGet_pml_x_sgx ()
 Get the pml_x_sgx matrix from the container.
TRealMatrixGet_pml_y_sgy ()
 Get the pml_y_sgy matrix from the container.
TRealMatrixGet_pml_z_sgz ()
 Get the pml_z_sgz matrix from the container.
TRealMatrixGet_pml_x ()
 Get the pml_x matrix from the container.
TRealMatrixGet_pml_y ()
 Get the pml_y matrix from the container.
TRealMatrixGet_pml_z ()
 Get the pml_z matrix from the container.
TRealMatrixGet_dxudxn ()
 Get the dxudxn matrix from the container.
TRealMatrixGet_dyudyn ()
 Get the dyudyn matrix from the container.
TRealMatrixGet_dzudzn ()
 Get the dzudzn matrix from the container.
TRealMatrixGet_dxudxn_sgx ()
 Get the dxudxn_sgx matrix from the container.
TRealMatrixGet_dyudyn_sgy ()
 Get the dyudyn_sgy matrix from the container.
TRealMatrixGet_dzudzn_sgz ()
 Get the dzudzn_sgz matrix from the container.
TRealMatrixGet_BonA ()
 Get the BonA matrix from the container.
TRealMatrixGet_absorb_tau ()
 Get the absorb_tau matrix from the container.
TRealMatrixGet_absorb_eta ()
 Get the absorb_eta matrix from the container.
TRealMatrixGet_absorb_nabla1 ()
 Get the absorb_nabla1 matrix from the container.
TRealMatrixGet_absorb_nabla2 ()
 Get the absorb_nabla2 matrix from the container.
TLongMatrixGet_sensor_mask_ind ()
 Get the sensor_mask_ind matrix from the container.
TLongMatrixGet_u_source_index ()
 Get the u_source_index matrix from the container.
TLongMatrixGet_p_source_index ()
 Get the p_source_index matrix from the container.
TLongMatrixGet_delay_mask ()
 Get the delay_mask matrix from the container.
TRealMatrixGet_transducer_source_input ()
 Get the transducer_source_input matrix from the container.
TRealMatrixGet_p_source_input ()
 Get the p_source_input matrix from the container.
TRealMatrixGet_p0_source_input ()
 Get the p0_source_input from the container.
TRealMatrixGet_ux_source_input ()
 Get the ux_source_input matrix from the container.
TRealMatrixGet_uy_source_input ()
 Get the uy_source_input matrix from the container.
TRealMatrixGet_uz_source_input ()
 Get the uz_source_input matrix from the container.
TRealMatrixGet_Temp_1_RS3D ()
 Get the Temp_1_RS3D matrix from the container.
TRealMatrixGet_Temp_2_RS3D ()
 Get the Temp_2_RS3D matrix from the container.
TRealMatrixGet_Temp_3_RS3D ()
 Get the Temp_3_RS3D matrix from the container.
TRealMatrixGet_p_sensor_rms ()
 Get the p_sensor_rms from the container.
TRealMatrixGet_p_sensor_max ()
 Get the p_sensor_max from the container.
TRealMatrixGet_ux_sensor_rms ()
 Get the ux_sensor_rms from the container.
TRealMatrixGet_uy_sensor_rms ()
 Get the uy_sensor_rms from the container.
TRealMatrixGet_uz_sensor_rms ()
 Get the uz_sensor_rms from the container.
TRealMatrixGet_ux_sensor_max ()
 Get the ux_sensor_max from the container.
TRealMatrixGet_uy_sensor_max ()
 Get the uy_sensor_max from the container.
TRealMatrixGet_uz_sensor_max ()
 Get the uz_sensor_max from the container.
TRealMatrixGet_Ix_sensor_avg ()
 Get the Ix_sensor_avg from the container.
TRealMatrixGet_Iy_sensor_avg ()
 Get the Iy_sensor_avg from the container.
TRealMatrixGet_Iz_sensor_avg ()
 Get the Iz_sensor_avg from the container.
TRealMatrixGet_Ix_sensor_max ()
 Get the Ix_sensor_max from the container.
TRealMatrixGet_Iy_sensor_max ()
 Get the Iy_sensor_max from the container.
TRealMatrixGet_Iz_sensor_max ()
 Get the Iz_sensor_max from the container.
TRealMatrixGet_p_sensor_i_1_raw ()
 Get the p_sensor_i_1_raw (the i-1 step) from the container.
TRealMatrixGet_ux_sensor_i_1_agr_2 ()
 Get the ux_sensor_i_1_agr_2 (the i-1 step, and average over points in staggered grid) from the container.
TRealMatrixGet_uy_sensor_i_1_agr_2 ()
 Get the uy_sensor_i_1_agr_2 (the i-1 step, and average over points in staggered grid) from the container.
TRealMatrixGet_uz_sensor_i_1_agr_2 ()
 Get the uz_sensor_i_1_agr_2 (the i-1 step, and average over 2 points in staggered grid) from the container.
TFFTWComplexMatrixGet_FFT_X_temp ()
 Get the FFT_X_temp from the container.
TFFTWComplexMatrixGet_FFT_Y_temp ()
 Get the FFT_Y_temp from the container.
TFFTWComplexMatrixGet_FFT_Z_temp ()
 Get the FFT_Z_temp from the container.

Protected Attributes

TOutputHDF5Streamp_sensor_raw_OutputStream
 pressure raw data output stream (timeseries)
TOutputHDF5Streamux_sensor_raw_OutputStream
 ux raw data output stream (timeseries)
TOutputHDF5Streamuy_sensor_raw_OutputStream
 uy raw data output stream (timeseries)
TOutputHDF5Streamuz_sensor_raw_OutputStream
 uz raw data output stream (timeseries)

Private Attributes

TMatrixContainer MatrixContainer
 Matrix container with all the matrix classes.
int t_index
 actual time index (time step of the simulation
int ActPercent
 Percentage of the simulation done.
TParametersParameters
 Global parameters of the simulation.
TTimeMesssure TotalTime
 Total time of the simulation.
TTimeMesssure PreProcessingTime
 Pre-processing time of the simulation.
TTimeMesssure DataLoadTime
 Data load time of the simulation.
TTimeMesssure SimulationTime
 Simulation time of the simulation.
TTimeMesssure PostProcessingTime
 Post-processing time of the simulation.
TTimeMesssure IterationTime
 Iteration time of the simulation.

Detailed Description

Definition at line 56 of file KSpaceFirstOrder3DSolver.h.


Constructor & Destructor Documentation

TKSpaceFirstOrder3DSolver::TKSpaceFirstOrder3DSolver ( )

Constructor of the class.

Definition at line 66 of file KSpaceFirstOrder3DSolver.cpp.

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TKSpaceFirstOrder3DSolver::~TKSpaceFirstOrder3DSolver ( ) [virtual]

Destructor of the class.

Definition at line 91 of file KSpaceFirstOrder3DSolver.cpp.

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Member Function Documentation

void TKSpaceFirstOrder3DSolver::AllocateMemory ( ) [virtual]

The method allocates the matrix container and create all matrices and creates all output streams.

Definition at line 101 of file KSpaceFirstOrder3DSolver.cpp.

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void TKSpaceFirstOrder3DSolver::Caclucalte_dt_rho0_non_uniform ( ) [protected]

Prepare dt./ rho0 for non-uniform grid.

Definition at line 688 of file KSpaceFirstOrder3DSolver.cpp.

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void TKSpaceFirstOrder3DSolver::Calculate_p0_source ( ) [protected]

Calculate p0 source when necessary.

Definition at line 774 of file KSpaceFirstOrder3DSolver.cpp.

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void TKSpaceFirstOrder3DSolver::Calculate_SumRho_BonA_SumDu_SSE2 ( TRealMatrix RHO_Temp,
TRealMatrix BonA_Temp,
TRealMatrix Sum_du 
) [protected]

Calculate three temporary sums in the new pressure formula
non-linear absorbing case, SSE2 version.

Parameters:
[out]RHO_Temp- rhox_sgx + rhoy_sgy + rhoz_sgz
[out]BonA_Temp- BonA + rho ^2 / 2 rho0 + (rhox_sgx + rhoy_sgy + rhoz_sgz)
[out]Sum_du- rho0* (duxdx + duydy + duzdz)

Definition at line 1559 of file KSpaceFirstOrder3DSolver.cpp.

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void TKSpaceFirstOrder3DSolver::Calculate_SumRho_SumRhoDu ( TRealMatrix Sum_rhoxyz,
TRealMatrix Sum_rho0_du 
) [protected]

Calculate two temporary sums in the new pressure formula, linear absorbing case.

Parameters:
[out]Sum_rhoxyz- rhox_sgx + rhoy_sgy + rhoz_sgz
[out]Sum_rho0_du- rho0* (duxdx + duydy + duzdz);

Definition at line 1685 of file KSpaceFirstOrder3DSolver.cpp.

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void TKSpaceFirstOrder3DSolver::Compute ( ) [virtual]

This method computes k-space First Order 3D simulation. It launches calculation on a given dataset going through FFT initialization, pre-processing, main loop and post-processing phases.

Definition at line 224 of file KSpaceFirstOrder3DSolver.cpp.

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void TKSpaceFirstOrder3DSolver::Compute_Absorb_nabla1_2_SSE2 ( TFFTWComplexMatrix FFT_1,
TFFTWComplexMatrix FFT_2 
) [protected]

Compute absorbing term with abosrb_nabla1 and absorb_nabla2, SSE2 version
Calculate absorb_nabla1 .* fft_1
Calculate absorb_nabla2 .* fft2

Parameters:
[in,out]FFT_1
[in,out]FFT_2

Definition at line 1757 of file KSpaceFirstOrder3DSolver.cpp.

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void TKSpaceFirstOrder3DSolver::Compute_c2 ( ) [protected]

Compute c^2.

Definition at line 860 of file KSpaceFirstOrder3DSolver.cpp.

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void TKSpaceFirstOrder3DSolver::Compute_ddx_kappa_fft_p ( TRealMatrix X_Matrix,
TFFTWComplexMatrix FFT_X,
TFFTWComplexMatrix FFT_Y,
TFFTWComplexMatrix FFT_Z,
TRealMatrix kappa,
TComplexMatrix ddx,
TComplexMatrix ddy,
TComplexMatrix ddz 
) [protected]

Compute part of the new velocity term - gradient in p represented by: bsxfun(@times, ddx_k_shift_pos, kappa .* p_k)

Parameters:
[in]X_Matrix- 3D pressure matrix
[out]FFT_X- matrix to store input for iFFT (p) /dx
[out]FFT_Y- matrix to store input for iFFT (p) /dy
[out]FFT_Z- matrix to store input for iFFT (p) /dz
[in]kappa- Real matrix of kappa
[in]ddx- precomputed value of ddx_k_shift_pos
[in]ddy- precomputed value of ddy_k_shift_pos
[in]ddz- precomputed value of ddz_k_shift_pos

Definition at line 898 of file KSpaceFirstOrder3DSolver.cpp.

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void TKSpaceFirstOrder3DSolver::Compute_duxyz ( ) [protected]

Compute new values for duxdx, duydy, dzdz

Definition at line 970 of file KSpaceFirstOrder3DSolver.cpp.

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void TKSpaceFirstOrder3DSolver::Compute_MainLoop ( ) [protected]

Compute the main time loop of KSpaceFirstOrder3D.

Definition at line 2327 of file KSpaceFirstOrder3DSolver.cpp.

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void TKSpaceFirstOrder3DSolver::Compute_new_p_linear ( ) [protected]

Compute new p for linear case.

Definition at line 2150 of file KSpaceFirstOrder3DSolver.cpp.

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void TKSpaceFirstOrder3DSolver::Compute_new_p_nonlinear ( ) [protected]

Compute new p for non-linear case.

Definition at line 2103 of file KSpaceFirstOrder3DSolver.cpp.

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void TKSpaceFirstOrder3DSolver::Compute_rhoxyz_linear ( ) [protected]

Calculate new values of rhox, rhoy and rhoz for linear case.

Definition at line 1370 of file KSpaceFirstOrder3DSolver.cpp.

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void TKSpaceFirstOrder3DSolver::Compute_rhoxyz_nonlinear ( ) [protected]

Calculate new values of rhox, rhoy and rhoz for non-linear case.

Definition at line 1160 of file KSpaceFirstOrder3DSolver.cpp.

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void TKSpaceFirstOrder3DSolver::FreeMemory ( ) [virtual]

The method frees all memory allocated by the class.

Definition at line 136 of file KSpaceFirstOrder3DSolver.cpp.

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void TKSpaceFirstOrder3DSolver::Generate_absorb_tau_absorb_eta_matrix ( ) [protected]

Generate absorb_tau and absorb_eta in for heterogenous media.

Definition at line 597 of file KSpaceFirstOrder3DSolver.cpp.

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void TKSpaceFirstOrder3DSolver::Generate_kappa ( ) [protected]

Generate kappa matrix for lossless mode.

Definition at line 432 of file KSpaceFirstOrder3DSolver.cpp.

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void TKSpaceFirstOrder3DSolver::Generate_kappa_absorb_nabla1_absorb_nabla2 ( ) [protected]

Generate kappa, absorb_nabla1, absorb_nabla2 for absorbing media.

Definition at line 503 of file KSpaceFirstOrder3DSolver.cpp.

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void TKSpaceFirstOrder3DSolver::InitializeFFTWPlans ( ) [protected]

Initialize FFTW plans.

Definition at line 341 of file KSpaceFirstOrder3DSolver.cpp.

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void TKSpaceFirstOrder3DSolver::LoadInputData ( ) [virtual]

Load data from the input file provided by the Parameter class and creates the output time series streams.

Definition at line 171 of file KSpaceFirstOrder3DSolver.cpp.

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void TKSpaceFirstOrder3DSolver::PreProcessingPhase ( ) [protected]

Compute pre-processing phase
Initialize all indices, pre-compute constants such as c^2, rho0_sg* x dt and create kappa, absorb_eta, absorb_tau, absorb_nabla1, absorb_nabla2 matrices

Definition at line 366 of file KSpaceFirstOrder3DSolver.cpp.

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void TKSpaceFirstOrder3DSolver::PrintFullNameCodeAndLicense ( FILE *  file)

Print Full code name and the license

Parameters:
file- file to print the data (stdout)

Definition at line 318 of file KSpaceFirstOrder3DSolver.cpp.

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void TKSpaceFirstOrder3DSolver::PrintParametersOfSimulation ( FILE *  file) [virtual]

Print parameters of the simulation.

Parameters:
[in,out]file- where to print the parameters

Definition at line 281 of file KSpaceFirstOrder3DSolver.cpp.

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size_t TKSpaceFirstOrder3DSolver::ShowMemoryUsageInMB ( ) [virtual]

Get peak memory usage.

Returns:
Peak memory usage in MBs.

Definition at line 300 of file KSpaceFirstOrder3DSolver.cpp.

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void TKSpaceFirstOrder3DSolver::StoreIntensityData ( ) [protected]

Store intensity data. This has to be calculated using spatial and temporary staggered grid.

Definition at line 2687 of file KSpaceFirstOrder3DSolver.cpp.

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void TKSpaceFirstOrder3DSolver::Sum_new_p_nonlinear_lossless ( ) [protected]

Sum sub-terms for new p, non-linear lossless case.

Definition at line 1977 of file KSpaceFirstOrder3DSolver.cpp.

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void TKSpaceFirstOrder3DSolver::Sum_Subterms_linear ( TRealMatrix Absorb_tau_temp,
TRealMatrix Absorb_eta_temp,
TRealMatrix Sum_rhoxyz 
) [protected]

Sum sub-terms to calculate new pressure, linear case.

Parameters:
[in]Absorb_tau_temp- sub-term with absorb_tau
[in]Absorb_eta_temp- sub-term with absorb_eta
[in]Sum_rhoxyz- rhox_sgx + rhoy_sgy + rhoz_sgz

Definition at line 1900 of file KSpaceFirstOrder3DSolver.cpp.

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void TKSpaceFirstOrder3DSolver::Sum_Subterms_nonlinear ( TRealMatrix Absorb_tau_temp,
TRealMatrix Absorb_eta_temp,
TRealMatrix BonA_temp 
) [protected]

Sum sub-terms to calculate new pressure, non-linear case.

Parameters:
[in]Absorb_tau_temp-
[in]Absorb_eta_temp- BonA + rho ^2 / 2 rho0 + (rhox_sgx + rhoy_sgy + rhoz_sgz)
[in]BonA_temp- rho0* (duxdx + duydy + duzdz)

Definition at line 1824 of file KSpaceFirstOrder3DSolver.cpp.

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void TKSpaceFirstOrder3DSolver::WriteOutputDataInfo ( ) [protected]

Write statistics and the header into the output file.

Definition at line 2809 of file KSpaceFirstOrder3DSolver.cpp.

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The documentation for this class was generated from the following files:
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