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Extract profile spherical velocity and data load #386

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a7e5179
Enhance 'GAMER_ExtractProfile' to read hybrid scheme data
vivi235711 Sep 12, 2023
70bd31d
Improve the differential accuracy in GAMER_ExtractProfile using Richa…
vivi235711 Sep 12, 2023
b8e2b7c
Remove the center of mass velocity for evaluating the shell-average o…
vivi235711 Sep 12, 2023
ff02372
Add option 'O' to 'GAMER_ExtractProfile' for generating spherical vel…
vivi235711 Sep 13, 2023
73abe31
Enable differential accuracy as an option in GAMER_ExtractProfile
vivi235711 Sep 14, 2023
cad6826
Correct CMV calculation, changed sin&cos to SIN&COS, and skip density…
vivi235711 Oct 11, 2023
b2b39d5
Remove CMV using phase shift
vivi235711 Oct 25, 2023
bcfdb80
Change to wave function derivative to calculate internal velocity; Ou…
vivi235711 Oct 25, 2023
c475678
Correct velocity calculation
vivi235711 Oct 26, 2023
67aae0c
Remove center of mass velocity as an option 'C'
vivi235711 Oct 29, 2023
dc0f00b
Fix error of unsupported model
vivi235711 Dec 18, 2023
7d26a85
Merge branch 'psidm' of https://github.com/hyschive/gamer-fork into e…
vivi235711 May 14, 2024
9003366
Merge branch 'main' of https://github.com/gamer-project/gamer into ex…
vivi235711 Dec 19, 2024
372ff76
Style: Align code
vivi235711 Feb 8, 2025
bed46c1
Fix: HDF5 loading with ELBDM_Scheme
vivi235711 Feb 10, 2025
b4d08b7
Refactor code based on @hsinhaoHHuang's comment
vivi235711 Feb 11, 2025
59ad25d
Support: OutputSphVel in Hydro
vivi235711 Feb 12, 2025
f9262bf
Change RMS velocity to mass-weighted
vivi235711 Mar 6, 2025
239d21c
Turn on ELBDM_GetVir when -O is on in ELBDM
vivi235711 Jan 15, 2026
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2 changes: 2 additions & 0 deletions tool/analysis/gamer_extract_profile/GAMER_Functions/LoadData.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -325,9 +325,11 @@ void LoadData()
if ( LoadPot ) NOut ++;

# if ( MODEL == HYDRO )
if ( OutputSphVel ) NOut += 3;
# elif ( MODEL == MHD )
# elif ( MODEL == ELBDM )
if ( ELBDM_GetVir ) NOut += 8;
if ( OutputSphVel ) NOut += 6;
# else
# error : ERROR : unsupported MODEL !!
# endif // MODEL
Expand Down
108 changes: 78 additions & 30 deletions tool/analysis/gamer_extract_profile/GAMER_Functions/LoadData_HDF5.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -94,7 +94,7 @@ void LoadData_HDF5( const char *FileName )
double ELBDM_PlanckConst;
# endif

hid_t H5_FileID, H5_SetID_KeyInfo, H5_TypeID_KeyInfo, H5_SetID_InputPara, H5_TypeID_InputPara;
hid_t H5_FileID, H5_SetID_KeyInfo, H5_TypeID_KeyInfo, H5_SetID_InputPara, H5_TypeID_InputPara, H5_SetID_Makefile, H5_TypeID_Makefile;
hid_t H5_SetID_Cr, H5_SetID_Son;
herr_t H5_Status;

Expand All @@ -105,7 +105,7 @@ void LoadData_HDF5( const char *FileName )
Aux_Error( ERROR_INFO, "failed to open the restart HDF5 file \"%s\" !!\n", FileName );


// 1-2. load the dataset and datatype of KeyInfo and InputPara
// 1-2. load the dataset and datatype of KeyInfo and InputPara and Makefile
H5_SetID_KeyInfo = H5Dopen( H5_FileID, "Info/KeyInfo", H5P_DEFAULT );
if ( H5_SetID_KeyInfo < 0 )
Aux_Error( ERROR_INFO, "failed to open the dataset \"%s\" !!\n", "Info/KeyInfo" );
Expand All @@ -122,6 +122,13 @@ void LoadData_HDF5( const char *FileName )
if ( H5_TypeID_InputPara < 0 )
Aux_Error( ERROR_INFO, "failed to open the datatype of \"%s\" !!\n", "Info/InputPara" );

H5_SetID_Makefile = H5Dopen( H5_FileID, "Info/Makefile", H5P_DEFAULT );
if ( H5_SetID_Makefile < 0 )
Aux_Error( ERROR_INFO, "failed to open the dataset \"%s\" !!\n", "Info/Makefile" );

H5_TypeID_Makefile = H5Dget_type( H5_SetID_Makefile );
if ( H5_TypeID_Makefile < 0 )
Aux_Error( ERROR_INFO, "failed to open the datatype of \"%s\" !!\n", "Info/Makefile" );

// 1-3. load all target fields in KeyInfo and InputPara one-by-one (by all ranks)
LoadField( "FormatVersion", &FormatVersion, H5_SetID_KeyInfo, H5_TypeID_KeyInfo, Fatal, NullPtr, -1, NonFatal );
Expand All @@ -132,34 +139,35 @@ void LoadData_HDF5( const char *FileName )
if ( FormatVersion < 2200 )
Aux_Error( ERROR_INFO, "unsupported data format version (only support version >= 2200) !!\n" );

LoadField( "Model", &Model_RS, H5_SetID_KeyInfo, H5_TypeID_KeyInfo, Fatal, &Model_RT, 1, Fatal );
LoadField( "Float8", &Float8_RS, H5_SetID_KeyInfo, H5_TypeID_KeyInfo, Fatal, &Float8_RT, 1, Fatal );
LoadField( "NLevel", &NLevel_RS, H5_SetID_KeyInfo, H5_TypeID_KeyInfo, Fatal, &NLevel_RT, 1, Fatal );
LoadField( "PatchSize", &PatchSize_RS, H5_SetID_KeyInfo, H5_TypeID_KeyInfo, Fatal, &PatchSize_RT, 1, Fatal );
LoadField( "NCompFluid", &NCompFluid_RS, H5_SetID_KeyInfo, H5_TypeID_KeyInfo, Fatal, &NCompFluid_RT, 1, Fatal );
LoadField( "NCompPassive", &NCompPassive_RS, H5_SetID_KeyInfo, H5_TypeID_KeyInfo, Fatal, &NCompPassive_RT, 1, Fatal );

LoadField( "Gravity", &Gravity, H5_SetID_KeyInfo, H5_TypeID_KeyInfo, Fatal, NullPtr, -1, NonFatal );
LoadField( "Particle", &Particle, H5_SetID_KeyInfo, H5_TypeID_KeyInfo, Fatal, NullPtr, -1, NonFatal );
LoadField( "DumpID", &DumpID, H5_SetID_KeyInfo, H5_TypeID_KeyInfo, Fatal, NullPtr, -1, NonFatal );
LoadField( "NX0", NX0_TOT, H5_SetID_KeyInfo, H5_TypeID_KeyInfo, Fatal, NullPtr, -1, NonFatal );
LoadField( "NPatch", NPatchTotal, H5_SetID_KeyInfo, H5_TypeID_KeyInfo, Fatal, NullPtr, -1, NonFatal );
LoadField( "Step", &Step, H5_SetID_KeyInfo, H5_TypeID_KeyInfo, Fatal, NullPtr, -1, NonFatal );
LoadField( "Time", Time, H5_SetID_KeyInfo, H5_TypeID_KeyInfo, Fatal, NullPtr, -1, NonFatal );
LoadField( "CellSize", amr.dh, H5_SetID_KeyInfo, H5_TypeID_KeyInfo, Fatal, NullPtr, -1, NonFatal );
LoadField( "BoxScale", amr.BoxScale, H5_SetID_KeyInfo, H5_TypeID_KeyInfo, Fatal, NullPtr, -1, NonFatal );
LoadField( "BoxSize", amr.BoxSize, H5_SetID_KeyInfo, H5_TypeID_KeyInfo, Fatal, NullPtr, -1, NonFatal );

LoadField( "Opt__BC_Flu", ExtBC_RS, H5_SetID_InputPara, H5_TypeID_InputPara, Fatal, NullPtr, -1, NonFatal );
LoadField( "Model", &Model_RS, H5_SetID_KeyInfo, H5_TypeID_KeyInfo, Fatal, &Model_RT, 1, Fatal );
LoadField( "Float8", &Float8_RS, H5_SetID_KeyInfo, H5_TypeID_KeyInfo, Fatal, &Float8_RT, 1, Fatal );
LoadField( "NLevel", &NLevel_RS, H5_SetID_KeyInfo, H5_TypeID_KeyInfo, Fatal, &NLevel_RT, 1, Fatal );
LoadField( "PatchSize", &PatchSize_RS, H5_SetID_KeyInfo, H5_TypeID_KeyInfo, Fatal, &PatchSize_RT, 1, Fatal );
LoadField( "NCompFluid", &NCompFluid_RS, H5_SetID_KeyInfo, H5_TypeID_KeyInfo, Fatal, &NCompFluid_RT, 1, Fatal );
LoadField( "NCompPassive", &NCompPassive_RS, H5_SetID_KeyInfo, H5_TypeID_KeyInfo, Fatal, &NCompPassive_RT, 1, Fatal );

LoadField( "Gravity", &Gravity, H5_SetID_KeyInfo, H5_TypeID_KeyInfo, Fatal, NullPtr, -1, NonFatal );
LoadField( "Particle", &Particle, H5_SetID_KeyInfo, H5_TypeID_KeyInfo, Fatal, NullPtr, -1, NonFatal );
LoadField( "DumpID", &DumpID, H5_SetID_KeyInfo, H5_TypeID_KeyInfo, Fatal, NullPtr, -1, NonFatal );
LoadField( "NX0", NX0_TOT, H5_SetID_KeyInfo, H5_TypeID_KeyInfo, Fatal, NullPtr, -1, NonFatal );
LoadField( "NPatch", NPatchTotal, H5_SetID_KeyInfo, H5_TypeID_KeyInfo, Fatal, NullPtr, -1, NonFatal );
LoadField( "Step", &Step, H5_SetID_KeyInfo, H5_TypeID_KeyInfo, Fatal, NullPtr, -1, NonFatal );
LoadField( "Time", Time, H5_SetID_KeyInfo, H5_TypeID_KeyInfo, Fatal, NullPtr, -1, NonFatal );
LoadField( "CellSize", amr.dh, H5_SetID_KeyInfo, H5_TypeID_KeyInfo, Fatal, NullPtr, -1, NonFatal );
LoadField( "BoxScale", amr.BoxScale, H5_SetID_KeyInfo, H5_TypeID_KeyInfo, Fatal, NullPtr, -1, NonFatal );
LoadField( "BoxSize", amr.BoxSize, H5_SetID_KeyInfo, H5_TypeID_KeyInfo, Fatal, NullPtr, -1, NonFatal );

LoadField( "Opt__BC_Flu", ExtBC_RS, H5_SetID_InputPara, H5_TypeID_InputPara, Fatal, NullPtr, -1, NonFatal );
if ( Gravity ) {
LoadField( "Opt__Output_Pot", &LoadPot, H5_SetID_InputPara, H5_TypeID_InputPara, Fatal, NullPtr, -1, NonFatal ); }
LoadField( "Opt__Output_Pot", &LoadPot, H5_SetID_InputPara, H5_TypeID_InputPara, Fatal, NullPtr, -1, NonFatal ); }
if ( Particle ) {
LoadField( "Opt__Output_ParDens", &OutputParDens, H5_SetID_InputPara, H5_TypeID_InputPara, Fatal, NullPtr, -1, NonFatal ); }
LoadField( "Opt__Output_ParDens", &OutputParDens, H5_SetID_InputPara, H5_TypeID_InputPara, Fatal, NullPtr, -1, NonFatal ); }
# if ( MODEL == HYDRO )
LoadField( "Gamma", &GAMMA, H5_SetID_InputPara, H5_TypeID_InputPara, Fatal, NullPtr, -1, NonFatal );
LoadField( "Gamma", &GAMMA, H5_SetID_InputPara, H5_TypeID_InputPara, Fatal, NullPtr, -1, NonFatal );
# elif ( MODEL == ELBDM )
LoadField( "ELBDM_Mass", &ELBDM_Mass, H5_SetID_InputPara, H5_TypeID_InputPara, Fatal, NullPtr, -1, NonFatal );
LoadField( "ELBDM_PlanckConst", &ELBDM_PlanckConst, H5_SetID_InputPara, H5_TypeID_InputPara, Fatal, NullPtr, -1, NonFatal );
LoadField( "ELBDM_Mass", &ELBDM_Mass, H5_SetID_InputPara, H5_TypeID_InputPara, Fatal, NullPtr, -1, NonFatal );
LoadField( "ELBDM_PlanckConst", &ELBDM_PlanckConst, H5_SetID_InputPara, H5_TypeID_InputPara, Fatal, NullPtr, -1, NonFatal );
LoadField( "ELBDMScheme", &ELBDM_Scheme, H5_SetID_Makefile, H5_TypeID_Makefile, NonFatal, NullPtr, -1, NonFatal );

ELBDM_ETA = ELBDM_Mass / ELBDM_PlanckConst;
# endif
Expand All @@ -183,6 +191,9 @@ void LoadData_HDF5( const char *FileName )
char Key[MaxString];
sprintf( Key, "FieldLabel%02d", v );

# if ( MODEL == ELBDM)
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@hsinhaoHHuang hsinhaoHHuang Mar 24, 2026

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Suggested change
# if ( MODEL == ELBDM)
# if ( MODEL == ELBDM )

if ( ELBDM_Scheme == 2 && v == 2 ) continue;
# endif
LoadField( Key, &FieldName_In[v], H5_SetID_InputPara, H5_TypeID_InputPara, Fatal, NullPtr, -1, NonFatal );
}
}
Expand Down Expand Up @@ -256,9 +267,11 @@ void LoadData_HDF5( const char *FileName )
OutputParDens = 0;

# if ( MODEL == HYDRO )
if ( OutputSphVel ) NOut += 3;
# elif ( MODEL == MHD )
# elif ( MODEL == ELBDM )
if ( ELBDM_GetVir ) NOut += 8;
if ( OutputSphVel ) NOut += 6;
# else
# error : ERROR : unsupported MODEL !!
# endif // MODEL
Expand Down Expand Up @@ -383,7 +396,12 @@ void LoadData_HDF5( const char *FileName )
if ( FormatVersion >= 2300 )
{
for (int v=0; v<NCOMP_TOTAL; v++)
sprintf( FieldName[v], "%s", FieldName_In[v] );
{
# if ( MODEL == ELBDM )
if ( ELBDM_Scheme == 2 && v == 2 ) continue;
# endif
sprintf( FieldName[v], "%s", FieldName_In[v] );
}
}

else
Expand Down Expand Up @@ -441,6 +459,9 @@ void LoadData_HDF5( const char *FileName )

for (int v=0; v<NCOMP_TOTAL; v++)
{
# if ( MODEL == ELBDM )
if ( ELBDM_Scheme == 2 && v == 2 ) continue;
# endif
H5_SetID_Field[v] = H5Dopen( H5_GroupID_GridData, FieldName[v], H5P_DEFAULT );
if ( H5_SetID_Field[v] < 0 ) Aux_Error( ERROR_INFO, "failed to open the dataset \"%s\" !!\n", FieldName[v] );
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}
Expand Down Expand Up @@ -477,9 +498,15 @@ void LoadData_HDF5( const char *FileName )
}

// free HDF5 objects
for (int v=0; v<NCOMP_TOTAL; v++) H5_Status = H5Dclose( H5_SetID_Field[ v] );
if ( OutputPot ) H5_Status = H5Dclose( H5_SetID_Field[NCOMP_TOTAL+0] );
if ( OutputParDens ) H5_Status = H5Dclose( H5_SetID_Field[NCOMP_TOTAL+1] );
for (int v=0; v<NCOMP_TOTAL; v++)
{
# if ( MODEL == ELBDM )
if ( ELBDM_Scheme == 2 && v == 2 ) continue;
# endif
H5_Status = H5Dclose( H5_SetID_Field[v] );
}
if ( OutputPot ) H5_Status = H5Dclose( H5_SetID_Field[NCOMP_TOTAL+0] );
if ( OutputParDens ) H5_Status = H5Dclose( H5_SetID_Field[NCOMP_TOTAL+1] );

H5_Status = H5Gclose( H5_GroupID_GridData );
H5_Status = H5Fclose( H5_FileID );
Expand Down Expand Up @@ -770,11 +797,32 @@ void LoadOnePatch( const hid_t H5_FileID, const int lv, const int GID, const boo
// load the fluid data
for (int v=0; v<NCOMP_TOTAL; v++)
{
# if ( MODEL == ELBDM )
// Hybrid Scheme : Only has dens and phase parts
if ( ELBDM_Scheme == 2 && v == 2 ) continue;
# endif
H5_Status = H5Dread( H5_SetID_Field[v], H5T_GAMER_REAL, H5_MemID_Field, H5_SpaceID_Field, H5P_DEFAULT,
amr.patch[lv][PID]->fluid[v] );
if ( H5_Status < 0 )
Aux_Error( ERROR_INFO, "failed to load a field variable (lv %d, GID %d, v %d) !!\n", lv, GID, v );
}
// Transfer dens and phase to real and imag
# if ( MODEL == ELBDM )
if ( ELBDM_Scheme == 2 )
{
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Suggested change
{
{

real Dens, Phas, Im, Re;
for (int k=0; k<PATCH_SIZE; k++) {
for (int j=0; j<PATCH_SIZE; j++) {
for (int i=0; i<PATCH_SIZE; i++) {
Dens = amr.patch[lv][PID]->fluid[0][k][j][i];
Phas = amr.patch[lv][PID]->fluid[1][k][j][i];
Im = SQRT(Dens) * SIN(Phas);
Re = SQRT(Dens) * COS(Phas);
amr.patch[lv][PID]->fluid[IMAG][k][j][i] = Im;
amr.patch[lv][PID]->fluid[REAL][k][j][i] = Re;
}}}
}
# endif

// load the potential data
if ( OutputPot )
Expand Down
2 changes: 2 additions & 0 deletions tool/analysis/gamer_extract_profile/Header/Global.h
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Expand Up @@ -16,10 +16,12 @@ extern bool UseTree;
extern bool NeedGhost;
extern bool GetAvePot;
extern double NewtonG;
extern bool OutputSphVel;

#if ( MODEL == ELBDM )
extern bool ELBDM_GetVir;
extern double ELBDM_ETA;
extern int ELBDM_Scheme;
#endif


Expand Down
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