Add ELBDM/UniformGranule test problem #135

HsunYeong · 2024-10-01T06:28:53Z

Add a test problem to simulate periodic box with homogeneous FDM granule initial condition.

vivi235711

Hi, I left some comments here.

example/test_problem/ELBDM/UniformGranule/Input__UM_IC_RefineRegion

example/test_problem/ELBDM/UniformGranule/Input__Parameter

src/TestProblem/ELBDM/UniformGranule/Init_TestProb_ELBDM_UniformGranule.cpp

example/test_problem/ELBDM/UniformGranule/python_script/get_vel_dispersion.py

example/test_problem/ELBDM/UniformGranule/python_script/plot_correlation.py

src/TestProblem/ELBDM/UniformGranule/Init_TestProb_ELBDM_UniformGranule.cpp

src/TestProblem/ELBDM/UniformGranule/Aux_ComputeProfile_with_Sigma.cpp

vivi235711

Hi. I left some comment here.
Because I'm not familiar with the correlation function, could you please share the reference about how to calculate it? I confused why divided by std^2 or mean^2.

src/TestProblem/ELBDM/UniformGranule/Aux_ComputeProfile_with_Sigma.cpp

src/TestProblem/ELBDM/UniformGranule/Aux_ComputeCorrelation.cpp

example/test_problem/ELBDM/UniformGranule/python_script/get_vel_dispersion.py

example/test_problem/ELBDM/UniformGranule/python_script/plot_correlation.py

vivi235711

I only have one minor comment.

src/TestProblem/ELBDM/UniformGranule/Init_TestProb_ELBDM_UniformGranule.cpp

ChunYen-Chen · 2025-01-08T09:55:51Z

@HsunYeong
Could you update the download link of the uniform-granule.tar.gz according to gamer-project#390? I have uploaded uniform-granule.tar.gz to ythub. The link to uniform-granule.tar.gz is

https://hub.yt/api/v1/item/677cc1c3999605c485c8de80/download

An example of the download script:

#!/bin/bash

LOCAL_FILENAME="uniform-granule"
FILE_ID="677cc1c3999605c485c8de80"

# 1. download
curl https://hub.yt/api/v1/item/${FILE_ID}/download -o "${LOCAL_FILENAME}.tar.gz"

# 2. unzip
tar -zxvf ${LOCAL_FILENAME}.tar.gz
rm ${LOCAL_FILENAME}.tar.gz

See also gamer-project#408.

hyschive

@HsunYeong Thanks for the contribution! I've added some comments, mostly regarding wording and formatting.

The only major suggestion is to file a separate PR to add support for computing standard deviation in Aux_ComputeProfile.cpp.

Additionally, please merge the latest psidm branch.

hyschive · 2025-03-01T01:53:21Z

example/test_problem/ELBDM/UniformGranule/Input__Parameter

+NX0_TOT_X                     128         # number of base-level cells along x
+NX0_TOT_Y                     128         # number of base-level cells along y
+NX0_TOT_Z                     128         # number of base-level cells along z


Increase to 256 to match the updated default value in psidm-uniform-granule-ic/input_parameter

hyschive · 2025-03-01T02:03:01Z

example/test_problem/ELBDM/UniformGranule/generate_make.sh

+${PYTHON} configure.py --machine=eureka_intel --mpi=true --hdf5=true --fftw=FFTW3 --gpu=true \
+                       --model=ELBDM --gravity=true --passive=1


Please merge the latest psidm branch, which supports a default --machine.

Suggested change

${PYTHON} configure.py --machine=eureka_intel --mpi=true --hdf5=true --fftw=FFTW3 --gpu=true \

--model=ELBDM --gravity=true --passive=1

${PYTHON} configure.py --mpi=true --hdf5=true --fftw=FFTW3 --gpu=true \

--model=ELBDM --gravity=true --passive=1 "$@"

hyschive · 2025-03-01T02:06:19Z

example/test_problem/ELBDM/UniformGranule/Input__Parameter

+UNIT_L            3.0856800e+21           # length unit        (<=0 -> set to UNIT_V*UNIT_T or (UNIT_M/UNIT_D)^(1/3)) [-1.0]
+UNIT_M                       -1.0         # mass unit          (<=0 -> set to UNIT_D*UNIT_L^3)                        [-1.0]
+UNIT_T                       -1.0         # time unit          (<=0 -> set to UNIT_L/UNIT_V)                          [-1.0]
+UNIT_V            1.0000000e+05           # velocity unit      (<=0 -> set to UNIT_L/UNIT_T)                          [-1.0]
+UNIT_D            6.7698980e-22           # mass density unit  (<=0 -> set to UNIT_M/UNIT_L^3)                        [-1.0]


To align with the default setup in psidm-uniform-granule-ic/input_parameter

Suggested change

UNIT_L 3.0856800e+21 # length unit (<=0 -> set to UNIT_V*UNIT_T or (UNIT_M/UNIT_D)^(1/3)) [-1.0]

UNIT_M -1.0 # mass unit (<=0 -> set to UNIT_D*UNIT_L^3) [-1.0]

UNIT_T -1.0 # time unit (<=0 -> set to UNIT_L/UNIT_V) [-1.0]

UNIT_V 1.0000000e+05 # velocity unit (<=0 -> set to UNIT_L/UNIT_T) [-1.0]

UNIT_D 6.7698980e-22 # mass density unit (<=0 -> set to UNIT_M/UNIT_L^3) [-1.0]

UNIT_L 3.0856800e+21 # length unit (<=0 -> set to UNIT_V*UNIT_T or (UNIT_M/UNIT_D)^(1/3)) [-1.0]

UNIT_M 1.9890000e+43 # mass unit (<=0 -> set to UNIT_D*UNIT_L^3) [-1.0]

UNIT_T -1.0 # time unit (<=0 -> set to UNIT_L/UNIT_V) [-1.0]

UNIT_V 1.0000000e+05 # velocity unit (<=0 -> set to UNIT_L/UNIT_T) [-1.0]

UNIT_D -1.0 # mass density unit (<=0 -> set to UNIT_M/UNIT_L^3) [-1.0]

hyschive · 2025-03-01T02:31:01Z

example/test_problem/ELBDM/UniformGranule/python_script/plot_slice.py

Support MPI parallelization by adding something like the following lines. Please refer to Plummer/plot_script/plot_gas.py.

yt.enable_parallelism() ts = yt.DatasetSeries( [ prefix+'/Data_%06d'%idx for idx in range(idx_start, idx_end+1, didx) ] ) for ds in ts.piter():

hyschive · 2025-03-01T02:45:55Z

example/test_problem/ELBDM/UniformGranule/Input__Parameter

+NX0_TOT_Y                     128         # number of base-level cells along y
+NX0_TOT_Z                     128         # number of base-level cells along z
+OMP_NTHREAD                  -1           # number of OpenMP threads (<=0=auto) [-1] ##OPENMP ONLY##
+END_T                         1.00e0      # end physical time (<0=auto -> must be set by test problems or restart) [-1.0]


This is a bit too long for the default initial condition with a wavelength of 0.00669212 and a velocity of 6, corresponding to a characteristic timescale of roughly 0.00669212/6 ~ 1e-3. I suggest END_T=2.0e-3 and OUTPUT_DT=4.0e-5.

hyschive · 2025-03-01T07:32:16Z

src/TestProblem/ELBDM/UniformGranule/Init_TestProb_ELBDM_UniformGranule.cpp

+
+      if ( MPI_Rank == 0 )  Aux_Message( stdout, "InitialTime = %13.6e \n", InitialTime );
+
+//    compute the enter position for passive field


Suggested change

// compute the enter position for passive field

// determine the central position for computing correlation function

hyschive · 2025-03-01T07:33:58Z

src/TestProblem/ELBDM/UniformGranule/Init_TestProb_ELBDM_UniformGranule.cpp

+      if ( MPI_Rank == 0 )  Aux_Message( stdout, "InitialTime = %13.6e \n", InitialTime );
+
+//    compute the enter position for passive field
+      if ( MPI_Rank == 0 )  Aux_Message( stdout, "Calculate halo center for passive field:\n");


Suggested change

if ( MPI_Rank == 0 ) Aux_Message( stdout, "Calculate halo center for passive field:\n");

if ( MPI_Rank == 0 ) Aux_Message( stdout, "Calculate the initial center-of-mass position:\n");

hyschive · 2025-03-01T07:34:31Z

src/TestProblem/ELBDM/UniformGranule/Init_TestProb_ELBDM_UniformGranule.cpp

+      }
+      Aux_FindWeightedAverageCenter( Center, CoM_ref, COM_MAX_R, COM_MIN_RHO, _TOTAL_DENS, COM_TOLERR_R, COM_MAX_ITER, &FinaldR, &FinalNIter );
+
+      if ( MPI_Rank == 0 )  Aux_Message( stdout, "Center of passive field is ( %14.11e,%14.11e,%14.11e )\n", Center[0], Center[1], Center[2] );


Suggested change

if ( MPI_Rank == 0 ) Aux_Message( stdout, "Center of passive field is ( %14.11e,%14.11e,%14.11e )\n", Center[0], Center[1], Center[2] );

if ( MPI_Rank == 0 ) Aux_Message( stdout, "Initial center-of-mass position is ( %14.11e,%14.11e,%14.11e )\n", Center[0], Center[1], Center[2] );

hyschive · 2025-03-01T07:44:09Z

src/TestProblem/ELBDM/UniformGranule/Init_TestProb_ELBDM_UniformGranule.cpp

+      if ( MPI_Rank == 0 )  Aux_Message( stdout, "Center of passive field is ( %14.11e,%14.11e,%14.11e )\n", Center[0], Center[1], Center[2] );
+
+//    commpute density profile for passive field
+      if ( MPI_Rank == 0 )  Aux_Message( stdout, "Calculate density profile for passive field:\n");


Suggested change

if ( MPI_Rank == 0 ) Aux_Message( stdout, "Calculate density profile for passive field:\n");

if ( MPI_Rank == 0 ) Aux_Message( stdout, "Calculate initial density profile:\n");

hyschive · 2025-03-01T07:58:40Z

src/TestProblem/ELBDM/UniformGranule/Init_TestProb_ELBDM_UniformGranule.cpp

+   }
+   if ( OPT__BC_POT != BC_POT_PERIODIC )
+      Aux_Error( ERROR_INFO, "must set periodic BC for gravity --> reset OPT__BC_POT to 1 !!\n" );
+


Add a sanity check on OPT__RECORD_USER when enabling ComputeCorrelation.

hyschive · 2025-03-01T08:11:42Z

example/test_problem/ELBDM/UniformGranule/Input__Parameter

+OPT__RECORD_PERFORMANCE       1           # record the code performance [1]
+OPT__MANUAL_CONTROL           1           # support manually dump data, stop run, or pause run during the runtime
+                                          # (by generating the file DUMP_GAMER_DUMP, STOP_GAMER_STOP, PAUSE_GAMER_PAUSE, respectively) [1]
+OPT__RECORD_CENTER            1           # record the position of maximum density, minimum potential, and center of mass [0]


Why enable this? Note that it's executed after Init_User_Ptr

hyschive · 2025-03-01T08:13:34Z

example/test_problem/ELBDM/UniformGranule/README

How about mentioning that one must turn on OPT__RECORD_USER and set COM_* properly for ComputeCorrelation?

HsunYeong added 4 commits July 8, 2024 10:45

Add UniformGranule test problem

7a8e56c

update test problem

07d4526

minor

6ea4640

Merge branch 'psidm' into psidm-uniform-granule

3d6c231

vivi235711 reviewed Nov 12, 2024

View reviewed changes

HsunYeong added 6 commits November 13, 2024 12:27

correct unit and update description

27d67f2

update description

f6363cf

remove Input__UM_IC_RefineRegion since UM_IC only has one level

78d64f1

remove unused Input__Flag_* files

82dc818

minor

e8b027c

Merge branch 'psidm' into psidm-uniform-granule

ed56f83

vivi235711 reviewed Nov 19, 2024

View reviewed changes

HsunYeong added 2 commits November 21, 2024 14:28

minor

491c090

improve code alignment

910b4df

vivi235711 approved these changes Nov 22, 2024

View reviewed changes

src/TestProblem/ELBDM/UniformGranule/Init_TestProb_ELBDM_UniformGranule.cpp Outdated Show resolved Hide resolved

improve code alignment

b4fe124

update download link

728d789

hyschive assigned vivi235711 Jan 15, 2025

hyschive added the psidm Wave dark matter label Jan 15, 2025

ChunYen-Chen mentioned this pull request Jan 22, 2025

Update IC links gamer-project/gamer#408

Merged

Merge branch 'psidm' into psidm-uniform-granule

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hyschive requested changes Mar 1, 2025

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hyschive reviewed Mar 1, 2025

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Add ELBDM/UniformGranule test problem #135

Add ELBDM/UniformGranule test problem #135

HsunYeong commented Oct 1, 2024

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		${PYTHON} configure.py --machine=eureka_intel --mpi=true --hdf5=true --fftw=FFTW3 --gpu=true \
		--model=ELBDM --gravity=true --passive=1


		if ( MPI_Rank == 0 ) Aux_Message( stdout, "InitialTime = %13.6e \n", InitialTime );

		// compute the enter position for passive field

	// compute the enter position for passive field
	// determine the central position for computing correlation function

Add ELBDM/UniformGranule test problem #135

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