Add DynamicalFriction Test Problem #252

ej-1211 · 2023-10-17T09:42:34Z

No description provided.

hsinhaoHHuang

I am really sorry for the delayed review. 😢
Thank you for your patience.
I've had a quick look at this PR recently.

I can run the three default cases and reproduce similar results in this page.
However, the figure for the Quick_Burkert is not 100% identical with the reference. Here is my results:

I am not sure why and I didn't figure out what may went wrong.

I provided some suggestions in the inline comments. Please take a look.
Please let me know if my messages are not clear or I misunderstood anything. 🙏 Thanks!

example/test_problem/Hydro/DynamicalFriction/Input__Parameter_NFW_interpolation

src/TestProblem/Hydro/DynamicalFriction/Init_TestProb_Hydro_DynamicalFriction.cpp

example/test_problem/Hydro/DynamicalFriction/clean.sh

example/test_problem/Hydro/DynamicalFriction/generate_make.sh

example/test_problem/Hydro/DynamicalFriction/Input__TestProb_NFW_interpolation

example/test_problem/Hydro/DynamicalFriction/Tools/Density_Profile_Barry_table_for_GAMER.txt

example/test_problem/Hydro/DynamicalFriction/Tools/plot_trajectory_movie.py

hsinhaoHHuang · 2024-02-03T03:43:08Z

example/test_problem/Hydro/DynamicalFriction/Input__TestProb_NFW_interpolation

+# (1) HALO and STELLAR Parameters
+HALO_TYPE             NFW                       #* [Burkert]
+HALO_RHO_0            1.96311939345708e-03          #* [Msun/pc^3][665.3026853292199e-3]
+HALO_Rs               5.48799489144317e+03                        #*Scale radius for the profile [pc][0.25e3]
+HALO_Rt               35e3                         #*Truncate radius for the halo [pc][6e3] 
+
+STELLAR_TYPE          None	                    #*[None]
+STELLAR_RHO_0         0	                            #*[Msun/pc^3][0]
+STELLAR_Rs            0	                            #*[pc][0]
+STELLAR_Rt            0                             #*[pc][0]
+


I found there are several parameters (e.g. HALO_*, STELLAR_*, PURE_TABLE) in Input__TestProb that are not used and are even not read by GAMER. This is weird for me.
The */+/! notation for the variables is also quite not consistent with other test problems in GAMER. I think the input and the output for the Python script are put in the same file is confusing.
Also, it would be better if the default run is as simple as possible such that users can run it without doing many steps.

Therefore, I suggest two workflows for this test problem to improve it.
I personally prefer the 1st one because it is simpler for the user.
But I think the 2nd one is easier to implement from your current code.

The 1st suggestion:

Put the calculation in A_SET_IC.py (generating density profile and deciding initial parameters) inside the GAMER source code.

Maybe take the Plummer test problem as the reference, see src/TestProblem/Hydro/Plummer/Par_Init_ByFunction_Plummer.cpp.

Combine C_Chandrasekhar_dynamical_friction.py and D_Compare.py into the same file to handle the simulation analysis.

Steps:

In Input__Testprob

GC_SmallGas

FIX_CENTER

SEARCH_RADIUS

Cloud_Center

HALO_TYPE, HALO_Rs, HALO_Rt, HALO_Rho0

STELLAR_TYPE, STELLAR_Rs, STELLAR_Rt, STELLAR_Rho0

GC_MASS, GC_Initial_R

PURE_TABLE

In Init_TestProb_Hydro_DynamicalFriction()

Goal:

to read the parameters to set the fluid

to read the parameters to record the center

to read the parameters for the GC

Input:

GC_SmallGas

GC_MASS, GC_Initial_R

FIX_CENTER

SEARCH_RADIUS

Par_Init_ByFunction_GC()

Goal:

to set the initial condition of the halo

to set the initial condition of the GC

to set the derived parameters from the input model

Input

Cloud_Center

HALO_TYPE, HALO_Rs, HALO_Rt, HALO_Rho0

STELLAR_TYPE, STELLAR_Rs, STELLAR_Rt, STELLAR_Rho0

GC_MASS, GC_Initial_R

PURE_TABLE

Derived Parameters

Density profile and mass profile of the halo

GC_POS

GC_VEL

Cloud_BulkVel

Cloud_Rho0

Cloud_R0

Cloud_MaxR

Init_ExtPot_GC()

Goal:

to set the external potential

Input:

DynamicialFriction_ExtPot_Rho0

DynamicalFriction_ExtPot_R

DynamicalFriction_ExtPot_Center

DynamicalFriction_ExtPot_MFrac

Aux_Record_User_GC()

Goal:

to record the position of minimum potential

to record the position of GC

Input:

FIX_CENTER

SEARCH_RADIUS

Output:

table of the position of the minimum potential

table of the position of the GC

plot_compare.py

Goal:

to provide the Chandrasekhar prediction

to plot the comparison of Chandrasekhar's prediction and the simulation results.

Input:

Chandrasekhar_result_r-t

table of the position of the minimum potential

table of the position of the GC

BOX_SIZE, NXO_TOT_X, END_T

LN_LAMBDA_BMAX_FACTOR, LN_LAMBDA_BMIN_FACTOR

GC_Sortening

Output:

Chandrasekhar_result_r-t

radius-time comparison figures

The 2nd suggestion:

Combine A_SET_IC.py and C_Chandrasekhar_dynamical_friction.py to calculate the initial parameters and analytical prediction.

Set the parameters manually in Input__TestProb and only feed needed parameters to GAMER.

Use a script to analyze the results.

Steps

Use a Python script to get the initial parameters

Goal:

to provide a density profile of the halo as the initial condition

to provide the initial parameters for halos and GC

to provide the Chandrasekhar prediction

Input

Cloud_Center

HALO_TYPE, HALO_Rs, HALO_Rt, HALO_Rho0

STELLAR_TYPE, STELLAR_Rs, STELLAR_Rt, STELLAR_Rho0

GC_MASS, GC_Initial_R

PURE_TABLE

BOX_SIZE, NXO_TOT_X, END_T

LN_LAMBDA_BMAX_FACTOR, LN_LAMBDA_BMIN_FACTOR

GC_Sortening

Output

Density profile file

Mass profile file

GC_POS

GC_VEL

Cloud_BulkVel

Cloud_Rho0

Cloud_R0

Cloud_MaxR

Chandrasekhar_result_r-t

In Input__TestProb

GC_SmallGas

FIX_CENTER

SEARCH_RADIUS

Density profile of the halo

Here, maybe we can provide the generated density profiles in this test problem directory and the recommended parameters in README for the three default cases to save the user’s time.

Cloud_BulkVel

Cloud_Rho0

Cloud_R0

Cloud_MaxR

GC_MASS

GC_POS

GC_VEL

Init_TestProb_Hydro_DynamicalFriction()

Goal:

to read the parameters to set the fluid

to read the parameters to record the center

to read the parameters for the GC

Input:

GC_SmallGas

FIX_CENTER

SEARCH_RADIUS

GC_MASS

GC_POS

GC_VEL

Par_Init_ByFunction_GC()

Goal:

to set the initial condition of the halo

to set the initial condition of the GC

Input

Density profile of the halo

Cloud_BulkVel

Cloud_Rho0

Cloud_R0

Cloud_MaxR

GC_MASS

GC_POS

GC_VEL

Init_ExtPot_GC()

Goal:

to set the external potential

Input:

DynamicialFriction_ExtPot_Rho0

DynamicalFriction_ExtPot_R

DynamicalFriction_ExtPot_Center

DynamicalFriction_ExtPot_MFrac

Aux_Record_User_GC()

Goal:

to record the position of the minimum potential

to record the position of the GC

Input:

FIX_CENTER

SEARCH_RADIUS

Output:

table of the position of the minimum potential

table of the position of the GC

plot_compare.py

Goal:

to plot the comparison of Chandrasekhar's prediction and the simulation results.

Input:

Chandrasskhar_result_r-t

table of the position of the minimum potential

table of the position of the GC

BOX_SIZE, NX0_TOT_X0

Output:

radius-time comparison figures

hyschive · 2024-02-05T14:41:09Z

@JeiwHuang Thanks for the extremely careful and thorough review!

@ej-1211: I agree with @JeiwHuang's most comments. For example,

Simplify the initial condition construction, if possible, by utilizing the built-in tools in gamer (e.g., Aux_ComputeProfile()).
Make variable names more descriptive
Add comments whenever appropriate
Follow the gamer coding format (e.g., no tabs, three-space indent, code alignment)
Minimize redundant code lines

If you have any questions or different opinions, please feel free to speak out 😉

…micalFriction()

ej-1211 · 2024-03-07T00:14:42Z

Followed the 1st suggestion above (working but not in GAMER coding style yet)
Aux_Record_User_DynamicalFriction() in Init_TestProb_Hydro_DynamicalFriction.cpp is done
- Remove unnesassary Record__RESULT_Previous_Center.txt
- changed RESULT to Result
- remove .txt from the output file name
- GAMER coding style done
  - three space indenting
  - { } in if else statement
- Aligned the Record__Result_* header and added #
- changed FixCenter to boolean and turn to if ( FixCenter )

ej-1211 · 2024-03-09T00:01:47Z

Separate Input__TestProb to Input__TestProb and Input__Profile_Params
- Input__Profile_Params is for ParticleEquilibriumIC Test problem
- reduced the amount of unregcognize parameter
Update the input file in /example
- Only save one set of Input__*
Add a feature that can automatically update Cloud_BulkVel* in Input__Profile_Params, which is calculated in the GAMER routine
Add "Stellar" part back

ej-1211 · 2024-03-11T01:57:42Z

Change from /b_min_factor and /b_max_factor to *b_min_factor and *b_max_factor
Throw away the datetime in the result file
read the parameter from the log file and the Record__Note File
removed A_ C_ X_

ej-1211 · 2024-03-26T23:57:42Z

@hsinhaoHHuang (@hyschive) Sorry for the late update, I have chosen the 1st suggestion above and have already fixed most of the problems (comments and suggestions) above, besides the fixing, in this version, we

Add the function of subtracting GC's potential so that it will be more accurate to find the center
Three cases (NFW, Burkert, DoublePowerLaw) are tested again and results are inside README
deleted the unnecessary script (python and .cpp) and unsupported feature

Please review my pull request again and please tell me if you have any suggestion!
Thank you very much !!!!

hsinhaoHHuang

Hi @ej-1211, Thanks for your update!

I have finished my second review and left some comments.
Please take another look, and please let me know if I didn't make myself clear.
Thanks!

Here is the result I got from the default set-up (DoublePowerLaw)
The vertical lines look a little weird to me but I am not sure whether this is expected.

example/test_problem/Hydro/DynamicalFriction/Input__Parameter

example/test_problem/Hydro/DynamicalFriction/Input__Profile_Params

example/test_problem/Hydro/DynamicalFriction/Input__TestProb

hsinhaoHHuang · 2024-04-04T07:40:32Z

example/test_problem/Hydro/DynamicalFriction/Input__TestProb

+SEARCH_RADIUS              2                             # search radius for the potential minimum search (unit:spatial resolution)
+                                                         # If FIX_CENTER = 1, this parameter is useless
+# (1) HALO and STELLAR Parameters
+HALO_TYPE                  DoublePowerLaw                # the type of the halo (NFW,Burkert,King,DoublePowerLaw)[DoublePowerLaw]


How about adding space between different halo types (i.e. (NFW, Burkert, King, DoublePowerLaw))?

@hsinhaoHHuang Do you mean in the comment area? If the answer is yes, I have fixed it!

hsinhaoHHuang · 2024-04-15T10:25:49Z

src/TestProblem/Hydro/DynamicalFriction/Init_TestProb_Hydro_DynamicalFriction.cpp

+      Aux_Message( stdout, "  GC small Gas        = %13.5e\n", GC_SmallGas );
+      Aux_Message( stdout, "  GC initial radius   = %13.5e\n", GC_R );
+      Aux_Message( stdout, "  GC Mass             = %13.5e\n", GC_MASS );
+      Aux_Message( stdout, "  Fix Center          = %d\n",     FixCenter );
+      Aux_Message( stdout, "  Search Radius       = %13.5e\n",  SearchRadius );
+      Aux_Message( stdout, "  Pure Table          = %d\n",     PURE_TABLE );
+      Aux_Message( stdout, "  Density Table Name  = %s\n",     TableName );
+      Aux_Message( stdout, "  Halo Type           = %s\n",     HaloType );
+      Aux_Message( stdout, "  HALO_RHO_0          = %13.5e\n", Halo_Rho0 );
+      Aux_Message( stdout, "  HALO_Rs             = %13.5e\n", Halo_Rs );
+      Aux_Message( stdout, "  HALO_Rt             = %13.5e\n", Halo_Rt );
+      Aux_Message( stdout, "  Halo_Profle_Param_a = %13.5f\n", Halo_Profile_Param_a );
+      Aux_Message( stdout, "  Halo_Profle_Param_b = %13.5f\n", Halo_Profile_Param_b );
+      Aux_Message( stdout, "  Halo_Profle_Param_c = %13.5f\n", Halo_Profile_Param_c );


How about using %13.7e for better alignment?

hsinhaoHHuang · 2024-04-15T10:27:27Z

src/TestProblem/Hydro/DynamicalFriction/Init_TestProb_Hydro_DynamicalFriction.cpp

+      if ( MPI_Rank == 0 )
+         {
+         char Filename[MAX_STRING];
+         sprintf( Filename, "%s", "Record__Result_Center" );


How about specifying that it is the minimum potential in the filename?

hsinhaoHHuang · 2024-04-15T10:29:00Z

src/TestProblem/Hydro/DynamicalFriction/Init_TestProb_Hydro_DynamicalFriction.cpp

+         {
+            fprintf(File, "%15s\t%15s\t%15s\t%15s\n", "#          Time", " CenterX", " CenterY", " CenterZ");
+         }
+         fprintf(File, "%15.7f\t%15.7e\t%15.7e\t%15.7e\n",


How about also printing the Time as %15.7e?

src/TestProblem/Hydro/DynamicalFriction/Calculate_IC.cpp

hsinhaoHHuang · 2024-04-15T10:38:16Z

...est_problem/Hydro/DynamicalFriction/Tools/calculate_ChandrasekharDynamicalFrictionFormula.py

I got this warning:

IntegrationWarning: The maximum number of subdivisions (50) has been achieved. If increasing the limit yields no improvement it is advised to analyze the integrand in order to determine the difficulties. If the position of a local difficulty can be determined (singularity, discontinuity) one will probably gain from splitting up the interval and calling the integrator on the subranges. Perhaps a special-purpose integrator should be used.

hyschive · 2024-07-20T06:19:17Z

@ej-1211 Just a reminder. Let's get it done this summer 💪

Add DynamicalFriction Test Problem

6f7eeef

hyschive requested a review from koarakawaii October 18, 2023 14:34

hyschive assigned koarakawaii Oct 18, 2023

hyschive added enhancement particle Particles test Test problems labels Oct 18, 2023

ej-1211 and others added 2 commits December 24, 2023 17:47

Resolved merge conflicts

7754142

DF Test Problem : fix bug, add example

eb97e1d

hyschive requested review from hsinhaoHHuang and removed request for koarakawaii January 12, 2024 02:12

hyschive assigned hsinhaoHHuang and unassigned koarakawaii Jan 12, 2024

Resolved Merge conflicts with newest main branch

d9b1151

hsinhaoHHuang suggested changes Feb 3, 2024

View reviewed changes

Modify Init_TestProb_Hydro_DynamicalFriction.cpp/Aux_Record_User_Dyna…

10709dd

…micalFriction()

ej-1211 added 3 commits March 7, 2024 09:41

Modify Init_TestProb_Hydro_DynamicalFriction.cpp/Set_Parameter()

2dc9a27

Reduce 'unrecognize parameter' (0304_Test)

9c31200

change example/Input_*

2282be9

ej-1211 added 9 commits March 9, 2024 09:53

Code Style : SetParameter()

0f3ea51

Fix Input__* & Par_Init_() style

0e86680

fix Input__Parameter Input__TestProb and some minor things

7f04f9a

fix Init_ / delete useless parameter in Input_

396c713

Remove A_SET_IC.py & modify D_Compare.py

992946f

change D_Compare.py to plot_comparison & remove datetime import

308ee7a

Fix Trailing Space for Init_*

6095193

Fix trailing

81a1da1

Modification in example/../Tools, Reading from Record__Note

4099f1d

calculate Chandrasekhar & fix bmax bmin factor

2901f0c

ej-1211 added 15 commits March 11, 2024 10:02

changed 'some_function.py' to 'read_parameters.py'

d0ce152

fix clean.sh

fb686a5

Add AdjustGCPotential()

3c2202b

Fix massbase() & Input__Testprob

a97c401

Modify and adjust example script

69f1e11

Delete some unneccsasry file

c5cc064

Finalize Init_ file

2bf89ec

Add README

f56548d

delete .swp

43e9a62

Fix Alignment in Input__*

6e09449

add the ln_lambda_factor in README

d4d60e3

change E to e

8d3c2fe

Add comments on all python script

d05b0a9

make the return of DF calaulation be specific

8222055

align the qual sign in python script if it is near

dcbe53b

hsinhaoHHuang suggested changes Apr 15, 2024

View reviewed changes

ej-1211 added 5 commits April 19, 2024 20:53

change to the right scientific symbol and correct the GC's mass for DPDL

657b7cd

Fix the typo in Input__Parameter and Input__TestProb

a54655c

Fix README

ad053b4

Change Variable Capital problem and fix Input_TestProb

2ae24df

Fix Calculate_IC.cpp

7386486

minor change for indentaion and tabs

9aac252

hyschive requested a review from hsinhaoHHuang January 4, 2025 07:11

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Add DynamicalFriction Test Problem #252

Add DynamicalFriction Test Problem #252

ej-1211 commented Oct 17, 2023

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hyschive commented Jul 20, 2024

Add DynamicalFriction Test Problem #252

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Add DynamicalFriction Test Problem #252

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The 1st suggestion:

Steps:

The 2nd suggestion:

Steps

hyschive commented Feb 5, 2024

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