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61b318f
Port forward Stokes output, originally via Abhishek Joshi
Jan 26, 2021
d9527fa
Added functionality for vector parallel transport in ipolarray
avjoshi21 Mar 10, 2021
66d097a
Added code to reverse B field in model.c (when flag reverse_field in…
avjoshi21 Mar 10, 2021
e826531
Changes to record Stokes vector, e2 basis vector (constructed and par…
avjoshi21 Mar 10, 2021
7c987b3
added frontera.make from fix/frontera-complie
avjoshi21 Mar 12, 2021
8567d1d
edited to use frontera.make when on frontera
avjoshi21 Mar 12, 2021
54675e0
Merge branch 'hamr' into feature/stokes-output
Mar 22, 2021
27994ce
Merge branch 'hamr' into feature/stokes-output
Mar 22, 2021
e5860fb
Extra output of tensor quantities, some cleanup.
Mar 22, 2021
35b2ab8
Merge branch 'fix/dead-pixels' into feature/stokes-output
Mar 23, 2021
2c12768
Merge branch 'fix/dead-pixels' into feature/stokes-output
Mar 23, 2021
5651d7a
Merge branch 'fix/dead-pixels' into feature/stokes-output
Mar 23, 2021
a2217b5
add isothermal sphere model
gnwong Mar 26, 2021
5b5dc9d
Development continues
Apr 2, 2021
a770ed9
Merge dev back into stokes-output/reverse-B branch
Apr 2, 2021
1592030
add support for ressler iharm format
gnwong Apr 2, 2021
569992d
nits
gnwong Apr 9, 2021
713e029
remove 100M limit on rmax_geo
gnwong Apr 15, 2021
b527fa5
RIAF model from Pu & Broderick '18
Apr 17, 2021
966ed56
Finish cleaning up some debugging-only code
Apr 17, 2021
0255cf6
add base thermal sed for comparison purposes. agrees with draft after…
gnwong Apr 17, 2021
0589d51
add comparison inc data for thermal edf
gnwong Apr 17, 2021
6ffe54c
add kappa=4 isothermal sphere comparison values. (agrees with draft l…
gnwong Apr 17, 2021
1995a10
fix bug in parameter load
gnwong Apr 17, 2021
284a610
attempt to add edf parameters in reasonable way. this powerlaw abs se…
gnwong Apr 17, 2021
8664699
add (maybe incorrect) powerlaw fluxes
gnwong Apr 17, 2021
48981ff
add nuLnu to test output
gnwong Apr 18, 2021
b7a8eb7
add exponential radial coordinate for isothermal flat space sphere test
gnwong Apr 19, 2021
4908384
Disable automated run of the isothermal sphere model
Apr 19, 2021
c621f7d
add utility debug 'dump everything' function
gnwong Apr 21, 2021
f727da9
Fix RIAF function & add checks, fix some debugging fns/output
Apr 22, 2021
7943fdc
Clarify RIAF velocity behavior inside ISCO, check for unreasonable u^r
Apr 23, 2021
98fbc5c
Merge branch 'feature/isothermal-sphere' into feature/riaf-model
Apr 23, 2021
adb0c14
Move powerlaw and kappa parameters completely to model_radiation and …
Apr 23, 2021
4ee08f8
initialize coordinate names
gnwong Apr 25, 2021
fbf4041
add comparison riaf fluxes. note required high resolution.
gnwong Apr 25, 2021
33b2a0a
remove Kcon from dump_at_X since it's not actually used in to get the…
gnwong Apr 26, 2021
ab19346
Merge pull request #59 from AFD-Illinois/feature/isothermal-sphere
Apr 26, 2021
672ee7a
Merge pull request #63 from AFD-Illinois/feature/riaf-model
Apr 26, 2021
db2fa1f
add koral helper functions. might remove.
gnwong May 2, 2021
826d0c2
add forward and backward interpolation
gnwong May 2, 2021
8bbe9b6
add provisional grid interpolation routines with support for koral. d…
gnwong May 3, 2021
6166ec3
expose rmin_geo (required for simcoords
gnwong May 3, 2021
4d9d856
add proper assert include
gnwong May 3, 2021
82ba00b
Merge branch 'dev' into feature/stokes-output
May 20, 2021
50e267f
Enforce particular maximum polarization fractions in the emissivities…
May 24, 2021
22b9ca4
Overhaul analytic solution choices to be more systematic
May 25, 2021
c632b86
Explain reorthogonalization, rather than hand-waving. Use limiting s…
May 25, 2021
54cb4e2
Correct a citation(s)
May 25, 2021
6f1276d
Remove explicit zero case. Case 2->1 is stable and accurate if probab…
May 26, 2021
52681aa
Fix trivial merge conflict in comments
May 30, 2021
213c2d6
Merge branch 'master' into dev
May 30, 2021
b2d6a5b
Merge branch 'dev' into feature/revised-analytic-solution
May 30, 2021
08f4fd3
Fix trivial merge conflict
May 30, 2021
e52f219
Fix a typo and some omitted function stubs on merging master
May 31, 2021
e3668d1
Merge branch 'dev' into feature/revised-analytic-solution
May 31, 2021
123cef6
Merge branch 'dev' into feature/stokes-output
May 31, 2021
540293e
Replace cases with a single expression
May 31, 2021
12d2954
Fix a NaN in the kappa fits
Jun 1, 2021
e6f0e4f
Stabilize hypergeometric function application in Kappa fit, courtesy …
Jun 1, 2021
aaadb6e
Fix inlining and remove unused variable so GCC compiles correctly wit…
Jun 1, 2021
e2e22fb
Merge pull request #66 from AFD-Illinois/feature/revised-analytic-sol…
Jun 7, 2021
c414e99
Merge dev to variable kappa
Jun 7, 2021
410e233
Correct re-definitions in some models after the merge
Jun 7, 2021
a9cc5fa
Add j_I >= 0 constraint to unpolarized transport
Jun 20, 2021
02fc6a8
add more debug tooling and re-enable rhigh model
gnwong Jun 22, 2021
4a9580f
Fix an old bug that left some ghost zones uninitialized. Set a sensi…
Jun 22, 2021
7189f3d
Merge memory & transport fixes from dev back to var-kappa
Jun 22, 2021
f93fa02
Be slightly more wary of dividing by small numbers in new analytic ex…
Jun 24, 2021
fc6ed24
Use clang (AOCC) on Illinois BH29. Don't override user/module's HDF5…
Jun 25, 2021
08f2755
Remove unnecessary flags for BH cluster
Jun 25, 2021
4441b94
Avoid requiring that optimizing compilers be in environment
Jun 25, 2021
c79fb21
Merge branch 'dev' into feature/var-kappa
Jun 28, 2021
6f5fb5f
Preliminary kappa rotativities for polarized transport, see Marszewsk…
Jun 30, 2021
d27a4cf
Merge branch 'master' into dev
Jul 1, 2021
edd1aa8
vbump after merging master 1.4 fixes
Jul 1, 2021
c49057d
Merge branch 'dev' into feature/var-kappa
Jul 1, 2021
8ac4bab
Actually merge new master version
Jul 1, 2021
773d7ce
Merge branch 'dev' into feature/var-kappa
Jul 1, 2021
c9648f0
More NaN checks under debug, guards against Nlow==0.
Jul 1, 2021
327f161
Banish checks on thetae to debug builds where they will have context
Jul 1, 2021
46ec573
Some mitigations and much debug output related to kappa-distribution …
Jul 2, 2021
264ffe7
Merge dev and var-kappa work into stokes-output
Jul 2, 2021
0ee968c
Enforce max polarized emission properly
Jul 2, 2021
9540848
Why is it every time I say it won't be a dumb bug, it's a dumb bug? …
Jul 6, 2021
34ba772
Merge branch 'dev' into feature/stokes-output
Jul 6, 2021
056d42a
modify the way iharm model loader deals with mdot and add proper EKS …
gnwong Jul 11, 2021
f0b9fc4
remove extraneous print statement
gnwong Jul 11, 2021
d63fbef
add diagnostic print statements for comparison purposes.
gnwong Jul 11, 2021
4ea31f1
Better debug output for increasingly frequent NaNs in transport coeff…
Jul 13, 2021
e2368af
Merge branch 'feature/var-kappa' into unified-coefficients
Jul 19, 2021
6b14061
Merge branch 'feature/stokes-output' into unified-coefficients
Jul 19, 2021
b0eeef8
Overhaul emission coefficients
Jul 19, 2021
24ad6ff
Add the good parts of the dev branch changes to unified-coeffs
Jul 19, 2021
07834a4
Add back all original emission coefficients, pass the tests locally
Jul 20, 2021
649046f
Revert premature optimization
Jul 20, 2021
879a499
Fix compile after reverting calling convention
Jul 20, 2021
c96a622
Merge branch 'dev' into feature/ressler-support
gnwong Jul 20, 2021
c894cf7
Merge pull request #70 from AFD-Illinois/feature/ressler-support
gnwong Jul 20, 2021
3098dfa
Merge Ressler support to Stokes output branch, clean up extra print s…
Jul 20, 2021
64c939a
Fix old NaN in rho_Q fits which started showing up in pixels after an…
Jul 23, 2021
1e14c7a
Eliminate old print statements from Ressler branch (again?) and fix a…
Jul 30, 2021
276cd99
Merge simcoords into new unified coefficients branch
Jul 30, 2021
4ee575a
Tweaks for MKS2 systems after merging simcoords
Jul 30, 2021
245ce82
Clean up printing B field warning, as reversal is now off by default
Aug 3, 2021
f2905d6
Add a floor for cooling times (ceiling on temperature) shorter than t…
Aug 3, 2021
4d46002
Update unified branch with dev fixes
Aug 10, 2021
4495603
Fix some printed output when running on KORAL dumps. Add sigma, beta …
Aug 10, 2021
47e037b
Disable dynamical-time cooling by default, load BHAC dumps correctly …
Aug 13, 2021
83f4be6
Move rmin_geo and rmax_geo to coordinates.c. They still must be set …
Aug 13, 2021
e0500d9
Add Bremsstrahlung emission coefficients, via Ricardo Yarza's work on…
Sep 2, 2021
9af6c1d
Merge pull request #52 from AFD-Illinois/feature/stokes-output
Sep 2, 2021
d99a0b2
Merge dev back into unified-coeffs
Sep 2, 2021
91c4c49
Merge pull request #72 from AFD-Illinois/unified-coefficients
Sep 2, 2021
93adc10
Add variable kappa model courtesy of Razieh Emami. Floors for model s…
Sep 8, 2021
571f6df
Merge branch 'master' into dev
Sep 8, 2021
b31e015
Merge branch 'dev' of github:afd-illinois/ipole into dev
Sep 8, 2021
4f55564
Control behavior of variable kappa fits with parameters
Sep 17, 2021
1624448
Re-enable guard for zero emission angle in unpolarized transport, mak…
Sep 19, 2021
75d7ded
Fix NaN value when jX==Bnu==0
Oct 21, 2021
f1153e9
Fix NaN in a previously-missed spot we use the blackbody function, in…
Oct 26, 2021
3d48008
Merge pull request #75 from AFD-Illinois/fix/nan-thermal-abs
Oct 26, 2021
164a165
Update model_radiation.c
Jan 6, 2022
7214735
Fix test scripts on some machines by specifying python3
Jan 10, 2022
f3ca05d
Correct a very old typo
Jan 13, 2022
e760a4d
add sigma_cut_high to allow for sigmoid-like sigma cutoff
gnwong Feb 1, 2022
e13bae2
Merge pull request #77 from AFD-Illinois/feature/sigma-sigmoid
Feb 4, 2022
1e6e39b
add command line argument to target mdot
gnwong Apr 18, 2022
f6c1873
update code to automatically override M_unit -> 1 when mdot set befor…
gnwong Apr 19, 2022
715b459
Merge pull request #81 from AFD-Illinois/feature/target_mdot
gnwong Apr 19, 2022
c43fa2c
force rescale magnetic field after resetting M_unit
gnwong Apr 20, 2022
bd7679a
Merge pull request #82 from AFD-Illinois/feature/target_mdot
gnwong Apr 20, 2022
0c32905
added target to statically compile ipole. will need tweaks to find th…
avjoshi21 Apr 25, 2022
bc87ce6
fixed reverse field issue (thanks to Ben) where it wasn't iterating o…
avjoshi21 Jun 15, 2022
3778603
Merge pull request #83 from AFD-Illinois/fix/reverse_field
Jun 17, 2022
78ae984
fixed reverse field issue
avjoshi21 Jul 20, 2022
ccf6b68
Merge remote-tracking branch 'origin/dev' into feature/bh29-compile
avjoshi21 Sep 14, 2022
5b032c3
added field configuration to output header
avjoshi21 Sep 15, 2022
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5 changes: 4 additions & 1 deletion machines/bh-cluster.make
Original file line number Diff line number Diff line change
@@ -1 +1,4 @@
CFLAGS_CUSTOM = -D_DEFAULT_SOURCE -shlib
# For oneapi. Load with ". /opt/intel/oneapi/setvars.sh"
CC=/opt/intel/oneapi/compiler/2021.1.2/linux/bin/intel64/icc
CFLAGS=-xHost -Ofast -fstrict-aliasing -Wall -Werror -ipo -qopenmp
HDF5_DIR=/usr/lib/hpc/gnu7/hdf5/1.10.5
3 changes: 3 additions & 0 deletions machines/bh29.make
Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
# For AOCC. Load with ". /opt/AMD/aocc-compiler-3.0.0/setenv_AOCC.sh"
CC=/opt/AMD/aocc-compiler-3.0.0/bin/clang
CFLAGS=-std=gnu99 -O3 -march=native -mtune=native -flto -fopenmp -funroll-loops
11 changes: 7 additions & 4 deletions makefile
Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@ HDF5_DIR =
GSL_DIR =
# System /lib equivalent (can be /usr/lib, /lib64, /usr/lib64)
# Can leave this blank if it's included automatically by GCC
SYSTEM_LIBDIR = /lib64
SYSTEM_LIBDIR =

# Try pointing this to h5pcc or h5cc on your machine, before hunting down libraries
CC=h5cc
Expand Down Expand Up @@ -45,7 +45,7 @@ ifneq (,$(findstring stampede2,$(HOST)))
-include $(MAKEFILE_PATH)/machines/stampede2.make
endif
ifneq (,$(findstring frontera,$(HOST)))
-include $(MAKEFILE_PATH)/machines/frontera.make
-include $(MAKEFILE_PATH)/machines/frontera.make
endif
# Hack to check only whether host begins with bh*
ifneq (,$(findstring beginsbh,begins$(HOST)))
Expand Down Expand Up @@ -91,12 +91,12 @@ LIB = $(MATH_LIB) $(GSL_LIB)
# Add HDF and MPI directories only if compiler doesn't
ifneq ($(strip $(HDF5_DIR)),)
INC += -I$(HDF5_DIR)/include/
LIBDIR += -L$(HDF5_DIR)/lib/
LIBDIR += -L$(HDF5_DIR)/lib64/
LIB += $(HDF5_LIB)
endif
ifneq ($(strip $(GSL_DIR)),)
INC += -I$(GSL_DIR)/include/
LIBDIR += -L$(GSL_DIR)/lib/
LIBDIR += -L$(GSL_DIR)/lib64/
endif
ifneq ($(strip $(SYSTEM_LIBDIR)),)
# Prefer user libraries (above) to system
Expand All @@ -113,6 +113,9 @@ build: $(EXE)
@$(ECHO) "CFLAGS: $(CFLAGS)"
@$(ECHO) "MD5: $(shell $(MD5) $(EXE))"

static: CFLAGS += -static
static: build

debug: CFLAGS += -g -Wall -Werror -Wno-unused-variable -Wno-unused-but-set-variable
debug: CFLAGS += -DDEBUG=1
debug: build
Expand Down
15 changes: 7 additions & 8 deletions model/analytic/model.c
Original file line number Diff line number Diff line change
Expand Up @@ -16,10 +16,7 @@ double Te_unit;
// This one is useful
double RHO_unit;

// Model parameters: public
double rmax_geo = 1000.0;
// Model parameters: private
static double rmin_geo = 0;
static double MBH_solar = 4.e6;
static double RHO_unit_in = 0;

Expand Down Expand Up @@ -58,7 +55,7 @@ void try_set_model_parameter(const char *word, const char *value)
set_by_word_val(word, value, "model", &model, TYPE_INT);
set_by_word_val(word, value, "MBH", &MBH_solar, TYPE_DBL);
set_by_word_val(word, value, "rho_unit", &RHO_unit_in, TYPE_DBL);
// TODO NEED to move this into main parameters
// TODO move these calls into the main parameters
set_by_word_val(word, value, "rmax_geo", &rmax_geo, TYPE_DBL);
set_by_word_val(word, value, "rmin_geo", &rmin_geo, TYPE_DBL);

Expand Down Expand Up @@ -137,7 +134,8 @@ void set_units()
Rh = 1 + sqrt(1. - a * a);
Rin = Rh;
Rout = 1000.0;
// Limit rmax_geo?
rmin_geo = 1.;
rmax_geo = 10000.;

double z1 = 1. + pow(1. - a * a, 1. / 3.) * (pow(1. + a, 1. / 3.) + pow(1. - a, 1. / 3.));
double z2 = sqrt(3. * a * a + z1 * z1);
Expand Down Expand Up @@ -317,8 +315,9 @@ int radiating_region(double X[NDIM])
// Define these to specify a fluid model: e- density/temperature for
// synchrotron radiation based on an energy distribution
double get_model_thetae(double X[NDIM]) {return 0;}
void get_model_powerlaw_vals(double X[NDIM], double *p, double *n,
double *gamma_min, double *gamma_max, double *gamma_cut) {return;}

double get_model_sigma(double X[NDIM]) {return 0;}
double get_model_beta(double X[NDIM]) {return 0;}
void update_data(double *tA, double *tB) {return;}
void update_data_until(double *tA, double *tB, double tgt) {return;}
// This is only called for trace file output, and doesn't really apply to analytic models
void get_model_primitives(double X[NDIM], double *p) {return;}
3 changes: 0 additions & 3 deletions model/analytic/model_params.h
Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,4 @@

#define THIN_DISK (0)

// Necessary model parameters, can be used or not
extern double rmax_geo;

#endif /* MODEL_PARAMS_H */
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