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merge develop into master #59

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merged 77 commits into from
Mar 26, 2024
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874bc21
<WIP> add lib_make_convolution.py and sim_trhepd_rheed_mb_connect.py
H-Iwamoto-research Jul 20, 2023
f0cb3ee
add: solver="sim-trhepd-rheed-mb_connect" is available.
H-Iwamoto-research Jul 27, 2023
46c3880
normalization = "MS_NORM_SET_WGT" and Rfactor_type = "A" is aveilable.
H-Iwamoto-research Aug 2, 2023
fc9322f
mod : Keep the rocking curve data as "self.calc_rocking_curve".
H-Iwamoto-research Aug 13, 2023
109a33c
Only MPIrank=0 process executes _check_template.
H-Iwamoto-research Aug 26, 2023
b8cb487
Update sim-trhepd-rheed.rst
H-Iwamoto-research Sep 7, 2023
91c031b
fix : iset and LogXXX_XXX directory
H-Iwamoto-research Sep 7, 2023
29a5e27
fix errors in sim-trhepd-rheed.rst
H-Iwamoto-research Sep 8, 2023
e376f02
Removed redundant comments and debugging code.
H-Iwamoto-research Sep 10, 2023
ad1c34c
Add test data of sim_trepd_rheed_mb_connect.
H-Iwamoto-research Sep 13, 2023
655ba3b
Edited about "detail_timer"
H-Iwamoto-research Sep 13, 2023
c2c6255
Added comment of "surf_tempalte_width_for_fortran" and "bulk_out_widt…
H-Iwamoto-research Sep 13, 2023
add625a
Added comment about "emp_str".
H-Iwamoto-research Sep 13, 2023
4724feb
Get "generate_rocking_curve" in "Class Input" and "Class Output".
H-Iwamoto-research Sep 14, 2023
499b10a
Rename the file from RockingCurve.txt to RockingCurve_calculated.txt
H-Iwamoto-research Sep 18, 2023
976feb1
Change in operation to remove headers in computed data files.
H-Iwamoto-research Sep 20, 2023
3755365
delete 'RC_data_cnv' in sim_trhepd_rheed_mb_connect.py
H-Iwamoto-research Sep 20, 2023
5e1a921
Modification of the reference data (= experiment data) reading section.
H-Iwamoto-research Sep 26, 2023
168da7d
"limitation" is available.
H-Iwamoto-research Sep 28, 2023
8ef6af7
Merge branch 'limitation' into TRHEPD_manybeam_with_limitation
H-Iwamoto-research Sep 28, 2023
db51b93
Modification of the calculate data reading section.
H-Iwamoto-research Oct 3, 2023
4147260
delete row_number
H-Iwamoto-research Oct 4, 2023
2a55492
delete degree_max and degree_list
H-Iwamoto-research Oct 4, 2023
fd8fcc5
Rename the variable "self.log_mode" to "self.isLogmode".
H-Iwamoto-research Oct 4, 2023
dc462c1
Calculate "angle_interval" in the "for" loop of the convolution calcu…
H-Iwamoto-research Oct 4, 2023
8c4a416
normalization == "MAX" is disabled.
H-Iwamoto-research Oct 4, 2023
6b95b24
Changes to R-factor calculation and normalization.
H-Iwamoto-research Oct 12, 2023
21d9643
Changes related to RockingCurve_calculated.txt.
H-Iwamoto-research Oct 12, 2023
8f3a9e0
Renewal of normalization options
H-Iwamoto-research Oct 12, 2023
5e13d6f
Merge branch 'TRHEPD_manybeam' into TRHEPD_manybeam_with_limitation
H-Iwamoto-research Oct 13, 2023
d368b93
change solver name
H-Iwamoto-research Oct 14, 2023
d827956
Merge branch 'TRHEPD_manybeam' into TRHEPD_manybeam_with_limitation
H-Iwamoto-research Oct 14, 2023
1f91598
delete sim_trhepd_rheed_mb_connect.py
H-Iwamoto-research Oct 14, 2023
3d85410
delete sim_trhepd_rheed_mb_connect.py
H-Iwamoto-research Oct 14, 2023
4e7c966
Edited about self.Rfactor_type="B".
H-Iwamoto-research Oct 14, 2023
771511e
Minor changes to RockingCurve_calculated.txt
H-Iwamoto-research Oct 14, 2023
85f47ad
Delete unused function "_g"
H-Iwamoto-research Oct 14, 2023
f65713c
Removed redundant comments.
H-Iwamoto-research Oct 14, 2023
2dc0040
Merge branch 'TRHEPD_manybeam' into TRHEPD_manybeam_with_limitation
H-Iwamoto-research Oct 15, 2023
b59a903
Change of limitation on montecarlo
H-Iwamoto-research Oct 17, 2023
1d268cf
Change of limitation on minsearch.
H-Iwamoto-research Oct 17, 2023
830b7ec
Merge branch 'limitation' into TRHEPD_manybeam_with_limitation
H-Iwamoto-research Oct 17, 2023
96d2708
Add limitation section
H-Iwamoto-research Oct 30, 2023
a7019bb
bug fix
H-Iwamoto-research Oct 30, 2023
605f16b
Added sample of limitaiton
H-Iwamoto-research Oct 31, 2023
656c2e8
Rename best_result.txt -> ref.txt (in sample/analytical/limitation)
H-Iwamoto-research Oct 31, 2023
d8373e7
fix input.toml
H-Iwamoto-research Oct 31, 2023
980e7a3
Add file
H-Iwamoto-research Nov 1, 2023
9982dd0
Add tutorial of limitation
H-Iwamoto-research Nov 1, 2023
0afb0e6
normalization = "MULTI_SPOT" -> normalization = "MANY_BEAM"
H-Iwamoto-research Nov 3, 2023
d4a2650
Merge remote-tracking branch 'TRHEPD_manybeam' into TRHEPD_manybeam_w…
H-Iwamoto-research Nov 3, 2023
e092320
update document
H-Iwamoto-research Nov 11, 2023
63980bc
add comment
H-Iwamoto-research Nov 11, 2023
9e5ac83
add TypeHint
H-Iwamoto-research Nov 11, 2023
5c34d84
Adjustment of variable types
H-Iwamoto-research Nov 12, 2023
70c842b
Adjustment of variable types
H-Iwamoto-research Nov 12, 2023
b149b23
Slight adjustments to the document
H-Iwamoto-research Nov 13, 2023
da11583
Merge remote-tracking branch 'origin/TRHEPD_manybeam' into TRHEPD_man…
H-Iwamoto-research Nov 13, 2023
d2675f1
Merge remote-tracking branch 'origin/limitation' into TRHEPD_manybeam…
H-Iwamoto-research Nov 13, 2023
d2c927b
reformat
yomichi Feb 22, 2024
14846c5
update docs
yomichi Feb 22, 2024
3366b6b
update samples
yomichi Feb 28, 2024
3aecea4
update error messages
yomichi Feb 28, 2024
0fbcf9c
set run_scheme=subprocess as default for sim-trhepd-rheed
yomichi Mar 13, 2024
0b2014e
move STR manybeam samples
yomichi Mar 13, 2024
3c36082
fix script
yomichi Mar 13, 2024
b17831d
update tutorials (fix file paths)
yomichi Mar 13, 2024
d65ba59
update samples
yomichi Mar 13, 2024
d99a9b2
Merge pull request #56 from issp-center-dev/TRHEPD_manybeam_with_limi…
yomichi Mar 13, 2024
4571a8e
fix meshgrid
yomichi Mar 13, 2024
390c51c
don't check dimension (for transform)
yomichi Mar 13, 2024
ace0e6f
Merge pull request #58 from issp-center-dev/fix_57
yomichi Mar 13, 2024
33bd631
update gitignore
yomichi Mar 13, 2024
5c47712
(sim-trhepd-rheed) accept an integer for cal_number / exp_number
yomichi Mar 25, 2024
99c78ec
update
yomichi Mar 25, 2024
96f56c9
v2.2.0
yomichi Mar 26, 2024
9990bdc
update readme
yomichi Mar 26, 2024
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H-Iwamoto-research committed Nov 11, 2023

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commit 63980bcee17dd4bf4dbb2b332b40c60e60f7a0f6
13 changes: 9 additions & 4 deletions src/py2dmat/solver/sim_trhepd_rheed.py
Original file line number Diff line number Diff line change
@@ -175,7 +175,8 @@ def __init__(self, info, d_timer):
self.dimension = info.solver["dimension"]
else:
self.dimension = info.base["dimension"]


#read info
info_s = info.solver
self.run_scheme = info_s["run_scheme"]
self.generate_rocking_curve = info_s.get("generate_rocking_curve", False)
@@ -573,6 +574,7 @@ def __init__(self, info, d_timer):
msg ="ERROR: normalization must be "
msg+="MANY_BEAM or TOTAL"
raise exception.InputError(msg)

# solver.config
info_config = info_s.get("config", {})
self.surface_output_file = info_config.get(
@@ -722,7 +724,7 @@ def _post(self, fitted_x_list):
time_end = time.perf_counter()
self.detail_timer["calculate_R-factor"] += time_end - time_sta

#generate rocking curve
#generate RockingCurve_calculated.txt
dimension = self.dimension
string_list = self.string_list
cal_number = self.cal_number
@@ -820,8 +822,7 @@ def _calc_I_from_file(self):
self.isWarning_calcnline = True
calc_number_of_g_angles = calculated_nlines

# Define the array for the rocking curve data.
# Note the components with (beam-index)=0 are the degree data
# Define the array for the original calculated data.
RC_data_org = np.zeros((calc_number_of_g_angles, calc_number_of_beams_org+1))
for g_angle_index in range(calc_number_of_g_angles):
line_index = (calculated_first_line - 1) + g_angle_index
@@ -838,6 +839,7 @@ def _calc_I_from_file(self):

if self.isLogmode : time_sta = time.perf_counter()
verbose_mode = False
# convolution
data_convolution = lib_make_convolution.calc(
RC_data_org,
calc_number_of_beams_org,
@@ -860,6 +862,8 @@ def _calc_I_from_file(self):
glancing_angle = data_convolution[:,0]

beam_number_reference = len(cal_number)

# Normalization of calculated data.
for loop_index in range(beam_number_reference):
cal_index = cal_number[loop_index]
conv_I_calculated = data_convolution[:,cal_index]
@@ -892,6 +896,7 @@ def _calc_I_from_file(self):
[conv_I_calculated_normalized]]
)
if loop_index == beam_number_reference-1: #first loop
#calculate spot_weight
self.spot_weight = ( conv_I_calculated_norm_l
/ sum(conv_I_calculated_norm_l) )**2
elif self.normalization=="MANY_BEAM" and self.weight_type=="manual":