From 66efd3dea9482a69681be33b05e9ed442a6c0578 Mon Sep 17 00:00:00 2001
From: "Joachim Wuttke (o)" <j.wuttke@fz-juelich.de>
Date: Tue, 11 Apr 2023 18:18:03 +0200
Subject: [PATCH 1/5] purge devtools: rm line counting tools
---
devtools/linecount/baloc/__init__.py | 3 -
devtools/linecount/baloc/file_types.py | 122 -----------------
devtools/linecount/baloc/history_collector.py | 128 ------------------
devtools/linecount/baloc/history_plot.py | 63 ---------
devtools/linecount/lines_of_code.py | 58 --------
5 files changed, 374 deletions(-)
delete mode 100644 devtools/linecount/baloc/__init__.py
delete mode 100644 devtools/linecount/baloc/file_types.py
delete mode 100644 devtools/linecount/baloc/history_collector.py
delete mode 100644 devtools/linecount/baloc/history_plot.py
delete mode 100755 devtools/linecount/lines_of_code.py
diff --git a/devtools/linecount/baloc/__init__.py b/devtools/linecount/baloc/__init__.py
deleted file mode 100644
index c8a9d7cc449..00000000000
--- a/devtools/linecount/baloc/__init__.py
+++ /dev/null
@@ -1,3 +0,0 @@
-from .file_types import *
-from .history_collector import *
-from .history_plot import *
diff --git a/devtools/linecount/baloc/file_types.py b/devtools/linecount/baloc/file_types.py
deleted file mode 100644
index 9a86fccbd53..00000000000
--- a/devtools/linecount/baloc/file_types.py
+++ /dev/null
@@ -1,122 +0,0 @@
-"""
-Contains machinery to convert BornAgain filename to the type of the content
-"""
-
-class FileTypes:
- """
- Enumerator class to hold file types
- """
- CORE, FTEST, UTEST, PYCODE, MACROS, GUI, PYAPI, THIRD, UNDEF, TOTAL = range(10)
- descr=["Core", "Functional Tests", "Unit Tests", "*.py", "macros", "GUI", "PythonAPI", "Third", "Undef"]
- @staticmethod
- def loc_for_type():
- result = []
- for i in range(FileTypes.TOTAL):
- result.append(0)
- return result
-
-
-def filePython(x):
- if ".py" in x and not ".pypp." in x: return True
- return False
-
-
-def fileCpp(x):
- if ".h" in x or ".cpp" in x: return True
- return False
-
-
-def dirCore(x):
- # if "/Core/Algorithms" in x: return True
- # if "/Core/FormFactors" in x: return True
- # if "/Core/Samples" in x: return True
- # if "/Core/StandardSamples" in x: return True
- # if "/Core/Tools" in x: return True
- # if "/Core/Fitting" in x: return True
- # if "/Core/inc" in x: return True
- # if "/Core/src" in x: return True
- # if "/Core/InputOutput" in x: return True
- # if "/Core/Geometry" in x: return True
- # if "/Fit/Factory" in x: return True
- # if "/Fit/FitKernel" in x: return True
- # if "/Fit/StandardFits" in x: return True
- # if "/Core/Geometry" in x: return True
- if "/Core/" in x: return True
- if "/Fit/" in x: return True
-
- return False
-
-
-def dirPyAPI(x):
- if "/Core/PythonAPI" in x: return True
- if "/Fit/PythonAPI" in x: return True
- return False
-
-
-def dirFuncTest(x):
- # if "/App/" in x: return True
- if "/Tests/Functional" in x: return True
- if "/Tests/PerformanceTests" in x: return True
- if "/Tests/FunctionalTests/TestCore" in x: return True
- if "/Tests/FunctionalTests/TestFit" in x: return True
- if "/Tests/FunctionalTests/TestPyCore" in x: return True
- if "/Tests/FunctionalTests/TestPyFit" in x: return True
- if "/Core/TestMachinery" in x: return True
- return False
-
-
-def dirGUI(x):
- if "/GUI/coregui" in x and not "widgetbox" in x and not "qttools" in x: return True
- if "/GUI/main" in x: return True
- if "/AppGUI/coregui" in x: return True
- if "/BASuite" in x: return True
- return False
-
-
-def dirThirdParty(x):
- if "/ThirdParty" in x: return True
- return False
-
-
-def dirSkip(x):
- if "/pub/core" in x: return True
- return False
-
-
-def dirUnitTests(x):
- if "/UnitTests/" in x: return True
- if "/Tests/UnitTests/TestCore/" in x: return True
- if "/Tests/UnitTests/TestFit/" in x: return True
- if "/Tests/UnitTests/" in x: return True
- return False
-
-
-def filetype(x):
- """
- Returns type of file
- """
- result = FileTypes.UNDEF
-
- if dirSkip(x):
- return result
-
- if dirPyAPI(x):
- result = FileTypes.PYAPI
-
- elif dirThirdParty(x):
- result = FileTypes.THIRD
-
- elif (fileCpp(x) or filePython(x)) and dirFuncTest(x):
- result = FileTypes.FTEST
-
- elif fileCpp(x) and dirCore(x):
- result = FileTypes.CORE
-
- elif dirUnitTests(x):
- result = FileTypes.UTEST
-
- elif dirGUI(x):
- result = FileTypes.GUI
-
- return result
-
diff --git a/devtools/linecount/baloc/history_collector.py b/devtools/linecount/baloc/history_collector.py
deleted file mode 100644
index 8ac42f65e6d..00000000000
--- a/devtools/linecount/baloc/history_collector.py
+++ /dev/null
@@ -1,128 +0,0 @@
-"""
-Process gitlog and create a file with number of lines of code.
-"""
-from datetime import datetime
-from .file_types import FileTypes, filetype
-import re
-from email.utils import parsedate
-import subprocess
-
-
-def gitlog():
- """
- Execute gitlog command and make generator over lines in the log
- """
- p = subprocess.Popen(['git', 'log', 'develop', '--reverse', '-p'], stdout=subprocess.PIPE)
- for line in iter(p.stdout.readline, b''):
- decoded = line.decode('latin1')
- if decoded and len(decoded):
- yield decoded.strip()
-
-
-class Commit:
- """
- Contains commit info and accumulated number of lines of code (file type dependent).
- """
- def __init__(self):
- self.date = datetime.today()
- self.added_lines = 0
- self.removed_lines = 0
- self.loc_for_type = FileTypes.loc_for_type()
- self.hsh = None
- self.who = None
- self.cmt = None
-
- def increment_loc(self, file_type):
- self.loc_for_type[file_type] += 1
- self.added_lines += 1
-
- def decrement_loc(self, file_type):
- self.loc_for_type[file_type] -= 1
- self.removed_lines += 1
-
-
-class DayHistory:
- """
- Number of lines added or deleted for given day.
- """
- def __init__(self, date, locs):
- self.date = date
- self.loc_for_type = locs
-
-
-class HistoryCollector:
- def __init__(self):
- self.last_commit = Commit()
- self.data = []
- self.locs = 0
- self.fc = 0
- self.file_type_ppp = FileTypes.UNDEF
- self.file_type_mmm = FileTypes.UNDEF
- self.start_date = datetime(2012, 4, 1)
- self.days_history = {} # DayHistory vs. number of days since beginning of coding
-
- def pop(self):
- if not self.last_commit.added_lines:
- return
- pstr="%s %8u %5s %5s %7s %s"%(self.last_commit.date, self.locs, '+' + str(self.last_commit.added_lines), '-' + str(self.last_commit.removed_lines), self.last_commit.hsh, self.last_commit.who)
- print(pstr)
- delta = (self.last_commit.date - self.start_date).days
- self.days_history[delta] = DayHistory(self.last_commit.date, self.last_commit.loc_for_type)
-
- tmp = list(self.last_commit.loc_for_type)
- self.last_commit = Commit()
- self.last_commit.loc_for_type = tmp
-
- def run(self):
- nnn = 0
- for x in gitlog():
- nnn += 1
- if x.startswith('commit'):
- self.pop()
- self.last_commit.hsh = x[7:14]
-
- if x.startswith('Author'):
- self.last_commit.who = x.replace("Author: ", '').replace('\n', '')
- self.last_commit.who = re.sub(">.*", "", self.last_commit.who)
- self.last_commit.who = re.sub(".*<", "", self.last_commit.who)
-
- if x.startswith('Date'):
- self.fc = 1
- self.last_commit.date = datetime(*parsedate(x[5:])[:7])
-
- if self.fc == 2:
- self.last_commit.cmt = x[:-1]
- self.fc = 0
-
- if self.fc == 1:
- if len(x) == 1:
- self.fc = 2
-
- if x.startswith('+++'):
- self.file_type_ppp = filetype(x)
-
- if x.startswith('---'):
- self.file_type_mmm = filetype(x)
-
- if x.startswith('+') and not x.startswith('+++'):
- self.last_commit.increment_loc(self.file_type_ppp)
- if self.file_type_ppp <FileTypes.PYAPI:
- self.locs += 1
-
- if x.startswith('-') and not x.startswith('---'):
- self.last_commit.decrement_loc(self.file_type_mmm)
- if self.file_type_mmm < FileTypes.PYAPI:
- self.locs -= 1
-
- # if nnn>1000000:
- # break
-
- self.pop()
-
- def save_report(self, filename):
- print("Saving report in {0}".format(filename))
- with open(filename, 'w') as the_file:
- for key in self.days_history:
- dayhist = self.days_history[key]
- pstr = "%s %s \n" % (str(dayhist.date), ' '.join(str(e) for e in dayhist.loc_for_type))
- the_file.write(pstr)
diff --git a/devtools/linecount/baloc/history_plot.py b/devtools/linecount/baloc/history_plot.py
deleted file mode 100644
index 73eabfc5792..00000000000
--- a/devtools/linecount/baloc/history_plot.py
+++ /dev/null
@@ -1,63 +0,0 @@
-import matplotlib.pyplot as plt
-import seaborn as sns
-from datetime import datetime
-from .file_types import FileTypes, filetype
-
-
-selected_file_type = [FileTypes.CORE, FileTypes.FTEST, FileTypes.UTEST, FileTypes.GUI, FileTypes.PYAPI]
-
-
-def read_history(filename):
- xvals = [] # Time
- ydata = {} # id of file type .vs. LOC .vs. time
- for x in selected_file_type:
- ydata[x] = []
-
- print("Reading file {0}".format(filename))
- with open(filename, 'r') as the_file:
- for line in the_file:
- parts = line.strip().split()
- date = datetime.strptime(parts[0] + " " + parts[1], '%Y-%m-%d %H:%M:%S')
- xvals.append(date)
- for x in selected_file_type:
- ydata[x].append(int(parts[2+x]))
-
- yvals = []
- descr = []
- for key in ydata:
- descr.append(FileTypes.descr[key])
- yvals.append(ydata[key])
-
- # printing summary of LOC
- for x in range(0, len(yvals)):
- print("{:18} : {:10}".format(descr[x], yvals[x][-1]))
-
- return xvals, yvals, descr
-
-
-def history_plot(filename):
- xvals, yvals, descr = read_history(filename)
-
- # figure size
- my_dpi = 96
- plt.figure(figsize=(1600*1.2 / my_dpi, 900*1.2 / my_dpi), dpi=my_dpi)
- plt.style.use('seaborn-bright')
-
- # making stackplot
- plt.stackplot(xvals, yvals)
- pal = ["#3399ff", "#ffcc00", "#ff0000", "#0033ff", "#999999"]
- plt.stackplot(xvals, yvals, labels=descr, colors=pal)
-
- # styling axes and grid
- plt.grid(color='gray', linestyle='dashed')
- ax = plt.gca()
- ax.set_axisbelow(True)
- plt.ylim(0.0, 220e+03)
- plt.tick_params(axis='both', which='major', labelsize=14)
-
- # making inverse legend
- handles, labels = ax.get_legend_handles_labels()
- ax.legend(handles[::-1], labels[::-1], loc='upper left', prop={'size': 18})
-
- # saving plot
- plt.savefig('lines_of_code.png', dpi=my_dpi, bbox_inches='tight')
diff --git a/devtools/linecount/lines_of_code.py b/devtools/linecount/lines_of_code.py
deleted file mode 100755
index 2366fa6f5a4..00000000000
--- a/devtools/linecount/lines_of_code.py
+++ /dev/null
@@ -1,58 +0,0 @@
-#!/usr/bin/env python3
-"""
-Creates picture with number of lines of code.
-Usage: python3 lines_of_code.py
-
-The command should be executed in the directory where lines_of_code.py is located
-(i.e. in <BornAgain>/devtools/linecount)
-"""
-import sys
-if sys.version_info < (3, 0):
- exit("Requires python3, exiting ...")
-import os
-from baloc import HistoryCollector
-from baloc import history_plot
-import matplotlib.pyplot as plt
-
-
-gitlog_filename = "gitlog.tmp"
-
-
-def process_loc_number(targetfolder="../..", gitlog=gitlog_filename):
- prevfolder = os.getcwd()
- os.chdir(targetfolder)
-
- collector = HistoryCollector()
- collector.run()
- collector.save_report(os.path.join(prevfolder, gitlog))
-
- os.chdir(prevfolder)
-
-
-def plot_loc_number(gitlog=gitlog_filename):
- history_plot(gitlog)
- plt.show()
-
-
-if __name__ == '__main__':
- print('-' * 80)
- print("Generating picture for number of lines of code")
- print('-' * 80)
- print(" ")
- print("Possible options:")
- print("[0] - Generate {0} and picture.".format(gitlog_filename))
- print("[1] - Generate only {0}.".format(gitlog_filename))
- print("[2] - Generate picture using existing {0}.".format(gitlog_filename))
- print("[3] - Exit")
-
- var = int(input("Enter your choice [0]: ") or "0")
-
- if var == 0:
- process_loc_number()
- plot_loc_number()
- elif var == 1:
- process_loc_number()
- elif var == 2:
- plot_loc_number()
- else:
- exit("Good bye")
--
GitLab
From 06c790a1be052e12f78daa09013330f182541641 Mon Sep 17 00:00:00 2001
From: "Joachim Wuttke (o)" <j.wuttke@fz-juelich.de>
Date: Tue, 11 Apr 2023 18:21:56 +0200
Subject: [PATCH 2/5] devtools: script names uniformly with hyphen
---
Tests/Suite/Persist/Check.cpp | 4 ++--
devtools/view/{plot_diff_int.py => plot-diff.py} | 0
devtools/view/{plot_int.py => plot-int.py} | 0
devtools/view/{plot_numpy_array.py => plot-np-array.py} | 0
4 files changed, 2 insertions(+), 2 deletions(-)
rename devtools/view/{plot_diff_int.py => plot-diff.py} (100%)
rename devtools/view/{plot_int.py => plot-int.py} (100%)
rename devtools/view/{plot_numpy_array.py => plot-np-array.py} (100%)
diff --git a/Tests/Suite/Persist/Check.cpp b/Tests/Suite/Persist/Check.cpp
index 7a40ca9d0b2..4c09ffd4b9f 100644
--- a/Tests/Suite/Persist/Check.cpp
+++ b/Tests/Suite/Persist/Check.cpp
@@ -61,9 +61,9 @@ bool checkSimulation(const std::string& name, ISimulation& direct_simulation, co
BaseUtils::Filesystem::jointPath(BATesting::TestOutDir_Suite(), name + ".int.gz");
IOFactory::writeDatafield(*result_data, out_fname);
std::cout << "Notes:\n- to visualize an intensity map, use " << BABuild::srcDir()
- << "/devtools/view/plot_int.py\n"
+ << "/devtools/view/plot-int.py\n"
<< "- to plot a difference image, use " << BABuild::srcDir()
- << "/devtools/view/plot_diff_int.py\n"
+ << "/devtools/view/plot-diff.py\n"
<< "- if the new simulation result\n"
<< " " << out_fname << "\n"
<< " is correct, then move it to the reference directory\n"
diff --git a/devtools/view/plot_diff_int.py b/devtools/view/plot-diff.py
similarity index 100%
rename from devtools/view/plot_diff_int.py
rename to devtools/view/plot-diff.py
diff --git a/devtools/view/plot_int.py b/devtools/view/plot-int.py
similarity index 100%
rename from devtools/view/plot_int.py
rename to devtools/view/plot-int.py
diff --git a/devtools/view/plot_numpy_array.py b/devtools/view/plot-np-array.py
similarity index 100%
rename from devtools/view/plot_numpy_array.py
rename to devtools/view/plot-np-array.py
--
GitLab
From 866e9134cbaf98842c45dab4f2590006632c0a01 Mon Sep 17 00:00:00 2001
From: "Joachim Wuttke (o)" <j.wuttke@fz-juelich.de>
Date: Tue, 11 Apr 2023 18:23:52 +0200
Subject: [PATCH 3/5] devtools: rm MPI scripts
---
devtools/mpi/pytests/mpi_cpp_test.py | 76 --------------------
devtools/mpi/pytests/mpi_test.py | 103 ---------------------------
devtools/mpi/pytests/version.py | 2 -
devtools/mpi/supermuc.sh | 17 -----
4 files changed, 198 deletions(-)
delete mode 100644 devtools/mpi/pytests/mpi_cpp_test.py
delete mode 100644 devtools/mpi/pytests/mpi_test.py
delete mode 100644 devtools/mpi/pytests/version.py
delete mode 100644 devtools/mpi/supermuc.sh
diff --git a/devtools/mpi/pytests/mpi_cpp_test.py b/devtools/mpi/pytests/mpi_cpp_test.py
deleted file mode 100644
index ccc8774a3d5..00000000000
--- a/devtools/mpi/pytests/mpi_cpp_test.py
+++ /dev/null
@@ -1,76 +0,0 @@
-# Mixture of cylinders and prisms without interference
-
-from mpi4py import MPI # this line has to be first
-import numpy
-import matplotlib
-import pylab
-from libBornAgainCore import *
-
-comm = MPI.COMM_WORLD
-world_size = comm.Get_size()
-world_rank = comm.Get_rank()
-
-
-def get_sample():
- """
- Build and return the sample representing cylinders and pyramids on top of
- substrate without interference.
- """
- # defining materials
- m_air = HomogeneousMaterial("Air", 0.0, 0.0)
- m_substrate = HomogeneousMaterial("Substrate", 6e-6, 2e-8)
- m_particle = HomogeneousMaterial("Particle", 6e-4, 2e-8)
-
- # collection of particles
- cylinder_ff = FormFactorCylinder(5*nanometer, 5*nanometer)
- cylinder = Particle(m_particle, cylinder_ff)
- prism_ff = FormFactorPrism3(10*nanometer, 5*nanometer)
- prism = Particle(m_particle, prism_ff)
- particle_layout = ParticleLayout()
- particle_layout.addParticle(cylinder, 0.5)
- particle_layout.addParticle(prism, 0.5)
-
- # air layer with particles and substrate form multi layer
- air_layer = Layer(m_air)
- air_layer.addLayout(particle_layout)
- substrate_layer = Layer(m_substrate)
- multi_layer = MultiLayer()
- multi_layer.addLayer(air_layer)
- multi_layer.addLayer(substrate_layer)
- return multi_layer
-
-
-def get_simulation():
- """
- Create and return GISAS simulation with beam and detector defined
- """
- simulation = GISASSimulation()
- simulation.setDetectorParameters(100, -1.0*degree, 1.0*degree, 100, 0.0*degree, 2.0*degree)
- simulation.setBeamParameters(1.0*angstrom, 0.2*degree, 0.0*degree)
- sample = get_sample()
- simulation.setSample(sample)
-
- return simulation
-
-
-def run_simulation():
- """
- Run simulation and plot results
- """
- simulation = get_simulation()
-
- if(world_size == 1):
- print("Not an MPI environment, run with 'mpirun -n 4 python ompi_sim_example.py'")
- exit(0)
-
- simulation.runMPISimulation()
-
- if(world_rank == 0):
- sumresult = simulation.result().array()
- print(sumresult)
- # pylab.imshow(sumresult + 1, norm=matplotlib.colors.LogNorm(), extent=[-1.0, 1.0, 0, 2.0])
- # pylab.show()
-
-
-if __name__ == '__main__':
- run_simulation()
diff --git a/devtools/mpi/pytests/mpi_test.py b/devtools/mpi/pytests/mpi_test.py
deleted file mode 100644
index 367c46d41a7..00000000000
--- a/devtools/mpi/pytests/mpi_test.py
+++ /dev/null
@@ -1,103 +0,0 @@
-# Mixture of cylinders and prisms without interference (IsGISAXS example ex-1)
-
-from mpi4py import MPI # this line has to be first
-import numpy
-import matplotlib
-import pylab
-from libBornAgainCore import *
-
-comm = MPI.COMM_WORLD
-world_size = comm.Get_size()
-world_rank = comm.Get_rank()
-
-
-def get_sample():
- """
- Build and return the sample representing cylinders and pyramids on top of
- substrate without interference.
- """
- # defining materials
- m_air = HomogeneousMaterial("Air", 0.0, 0.0)
- m_substrate = HomogeneousMaterial("Substrate", 6e-6, 2e-8)
- m_particle = HomogeneousMaterial("Particle", 6e-4, 2e-8)
-
- # collection of particles
- cylinder_ff = FormFactorCylinder(5*nanometer, 5*nanometer)
- cylinder = Particle(m_particle, cylinder_ff)
- prism_ff = FormFactorPrism3(10*nanometer, 5*nanometer)
- prism = Particle(m_particle, prism_ff)
- particle_layout = ParticleLayout()
- particle_layout.addParticle(cylinder, 0.5)
- particle_layout.addParticle(prism, 0.5)
-
- # air layer with particles and substrate form multi layer
- air_layer = Layer(m_air)
- air_layer.addLayout(particle_layout)
- substrate_layer = Layer(m_substrate)
- multi_layer = MultiLayer()
- multi_layer.addLayer(air_layer)
- multi_layer.addLayer(substrate_layer)
- return multi_layer
-
-
-def get_simulation():
- """
- Create and return GISAXS simulation with beam and detector defined
- """
- simulation = GISASSimulation()
- simulation.setDetectorParameters(100, -1.0*degree, 1.0*degree, 100, 0.0*degree, 2.0*degree)
- simulation.setBeamParameters(1.0*angstrom, 0.2*degree, 0.0*degree)
- sample = get_sample()
- simulation.setSample(sample)
-
- return simulation
-
-
-def run_simulation():
- """
- Run simulation and plot results
- """
- simulation = get_simulation()
-
- if(world_size == 1):
- print("Not a MPI environment, run with 'mpirun -n 4 python ompi_sim_example.py'")
- exit(0)
-
- if(world_rank != 0):
- options = simulation.getOptions()
- thread_info = ThreadInfo()
- thread_info.n_threads = options.getNumberOfThreads()
- thread_info.n_batches = world_size - 1
- thread_info.current_batch = world_rank - 1
- options.setThreadInfo(thread_info)
- simulation.setOptions(options)
- print("preparing to run ", thread_info.n_batches, thread_info.current_batch)
- simulation.runSimulation()
- print("preparing to send")
- comm.Send(simulation.result().array(), 0)
-
- if(world_rank == 0):
- sumresult = simulation.result().array()
- print(sumresult)
- sumresult = numpy.zeros(sumresult.shape)
- print(sumresult)
-
- print("preparing to receive")
- for i_proc in range(1, world_size):
- print(" ... receiving", i_proc)
- result = numpy.zeros(sumresult.shape)
- comm.Recv(result, i_proc)
- sumresult += result
- print(sumresult)
-
- if(world_rank == 0):
- print(sumresult)
- # pylab.imshow(sumresult + 1, norm=matplotlib.colors.LogNorm(), extent=[-1.0, 1.0, 0, 2.0])
- # pylab.show()
-
-
-if __name__ == '__main__':
- run_simulation()
-
-
-
diff --git a/devtools/mpi/pytests/version.py b/devtools/mpi/pytests/version.py
deleted file mode 100644
index 261a6512c03..00000000000
--- a/devtools/mpi/pytests/version.py
+++ /dev/null
@@ -1,2 +0,0 @@
-import sys
-print(sys.version)
diff --git a/devtools/mpi/supermuc.sh b/devtools/mpi/supermuc.sh
deleted file mode 100644
index ce93ec8cdb5..00000000000
--- a/devtools/mpi/supermuc.sh
+++ /dev/null
@@ -1,17 +0,0 @@
-# Setup for BornAgain compilation at SuperMUC LRZ cluster
-
-
-module load git
-module load gcc/4.7
-module load cmake/2.8
-module load fftw/mpi/3.3
-module load gsl
-#module load python/2.7_anaconda
-
-export LD_LIBRARY_PATH=/home/hpc/pr87me/di29sok/software/boost_1_55_0.gcc47/lib:$LD_LIBRARY_PATH
-
-export FFTW3=$FFTW_BASE
-export GSL_DIR=$GSL_BASE
-export BOOST_ROOT=/home/hpc/pr87me/di29sok/software/boost_1_55_0.gcc47
-
-
--
GitLab
From e42cc010278df81bb1c1c6e3a1bb0580d8843d81 Mon Sep 17 00:00:00 2001
From: "Joachim Wuttke (o)" <j.wuttke@fz-juelich.de>
Date: Tue, 11 Apr 2023 18:24:44 +0200
Subject: [PATCH 4/5] devtools: update README
---
devtools/README.md | 5 +----
1 file changed, 1 insertion(+), 4 deletions(-)
diff --git a/devtools/README.md b/devtools/README.md
index bdfb625a80e..19f7ec8d2fa 100644
--- a/devtools/README.md
+++ b/devtools/README.md
@@ -1,4 +1 @@
-Various tools for BornAgain developers.
-
-Note that this directory receives only little, and irregular, attention.
-Much of the material is outdated or obsolete.
+Various tools for BornAgain maintainers.
--
GitLab
From 3f2f83102b1e433a5e7fd2a435202a01e9b99f11 Mon Sep 17 00:00:00 2001
From: "Joachim Wuttke (o)" <j.wuttke@fz-juelich.de>
Date: Tue, 11 Apr 2023 18:25:08 +0200
Subject: [PATCH 5/5] devtools: rm outdated architecture analyses
---
devtools/architecture/DepthProbe.md | 32 -----
devtools/architecture/Lattice.md | 21 ---
.../architecture/ParameterDistribution.md | 117 ----------------
devtools/architecture/Scattering.md | 126 ------------------
4 files changed, 296 deletions(-)
delete mode 100644 devtools/architecture/DepthProbe.md
delete mode 100644 devtools/architecture/Lattice.md
delete mode 100644 devtools/architecture/ParameterDistribution.md
delete mode 100644 devtools/architecture/Scattering.md
diff --git a/devtools/architecture/DepthProbe.md b/devtools/architecture/DepthProbe.md
deleted file mode 100644
index 2ee5e194979..00000000000
--- a/devtools/architecture/DepthProbe.md
+++ /dev/null
@@ -1,32 +0,0 @@
-## How does BornAgain compute depth profiles
-
-Analysis of BornAgain v1.19.0
-
-### Simulation computes an incoherent sum
-
-We consider a simulation handled by class `DepthProbeSimulation < ISimulation`
-(where `<` indicates inheritance).
-
-The function `ISimulation::runSimulation`
-- calls `ISimulation::prepareSimulation`, which
- - does nothing of interest, except for sample builders
-- loops over parameter combinations, thereby performing an incoherent summation:
- - for each parameter set, `runSingleSimulation`;
-- calls `DepthProbeSimulation::moveDataFromCache` to collect results.
- - also calls `transferResultsToIntensityMap`, which does nothing except for `OffSpecSimulation`.
-
-`ISimulation::runSingleSimulation` handles the multithreaded parallel computation
-for batches of detector pixels (`SimulationElement`s). It
-- uses `DepthProbeSimulation::generateSingleThreadedComputation`
- to create instances of `DepthProbeComputation < IComputation`;
-- for each instance, runs `IComputation.run`;
-- calls `ISimulation2D::normalize`;
-- calls `ISimulation2D::addBackgroundIntensity`.
-
-The `IComputation` constructor creates the member `ProcessedSample m_processed_sample`.
-
-The `DepthProbeComputation` constructor
- sets the member `DepthProbeComputationTerm m_computation_term`
- using `ProcessedSample` ...?...
-
-`DepthProbeComputationTerm::compute` computes intensities for all z at one alpha_i.
diff --git a/devtools/architecture/Lattice.md b/devtools/architecture/Lattice.md
deleted file mode 100644
index 8c6d38792c4..00000000000
--- a/devtools/architecture/Lattice.md
+++ /dev/null
@@ -1,21 +0,0 @@
-## Lattices
-
-Typical sample construction with a 3d lattice:
-```
- lattice = ba.FCCLattice(30*nm).transformed(rot.getTransform3D())
- peak_shape = ba.MisesFisherGaussPeakShape(peak_intensity, peak_width, zenith, kappa, kappa2)
- iff = ba.InterferenceFunction3DLattice(lattice)
- iff.setPositionVariance(1.)
- iff.setPeakShape(peak_shape)
-
- layout = ba.ParticleLayout()
- layout.addParticle(particle)
- layout.setTotalParticleSurfaceDensity(.01)
- layout.setInterferenceFunction(iff)
- layout.setWeight(1.0)
-
- vacuum_layer = ba.Layer(m_vacuum)
- vacuum_layer.addLayout(layout)
-```
-
-`bake::FCCLattice` returns a `Lattice3d` with an fcc primitive cell.
diff --git a/devtools/architecture/ParameterDistribution.md b/devtools/architecture/ParameterDistribution.md
deleted file mode 100644
index 1c774260c98..00000000000
--- a/devtools/architecture/ParameterDistribution.md
+++ /dev/null
@@ -1,117 +0,0 @@
-## Parameter distributions
-
-Analysis of BornAgain develop, per 3dec20.
-
-It seems there are two different ways for handling parameter distributions,
-the one specifically for particle distributions, the other one more generic.
-
-### Particle distribution
-
-#### Typical use
-
-Typical use of parameter distributions is described in
-`Examples/Python/sim01_Particles/CylindersWithSizeDistribution.py`:
-```
-def get_sample():
- # Define materials and form factor ...
-
- # Define particles
- particle = ba.Particle(material_Particle, ff)
-
- # Define particles with parameter following a distribution
- distr_1 = ba.DistributionGaussian(5.0*nm, 1.0*nm)
- par_distr_1 = ba.ParameterDistribution(
- "/Particle/Cylinder/Radius", distr_1, 100, 2.0)
- particle_distrib = ba.ParticleDistribution(particle, par_distr_1)
-
- # Define particle layouts
- layout = ba.ParticleLayout()
- layout.addParticle(particle_distrib, 1.0)
-
- # Define layers
- layer = ba.Layer(material_Vacuum)
- layer.addLayout(layout)
-
- # Define sample
- sample = ba.MultiLayer()
- sample.addLayer(layer)
-
- return sample
-
-
-def get_simulation():
- simulation = ba.ScatteringSimulation()
- simulation.setDetectorParameters(200, 0.0*deg, 2.0*deg, 200, 0.0*deg, 2.0*deg)
- simulation.setBeamParameters(1.0*angstrom, 0.2*deg, 0.0*deg)
- return simulation
-
-
-def run_simulation():
- simulation = get_simulation()
- simulation.setSample(get_sample())
- simulation.runSimulation()
- return simulation.result()
-```
-
-#### What goes on behind the scenes?
-
-Class hierarchy:
-```
-IParametricComponent
-- INode
- - ISampleNode
- - IAbstractParticle
- - ParticleDistribution (final)
- - IParticle
- - Particle (final)
- - CoreAndShell (final)
- ... (all final)
-- ISampleBuilder
-- DistributionHandler (final)
-- ParameterDistribution (final)
-```
-
-As we see from the `CylindersWithSizeDistribution` example,
-a `ParticleDistribution` is bound to a `ParticleLayout`.
-The drawing of `IParticle`s from the distribution happens here:
-
-```
-SafePointerVector<IParticle> ParticleLayout::particles() const {
- SafePointerVector<IParticle> particle_vector;
- for (const auto* particle : m_particles) {
- if (const auto* p_part_distr = dynamic_cast<const ParticleDistribution*>(particle)) {
- SafePointerVector<IParticle> generated_particles = p_part_distr->generateParticles();
- for (const IParticle* particle : generated_particles)
- particle_vector.push_back(particle->clone());
- } else if (const auto* p_iparticle = dynamic_cast<const IParticle*>(particle)) {
- particle_vector.push_back(p_iparticle->clone());
- }
- }
- return particle_vector;
-}
-```
-
-### Generic distribution handler
-
-This mechanism acts almost on top of the simulation model hierarchy.
-
-`ISimulation` has member `DistributionHandler m_distribution_handler`.
-It is modified through `ISimulation::addParameterDistribution`.
-This function is called explicitly by some standard simulations and Python scripts
-(e.g. `sim03_Structures/Interference2DLatticeSumOfRotated.py`),
-but not in the above simple example.
-
-
-```
-void ISimulation::runSimulation() {
- ...
- size_t param_combinations = m_distribution_handler.getTotalNumberOfSamples();
- std::unique_ptr<ParameterPool> param_pool(createParameterTree());
- for (size_t index = 0; index < param_combinations; ++index) {
- double weight = m_distribution_handler.setParameterValues(param_pool.get(), index);
- runSingleSimulation(batch_start, batch_size, weight);
- }
- m_distribution_handler.setParameterToMeans(param_pool.get());
- ...
-}
-```
diff --git a/devtools/architecture/Scattering.md b/devtools/architecture/Scattering.md
deleted file mode 100644
index ca15543a9f9..00000000000
--- a/devtools/architecture/Scattering.md
+++ /dev/null
@@ -1,126 +0,0 @@
-## How does BornAgain compute scattering?
-
-Analysis of BornAgain develop
-- per 18nov20, after merge of https://github.com/scgmlz/BornAgain/pull/1105
-- partly checked and improved 24jun21
-
-### Run parallel simulations
-
-We consider a GISAS simulation, handled by class `ScatteringSimulation < ISimulation2D < ISimulation`
-(where `<` indicates inheritance).
-
-The function `ScatteringSimulation::runSimulation`
-- calls `ISimulation::prepareSimulation`;
- - calls `Instrument::initDetector`,
- - calls `ISimulation2D::prepareSimulation`
- - calls `ISimulation::prepareSimulation`
- - does nothing of interest, except for sample builders
- - calls `IDetector2D::createContext`
-- loops over parameter combinations, thereby performing an incoherent summation:
- - for each parameter set, `runSingleSimulation`;
-- calls `ISimulation2D::moveDataFromCache` to collect results.
- - also calls `transferResultsToIntensityMap`, which does nothing except for `OffSpecSimulation`.
-
-`ScatteringSimulation::prepareSimulation` seems to be mostly concerned with `SampleBuilder`s.
-
-`ISimulation::runSingleSimulation` handles the multithreaded parallel computation
-for batches of detector pixels (`SimulationElement`s). It
-- uses `ISimulation2D::generateSingleThreadedComputation`
- to create instances of `DWBAComputation < IComputation`;
-- for each instance, runs `IComputation.run`;
-- calls `ISimulation2D::normalize`;
-- calls `ISimulation2D::addBackgroundIntensity`.
-
-The `IComputation` constructor creates the member `up<ProcessedSample> m_processed_sample`
- by calling the c'tor `ProcessedSample(sample, sim_options, forcePolarized)`
-
-The `DWBAComputation` constructor
-populates the member `DWBASingleComputation m_single_computation`:
-- For each `ProcessedLayout` in `m_processed_sample->layouts()`,
- the vector `DWBASingleComputation::m_layout_comps`
- is given a `new ParticleLayoutComputation` member;
-- if `m_processed_sample->hasRoughness()`,
- then `DWBASingleComputation::m_roughness_comp`
- points to a `new RoughMultiLayerComputation`.
-
-`IComputation::run` calls `DWBAComputation::runProtected`,
- which for each `SimulationElement` in the batch calls `m_single_computation.compute`.
-
-### Compute scattering as incoherent sum
-
-`DWBASingleComputation::compute(SimulationElement& ele)`
-Computes Fresnel coefficients (`Fluxes`),
- and transfers them to `ele`.
- They will be used at the very end of the call following call chains
- - in `ComputeDWBA::computeFF` for scattering from particles
-
-Then it performs an incoherent summation
- by calling functions `compute(ele)`
- that increment `ele.m_intensity`.
-This is done
-- from each `ProcessedLayout`,
-- from each rough interface,
-- from transmission(?) and specular reflection.
-
-### Scattering from a particle layout
-
-The `ParticleLayoutComputation` constructor
-points the member `m_interference_function_strategy`
- to a `new DecouplingApproximationStrategy`,
-unless we are simulating a radial paracrystal,
- for which the `SSCApproximationStrategy` is used.
-
-`ParticleLayoutComputation::compute`
- increments `SimulationElement::m_intensity`
- by a scattering intensity times the `ProcessedLayout::surfaceDensity()`.
-The intensity is computed by `IInterferenceFunctionStrategy::evaluate`.
-Except for Monte-Carlo integration,
- this wraps just one call to `IInterferenceFunctionStrategy::evaluateSinglePoint`.
-For unpolarized scattering, and except for radial paracrystals,
- the next call goes to `DecouplingApproximationStrategy::scalarCalculation`.
-
-`DecouplingApproximationStrategy::scalarCalculation`
- performs a coherent and an incoherent summation
- over scattering amplitudes `ff`
- obtained by calling `FormFactorCoherentSum::summedFF`
- on members of `ProcessedLayout::formFactorList()`.
-The mixed sum is sum
-
-> |ff|^2 + |sum ff|^2 * (coherence_factor - 1)
-
-where coherence_factor is computed by `IInterferenceFunction::evaluate`.
-
-Except for superlattices, there is no "inner" structure,
-and therefore `IInterferenceFunction::evaluate` just wraps `IInterferenceFunction::iff_no_inner`,
-so that
-
-> coherence_factor = DWfactor(q) * (iff_without_dw(q) * outer_iff - 1) + 1.
-
-By default, outer_iff = 1, so that
-
-> coherence_factor = DWfactor(q) * (iff_without_dw - 1) + 1.
-
-For the simplest of all interference functions,
-`InterferenceFunctionNone::iff_without_dw` just returns 1, so that
-
-> coherence_factor = 1.
-
-### Computing the particle formfactor
-
-`FormFactorCoherentSum::summedFF` returns the sum over `FormFactorCoherentPart::coherentFF`.
-
-`FormFactorCoherentPart::coherentFF` makes use of `SimulationElement::fresnelMap`
-to compute `in` and `out` coefficients.
-
-`FormFactorCoherentPart` wraps an `IComputeFF` and additionally holds
-member `m_layer_index`
-that is set by `FormFactorCoherentPart::setSpecularInfo`.
-This information is forwarded by calling `IComputeFF::setSpecularInfo`,
-which does nothing, unless overridden in `ComputeDWBA`.
-
-After this preparation, `ComputeDWBA::computeFF`
-computes the coherent sum over the four DWBA terms.
-Each of them uses the scattering amplitude from `IFormFactor::evaluate`,
-which is pure virtual, overridden by `IFormFactorBorn::evaluate`,
-which calls `IFormFactorBorn::evaluate_for_q`,
-which is pure virtual, overriden by shape-specific classes like `FormFactorSphere`.
--
GitLab