Warning, /geant4/examples/advanced/dna/moleculardna/History is written in an unsupported language. File is not indexed.
0001 # Example molecularDNA History
0002
0003 See `CONTRIBUTING.rst` for details of **required** info/format for each entry,
0004 which **must** added in reverse chronological order (newest at the top).
0005 It must **not** be used as a substitute for writing good git commit messages!
0006
0007 -------------------------------------------------------------------------------
0008
0009 ## 2025-06-03 H. Tran (molecularDNA-V11-03-09)
0010 - fixed updated reaction list for each DNA reactions.
0011
0012 ## 2025-05-05 H. Tran (molecularDNA-V11-03-08)
0013 - fixed compilation warnings on cxx23
0014
0015 ## 2025-04-01 H. Tran (molecularDNA-V11-03-07)
0016 - updated the new implementation of IRT-syn model.
0017 - Deleted the Max Time Step parameter.
0018
0019 ## 2025-02-17 S. Incerti, K. Chatzipapas, H. Tran (molecularDNA-V11-03-06)
0020 - Added moleculardna macro, ROOT macro and geomety files for the simulation of phages
0021 - Updated direct damage range for plasmid.mac and cylinders.mac
0022 - Added fiber.mac
0023 - Increased max number of arguments in main
0024
0025 ## 2025-02-11 S. Incerti, K. Chatzipapas (molecularDNA-V11-03-05)
0026 - Added protection to all ROOT macros to avoid nan in error calculation
0027
0028 ## 2025-02-11 K. Chatzipapas, S. Incerti (molecularDNA-V11-03-04)
0029 - Added message in README related to ROOT import from python
0030
0031 ## 2025-01-30 S. Incerti (molecularDNA-V11-03-03)
0032 - Added possibility to activate parallel word using dedicated flag from executable
0033
0034 ## 2025-01-23 S. Incerti (molecularDNA-V11-03-02)
0035 - Increased default statistics in ecoli.mac
0036
0037 ## 2025-01-03 S. Incerti (molecularDNA-V11-03-01)
0038 - Added auto to cylinders.C
0039
0040 ## 2024-12-13 K. Chatzipapas (molecularDNA-V11-03-00)
0041 - Correct segmentation error of the root macrofile
0042 "human_cell.C", "ecoli.C", "human_cell_alphas.C",
0043 "human_cell_chromosome.C" and "plasmid.C". This error
0044 was caused when low damage had been produced.
0045 - Define the definition of one missing variable in the
0046 "human_cell.C", "ecoli.C", "human_cell_alphas.C",
0047 "human_cell_chromosome.C" and "plasmid.C".
0048
0049 ## 2024-11-05 H. Tran (molecularDNA-V11-02-13)
0050 - added missing plasmid analysis root macro file
0051
0052 ## 2024-11-04 S. Incerti (molecularDNA-V11-02-12)
0053 - updated README and .README
0054
0055 ## 2024-10-31 K. Chatzipapas (molecularDNA-V11-02-11)
0056 - Adding chromosomal geometry related files
0057 human_cell_chromosome.mac
0058 human_cell_chromosome.C
0059 human_cell_chromosome.py
0060 human_cell_chromosome.txt
0061
0062 ## 2024-10-22 Hoang Tran (molecularDNA-V11-02-10)
0063 - Corrected README files for plasmid geometry.
0064
0065 ## 2024-10-17 Hoang Tran (molecularDNA-V11-02-09)
0066 - Moved from extended example to advanced example.
0067
0068 ## 2024-10-07 Hoang Tran (molecularDNA-V11-02-08)
0069 - Added plasmid geometry
0070
0071 ## 2024-10-03 Hoang Tran (molecularDNA-V11-02-07)
0072 - Modified the molecule names of OH, HO2, O in MoleculeDefinition.
0073 Each molecule configuration has a molecule definition.
0074
0075 ## 2024-10-02 S. Incerti (molecularDNA-V11-02-06)
0076 - added more comments in ChromosomeMessenger for rod
0077
0078 ## 2024-09-16 S. Incerti (molecularDNA-V11-02-05)
0079 - fixed coding conventions violations
0080
0081 ## 2024-09-06 S. Incerti (molecularDNA-V11-02-04)
0082 - updated README
0083
0084 ## 2024-09-05 S. Incerti (molecularDNA-V11-02-03)
0085 - commented Geant4 macros
0086 - commented README
0087
0088 ## 2024-08-20 H. Tran (molecularDNA-V11-02-02)
0089 - modification of TimeStepModel interface
0090 - used the physico-chemistry builder
0091 - edited README files
0092
0093 ## 2024-07-29 S. Incerti (molecularDNA-V11-02-01)
0094 - Fixed bug in DNAGeometryMessenger
0095
0096 ## 2024-04-18 H. Tran (molecularDNA-V11-02-00)
0097 - Updated /dnageom/interactionDirectRange to 2.0 angstrom
0098
0099 ## 2023-11-09 H. Tran (molecularDNA-V11-01-08)
0100 - Added info in .README.txt and README files
0101
0102 ## 2023-11-07 I. Hrivnacova (molecularDNA-V11-01-07)
0103 - Fixed formatting in .README.txt
0104
0105 ## 2023-09-13 I. Hrivnacova (molecularDNA-V11-01-06)
0106 - Removed unused public data member
0107 PrimaryGeneratorSourceGRASCSV::nLineCounter
0108
0109 ## 2023-08-28 Hoang Tran (molecularDNA-V11-01-05)
0110 - add the geometry files for HTB177 and MCF-7 cell lines.
0111
0112 ## 2023-05-31 Hoang Tran (molecularDNA-V11-01-04)
0113 - restore the correction of the material bug
0114
0115 ## 2023-04-20 Ronny Stanzani (molecularDNA-V11-01-03)
0116 - Add the ability to read particles from a space phase file (csv)
0117 - Overall code revision with clang-tidy
0118
0119 ## 2023-02-07 Hoang Tran (molecularDNA-V11-01-02)
0120 - correct the material bug in moleculardna example
0121 - add /scheduler/endTime 1 us in ecoli.mac and cylinders.mac
0122
0123 ## 2023-01-13 Ben Morgan (molecularDNA-V11-01-01)
0124 - Migrate data download to CERN EOS area for examples
0125
0126 ## 2022-12-12 Hoang Tran (molecularDNA-V11-01-00)
0127 - update ecoli.mac file (Nathanael's parameter)
0128
0129 ## 2022-11-15 Hoang Tran (molecularDNA-V11-00-11)
0130 - correct ecoli.mac file
0131
0132 ## 2022-10-24 Konstantinos Chatzipapas (molecularDNA-V11-00-10)
0133 - Add repair-survival-models
0134 - molecularDNArepair.py
0135 - molecularDNAsurvival.py (beta)
0136 - Update ecoli files (fix bug)
0137 - Update vis.mac and cylinders.mac
0138
0139 ## 2022-09-20 Hoang Tran (molecularDNA-V11-00-09)
0140 - Fixed the examples naming conventions violations
0141 - reduce event number of ecoli.mac
0142
0143 ## 2022-08-30 Vladimir Ivanchenko (molecularDNA-V11-00-08)
0144 - ChemistryList - added forgotten header
0145
0146 ## 2022-08-27 Hoang Tran (molecularDNA-V11-00-07)
0147 - Fix smart pointer warning in gcc 12.1.
0148 - Fix typo in the human_cell.C.
0149
0150 ## 2022-07-12 Konstantinos Chatzipapas (molecularDNA-V11-00-06)
0151 - Fix ecoli.C minor bug on filename.
0152
0153 ## 2022-06-10 Sergio Losilla (molecularDNA-V11-00-05)
0154 - Added missing headers.
0155
0156 ## 2022-05-03 Konstantinos Chatzipapas (molecularDNA-V11-00-04)
0157 - add ecoli.C macro file
0158 - add createSDD.py
0159
0160 ## 2022-04-14 Hoang Tran (molecularDNA-V11-00-03)
0161 - correct a minor mistake in AnalysisManager
0162 - Add Complexity Frequency in cylinder.C
0163 - add human_cell.C macro file
0164
0165 ## 2022-02-27 Vladimir Ivanchenko (molecularDNA-V11-00-02)
0166 - PhysicsList - added DecayPhysics and RadioactiveDecayPhysics
0167 - ParallelWorldPhysics - minor clean-up
0168 - molecular.cc - updated according to the recent recommendations:
0169 removed ifdef, removed RanecuEngine, use visualisation in
0170 the interactive session only, use G4RunManagerFactory
0171
0172 ## 2022-02-17 Hoang Tran (molecularDNA-V11-00-01)
0173 - modify Chemistry list
0174 - timeout for the geometry data download
0175 - the exception message in DNAGeometryMessenger::SetNewValue
0176
0177 ## 2022-01-07 Hoang Tran (molecularDNA-V11-00-00)
0178 - initial tag
