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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 ## 2026-02-11 S. Incerti (molecularDNA-V11-03-16)
0010 - fixed display of error for SSBm_yield in ROOT macros
0011
0012 ## 2025-11-02 B. Munkhbaatar, S. Incerti, D. Sakata, H. Tran, (molecularDNA-V11-03-15)
0013 - Fixed the wrong gap: a gap (distance between 2 hits) can be 0 (bugzilla #2681)
0014 - Added protection for over counting damage
0015 - Fixed the printed info by Batmunkh
0016 - Updated of ROOT macros for statistical analysis of errors
0017 - Updated of absorbed dose calculation in ROOT macros to avoid double counting of
0018 energy deposition in DNA geometry, and inclusion of error on the dose
0019
0020 ## 2025-10-09 K. Chatzipapas, S. Incerti (molecularDNA-V11-03-14)
0021 - Fixed cell geometry in human_cell_chromosomes.mac.
0022
0023 ## 2025-09-17 Le Tuan Anh (molecularDNA-V11-03-13)
0024 - Commented out "system ("hadd -O -f molecular-dna.root molecular-dna_t*.root")"
0025 in all ROOT analysis macros.
0026
0027 ## 2025-08-26 H. Tran (molecularDNA-V11-03-12)
0028 - restored the Maximum Time Step parameter in the chemistry
0029 - merged the output files from different threads to a single file
0030 - fixed the memory leak in the PrimaryGeneratorAction for phase_space
0031
0032 ## 2025-07-22 S. Incerti (molecularDNA-V11-03-11)
0033 - added /scheduler/verbose 0 to all human* macros
0034
0035 ## 2025-07-17 S. Incerti (molecularDNA-V11-03-10)
0036 - fixed phase_space_test.mac.
0037
0038 ## 2025-06-03 H. Tran (molecularDNA-V11-03-09)
0039 - fixed updated reaction list for each DNA reactions.
0040
0041 ## 2025-05-05 H. Tran (molecularDNA-V11-03-08)
0042 - fixed compilation warnings on cxx23
0043
0044 ## 2025-04-01 H. Tran (molecularDNA-V11-03-07)
0045 - updated the new implementation of IRT-syn model.
0046 - Deleted the Max Time Step parameter.
0047
0048 ## 2025-02-17 S. Incerti, K. Chatzipapas, H. Tran (molecularDNA-V11-03-06)
0049 - Added moleculardna macro, ROOT macro and geomety files for the simulation of phages
0050 - Updated direct damage range for plasmid.mac and cylinders.mac
0051 - Added fiber.mac
0052 - Increased max number of arguments in main
0053
0054 ## 2025-02-11 S. Incerti, K. Chatzipapas (molecularDNA-V11-03-05)
0055 - Added protection to all ROOT macros to avoid nan in error calculation
0056
0057 ## 2025-02-11 K. Chatzipapas, S. Incerti (molecularDNA-V11-03-04)
0058 - Added message in README related to ROOT import from python
0059
0060 ## 2025-01-30 S. Incerti (molecularDNA-V11-03-03)
0061 - Added possibility to activate parallel word using dedicated flag from executable
0062
0063 ## 2025-01-23 S. Incerti (molecularDNA-V11-03-02)
0064 - Increased default statistics in ecoli.mac
0065
0066 ## 2025-01-03 S. Incerti (molecularDNA-V11-03-01)
0067 - Added auto to cylinders.C
0068
0069 ## 2024-12-13 K. Chatzipapas (molecularDNA-V11-03-00)
0070 - Correct segmentation error of the root macrofile
0071 "human_cell.C", "ecoli.C", "human_cell_alphas.C",
0072 "human_cell_chromosome.C" and "plasmid.C". This error
0073 was caused when low damage had been produced.
0074 - Define the definition of one missing variable in the
0075 "human_cell.C", "ecoli.C", "human_cell_alphas.C",
0076 "human_cell_chromosome.C" and "plasmid.C".
0077
0078 ## 2024-11-05 H. Tran (molecularDNA-V11-02-13)
0079 - added missing plasmid analysis root macro file
0080
0081 ## 2024-11-04 S. Incerti (molecularDNA-V11-02-12)
0082 - updated README and .README
0083
0084 ## 2024-10-31 K. Chatzipapas (molecularDNA-V11-02-11)
0085 - Adding chromosomal geometry related files
0086 human_cell_chromosome.mac
0087 human_cell_chromosome.C
0088 human_cell_chromosome.py
0089 human_cell_chromosome.txt
0090
0091 ## 2024-10-22 Hoang Tran (molecularDNA-V11-02-10)
0092 - Corrected README files for plasmid geometry.
0093
0094 ## 2024-10-17 Hoang Tran (molecularDNA-V11-02-09)
0095 - Moved from extended example to advanced example.
0096
0097 ## 2024-10-07 Hoang Tran (molecularDNA-V11-02-08)
0098 - Added plasmid geometry
0099
0100 ## 2024-10-03 Hoang Tran (molecularDNA-V11-02-07)
0101 - Modified the molecule names of OH, HO2, O in MoleculeDefinition.
0102 Each molecule configuration has a molecule definition.
0103
0104 ## 2024-10-02 S. Incerti (molecularDNA-V11-02-06)
0105 - added more comments in ChromosomeMessenger for rod
0106
0107 ## 2024-09-16 S. Incerti (molecularDNA-V11-02-05)
0108 - fixed coding conventions violations
0109
0110 ## 2024-09-06 S. Incerti (molecularDNA-V11-02-04)
0111 - updated README
0112
0113 ## 2024-09-05 S. Incerti (molecularDNA-V11-02-03)
0114 - commented Geant4 macros
0115 - commented README
0116
0117 ## 2024-08-20 H. Tran (molecularDNA-V11-02-02)
0118 - modification of TimeStepModel interface
0119 - used the physico-chemistry builder
0120 - edited README files
0121
0122 ## 2024-07-29 S. Incerti (molecularDNA-V11-02-01)
0123 - Fixed bug in DNAGeometryMessenger
0124
0125 ## 2024-04-18 H. Tran (molecularDNA-V11-02-00)
0126 - Updated /dnageom/interactionDirectRange to 2.0 angstrom
0127
0128 ## 2023-11-09 H. Tran (molecularDNA-V11-01-08)
0129 - Added info in .README.txt and README files
0130
0131 ## 2023-11-07 I. Hrivnacova (molecularDNA-V11-01-07)
0132 - Fixed formatting in .README.txt
0133
0134 ## 2023-09-13 I. Hrivnacova (molecularDNA-V11-01-06)
0135 - Removed unused public data member
0136 PrimaryGeneratorSourceGRASCSV::nLineCounter
0137
0138 ## 2023-08-28 Hoang Tran (molecularDNA-V11-01-05)
0139 - add the geometry files for HTB177 and MCF-7 cell lines.
0140
0141 ## 2023-05-31 Hoang Tran (molecularDNA-V11-01-04)
0142 - restore the correction of the material bug
0143
0144 ## 2023-04-20 Ronny Stanzani (molecularDNA-V11-01-03)
0145 - Add the ability to read particles from a space phase file (csv)
0146 - Overall code revision with clang-tidy
0147
0148 ## 2023-02-07 Hoang Tran (molecularDNA-V11-01-02)
0149 - correct the material bug in moleculardna example
0150 - add /scheduler/endTime 1 us in ecoli.mac and cylinders.mac
0151
0152 ## 2023-01-13 Ben Morgan (molecularDNA-V11-01-01)
0153 - Migrate data download to CERN EOS area for examples
0154
0155 ## 2022-12-12 Hoang Tran (molecularDNA-V11-01-00)
0156 - update ecoli.mac file (Nathanael's parameter)
0157
0158 ## 2022-11-15 Hoang Tran (molecularDNA-V11-00-11)
0159 - correct ecoli.mac file
0160
0161 ## 2022-10-24 Konstantinos Chatzipapas (molecularDNA-V11-00-10)
0162 - Add repair-survival-models
0163 - molecularDNArepair.py
0164 - molecularDNAsurvival.py (beta)
0165 - Update ecoli files (fix bug)
0166 - Update vis.mac and cylinders.mac
0167
0168 ## 2022-09-20 Hoang Tran (molecularDNA-V11-00-09)
0169 - Fixed the examples naming conventions violations
0170 - reduce event number of ecoli.mac
0171
0172 ## 2022-08-30 Vladimir Ivanchenko (molecularDNA-V11-00-08)
0173 - ChemistryList - added forgotten header
0174
0175 ## 2022-08-27 Hoang Tran (molecularDNA-V11-00-07)
0176 - Fix smart pointer warning in gcc 12.1.
0177 - Fix typo in the human_cell.C.
0178
0179 ## 2022-07-12 Konstantinos Chatzipapas (molecularDNA-V11-00-06)
0180 - Fix ecoli.C minor bug on filename.
0181
0182 ## 2022-06-10 Sergio Losilla (molecularDNA-V11-00-05)
0183 - Added missing headers.
0184
0185 ## 2022-05-03 Konstantinos Chatzipapas (molecularDNA-V11-00-04)
0186 - add ecoli.C macro file
0187 - add createSDD.py
0188
0189 ## 2022-04-14 Hoang Tran (molecularDNA-V11-00-03)
0190 - correct a minor mistake in AnalysisManager
0191 - Add Complexity Frequency in cylinder.C
0192 - add human_cell.C macro file
0193
0194 ## 2022-02-27 Vladimir Ivanchenko (molecularDNA-V11-00-02)
0195 - PhysicsList - added DecayPhysics and RadioactiveDecayPhysics
0196 - ParallelWorldPhysics - minor clean-up
0197 - molecular.cc - updated according to the recent recommendations:
0198 removed ifdef, removed RanecuEngine, use visualisation in
0199 the interactive session only, use G4RunManagerFactory
0200
0201 ## 2022-02-17 Hoang Tran (molecularDNA-V11-00-01)
0202 - modify Chemistry list
0203 - timeout for the geometry data download
0204 - the exception message in DNAGeometryMessenger::SetNewValue
0205
0206 ## 2022-01-07 Hoang Tran (molecularDNA-V11-00-00)
0207 - initial tag
