# Example molecularDNA History

See `CONTRIBUTING.rst` for details of **required** info/format for each entry,
which **must** added in reverse chronological order (newest at the top).
It must **not** be used as a substitute for writing good git commit messages!

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## 2026-02-11 S. Incerti (molecularDNA-V11-03-16)
- fixed display of error for SSBm_yield in ROOT macros

## 2025-11-02 B. Munkhbaatar, S. Incerti, D. Sakata, H. Tran,  (molecularDNA-V11-03-15)
- Fixed the wrong gap: a gap (distance between 2 hits) can be 0 (bugzilla #2681)
- Added protection for over counting damage
- Fixed the printed info by Batmunkh
- Updated of ROOT macros for statistical analysis of errors
- Updated of absorbed dose calculation in ROOT macros to avoid double counting of
energy deposition in DNA geometry, and inclusion of error on the dose

## 2025-10-09 K. Chatzipapas, S. Incerti (molecularDNA-V11-03-14)
- Fixed cell geometry in human_cell_chromosomes.mac.

## 2025-09-17 Le Tuan Anh (molecularDNA-V11-03-13)
- Commented out "system ("hadd -O -f molecular-dna.root molecular-dna_t*.root")"  
  in all ROOT analysis macros.

## 2025-08-26 H. Tran (molecularDNA-V11-03-12)
- restored the Maximum Time Step parameter in the chemistry
- merged the output files from different threads to a single file
- fixed the memory leak in the PrimaryGeneratorAction for phase_space

## 2025-07-22 S. Incerti (molecularDNA-V11-03-11)
- added /scheduler/verbose 0 to all human* macros

## 2025-07-17 S. Incerti (molecularDNA-V11-03-10)
- fixed phase_space_test.mac.

## 2025-06-03 H. Tran (molecularDNA-V11-03-09)
- fixed updated reaction list for each DNA reactions.

## 2025-05-05 H. Tran (molecularDNA-V11-03-08)
- fixed compilation warnings on cxx23

## 2025-04-01 H. Tran (molecularDNA-V11-03-07)
- updated the new implementation of IRT-syn model.
- Deleted the Max Time Step parameter.

## 2025-02-17 S. Incerti, K. Chatzipapas, H. Tran (molecularDNA-V11-03-06)
- Added moleculardna macro, ROOT macro and geomety files for the simulation of phages
- Updated direct damage range for plasmid.mac and cylinders.mac
- Added fiber.mac
- Increased max number of arguments in main

## 2025-02-11 S. Incerti, K. Chatzipapas (molecularDNA-V11-03-05)
- Added protection to all ROOT macros to avoid nan in error calculation

## 2025-02-11 K. Chatzipapas, S. Incerti (molecularDNA-V11-03-04)
- Added message in README related to ROOT import from python

## 2025-01-30 S. Incerti (molecularDNA-V11-03-03)
- Added possibility to activate parallel word using dedicated flag from executable

## 2025-01-23 S. Incerti (molecularDNA-V11-03-02)
- Increased default statistics in ecoli.mac

## 2025-01-03 S. Incerti (molecularDNA-V11-03-01)
- Added auto to cylinders.C

## 2024-12-13 K. Chatzipapas (molecularDNA-V11-03-00)
- Correct segmentation error of the root macrofile
  "human_cell.C", "ecoli.C", "human_cell_alphas.C",
  "human_cell_chromosome.C" and "plasmid.C". This error
  was caused when low damage had been produced.
- Define the definition of one missing variable in the
  "human_cell.C", "ecoli.C", "human_cell_alphas.C",
  "human_cell_chromosome.C" and "plasmid.C".

## 2024-11-05 H. Tran (molecularDNA-V11-02-13)
- added missing plasmid analysis root macro file

## 2024-11-04 S. Incerti (molecularDNA-V11-02-12)
- updated README and .README

## 2024-10-31 K. Chatzipapas (molecularDNA-V11-02-11)
- Adding chromosomal geometry related files
  human_cell_chromosome.mac
  human_cell_chromosome.C
  human_cell_chromosome.py
  human_cell_chromosome.txt

## 2024-10-22 Hoang Tran (molecularDNA-V11-02-10)
- Corrected README files for plasmid geometry.

## 2024-10-17 Hoang Tran (molecularDNA-V11-02-09)
- Moved from extended example to advanced example.

## 2024-10-07 Hoang Tran (molecularDNA-V11-02-08)
- Added plasmid geometry

## 2024-10-03 Hoang Tran (molecularDNA-V11-02-07)
- Modified the molecule names of OH, HO2, O in MoleculeDefinition.
  Each molecule configuration has a molecule definition.

## 2024-10-02 S. Incerti (molecularDNA-V11-02-06)
- added more comments in ChromosomeMessenger for rod

## 2024-09-16 S. Incerti (molecularDNA-V11-02-05)
- fixed coding conventions violations

## 2024-09-06 S. Incerti (molecularDNA-V11-02-04)
- updated README

## 2024-09-05 S. Incerti (molecularDNA-V11-02-03)
- commented Geant4 macros
- commented README

## 2024-08-20 H. Tran (molecularDNA-V11-02-02)
- modification of TimeStepModel interface
- used the physico-chemistry builder
- edited README files

## 2024-07-29 S. Incerti (molecularDNA-V11-02-01)
- Fixed bug in DNAGeometryMessenger

## 2024-04-18 H. Tran (molecularDNA-V11-02-00)
- Updated /dnageom/interactionDirectRange to 2.0 angstrom

## 2023-11-09 H. Tran (molecularDNA-V11-01-08)
- Added info in .README.txt and README files

## 2023-11-07 I. Hrivnacova (molecularDNA-V11-01-07)
- Fixed formatting in .README.txt

## 2023-09-13 I. Hrivnacova (molecularDNA-V11-01-06)
- Removed unused public data member
  PrimaryGeneratorSourceGRASCSV::nLineCounter

## 2023-08-28 Hoang Tran (molecularDNA-V11-01-05)
- add the geometry files for HTB177 and MCF-7 cell lines.

## 2023-05-31 Hoang Tran (molecularDNA-V11-01-04)
- restore the correction of the material bug

## 2023-04-20 Ronny Stanzani (molecularDNA-V11-01-03)
- Add the ability to read particles from a space phase file (csv)
- Overall code revision with clang-tidy

## 2023-02-07 Hoang Tran (molecularDNA-V11-01-02)
- correct the material bug in moleculardna example
- add /scheduler/endTime 1 us in ecoli.mac and cylinders.mac

## 2023-01-13 Ben Morgan (molecularDNA-V11-01-01)
- Migrate data download to CERN EOS area for examples

## 2022-12-12 Hoang Tran (molecularDNA-V11-01-00)
- update ecoli.mac file (Nathanael's parameter)

## 2022-11-15 Hoang Tran (molecularDNA-V11-00-11)
- correct ecoli.mac file

## 2022-10-24 Konstantinos Chatzipapas (molecularDNA-V11-00-10)
- Add repair-survival-models
	- molecularDNArepair.py
	- molecularDNAsurvival.py (beta)
- Update ecoli files (fix bug)
- Update vis.mac and cylinders.mac

## 2022-09-20 Hoang Tran (molecularDNA-V11-00-09)
- Fixed the examples naming conventions violations
- reduce event number of ecoli.mac

## 2022-08-30 Vladimir Ivanchenko (molecularDNA-V11-00-08)
- ChemistryList - added forgotten header

## 2022-08-27 Hoang Tran (molecularDNA-V11-00-07)
- Fix smart pointer warning in gcc 12.1.
- Fix typo in the human_cell.C.

## 2022-07-12 Konstantinos Chatzipapas (molecularDNA-V11-00-06)
- Fix ecoli.C minor bug on filename.

## 2022-06-10 Sergio Losilla (molecularDNA-V11-00-05)
- Added missing headers.

## 2022-05-03 Konstantinos Chatzipapas (molecularDNA-V11-00-04)
- add ecoli.C macro file
- add createSDD.py

## 2022-04-14 Hoang Tran (molecularDNA-V11-00-03)
- correct a minor mistake in AnalysisManager
- Add Complexity Frequency in cylinder.C
- add human_cell.C macro file

## 2022-02-27 Vladimir Ivanchenko (molecularDNA-V11-00-02)
- PhysicsList - added DecayPhysics and RadioactiveDecayPhysics
- ParallelWorldPhysics - minor clean-up
- molecular.cc - updated according to the recent recommendations:
    removed ifdef, removed RanecuEngine, use visualisation in
    the interactive session only, use G4RunManagerFactory

## 2022-02-17 Hoang Tran (molecularDNA-V11-00-01)
- modify Chemistry list
- timeout for the geometry data download
- the exception message in DNAGeometryMessenger::SetNewValue

## 2022-01-07 Hoang Tran (molecularDNA-V11-00-00)
- initial tag