v1.9.3

New This Version

• Added .xyzi files, XYZ format files that include massless interaction points to allow for resuming annealing with these particles included.
• Updated default value of 0K Finale parameter to true.

v1.9.2

New This Version

• Added seed.log output file, which contains the long value used for seeding random number generation for a given simulation
  • If a user-defined seed is not provided, the system's timestamp is utilized for seeding and output
  • seed.log allows for increased reproducibility and testing of simulations
• The --set-seed parameter is now an alias for the --seed parameter, with the same functionality

v1.9.1

New This Version

• The --set-seed/-s command-line parameter is introduced, which allows a long argument to be used to seed TransRot's random number generators for reproducibility in calculations

Bugfixes/Changes:

• Refactored all reading of the configuration file to a new Config class
• Modularized all file-parsing to allow comments and empty space in the database and configuration files
  • Removed dummy-space requirements in the configuration file to allow user control
• Now allows reordering of settings in the configuration file
• Improved error-catching and descriptiveness for parsing errors in both database and configuration files
• Fixes a bug where the --input command-line parameter did not function properly

v1.9.0

New This Version

• Reintroduces customizable pairwise interaction parameters via an associated file (interaction_params.txt) and custom .txt file specification.
  • New file format allows users to specify which molecules should be treated the same and independently in interactions through the use of aliased identifiers.
  • File input is expected if the 'Choose All Interaction Parameters' flag in config.txt is enabled.
• The --params/-p command-line variable has been introduced to allow user control of the location of interaction_params.txt
• Every run of TransRot (regardless of whether the user specified custom pairwise interaction parameters) outputs an automatically generated interaction_params.txt file of the same format as when input
  • This file reports all pairwise (non-reflexive) interaction parameters used in the TransRot simulation.

v1.8.0

New This Version

• Accompanied by the release of Visual TransRot (VTR), an accompanying graphical user interface and process manager for TransRot
• All input files (config.txt, dbase.txt, Input.xyz) as well as output location can be configured on a per-run basis using command-line arguments
• All output non-movie .xyz files can now be used directly as Input.xyz with no modifications
• Added elapsed_time.log output file, which tracks a calculation's total elapsed time (used specifically for VTR)

Bugfixes/Changes:

• Fixed error where configurational heat capacities were reported as negative by altering their calculation
• Fixed inconsistency between particle definitions in dbase.txt and their use in config.txt by updating config requirements to separate particles and their counts to at least two spaces
• Changed Input.xyz particle definition format (line 2) in order remove ambiguity
  • Format for 4 Cl- ions and 4 NH4+ molecules is: 4 Cl- | 4 NH4+
• Reformatted all error messages to use System.err to allow for separate redirection for logs and errors

v1.7.1

Bugfixes/Changes:

• Fixed error where atom pairwise precalculations were done according to their symbol, causing atoms with the same symbol but different parameters would use the wrong parameters
  • Fixed by assigning each atom a unique identifier (UUID), which ensures all atoms are taken into account.

Removed:

• param_overrides.txt and functionality of overriding atom pairwise parameters
  • Due to the pairwise precalculation error described above, the atomic symbol by itself is not enough to distinguish atom pairs, and there currently is not a better descriptor available for users to describe these overrides.

v1.7.0

New This Version:

• New Config Options:
  • Write Configurational Heat Capacities (true/false): Enabling this option adds an additional file to the output, 'configurational_heat_capacities.txt'. For each distinct temperature, the file will contain a line with the temperature, the average energy at that temperature, and the configurational heat capacity at that temperature (C = (<V²> - < V >²) / (k_BT²)).
  • Number of Equilibration Configurations: When Static Temperature and Write Configurational Heat Capacities are both enabled, the first N energies will not be considered in the configurational heat capacity, where N is the value set for Number of Equilibration Configurations.

Bugfixes/Changes:

• When Static Temperature is enabled, Points per Tooth is now always considered as set to 1. (Previously, only Number of Teeth was set like this for static temperatures.)

Release v1.6.4

New This Version:

• interaction_params.txt will now be generated during initialization, recording all parameters used for pairwise interactions including units, Kappa value, atomic charges, and calculated pair potentials.

Release v1.6.3

Bugfixes/Changes:

• When running a 0K finale:
  • Magwalking is now disabled (bugfix)
  • Translation and rotation distances are set to 1/100 of their base values (#2)

Release v1.6.2

New This Version:

• When simulating 2 or more teeth, the output file containing the lowest energy structure will be copied to Min_Energy_Structure_X.xyz for easier access. X corresponds to the copied file; for example, Min_Energy_Structure_3.xyz would be a copy of Output3.xyz. (#1)