| e684772 | Simon O'Meara | 02 March 2023, 17:31:36 UTC | readme improved readme improved for the indoor air quality modelling section | 02 March 2023, 17:31:36 UTC |
| afc6428 | Simon O'Meara | 02 March 2023, 16:07:07 UTC | corrected address to README images images should now show via README | 02 March 2023, 16:07:07 UTC |
| f3b42b9 | Simon O'Meara | 02 March 2023, 16:01:49 UTC | improved README README now better describes indoor air quality modelling | 02 March 2023, 16:01:49 UTC |
| aa071f8 | Simon O'Meara | 23 February 2023, 07:49:34 UTC | accommodation coefficient updates partit_var module now imports the most up-to-date module for accommodation coefficient | 23 February 2023, 07:49:34 UTC |
| cec2c94 | Simon O'Meara | 22 February 2023, 19:11:58 UTC | tidied up automated calling calling can now deal with Windows and Mac conventions for separating parts of a path name | 22 February 2023, 19:11:58 UTC |
| 5088ac6 | simonom | 21 February 2023, 17:00:09 UTC | fixed time step bug now count on time steps is the same in ode_updater as it is in rec | 21 February 2023, 17:00:09 UTC |
| cf74a00 | Simon O'Meara | 14 February 2023, 11:10:06 UTC | initial concentrations on surfaces Users can now supply initial concentrations on the simulated surfaces (in addition to the gas phase), as described in README | 14 February 2023, 11:10:06 UTC |
| c3ceeda | Simon O'Meara | 13 February 2023, 10:24:18 UTC | fixed plotting bug Resolved bug that was affecting First-look plot when one size bin of particle present | 13 February 2023, 10:24:18 UTC |
| bc3a5bb | simonom | 23 January 2023, 11:08:50 UTC | fixed bug in CIMS form Corrected saving of NO, HO2 and RO2 concentrations when pressing the Save in CIMS Form button | 23 January 2023, 11:08:50 UTC |
| 45d49e1 | Simon O'Meara | 20 January 2023, 09:30:04 UTC | updated output useful to autoCONSTRAIN CHON file, concentration and change in concentration at a given time file, NO and HO2 and RO2_pool file | 20 January 2023, 09:30:04 UTC |
| 9c1d78e | Simon O'Meara | 21 December 2022, 17:46:34 UTC | fixed bugs affecting CIMS output previously major bugs to CIMS output button prevented proper running, but this button now working fine (and checked against CIMS plot button) | 21 December 2022, 17:46:34 UTC |
| e5a2e75 | simonom | 20 December 2022, 17:05:12 UTC | improving CIMS output so that CIMS-style output file created | 20 December 2022, 17:05:12 UTC |
| 731c40a | Simon O'Meara | 15 December 2022, 15:46:57 UTC | minor bugs in plotter.py Resolved some minor bugs inside plotter.py, related to plotting the air quality index | 15 December 2022, 15:46:57 UTC |
| 95a4a81 | Simon O'Meara | 13 December 2022, 13:07:48 UTC | AQI improved Many bugs inside air quality index estimation (inside plotter.py) fixed, so the air quality index button in GUI should work now | 13 December 2022, 13:07:48 UTC |
| 5bb9e51 | simonom | 12 December 2022, 16:48:17 UTC | air quality index added plotting function, fronted by a new button on GUI, to plot air quality index (as defined by UK-AIR website) | 12 December 2022, 16:48:17 UTC |
| 4ab380b | Simon O'Meara | 07 December 2022, 17:40:58 UTC | improved PRAM inputs Setup the PRAM inputs to represent an alpha-pinene+ozone with lights on flow reactor chamber experiment | 07 December 2022, 17:40:58 UTC |
| 2e31f38 | simonom | 30 November 2022, 10:57:25 UTC | improved SMILES generator improved SMILES generator to also include Nitrogen atoms | 30 November 2022, 10:57:25 UTC |
| d6aecdd | simonom | 29 November 2022, 15:18:56 UTC | Added xml input Inside PyCHAM/input/PRAM is a code for generating SMILE strings based on chemical scheme names that will automatically be appended to a user-specified xml file | 29 November 2022, 15:18:56 UTC |
| 9d27e00 | Simon O'Meara | 28 November 2022, 11:47:34 UTC | resolved bugs around multiple particle influxes Bugs were present in pp_dursim and plotting that prevented simulations with multiple particle injections operating. Resolved in this version | 28 November 2022, 11:47:34 UTC |
| e6f58d4 | Simon O'Meara | 22 November 2022, 18:04:00 UTC | improved exp. prep. Improved the ability of exp. prep. to output useful results from simulations designed to prepare for experiments, for example in laboratories | 22 November 2022, 18:04:00 UTC |
| 22cb8de | simonom | 21 November 2022, 16:46:11 UTC | Automatic production of experiment design table Following on from designing experiments in SAPHIR*, MAC and HIRAC, now there is a button to automatically generate the key information needed for aerosol chamber design | 21 November 2022, 16:46:11 UTC |
| 6184f19 | Simon O'Meara | 18 November 2022, 16:42:32 UTC | automated calling added the new automated_setup_and_call module can be called from the command line: python automated_setup_and_call.py. Which will call PyCHAM and run specified inputs without needing to interact with the GUI. For example, it can loop through realistic ranges of parameters to create a collection of outputs, ready for analysing multiple outputs across parameter space | 18 November 2022, 16:42:32 UTC |
| 6a9c3cf | Simon O'Meara | 15 November 2022, 18:01:23 UTC | ode solver bug fixes Corrected the treatment of dilution in ode_solv and ode_solv_wat as previously, with more than 1 wall bin, wall concentrations were being diluted due to air exchange. Also added a button to plot carbon reservoirs with time. | 15 November 2022, 18:01:23 UTC |
| 17cd87a | simonom | 08 November 2022, 13:26:22 UTC | ind_AQ_ex included Included the indoor air quality example inside inputs | 08 November 2022, 13:26:22 UTC |
| aaa441d | simonom | 04 November 2022, 17:04:04 UTC | atom_frac updated plotting script for atom fractions, so that inputs obtained from self rather than retr_out | 04 November 2022, 17:04:04 UTC |
| 57726a6 | simonom | 02 November 2022, 17:27:41 UTC | minor bugs minor bugs fixed, such as stopping plotting scripts from zeroing particle-phase concentrations of some components for proceeding plotting actions | 02 November 2022, 17:27:41 UTC |
| ceb99e8 | Simon O'Meara | 02 November 2022, 10:23:50 UTC | minor update fixed a bug in RO2 contribution plot and removed print command from ode_updater | 02 November 2022, 10:23:50 UTC |
| 0896c91 | Simon O'Meara | 01 November 2022, 19:47:08 UTC | moved dydt_rec Moved the call to dydt_rec so that it was positioned appropriately beside the call to rec module | 01 November 2022, 19:47:08 UTC |
| 30e4e75 | simonom | 01 November 2022, 16:22:52 UTC | moved save before cham_up saving results before calling cham_up in ode_updater means that saved results represent the condition before any instantaneous changes (such as particle injection) at the saved time. | 01 November 2022, 16:22:52 UTC |
| fe0c04b | simonom | 28 October 2022, 16:05:26 UTC | equation parsing updated the equation parsing to deal with chemical scheme that don't contain spaces around = signs and/or + signs, also updated to deal with chemical schemes that have spaces inside the reaction rate coefficient | 28 October 2022, 16:05:26 UTC |
| c31a3cc | simonom | 27 October 2022, 16:18:41 UTC | updated UVC transmission modified the effect of setting the UVC transmission factor so that it affects the whole UVC region (100-280nm), rather than just 254nm | 27 October 2022, 16:18:41 UTC |
| d543a86 | Simon O'Meara | 26 October 2022, 16:29:05 UTC | plotting bug fixes fixed some more bugs around plotting functions | 26 October 2022, 16:29:05 UTC |
| 8082d61 | simonom | 25 October 2022, 16:48:21 UTC | bugs Bugs around changes to retr_out and allowing multiple wall bins corrected | 25 October 2022, 16:48:21 UTC |
| a6984a4 | simonom | 21 October 2022, 16:56:23 UTC | bug fixes bug fixes, including allowing actinic flux files to be identified | 21 October 2022, 16:56:23 UTC |
| f4a7185 | simonom | 20 October 2022, 15:30:44 UTC | updated ind_aq_ex More emissions from cleaning activity | 20 October 2022, 15:30:44 UTC |
| 334afb9 | Simon O'Meara | 19 October 2022, 16:37:12 UTC | updated ind_aq_ex Improved indoor air quality example | 19 October 2022, 16:37:12 UTC |
| 0de1ed7 | simonom | 18 October 2022, 15:47:43 UTC | bug fixes Some bug fixes | 18 October 2022, 15:47:43 UTC |
| 304a2bd | simonom | 13 September 2022, 16:31:22 UTC | improved particle plotting size-segregated particle mass concentration plotting improved | 13 September 2022, 16:31:22 UTC |
| 85896e1 | Simon O'Meara | 13 September 2022, 06:57:50 UTC | removed indoor air quality test results Because this is relatively a very large folder that is not required in the shared version of PyCHAM | 13 September 2022, 06:57:50 UTC |
| 8e0bce8 | Simon O'Meara | 13 September 2022, 06:55:12 UTC | Minor bug fixes Some bug fixes, but also the addition of ind_AQ_ex to the input folder, which demonstrates how to simulate indoor air quality using PyCHAM | 13 September 2022, 06:55:12 UTC |
| b40f5d1 | simonom | 07 September 2022, 16:33:59 UTC | Better particle influx representation Continuous influx of particles can now happen from the start of the simulation | 07 September 2022, 16:33:59 UTC |
| d9d63e0 | simonom | 06 September 2022, 16:23:05 UTC | wavelength-dependent light transmission factors For example, when windows present | 06 September 2022, 16:23:05 UTC |
| 1bf4df7 | simonom | 02 September 2022, 16:24:09 UTC | bug fixes and constant influx Some bug fixes related to the new multi-wall functionality. Also, now possible to prescribe continuous influxes of components through a spreadsheet rather in the model variables file. | 02 September 2022, 16:24:09 UTC |
| aad0e3d | simonom | 22 August 2022, 14:48:39 UTC | Important multi-wall bugs fixed Important bugs were fixed that had resulted from the new multi-wall approach. But now verified as working against the model for single wall. | 22 August 2022, 14:48:39 UTC |
| 56c3074 | Simon O'Meara | 19 August 2022, 16:05:02 UTC | Minor bug fix & wall-specific volatility Fixed some bugs associated with the new function to model multiple wall bins. Also allowed user-defined vapour pressures for specific walls | 19 August 2022, 16:05:02 UTC |
| 5fe2950 | simonom | 18 August 2022, 15:22:44 UTC | Multiple Walls Now Allowed Changed many modules, including write_ode_solv and jac_setup, to allow n walls to undergo gas-wall partitioning, whereas previously only one wall was allowed | 18 August 2022, 15:22:44 UTC |
| 408fd20 | Simon O'Meara | 10 August 2022, 17:03:13 UTC | Pie chart better Increased font size for labels in pie chart of contributors to a particular phase | 10 August 2022, 17:03:13 UTC |
| 131b366 | simonom | 09 August 2022, 15:37:19 UTC | Minor bugs fixed For example, gas phase plotting was crossed with Van-Krevelen. | 09 August 2022, 15:37:19 UTC |
| b6b2c8b | Simon O'Meara | 05 August 2022, 16:01:59 UTC | Improved plotting Improved plotting related to particle phase. Also moved the indexing of HOM-RO2 to prop_calc and save rather than estimating inside plotter_gp. | 05 August 2022, 16:01:59 UTC |
| 327cbc3 | Simon O'Meara | 04 August 2022, 15:27:56 UTC | Volatility plotting improved Pie charts of top contributors now more informative | 04 August 2022, 15:27:56 UTC |
| a928c4d | simonom | 03 August 2022, 15:15:58 UTC | Pie Chart for Contributions Can now plot the contributions to mass fraction for the gas-phase for oxidised non-methane carbon-containing components at a given time for the top n components | 03 August 2022, 15:15:58 UTC |
| a345d5e | simonom | 02 August 2022, 15:48:16 UTC | VBS available for different phases The volatility basis set can now be generated for the gas or particle or gas+particle phases | 02 August 2022, 15:48:16 UTC |
| c03f6c7 | Simon O'Meara | 01 August 2022, 07:49:09 UTC | Minor bug fix Fixed bug that caused crash when user-defined number of size bins>1 but no particle number concentration defined by user | 01 August 2022, 07:49:09 UTC |
| e71082d | Simon O'Meara | 27 July 2022, 17:25:31 UTC | Minor bug fix Fixed a bug that stopped photolysis rates from being plotted after a simulation had been run | 27 July 2022, 17:25:31 UTC |
| 17196bd | Simon O'Meara | 21 July 2022, 20:55:20 UTC | Error messages from middle Debugged what happens when an error message arises from middle.py | 21 July 2022, 20:55:20 UTC |
| 041af29 | simonom | 08 July 2022, 10:45:37 UTC | solar declination angle Corrected the calculation of solar declination angle inside the zenith.py module. Previously this was at a fixed value that introduced major error for natural light simulations during winter. Credit to Thai Bao Ngoc for identifying this issue | 08 July 2022, 10:45:37 UTC |
| d61660b | Simon O'Meara | 08 June 2022, 17:08:54 UTC | mass defect improved plotting options for mass defect plots improved | 08 June 2022, 17:08:54 UTC |
| e693e81 | Simon O'Meara | 06 June 2022, 11:41:59 UTC | Van Krevelen Improved Options and functioning of the Van Krevelen plots have been improved | 06 June 2022, 11:41:59 UTC |
| 0b3e23c | Simon O'Meara | 31 May 2022, 17:48:51 UTC | Van Krevelen Van Krevelen plots can now be made with results from new simulations inside the plotting tab | 31 May 2022, 17:48:51 UTC |
| 4d4958c | Simon O'Meara | 30 May 2022, 14:51:08 UTC | eqn_interr improved Now eqn_interr module can cope with components that appear first in the chemical scheme as a reactant and then a product - or possibly never as a product | 30 May 2022, 14:51:08 UTC |
| 2aaba25 | Simon O'Meara | 26 May 2022, 13:15:49 UTC | SOA yield button SOA yield button now works | 26 May 2022, 13:15:49 UTC |
| 824392a | simonom | 25 May 2022, 16:42:29 UTC | Consumption Consumption calculation corrected | 25 May 2022, 16:42:29 UTC |
| b6fe281 | simonom | 23 May 2022, 15:30:06 UTC | Minor Corrections Like allowing setting of cosx and secx | 23 May 2022, 15:30:06 UTC |
| d3727c6 | simonom | 12 May 2022, 11:54:08 UTC | Radical plotting Improved plotting of radical analysis, so that a minimum carbon number for radicals can be set by the user | 12 May 2022, 11:54:08 UTC |
| 6278f11 | Simon O'Meara | 11 May 2022, 17:53:46 UTC | Ozone isopleths Improved functionality of plotting ozone isopleths | 11 May 2022, 17:53:46 UTC |
| d583b7d | Simon O'Meara | 09 May 2022, 11:22:29 UTC | Generation counting and input checking Generation counting can now deal with single carbon components. User input check now deals with bas chemical scheme markers. | 09 May 2022, 11:22:29 UTC |
| 5af59dc | Simon O'Meara | 06 May 2022, 13:23:19 UTC | Ozone isopleth Function added to plot tab that allows user to see the ozone isopleth across the NOx and VOC space relevant to the simulation in question | 06 May 2022, 13:23:19 UTC |
| 66943ee | simonom | 03 May 2022, 15:27:16 UTC | continuous influx of water To accelerate ODE solver computation time, and consistency with gas-particle partitioning treatment, any continuous injection and/or dilution of water is treated in the ode solver for gas-particle partitioning of water rather than in the ode solver for all other processes. | 03 May 2022, 15:27:16 UTC |
| e477642 | simonom | 28 April 2022, 12:49:53 UTC | generation numbers saved Generation numbers of each component are saved to output | 28 April 2022, 12:49:53 UTC |
| 6a09fa8 | simonom | 28 April 2022, 10:09:10 UTC | generation identification For all components, eqn_interr now identifies its generation number (where the unoxidised initial VOC is zero generation). Originally intended for distinguishing radicals of different generation. | 28 April 2022, 10:09:10 UTC |
| 2eadd22 | Simon O'Meara | 22 April 2022, 06:56:08 UTC | input check Improved checks on user input | 22 April 2022, 06:56:08 UTC |
| 0e0e143 | Simon O'Meara | 12 April 2022, 15:15:11 UTC | README improved Added an output section to README so that users can apply their own code to analyse results | 12 April 2022, 15:15:11 UTC |
| 1d448cb | Simon O'Meara | 31 March 2022, 11:48:29 UTC | radical plotting Improved plotting of RO2 and RO radicals in Radicals tab | 31 March 2022, 11:48:29 UTC |
| 4196a0d | simonom | 30 March 2022, 15:14:13 UTC | RO fluxes Under Plotting/Radicals tab users can now plot the flux of alkoxy radicals in order of flux and they can track all alkoxy radicals fluxes using the tracked_comp model variable (as explained in README) | 30 March 2022, 15:14:13 UTC |
| c20cd87 | Simon O'Meara | 30 March 2022, 09:59:15 UTC | Radical pool plots Improved ability to plot radical-related properties | 30 March 2022, 09:59:15 UTC |
| 98df373 | Simon O'Meara | 29 March 2022, 17:04:41 UTC | radicals & checks Can now plot contribution to certain radical pools in plotting tab. Also, improved the checks on reaction rate coefficients when checking user-supplied chemical schemes | 29 March 2022, 17:04:41 UTC |
| ea8a0e1 | Simon O'Meara | 25 March 2022, 18:26:53 UTC | small bug Fixed issue in init_conc that was causing crash when a component with initial concentration provided by user not recognised | 25 March 2022, 18:26:53 UTC |
| 75e5dd4 | simonom | 24 March 2022, 16:52:30 UTC | self.obs_file big fixed self.obs_file is cleared after each new selection of input files now | 24 March 2022, 16:52:30 UTC |
| 315275e | simonom | 24 March 2022, 11:05:22 UTC | README updated Very small clarification made to seedx model variable description | 24 March 2022, 11:05:22 UTC |
| 4968b54 | simonom | 24 March 2022, 10:56:16 UTC | README updated Updates to several sections of README including a new gas-particle partitioning section to improve user experience | 24 March 2022, 10:56:16 UTC |
| 57c11cf | Simon O'Meara | 16 March 2022, 11:24:45 UTC | fixed concentrations components Fixed default values for the indices of components with concentrations fixed to observed | 16 March 2022, 11:24:45 UTC |
| 13627b5 | simonom | 14 March 2022, 16:40:28 UTC | User dialogue Rather than crash if a component is provided that isn't present in the chemical scheme, followed by the observed and modelled plot button pressed, now an error message is shown | 14 March 2022, 16:40:28 UTC |
| 366ac51 | Simon O'Meara | 09 March 2022, 18:10:40 UTC | Merge branch 'master' of https://github.com/simonom/PyCHAM | 09 March 2022, 18:10:40 UTC |
| 0b3385c | Simon O'Meara | 09 March 2022, 18:10:23 UTC | fixed to observations Now able to fix the concentrations of certain components to an observation file, as described in README | 09 March 2022, 18:10:23 UTC |
| 5554fe0 | Simon O'Meara | 08 March 2022, 09:24:49 UTC | Merge pull request #22 from baongocthai/patch-2 gas-particle partitioning rate: species conc.<0 | 08 March 2022, 09:24:49 UTC |
| a5bd719 | baongocthai | 08 March 2022, 07:25:26 UTC | gas-particle partitioning rate: species conc.<0 Line 222 to calculate dd_trouble: gas-particle partitioning rate (molecules/cm3/s) for species with negative concentration - kimt has shape (no. of size bins, negative components) - Csit has shape (no. of size bins, negative components) Error occurs when running PyCHAM because, in line 222 calculation, kimt[isb,:] has different shape compared to Csit -> ValueError: operands could not be broadcast together between 2 matrix of different shapes Therefore, propose the following change: -> kimt[isb, :]) to kimt on line 222 | 08 March 2022, 07:25:26 UTC |
| db151aa | Simon O'Meara | 03 March 2022, 14:50:01 UTC | molar mass display can now see molar masses of components through drop-down button in simulate tab | 03 March 2022, 14:50:01 UTC |
| 1d630ec | Simon O'Meara | 03 March 2022, 10:51:44 UTC | Negative output allowed Functionality added in a backward compatible manner: ode solver results are allowed to be negative, if the negative value is relatively tiny. This allows complex systems to have components that tend toward zero but which must (according to the solver limits) fluctuate about zero to do this | 03 March 2022, 10:51:44 UTC |
| f86c2a1 | simonom | 02 March 2022, 17:20:50 UTC | stability check limited negativity allowed when checking for solver stability in ode_updater following call to ode_solv | 02 March 2022, 17:20:50 UTC |
| 49816a0 | Simon O'Meara | 01 March 2022, 17:23:30 UTC | time issue Fixed numerical issue with knowing when recording interval was reached when interval less than 1 second | 01 March 2022, 17:23:30 UTC |
| ced218c | simonom | 24 February 2022, 16:39:49 UTC | lat fix latitude corrected back to radians from degrees in zenith | 24 February 2022, 16:39:49 UTC |
| d7a3885 | simonom | 24 February 2022, 13:49:33 UTC | self improvement moved input file identifiers to self to make code tidier and reduce dependence on pickle | 24 February 2022, 13:49:33 UTC |
| 5308adb | Simon O'Meara | 23 February 2022, 19:19:24 UTC | zenith, README Corrected inputs to zenith call from photolysisRates module. Improved README for users who have light intensity expressed as Watts | 23 February 2022, 19:19:24 UTC |
| 23d08d3 | simonom | 23 February 2022, 14:24:12 UTC | self More variables moved to self for tidier code | 23 February 2022, 14:24:12 UTC |
| 5799122 | Simon O'Meara | 22 February 2022, 11:46:20 UTC | self improvement Moved more variables into self to make code tidier | 22 February 2022, 11:46:20 UTC |
| d7716ce | Simon O'Meara | 21 February 2022, 11:57:43 UTC | Photolysis Rate Checker Check for photolysis rates in simulate tab updated so that legend corresponds directly to MCM numbers, i.e., #1 in legend corresponds to J<1> in MCM | 21 February 2022, 11:57:43 UTC |
| 1834bbe | Simon O'Meara | 21 February 2022, 10:35:44 UTC | Model Variable Transferred some model variable objects into self | 21 February 2022, 10:35:44 UTC |
| b99cb46 | Simon O'Meara | 16 February 2022, 20:14:34 UTC | PRINT Removed excess print statement from gui module, updated MAC actinic flux file | 16 February 2022, 20:14:34 UTC |
| 043ce97 | Simon O'Meara | 16 February 2022, 14:55:18 UTC | xls improvement More checks on user input provided for plotting model results against observations | 16 February 2022, 14:55:18 UTC |
| 078feb3 | Simon O'Meara | 16 February 2022, 14:38:04 UTC | openpyxl openpyxl module added to module list in environment setup files | 16 February 2022, 14:38:04 UTC |
