PHREEQC plus
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About this app
Description & Use:
PHREEQC (authors: David L. Parkhurst, C.A.J. Appelo) is a favourite geochemical code used for speciation modelling. Our application brings the users the experience of extended capabilities due to integration of MOPAC (author: James JP Stewart), CHEMSOL (authors: Jan Florián, Arieh Warshel), XTB (authors: C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, J. Seibert, S. Spicher, S. Grimme, P. Shushkov, M. Stahn, H. Neugebauer, J.-M. Mewes, V. Asgeirsson, C. Bauer, J. Koopman) and DFTB+ (authors: B. Hourahine, B. Aradi, V. Blum, F. Bonafé, A. Buccheri, C. Camacho, C. Cevallos, M. Y. Deshaye, T. Dumitrică, A. Dominguez, S. Ehlert, M. Elstner, T. van der Heide, J. Hermann, S. Irle, J. J. Kranz, C. Köhler, T. Kowalczyk, T. Kubař, I. S. Lee, V. Lutsker, R. J. Maurer, S. K. Min, I. Mitchell, C. Negre, T. A. Niehaus, A. M. N. Niklasson, A. J. Page, A. Pecchia, G. Penazzi, M. P. Persson, J. Řezáč, C. G. Sánchez, M. Sternberg, M. Stöhr, F. Stuckenberg, A. Tkatchenko, V. W.-z. Yu, T. Frauenheim). Any custom species not present in the built-in databases can be calculated within the app and the results used in the model (in other words, a new, specific database can be constructed in each run separately). Furthermore, the current package contains numerous non-conventional databases utilizing both experimental as well as predicted / calculated data from big databases such as CHNOSZ, ModelSEED, Alexandria library, KEGG and other literal sources.
Except from the equilibrium state, the code supports also kinetics modelling, for which the respective keyword blocks can be generated automatically based on the previous transitional state computation. As an alternative for nonaqueous systems, FastChem Cond speciation modelling is available as well. All the programs features are available offline.
Warning about the computational accuracy: MOPAC represents a reasonable compromis between power of the device/calculation time and prediction accuracy for large variety of compound types ranging from small to mid-sized molecules. However, the accuracy is limited. In order to tune the resulting energies, COSMO model from MOPAC as well as CHEMSOL solvation models are integrated, although CHEMSOL is originally intented to be used in connection with the structures and charges calculated at higher levels of theory. Therefore, all the calculated equilibrium and rate constants should be treated with caution and regarded as a rough estimate in cases when no experimental data (from the included databases) are available. XTB and DFTB+ integration is experimental so far.
IMPORTANT !!!
Although this app is composed of open-source codes and resources, licenses for some components require the users to cite the original references when publishing the results. Please check all the licensing information under the buttons 'License' and 'About the app'.
All the users of the PHREEQC PLUS app comply by downloading, installing and using it with all the licensing conditions of the individual software components and take the responsibility for keeping them.
App source code: https://github.com/alanliska/PHREEQC-plus
Contact:
Compilation of the source code for Android as well as the Android app development was done by Alan Liška (alan.liska@jh-inst.cas.cz) and Veronika Růžičková (sucha.ver@gmail.com), J. Heyrovský Institute of Physical Chemistry of the CAS, v.v.i., Dolejškova 3/2155, 182 23 Praha 8, Czech Republic.
Website: http://www.jh-inst.cas.cz/~liska/MobileChemistry.htm
List of used third-party software:
ACPDFVIEW, ANDROID SHELL, BLAS, CHEMSOL, DFTB+, DFTD4, EIGEN3, FASTCHEM Cond, GMP, GRAPHVIEW, LAPACK, MCTC-LIB, MOPAC, MSTORE, MULTICHARGE, OPENBABEL, OPENBLAS, OPENMOPAC, OPSIN, PHREEQC, PLOTMS, PYTHON, QCXMS, S-DFTD3, STDA, TBLITE, TEST-DRIVE, TOML-F, TRANSPOSE, X11-BASIC, XTB, XTB4STDA.
More info on licenses & references - please refer to the licensing information inside of the app.
PHREEQC (authors: David L. Parkhurst, C.A.J. Appelo) is a favourite geochemical code used for speciation modelling. Our application brings the users the experience of extended capabilities due to integration of MOPAC (author: James JP Stewart), CHEMSOL (authors: Jan Florián, Arieh Warshel), XTB (authors: C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, J. Seibert, S. Spicher, S. Grimme, P. Shushkov, M. Stahn, H. Neugebauer, J.-M. Mewes, V. Asgeirsson, C. Bauer, J. Koopman) and DFTB+ (authors: B. Hourahine, B. Aradi, V. Blum, F. Bonafé, A. Buccheri, C. Camacho, C. Cevallos, M. Y. Deshaye, T. Dumitrică, A. Dominguez, S. Ehlert, M. Elstner, T. van der Heide, J. Hermann, S. Irle, J. J. Kranz, C. Köhler, T. Kowalczyk, T. Kubař, I. S. Lee, V. Lutsker, R. J. Maurer, S. K. Min, I. Mitchell, C. Negre, T. A. Niehaus, A. M. N. Niklasson, A. J. Page, A. Pecchia, G. Penazzi, M. P. Persson, J. Řezáč, C. G. Sánchez, M. Sternberg, M. Stöhr, F. Stuckenberg, A. Tkatchenko, V. W.-z. Yu, T. Frauenheim). Any custom species not present in the built-in databases can be calculated within the app and the results used in the model (in other words, a new, specific database can be constructed in each run separately). Furthermore, the current package contains numerous non-conventional databases utilizing both experimental as well as predicted / calculated data from big databases such as CHNOSZ, ModelSEED, Alexandria library, KEGG and other literal sources.
Except from the equilibrium state, the code supports also kinetics modelling, for which the respective keyword blocks can be generated automatically based on the previous transitional state computation. As an alternative for nonaqueous systems, FastChem Cond speciation modelling is available as well. All the programs features are available offline.
Warning about the computational accuracy: MOPAC represents a reasonable compromis between power of the device/calculation time and prediction accuracy for large variety of compound types ranging from small to mid-sized molecules. However, the accuracy is limited. In order to tune the resulting energies, COSMO model from MOPAC as well as CHEMSOL solvation models are integrated, although CHEMSOL is originally intented to be used in connection with the structures and charges calculated at higher levels of theory. Therefore, all the calculated equilibrium and rate constants should be treated with caution and regarded as a rough estimate in cases when no experimental data (from the included databases) are available. XTB and DFTB+ integration is experimental so far.
IMPORTANT !!!
Although this app is composed of open-source codes and resources, licenses for some components require the users to cite the original references when publishing the results. Please check all the licensing information under the buttons 'License' and 'About the app'.
All the users of the PHREEQC PLUS app comply by downloading, installing and using it with all the licensing conditions of the individual software components and take the responsibility for keeping them.
App source code: https://github.com/alanliska/PHREEQC-plus
Contact:
Compilation of the source code for Android as well as the Android app development was done by Alan Liška (alan.liska@jh-inst.cas.cz) and Veronika Růžičková (sucha.ver@gmail.com), J. Heyrovský Institute of Physical Chemistry of the CAS, v.v.i., Dolejškova 3/2155, 182 23 Praha 8, Czech Republic.
Website: http://www.jh-inst.cas.cz/~liska/MobileChemistry.htm
List of used third-party software:
ACPDFVIEW, ANDROID SHELL, BLAS, CHEMSOL, DFTB+, DFTD4, EIGEN3, FASTCHEM Cond, GMP, GRAPHVIEW, LAPACK, MCTC-LIB, MOPAC, MSTORE, MULTICHARGE, OPENBABEL, OPENBLAS, OPENMOPAC, OPSIN, PHREEQC, PLOTMS, PYTHON, QCXMS, S-DFTD3, STDA, TBLITE, TEST-DRIVE, TOML-F, TRANSPOSE, X11-BASIC, XTB, XTB4STDA.
More info on licenses & references - please refer to the licensing information inside of the app.
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What's new
Fixed compatibilty of the plotting options on Android 7 devices.
