n.n.n / 2020-12-19 ================== * Merge pull request #15 from ltalirz/cleanup * Updated VTK visualization to VTK 9 * update version number * repository cleanup v2.0.39 / 2020-12-05 ==================== * Bugfix: fixed the computation of the error bar (they were too high). * Fixed compilation under macOS Big Sur. v2.0.38 / 2020-05-27 ==================== * Updated the submit-scripts for large batch simulations in the 'scripts' directory * Updated partition factors for ReactionEnsembleAmmonia example * Added examples from a forthcoming bookchapter * Changed CO2 and N2 to shifted potentials in GenericZeolites and GenericMOFs * Modified RXMC to avoid under/overflow in acceptance rule. * Added option 'LnPartitionFunction' to enter ln(q/V) in units of ln(A^(-3)). * Added reference to the README * Fixed type: "gr/gr" should be "mg/g" * Added ITQ-29-2x2x2 * Added carbon monoxide * Incorporated changes to make it possible to change the volume of the unit cell along a particular direction/directions. * Do not check for energy-drift for MuPT-, MuPTPR-, and MuVT-ensembles * Fixed typo from 'J. Phys. Chem. B 1999, 103, 4508-4517' and changed torsion parameters 335.03 to 355.03 (as in 'J. Phys. Chem. B 1998, 102, 2569-2577') v2.0.37 / 2019-04-27 ==================== * Added FrameworkChangeMove CFCMC compatibility * Prepared for upload to github v2.0.36 / 2019-01-06 ==================== * Prepared for upload to github v2.0.35 / 2018-07-22 ==================== * Added CFWidomProbability move; Fixed binary-restart to be backwards-compatible (from 2.0.35 onwards) v2.0.34 / 2018-07-05 ==================== * Set pseudo-atom to charged if a framework-atom from a CIF-file is charged, even though the pseudo-atom was defined without charge * Fixed compiler error on some compilers (reported by N. Scott Bobbitt) v2.0.33 / 2018-06-29 ==================== * Updated bookkeeping for CFCMC and CB/CFCMC with grids v2.0.32 / 2018-06-29 ==================== * PDB-movies and CFCMC: Lambda is printed as the occupancy * Added CRYST1-line to allcomponents pdb * Modified VTK-files from 'SetAAFrames' to 'SetMultiSamples' (needed on some nvidia cards on linux) * Python version bump v2.0.31 / 2018-05-08 ==================== * Added LTA dcTST example * Minor fixes in documentation and example molecule definitions v2.0.30 / 2018-03-25 ==================== * Fixed degrees-of-freedom in GibbsIdentityChangeAdsorbateMove/GibbsIdentityChangeCationMove v2.0.29 / 2018-03-14 ==================== * Fixed Intra 1-4 bug for molecules (Reported by Hirad S. Salehi) v2.0.28 / 2018-03-05 ==================== * Changed criteria to detect identical framework-atoms when expanding spacegroup v2.0.27 / 2017-12-22 ==================== * Added examples for MuPT, MuPTPR and MuVT ensemble MD simulations. * Implemented MuVT, MuPT, and MuPTPR ensembles for MD simulations. v2.0.26 / 2017-09-27 ==================== * Fixed adsorbate/cations Fourier energy for CFCMC v2.0.25 / 2017-09-06 ==================== * Added host-guest and guest-guest to SampleEnergyHistogram v2.0.24 / 2017-07-17 ==================== * Fixed error in 'AddRealMatrix6x6' and 'SubtractRealMatrix6x6' (they are now symmetric) v2.0.23 / 2017-07-12 ==================== * Removed erroneous debug-stop in 'SelectRandomMoleculeOfType' v2.0.22 / 2017-06-26 ==================== * Report chemical potentials for individual components when using multiple phases in the new CFCMC GE v2.0.20 / 2017-06-18 ==================== * Fixed order of deletion in CFCRXMCLambdaChangeMove (previous fix only fixed half) * Added Tutorial in Examples and Docs v2.0.19 / 2017-05-09 ==================== * Changed condition for overlap for spacegroup-expanding back to previous definition v2.0.18 / 2017-04-04 ==================== * CFGibbsSwapFractionalMoleculeToOtherBoxMove: extended to handle flexible molecules v2.0.17 / 2017-04-01 ==================== * Extended CFGibbsFractionalToIntegerMove to multiple components v2.0.16 / 2017-04-01 ==================== * Fixed order of deletion in CFCRXMCLambdaChangeMove v2.0.15 / 2017-03-21 ==================== * Fixed errors in Hessian cation-cation minimization v2.0.14 / 2017-02-21 ==================== * Fixed memory allocation-error in core-shells (reported by Ismael) v2.0.13 / 2017-02-06 ==================== * Corrected CFMoleculePresent for new Gibbs CFCMC v2.0.12 / 2016-12-18 ==================== * Added check for enough reaction molecules in Gibbs-swap move * Omit CFCRXMCLambdaChangeMove when no reactions defined v2.0.11 / 2016-12-05 ==================== * Added check for enough reaction molecules in identity-change move * Fixed segmentation-fault in 'shell'-output * Added 'shell'-output for frameworks v2.0.10 / 2016-08-29 ==================== * Error fixed (by Ozgur Yazaydin) in BoxShapeChangeMove * Gibbs CFCMC example added using the new methodology of Poursaeidesfahani et al. (J. Chem. Theory Comput., 2016, 12 (4), pp 1481-1490) * Small corrections for spectra, and cases without adsorbates * Merge branch 'master' of ssh://itsaio.science.uva.nl/~raspa2-dev/RASPA-2.0 * Added ortho C11, C12, C13 strains * Added option to measure properties for CFCMC only when lambda is small ('MeasureLambdaBelow') v2.0.9 / 2016-07-04 =================== * Added option to measure properties for CFCMC only when lambda is small ('MeasureLambdaBelow') v2.0.8 / 2016-05-30 =================== * Fixes NPH-PR energy drift (reported by Ozgur Yazaydin * Fixed limit length of file-name in 'output.c' * Patch by Jure Varlec on configure.ac to allow specification different versions of blas, lapack and fftw v2.0.7 / 2016-04-14 =================== * Bug fixed by Ozgur Yazaydin in routine 'CalculateEnergyDifferenceFrameworkMoveCharge' * Added labeling of pseudo-atoms when reading cif-files from the chemical element when no explicit label (_atom_site_label) is given v2.0.6 / 2016-03-05 =================== * Added modified TraPPE potential (Salvador Rodriguez Gomez and Ismael Matito Martos) * Fixed error in binary restart for core-shell flexible framework v2.0.5 / 2016-02-24 =================== * Error in tail-corrections introduced in 2.0.2 fixed (reported by Ismael Matito Martos) * Added lambda-extrapolation to estimate the chemical potential for grand-canonical CFCMC v2.0.4 / 2016-02-12 =================== * Added lambda-extrapolation to estimate the chemical potential for grand-canonical CFCMC v2.0.3 / 2016-02-11 =================== * Fixed extrapolation in new Gibbs-CFCMC method and corrected inverse-density in ideal-gas term v2.0.2 / 2016-02-11 =================== * Fixed error in non-default number of trial-moves for CBMC-Gibbs; Added new CFCMC-method for Gibbs (Ali Poursaeidesfahani, Ariana Torres-Knoop, David Dubbeldam, Thijs J.H. Vlugt). * Fixed spaces in pdb-output v2.0.1 / 2015-11-26 =================== * Fixed enthalpy of adsorption for mixture and cations * Corrected an small error in the ideal-gas part of the fluctuation formula for the enthalpy of adsorption (at 300K it was about 0.5 kJ/mol off) * Added MIE potential with cutoff * Rewrite of Numerical-Recipes matrix-inverse as zero-based * Fixed error in cation-cation intra Coulomb total energy (reported by José Manuel Vicent Luna) * Added: enthalpy of adsorption corrected for CFMC * Added: total heat of adsorption from components of the mixture and their measured mol-fractions * Fixed binary-restart 'exchange the CF fractional particle' * Added: Enthalpy of adsorption for mixtures (Ali Poursaeidesfahani) * Add torsion potential: TRAPPE_DIHEDRAL_EXTENDED [5-parameters, p_0+p_1*cos(phi)+p_2*cos(2*phi)+p_3*cos(3*phi)+p_4*cos(4*phi)] * Added MC-move: to exchange the CF fractional particle of a random component with a random integer molecule of the same component * Uploaded to PyPI, can now be installed with 'pip install RASPA2' * ln -s COPYING LICENSE.txt * Updated README with links to public wiki * Recommiting Yamil Colon's warnings.c/h changes to new repo * Change default overlap-criteria in FreeEnergyProfile3D to remove artifacts in VTK pictures * Added PrintEnergyStatusToStdOut and changed DebugEnergyStatus to print energy in Kelvin * Added example 'UmbrellaSampling' * Added example 'minimization of MIL-53 with water' * Added pdf of the RASPA Molecular Simulation article * Added averages to SampleProjectedLengthsDistributionFunction() * Added SampleCOMDensityProfile3DVTKGrid to output the center-of-mass of molecule * Added pdf 'On the Inner workings of Monte Carlo codes' v2.0 / 2015-02-03 ================= * Initial Release RASPA-2.0