SIMUNE uses optimization procedures to generate high quality and high transferability pseudopotentials and corresponding basis sets. The pseudopotentials are created by minimizing the difference in the pseudopotential and all-electron energy between different electronic configurations. The optimization of the basis sets is based on the minimization of the average energy of a dimer system with different interatomic distances. This approach ensures the generation of a transferable basis set, and excellent performance in different environments molecules and bulk.
Added the date command to the beginning of the template script for remote jobs. Changed to give the charge value as an argument when assigning a RESP charge when invoking from the command line. Fixed a problem in which the charge and dipole moments were not displayed when reading a log file in which the GAMESS structural optimization calculation was completed in one cycle. Added the display of the excitation configuration of the selected peak in the UV-Vis spectrum window.
Fixed a bug that prevented the [MD]-[Insert Molecules] function from starting. Fixed a bug in which the aspect ratio was not calculated correctly for monoatomic models.
Changed the default group name as the composition name in [Select]-[Register Selected Group]. Enabled to choose between OpenBabel and Balloon for generating molecular structures in the [Tools]-[Draw Molecule] function. Enabled to save csv files to various graph display functions.
Enabled to assign Dreiding force field for molecules containing deuteriums. Enabled to recalculate only the energy for each structure in the Gromacs trajectory file xtc. Fixed a bug that prevented the [Assign force Field parameters] window from being displayed under some conditions. Fixed a problem in which the RMSD and radius of inertia calculation functions of the result analysis function did not work when [Enable double precision] was checked in the Gromacs keyword setting window.
Fixed a bug that prevented the selection of groups for each molecular species under some conditions in the results analysis function of Gromacs.
Fixed a bug in which Winmostar JM Job Manager would lock the folder containing the first bat file executed after startup. Enabled to resize the [Edit]-[Edit Charge] window. Changed so that the index of atoms is sorted inside the program when [Select]-[Register Selected Group] is executed. Changed to assign the names of monomers and polymers as the atom names and substructures in the mol2 file created by the Polymer Builder.
Changed not to create backup files in the working directory by default when Gromacs jobs are executed. Enabled to set whether to create backup files in the working directory when executing a Gromacs job. Changed not to overwrite the index ndx file for Gromacs continues job. Changed to show the values of specific heat and isothermal compressibility Cvm, Cvp, Betat in [Calc Ave] of the energy change function of LAMMPS as the integrated average value itself, instead of the average of the integrated average values.
Fixed an issue where the number of repeats was not cleared in [Solid]-[Generate Supercell]. Fixed a problem in which the coordinates of the following K points were inappropriate in the band structure calculation function of OpenMX. Fixed a bug that the connection with the remote host may fail in remote job submission in some environments. Changed not to regenerates bonds in the interface builder. Enabled to read XYZ files that contain tab characters.
Fixed a bug where the interface builder could generate unwanted bonds. Changed the names of working directories in some functions. Dipole Corr tab [Specification Change] Changed the name of the working directory for some processes. Changed to show the RMS of charges at the bottom of the molecule display area. Fixed a bug that sometimes caused an error when reading Gaussian fchk files. Fixed a problem in which the process was terminated abnormally when launched from the command prompt, depending on the path of the output file.
Fixed a problem that prevented chloroform solvent calculations with Gaussian 09 and Fixed a problem in which an error occurred when using the UFF force field with water molecules and the process did not proceed.
Fixed a problem in which Gromacs continuous execution could be interrupted if the output file size exceeds 2GB. Fixed a bug in the energy change function of LAMMPS that prevented the display of units for variables defined in the variable command e. Added a menu to register and delete fragments under the [Edit]-[Select Fragment] menu. If you are using a template, you will need to recreate the template. Fixed a bug that caused an access violation when Spglib failed to detect a space group.
Fixed a problem where the Generate Supercell would force the outer atoms of a cell to collapse inside the cell. Fixed a bug that caused Winmostar Job Manager to lock the folder where the first bat file started at startup is located. Enabled to change the minimum index that automatically switches to wire view when zooming and rotating the field of view in Preferece window.
Enabled to change the minimum index that automatically switches to wire view usually in the preferences. Enabled to change the scale of the X-axis the same scale of the measured spectra in the infrared Raman spectral window.
Enabled to adjusted the name and size of the components and the scale of the X-axis in the NMR spectrum window. Changed the isosurface display of S-orbitals gray only for Density or Surface. Enabled to set the dihedral angle of polymerization in all polymer builders. Changed to check the chirality of the model generated by Polymer Cell Builder and output to the log. Enabled to set the allowable distance between unbonded atoms for Polymer Cell Builder. Changed to show density in Interface Builder and Slab Builder.
Changed the design of the Generating Supercell. Changed to show the super cell information as text instead of the original cell information in the Generating Supercell.
Speeded up Energy Plot of MD. Fixed a bug that could cause an error when checking to see if bonds passes through the ring structures in Polymer Cell Builder. Fixed a problem in which an incorrect abc axis appeared in the molecular display area when the cell did not exist. Changed to use perspective view in the display preset Winmostar Cover Art.
Changed the layout of the BoltzTraP results display window. Added support for window size in [Tools]-[Draw Molecule]. Fixed a bug that the analysis of space groups using spglib did not work. Changed to set the reference value of the vacuum to the potential energy at the specified coordinates instead of the maximum value of the potential energy in the potential energy distribution function of Quantum ESPRESSO.
Changed the behavior of [Solid]-[Slab Builder] partially. Changed the default extension to mol in the save dialog of [Tools]-[Comformation Search Balloon ]. Enabled to output of cell sizes in Lattice records when saving in xyz format. Added a function to change all the atoms that could not be determined automatically deuterium etc.
Enabled to input the absolute coordinates of the center of gravity of an editing group. Enabled to add atomic luster in the molecule view area. Enabled to show only number or element name on label in molecule view area. Enabled to show abc coordinate axes in the molecule view area when the cell is not a rectangular shape. Enabled to change and save view settings at once. Enabled to show the structure in real time when changing parameters in [MD]-[Interface Builder], Enabled to finely control cell size in the horizontal direction of the interface in [MD]-[Interface Builder].
Enabled to finely control cell size in the distance between cells in [MD]-[Interface Builder]. Enabled to read the structure in the main window in [MD]-[Interface Builder]. Enabled to automatically reposition atoms outside of cells in [MD]-[Interface Builder]. Added a function to create supercells based on the occupancy of the CIF file. Enabled to calculate the vector perpendicular to the plane along a ring structure when the ring structure is selected as a group.
Enabled to output multiple frame SDF files from Animation window. Fixed a bug where Quick Optimization fails for the structure from mol and sdf files. Fixed a problem in which cleave plane of slab models failed on some crystals. Use [Solid]-[Slab Builder]. Fixed a problem in which insert vaccum in slab models failed on some crystals. Fixed a problem in which the conversion to primitive cells failed for some crystals. Fixed the bug of bound check error occurring when converting to a primitive cell with the group selected.
Changed to show detected space groups after converting to primitive cell. Enables to specify the tolerance of space group detection in the preferences.
Changed to use Spglib convert to primitive cells. Changed to not allow OpenMX to run without a simulation cell. Enabled to count down and cancel the automatic shutdown of Job Manager before shutting down. Abolished [File]-[Save Ligand inp File Fixed a bug in which saving mol2 files sometimes resulted in incorrect atomic types.
Fixed a problem in which depth cueing was sometimes not immediately reflected. Fixed a bug where changes were sometimes not reflected after loading and editing a Gaussian input file and saving it. Fixed a problem in which the calculated values in the [Calc Ave] of the energy change window of various MD solvers were slightly shift. Fixed a problem in Acpype charge assignment that resulted in incorrect bond information after sorting by molecular species.
Select lammps. Changed to use the same graph drawing function as the other functions in the BoltzTraP results window. Star MIT License. Branches Tags. Could not load branches. Could not load tags.
Pulay mixing 3. Method overview 2. Want to make it run faster? Try it! QuantumATK Contact. Note You will primarily use the graphical user interface QuantumATK for setting up and analyzing the results. Uncheck the Passivate dangling bonds with hydrogen checkbox. Select Armchair edge.
Select the structure 8 atoms wide. The script below shows how to evaluate the entropy: 1 2 3 4 5 6 7 8 9 10 11 12 Note In most cases the default values should work well. Send the resulting device configuration to the Script Generator. Add a ForceFieldCalculator. Add a SemiEmpiricalCalculator.
In the results box select Do not save and uncheck the Print results summary to log box. No changes need to be made to the PhononTransmissionSpectrum. Double-click the second SemiEmpiricalCalculator and select the Hamiltonian settings. In the Basis Set box select the Hancock. C ppPi basis set.
No changes need to be made to the TransmissionSpectrum. Transfer the script to the Job Manager and run the calculation. Skip to content. Star MIT License.
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