Release10#3
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…mmits in the future for sure...
…or change to code.
… the 'Pool size per FU' instead of the 'Pool size per FU' * formulaUnitsList.size()
…ls/XtalOpt into Formula_Unit_Functions Conflicts: src/globalsearch/sshconnection_cli.cpp src/xtalopt/ui/tab_init.cpp src/xtalopt/ui/tab_init.h src/xtalopt/ui/tab_init.ui src/xtalopt/ui/tab_opt.cpp src/xtalopt/ui/tab_opt.ui src/xtalopt/ui/tab_plot.h src/xtalopt/xtalopt.cpp src/xtalopt/xtalopt.h
…ab_init.cpp to make it more compatible with my version.
…xes include: rank all now ranks and prints files successfully. Print results file includes formula units and enthalpy is now enthalpy/FU. Also made Enthalpy_per_FU_T the default y-axis setting.
…ene pool- and for eliminating duplicate chains. Also made a few more compatibility changes since the merge with release9.
…he number of formula units. This was done so the getFormulaUnits algorithm doesn't have to be run every time. It is set with setFormulaUnits. In addition, the only structures that are duplicate checked and supercell checked now are optimized structures.
…on and causing several functions to use it. Also set xtals from mitosis to have a generation of the parent xtal plus 1. Also fixed a memory leak issue. generateSuperCell now returns a dynamically allocated xtal.
…ating an optimized structure, it will be primitive checked via generateNewXtal(). If a primitive xtal can be created that has fewer formula units than the original xtal, then it will be. It will also be set to optimized and will not undergo optimization.
…structure has been identified as a primitive reduction or a supercell. Also added some of the variables I have made to structure's assignment operator.
…quired to do this. Also added structureChanged() during reading in xtalopt.cpp so primitives will not be made upon resuming. The program still appears to have a freezing issue, however, for higher structure numbers. This needs to be looked into.
… gets one copy of each supercell per formula unit. This is so we don't include supercells that are duplicates of each other.
…ting some of the trivial sorting loops at the end.
…f 1 in the tab_init constructor. This prevents crashing when the user doesn't actually click inside the formula units box on the initial tab.
…pt data if the user starts the search in a directory that already contains XtalOpt data.
…irectories recursively with Qt. I also implemented in a couple of places... Finally, I made printRanked only print out optimized xtals.
…on calls still worked, but using uninitialized pointers is typically a bad idea...
… the structure.state file. In addition, I made a few functions const that were just for reading a private member variable. In addition, I made the function countStructuresOfEachFormulaUnit() a static function since it doesn't use the this pointer anywhere in the body.
…l, a supercell of the smaller FU xtal is placed in the larger FU xtal's gene pool. So, supercell generating functions were added among a few other minor changes.
…pes, and atom positions are saved in the structure.state file. This speeds up loading a LOT. If it doesn't find this information, however, xtalopt will attempt to resume the old way (reading the optimizer output)
… xtalopt.cpp just checks for the saveSuccessful tag in the structure.state file. saveSuccessful now also starts as false during the save and becomes true at the end of the save. Finally, fixed some issues where energy was not saved or being read correctly.
…for structures that are not periodic (for randomdock and gapc runs, for instance).
… than 3 meV/atom instead of 1 percent for it to be considered a significant enough difference. In addition, if the user changes the formula unit list to have a larger maxFU than before, the supercell generation checks are reset so that larger FU may have a chance at getting some of the smaller FU structures. Also fixed the concurrency issue where identical supercells were being generated unnecessarily. Finally, a supercell is generated from a structure ONLY if that structure is the lowest enthalpy structure for that formula unit. This prevents higher enthalpy supercells from being generated unnecessarily.
…talopt into spginitBeginnings
…p (according to spglib), and we try 3 times to do so. We also remove the 'forceMostGeneralWyckPos' check in spgGen
…ed that here from spgGen.
… to be between the minima and maxima after their volumes are adjusted.
…ts to generate the correct spacegroup in spgGen.
…on flags to the compilation of spgGen to speed it up a lot.
…into spginitBeginnings
…he when the next resume attempt was performed (on an xtalopt.state.old file, typically).
… performed correctly because the parameters of the fucntion were in the wrong order...
Fixed a bug in which spglib would crash if the xtal had one length that was 100x shorter than the other lengths. XtalOpt now just removes those xtals and does not perform the check on them. Also removed a little cmake output from spgGen.
Reduced the length comparison cutoff from 100x to 25x since crashing was observed when lengths were that different from each other.
If the angles of a generated xtal are very small, then, after Niggli reduction, one of the sides may be adjusted to be very small instead. This can cause spglib to crash. It's reasonable to not expect one side to be at least 25x greater than another side. So let's enforce that requirement.
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Push r10 updates