{"shas":[["97c91617ce01ea1c60752bcefebf16212311b4c6","b1063c6ecf4e141d62862c7361346d12e74c651f@mit.edu","Better error message for forbidden species\n\nWhen a species from the input file, or the RMG_database thermochemistry\nfolders, is marked as forbidden, a better error message is now supplied\nto the user.\n\nThis error message only concerns read-in species that exceed the maximum\nnumber of oxygens, radicals, or cycles (another already-in-place code checks\nfor the other options given to the user in the input file, e.g. maximum number\nof carbons).","Michael Harper"],["d79f6cdeb3373e2b96e71f1e4dd884e391819df4","b1063c6ecf4e141d62862c7361346d12e74c651f@mit.edu","Bug fix: Converting InChIs (or .mol files) to adjacency lists\n\nIf the number of bonds in a molecule exceeded 99, the InChI2AdjList (or\nMol2AdjList) function would fail.  This was due to the number of atoms and\nthe number of bonds running together in the .mol file (as pointed out by\nGRM).  As pointed out by RHW in the comments, this can be resolved by\nrecognizing every token takes 3 characters.\n\nMRH has implemented and tested the fix.  The case presented by GRM in the\nissue runs w/o error.\n\nCloses #93","Michael Harper"],["bf63343c0258c3d7358f02afd00075f355003fba","9bd490a4f453b93cf9fd9834a38e01d2badc8a91@mit.edu","Switch Makefile to use gfortran instead of g95. (not yet working)\n\nStarted experimenting with compile flags.\nCurrently GATPFit doesn't build.","Richard West"],["b2fe3616c435315a56b4bba8c861f7d4640fd001","9bd490a4f453b93cf9fd9834a38e01d2badc8a91@mit.edu","Fix broken whitespace in GATPFit\n\nThe gnu fortran compiler, following standards, could not compile \nthe lines that were too long. It also warned about nonconforming tab\ncharacters. These have all been replaced with spaces. Fixed-width\nfortran has to have the command start in column 7. Some files also\nhad extra linebreaks (from a dos2unix error I guess)","Richard West"],["dba53787dca7ced33784436d1b040fee0e9c2846","9bd490a4f453b93cf9fd9834a38e01d2badc8a91@mit.edu","Fix GATPFit Makefile (and change to gfortran)","Richard West"],["c865004f48fa89a3ca73e3be52bac26979185681","9bd490a4f453b93cf9fd9834a38e01d2badc8a91@mit.edu","Correct line endings in GATPFit code.\n\nThese are now all unix. With a mixture, gfortran cannot compile and link it.","Richard West"],["5903c38496006e285090ce082279050a7c9e9179","9bd490a4f453b93cf9fd9834a38e01d2badc8a91@mit.edu","Squash some potentially un-assigned variable warnings.","Richard West"],["612144a97113764f3bbe87d219842fe1991a8bbf","9bd490a4f453b93cf9fd9834a38e01d2badc8a91@mit.edu","Switch fame Makefile to gfortran, and squash some warnings.","Richard West"],["64d73e3b9ec15cecf1e3cf63d8056c39c8e46488","9bd490a4f453b93cf9fd9834a38e01d2badc8a91@mit.edu","All makefiles use gfortran and tweaked.\n\nAdd -backtrace to F90FLAGS if using gfortran>=4.3.\nAlso, the 'clean' target for Ant has been fixed.","Richard West"],["992469fd48dd47f678cf77e60cc87df64fc53ef0","9bd490a4f453b93cf9fd9834a38e01d2badc8a91@mit.edu","Nonconforming tab chacacter in frankie.","Richard West"],["a448692fcd6c627d0d58de467e861a94339f3ab1","9bd490a4f453b93cf9fd9834a38e01d2badc8a91@mit.edu","Remove --fpe-trap=overflow from Makefiles.\n\nThis causes FAME to throw a floating point exception, and yet after\ntrying to debug it for ages Josh an I gave up. If we don't compile with \nthis flag, then it at least runs. There *may* be a bug in fame, but there\nmay also be a bug in the compiler. This should probably be looked at again\nsome time.","Richard West"],["01119ba747c95ca0e21f03823eca99e84a3d95e5","9bd490a4f453b93cf9fd9834a38e01d2badc8a91@mit.edu","Fix index error in fame network.f90 revealed by -fbounds-check -frange-check \n\nCompiler flags are our friend :)","Richard West"],["506a84f0a25de363460734f5bc5d47d718820983","9bd490a4f453b93cf9fd9834a38e01d2badc8a91@mit.edu","Fix frankie bug. Was assigning 0's to unallocated memory.\n\nRooted out with compiler flags and valgrind.\n(Thanks Josh!)","Richard West"],["0635bd3f2daae5a2b06d688b2cebc0daf71e3165","d2efaa4c3e5af267960de800d4d586f2bce0207f@mit.edu","Replaced stop with goto in fame.f90 when invalid rate is encountered.\n\nThis appears to allow FAME to properly deallocate memory, avoiding memory\nleaks.","Josh Allen"],["1cfdf78dbc89ebbf0245a06bcd8b84121f907e46","9bd490a4f453b93cf9fd9834a38e01d2badc8a91@mit.edu","Add 'MACOS' option to master Makefile\n\nCall with `make MACOS=true` for a MacOSX 10.6+ 64-bit intel core2 optimized build.\n(only works from master makefile)","Richard West"],["a98c0e7d4dfc266923a9eb41731f22117699baa5","9bd490a4f453b93cf9fd9834a38e01d2badc8a91@mit.edu","Special cases for dassl and daspk Makefiles.\n\nDASSL and DASPK break if you use certain compiler flags like bounds checking\nbecause they do cunning things with array bounds. Assuming these codes to be\nbug-free, we turn off such checks for such things.\n\nAlso updated the daspk subproject to quell one other compiler warning.\n`git subproject update` to get it.","Richard West"],["ee68909353d446b205b06fc790f71d36f8c4e0dd","9bd490a4f453b93cf9fd9834a38e01d2badc8a91@mit.edu","Tiny tweaks to makefiles.\n\n-Wno-tabs is covered by -Wall (use -Wtabs to silence such warnings)\nThe F90FLAGS_NDEBUG is not used in fame","Richard West"],["b8ed7c935566bb4a7a94eef6283c8621ba5f7052","9bd490a4f453b93cf9fd9834a38e01d2badc8a91@mit.edu","Convert tabs to spaces in daspk and dassl codes.","Richard West"],["46fc5f2daad4ccb62d93b6f9dacc15c3d1a6f29e","9bd490a4f453b93cf9fd9834a38e01d2badc8a91@mit.edu","Remove --fpe-trap=zero,invalid from Makefiles (specifically for fame)\n\nThis is removed from the master makefile (and hence all called by it)\nand fame's Makefile. It seems to only be a problem for fame.\nIt'd be nicer to find the cause of the floating point exception rather \nthan just to not check for it, but for now this allows us to run.","Richard West"],["c860326c553de92eb4c1714d98ff3cde27c1e0c5","9bd490a4f453b93cf9fd9834a38e01d2badc8a91@mit.edu","All Makefiles work for both g95 and gfortran! Call eg. 'make F90=g95'\n\nIf you declare the F90 value when calling make, it is honoured.\nAll the compiler flags are inside conditionals.\n\nOptions are:\n make F90=g95\n make F90=gfortran\n make F90=gfortran MACOS=true","Richard West"]],"repo":"rwest/RMG-Java","actor":"rwest","ref":"refs/heads/allowCO3","size":25,"head":"ec99ae1b58a23484ed60e9e45030761a151110cb","actor_gravatar":"3463bcb0d9be3889166c718a5d2cc993","push_id":23246236}