{"action":"created","comment":{"url":"https://api.github.com/repos/vonDonnerstein/QuantumLab.jl/pulls/comments/200700158","pull_request_review_id":135060211,"id":200700158,"node_id":"MDI0OlB1bGxSZXF1ZXN0UmV2aWV3Q29tbWVudDIwMDcwMDE1OA==","diff_hunk":"@@ -0,0 +1,635 @@\n+module BasisSetModule\n+export BasisSet, readTX93, readGaussian, readGAMESSUS, readNWChem, readDalton\n+using ..BaseModule\n+using ..AtomModule\n+using StringParserPEG\n+\n+immutable PrimitiveGaussianBasisFunctionDefinition\n+    exponent::Float64\n+    prefactor::Float64\n+end\n+\n+immutable ContractedGaussianBasisFunctionDefinition\n+    lQuantumNumber::LQuantumNumber\n+    primitives::Array{PrimitiveGaussianBasisFunctionDefinition,1}\n+end\n+\n+immutable BasisSet\n+    definitions::Dict{Element,Array{ContractedGaussianBasisFunctionDefinition,1}}\n+end\n+\n+# Element Dictionary : Full name to Symbol\n+ ElementSymbols = Dict{String,String}(\n+\"HYDROGEN\" =>                 \"H\",\n+\"HELIUM\" =>                  \"He\",\n+\"LITHIUM\" =>                 \"Li\",\n+\"BERYLLIUM\" =>               \"Be\",\n+\"BORON\" =>                    \"B\",\n+\"CARBON\" =>                   \"C\",\n+\"NITROGEN\" =>                 \"N\",\n+\"OXYGEN\" =>                   \"O\",\n+\"FLUORINE\" =>                 \"F\",\n+\"NEON\" =>                    \"Ne\",\n+\"SODIUM\" =>                  \"Na\",\n+\"MAGNESIUM\" =>               \"Mg\", \n+\"ALUMINUM\" =>                \"Al\",\n+\"ALUMINIUM\" =>         \"Al\", \n+\"SILICON\" =>                 \"Si\", \n+\"PHOSPHOROUS\" =>               \"P\", \n+\"SULFUR\" =>                   \"S\", \n+\"CHLORINE\" =>                \"Cl\", \n+\"ARGON\" =>                   \"Ar\", \n+\"POTASSIUM\" =>                \"K\", \n+\"CALCIUM\" =>                 \"Ca\", \n+\"SCANDIUM\" =>                \"Sc\", \n+\"TITANIUM\" =>                \"Ti\", \n+\"VANADIUM\" =>                 \"V\", \n+\"CHROMIUM\" =>                \"Cr\", \n+\"MANGANESE\" =>               \"Mn\", \n+\"IRON\" =>                    \"Fe\", \n+\"COBALT\" =>                  \"Co\", \n+\"NICKEL\" =>                  \"Ni\", \n+\"COPPER\" =>                  \"Cu\", \n+\"ZINC\" =>                    \"Zn\", \n+\"GALLIUM\" =>                 \"Ga\", \n+\"GERMANIUM\" =>               \"Ge\", \n+\"ARSENIC\" =>                 \"As\", \n+\"SELENIUM\" =>                \"Se\", \n+\"BROMINE\" =>                 \"Br\", \n+\"KRYPTON\" =>                 \"Kr\", \n+\"RUBIDIUM\" =>                \"Rb\", \n+\"STRONTIUM\" =>               \"Sr\", \n+\"YTTRIUM\" =>                  \"Y\", \n+\"ZIRCONIUM\" =>               \"Zr\", \n+\"NIOBIUM\" =>                 \"Nb\", \n+\"MOLYBDENUM\" =>              \"Mo\", \n+\"TECHNETIUM\" =>              \"Tc\", \n+\"RUTHENIUM\" =>               \"Ru\", \n+\"RHODIUM\" =>                 \"Rh\", \n+\"PALLADIUM\" =>               \"Pd\", \n+\"SILVER\" =>                  \"Ag\", \n+\"CADMIUM\" =>                 \"Cd\", \n+\"INDIUM\" =>                  \"In\", \n+\"TIN\" =>                     \"Sn\", \n+\"ANTIMONY\" =>                \"Sb\", \n+\"TELLURIUM\" =>               \"Te\", \n+\"IODINE\" =>                   \"I\",\n+\"XENON\" =>                   \"Xe\", \n+\"CESIUM\" =>                  \"Cs\", \n+\"BARIUM\" =>                  \"Ba\", \n+\"LANTHANUM\" =>               \"La\", \n+\"CERIUM\" =>                  \"Ce\", \n+\"PRASEODYMIUM\" =>            \"Pr\", \n+\"NEODYMIUM\" =>               \"Nd\", \n+\"PROMETHIUM\" =>              \"Pm\", \n+\"SAMARIUM\" =>                \"Sm\", \n+\"EUROPIUM\" =>                \"Eu\", \n+\"GADOLINIUM\" =>              \"Gd\", \n+\"TERBIUM\" =>                 \"Tb\", \n+\"DYSPROSIUM\" =>              \"Dy\", \n+\"HOLMIUM\" =>                 \"Ho\", \n+\"ERBIUM\" =>                  \"Er\", \n+\"THULIUM\" =>                 \"Tm\", \n+\"YTTERBIUM\" =>               \"Yb\", \n+\"LUTETIUM\" =>                \"Lu\", \n+\"HAFNIUM\" =>                 \"Hf\", \n+\"TANTALUM\" =>                \"Ta\", \n+\"TUNGSTEN\" =>                 \"W\", \n+\"RHENIUM\" =>                 \"Re\", \n+\"OSMIUM\" =>                  \"Os\", \n+\"IRIDIUM\" =>                 \"Ir\", \n+\"PLATINUM\" =>                \"Pt\", \n+\"GOLD\" =>                    \"Au\", \n+\"MERCURY\" =>                 \"Hg\", \n+\"THALLIUM\" =>                \"Tl\", \n+\"LEAD\" =>                    \"Pb\", \n+\"BISMUTH\" =>                 \"Bi\", \n+\"POLONIUM\" =>                \"Po\", \n+\"ASTATINE\" =>                \"At\", \n+\"RADON\" =>                   \"Rn\", \n+\"FRANCIUM\" =>                \"Fr\", \n+\"RADIUM\" =>                  \"Ra\", \n+\"ACTINIUM\" =>                \"Ac\", \n+\"THORIUM\" =>                 \"Th\", \n+\"PROTACTINIUM\" =>            \"Pa\", \n+\"URANIUM\" =>                  \"U\",\n+\"NEPTUNIUM\" =>               \"Np\", \n+\"PLUTONIUM\" =>               \"Pu\", \n+\"AMERICIUM\" =>               \"Am\", \n+\"CURIUM\" =>                  \"Cm\", \n+\"BERKELIUM\" =>               \"Bk\", \n+\"CALIFORNIUM\" =>             \"Cf\", \n+\"EINSTEINIUM\" =>             \"Es\", \n+\"FERMIUM\" =>                 \"Fm\", \n+\"MENDELEVIUM\" =>             \"Md\", \n+\"NOBELIUM\" =>                \"No\", \n+\"LAWRENCIUM\" =>              \"Lr\", \n+\"RUTHERFORDIUM\" =>           \"Rf\", \n+\"DUBNIUM\" =>                 \"Db\", \n+\"SEABORGIUM\" =>              \"Sg\", \n+\"BOHRIUM\" =>                 \"Bh\", \n+\"HASSIUM\" =>                 \"Hs\", \n+\"MEITNERIUM\" =>              \"Mt\", \n+\"DARMSTADTIUM\" =>            \"Ds\", \n+\"ROENTGENIUM\" =>             \"Rg\", \n+\"COPERNICIUM\" =>             \"Cn\", \n+\"NIHONIUM\" =>                \"Nh\", \n+\"FLEROVIUM\" =>               \"Fl\", \n+\"MOSCOVIUM\" =>               \"Mc\", \n+\"LIVERMORIUM\" =>             \"Lv\", \n+\"TENNESSINE\" =>              \"Ts\", \n+\"OGANESSON\" =>               \"Og\", \n+)\n+\n+# Supplementary Functions for the PEG BasisSet Parsers\n+\n+\n+function dict(children) \n+  dicty = Dict() \n+for i = 1:length(children) \n+  dicty = merge(dicty,children[i]) \n+end \n+\n+return dicty\n+end\n+\n+function DictElements(children)\n+Elem = children[1][1]\n+contracteds = Vector()\n+for i=1:length(children)\n+ cont = BasisSetModule.ContractedGaussianBasisFunctionDefinition(children[i][2],children[i][3][1])\n+ push!(contracteds,cont)\n+end\n+\n+dictyElem = Dict(zip([Elem],[contracteds]))\n+\n+return dictyElem\n+end\n+\n+function bases(children)\n+bases = Vector()\n+for i=1:length(children)\n+if typeof(children[i]) == QuantumLab.BasisSetModule.ContractedGaussianBasisFunctionDefinition\n+  push!(bases,children[i])\n+elseif typeof(children[i]) == Array{QuantumLab.BasisSetModule.ContractedGaussianBasisFunctionDefinition,1}\n+  for j=1:length(children[i])\n+  push!(bases,children[i][j]) \n+  end\n+end\n+end\n+\n+return bases\n+end\n+\n+function SPOrbitals(children)\n+OrbS = Vector()\n+OrbP = Vector()\n+S = Vector()\n+P = Vector()\n+for i=1:length(children)\n+  S1 = children[i][1]\n+  push!(S,S1)\n+end\n+for i=1:length(children)\n+  S2 = children[i][2]\n+  push!(P,S2)\n+end\n+\n+OrbS = BasisSetModule.ContractedGaussianBasisFunctionDefinition(LQuantumNumber(\"S\"),S)\n+OrbP = BasisSetModule.ContractedGaussianBasisFunctionDefinition(LQuantumNumber(\"P\"),P)\n+#push!(Primitives,OrbS)\n+#push!(Primitives,OrbP)\n+\n+\n+Primitives = vcat(OrbS,OrbP)\n+return Primitives\n+end\n+\n+function dictDalton(children) \n+  dicty = Dict() \n+for i = 1:length(children)\n+  dicty = merge(dicty,children[i])\n+end \n+\n+return dicty\n+end\n+\n+\n+function basesDalton(children)\n+bases = Vector()\n+for i=1:length(children)\n+  for j=1:length(children[i])\n+  push!(bases,children[i][j]) \n+  end\n+end\n+\n+return bases\n+end\n+\n+\n+function CreateCorrectPrimitives(children)\n+Primitives = Vector()\n+A = zeros(length(children[2]),length(children[2][1]))\n+for i = 1:length(children[2]) \n+  for j = 1:length(children[2][i])\n+  A[i,j] = children[2][i][j]\n+  end\n+end \n+B = 0\n+\n+a = size(A)\n+C = [Vector{Any}() for _ in 1:a[2]-1]\n+\n+for j = 1:a[2]-1\n+  for i = 1:a[1]\n+    if A[i,j] == 0 \n+    continue\n+    else \n+    B = BasisSetModule.PrimitiveGaussianBasisFunctionDefinition(A[i,end],A[i,j])\n+    push!(C[j],B)\n+    end\n+  end\n+end \n+\n+\n+\n+D = Vector(length(C))\n+for i=1:length(C)\n+  D[i]=BasisSetModule.ContractedGaussianBasisFunctionDefinition(children[1],C[i])\n+end\n+return D\n+end\n+\n+function LinearFactors(children)\n+\n+LinearFactor=0\n+for i=1:length(children)\n+  if children[i][1] == 0\n+  continue\n+  else \n+  LinearFactor=children[i][1]\n+  end\n+end\n+return LinearFactor\n+end\n+############################################################################################################################################\n+# Main Functions","path":"BasisSetModule.jl","position":276,"original_position":276,"commit_id":"1a67d0d829d9e6389f4356838fae9ee7a2db19c6","original_commit_id":"1a67d0d829d9e6389f4356838fae9ee7a2db19c6","user":{"login":"vonDonnerstein","id":14938722,"node_id":"MDQ6VXNlcjE0OTM4NzIy","avatar_url":"https://avatars2.githubusercontent.com/u/14938722?v=4","gravatar_id":"","url":"https://api.github.com/users/vonDonnerstein","html_url":"https://github.com/vonDonnerstein","followers_url":"https://api.github.com/users/vonDonnerstein/followers","following_url":"https://api.github.com/users/vonDonnerstein/following{/other_user}","gists_url":"https://api.github.com/users/vonDonnerstein/gists{/gist_id}","starred_url":"https://api.github.com/users/vonDonnerstein/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/vonDonnerstein/subscriptions","organizations_url":"https://api.github.com/users/vonDonnerstein/orgs","repos_url":"https://api.github.com/users/vonDonnerstein/repos","events_url":"https://api.github.com/users/vonDonnerstein/events{/privacy}","received_events_url":"https://api.github.com/users/vonDonnerstein/received_events","type":"User","site_admin":false},"body":"I'd like to go over these functions in detail. This will probably be much easier once you have made the other adjustments, so I'll wait until then. Same holds for `runtests.jl` below. Thank you for updating your pull request (simply push your changes to sasadada:master).","created_at":"2018-07-06T16:10:03Z","updated_at":"2018-07-06T16:14:05Z","html_url":"https://github.com/vonDonnerstein/QuantumLab.jl/pull/11#discussion_r200700158","pull_request_url":"https://api.github.com/repos/vonDonnerstein/QuantumLab.jl/pulls/11","author_association":"OWNER","_links":{"self":{"href":"https://api.github.com/repos/vonDonnerstein/QuantumLab.jl/pulls/comments/200700158"},"html":{"href":"https://github.com/vonDonnerstein/QuantumLab.jl/pull/11#discussion_r200700158"},"pull_request":{"href":"https://api.github.com/repos/vonDonnerstein/QuantumLab.jl/pulls/11"}}},"pull_request":{"url":"https://api.github.com/repos/vonDonnerstein/QuantumLab.jl/pulls/11","id":199769338,"node_id":"MDExOlB1bGxSZXF1ZXN0MTk5NzY5MzM4","html_url":"https://github.com/vonDonnerstein/QuantumLab.jl/pull/11","diff_url":"https://github.com/vonDonnerstein/QuantumLab.jl/pull/11.diff","patch_url":"https://github.com/vonDonnerstein/QuantumLab.jl/pull/11.patch","issue_url":"https://api.github.com/repos/vonDonnerstein/QuantumLab.jl/issues/11","number":11,"state":"open","locked":false,"title":"Basis 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