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Added xyz file parser/lexer
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@ -12,7 +12,7 @@ let ang_mom = ['S' 'P' 'D' 'F' 'G' 'H' 'I' 'J' 'K' 'L' 'M' 'N' 'O'
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's' 'p' 'd' 'f' 'g' 'h' 'i' 'j' 'k' 'l' 'm' 'n' 'o' ]
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's' 'p' 'd' 'f' 'g' 'h' 'i' 'j' 'k' 'l' 'm' 'n' 'o' ]
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white
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white
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let integer = ['0'-'9']+
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let integer = ['0'-'9']+
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let real = '-'? integer '.' integer (['e' 'E'] '-'? integer)?
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let real = '-'? integer '.' integer (['e' 'E'] ('+'|'-')? integer)?
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rule read_all_rule = parse
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rule read_all_rule = parse
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3
Makefile
3
Makefile
@ -1,9 +1,10 @@
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.NOPARALLEL:
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.NOPARALLEL:
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INCLUDE_DIRS=Nuclei,Utils,Basis
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LIBS=
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LIBS=
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PKGS=
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PKGS=
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OCAMLCFLAGS="-g"
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OCAMLCFLAGS="-g"
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OCAMLBUILD=ocamlbuild -j 0 -cflags $(OCAMLCFLAGS) -lflags $(OCAMLCFLAGS) -I Utils -I Basis
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OCAMLBUILD=ocamlbuild -j 0 -cflags $(OCAMLCFLAGS) -lflags $(OCAMLCFLAGS) -Is $(INCLUDE_DIRS)
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MLLFILES=$(wildcard */*.mll) $(wildcard *.mll)
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MLLFILES=$(wildcard */*.mll) $(wildcard *.mll)
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MLYFILES=$(wildcard */*.mly) $(wildcard *.mly)
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MLYFILES=$(wildcard */*.mly) $(wildcard *.mly)
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MLFILES= $(wildcard */*.ml) $(wildcard *.ml)
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MLFILES= $(wildcard */*.ml) $(wildcard *.ml)
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1
Nuclei/Nuclei.ml
Normal file
1
Nuclei/Nuclei.ml
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@ -0,0 +1 @@
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type xyz_input = string * ( (string * (float array)) array)
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38
Nuclei/Nuclei_lexer.mll
Normal file
38
Nuclei/Nuclei_lexer.mll
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@ -0,0 +1,38 @@
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{
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open Nuclei_parser
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}
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let eol = ['\n']
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let white = [' ' '\t']+
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let word = [^' ' '\t' '\n']+
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let letter = ['A'-'Z' 'a'-'z']
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let integer = ['0'-'9']+
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let real = '-'? integer '.' integer (['e' 'E'] ('+'|'-')? integer)?
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rule read_all = parse
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| eof { EOF }
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| eol { EOL }
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| white as w { SPACE w }
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| integer as i { INTEGER (int_of_string i) }
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| real as f { FLOAT (float_of_string f) }
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| word as w { WORD w }
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{
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let debug () =
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let ic = open_in "caffeine.xyz" in
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let lexbuf = Lexing.from_channel ic in
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while true do
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let s =
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match read_all lexbuf with
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| EOL -> "EOL"
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| SPACE w -> "SPACE("^w^")"
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| INTEGER i -> "INTEGER("^(string_of_int i)^")"
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| FLOAT f -> "FLOAT("^(string_of_float f)^")"
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| WORD w -> "WORD("^w^")"
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| EOF -> "EOF"
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in
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print_endline s
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done;
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}
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55
Nuclei/Nuclei_parser.mly
Normal file
55
Nuclei/Nuclei_parser.mly
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@ -0,0 +1,55 @@
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/* Parses basis sets in GAMESS format */
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%{
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exception InputError of string
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%}
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%token EOL
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%token <string> SPACE
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%token <string> WORD
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%token <int> INTEGER
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%token <float> FLOAT
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%token EOF
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%start input
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%type <Nuclei.xyz_input> input
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%% /* Grammar rules and actions follow */
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input:
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| integer title atoms {
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let len = List.length $3 in
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if len <> $1 then
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let error_msg = Printf.sprintf "%d atoms entered, expected %d" len $1 in
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raise (InputError error_msg)
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else
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($2,Array.of_list $3)
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}
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integer:
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| INTEGER EOL { $1 }
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| INTEGER SPACE EOL { $1 }
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title:
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| title_list EOL { $1 }
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text:
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| WORD {$1 }
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| SPACE {$1 }
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| FLOAT {(string_of_float $1)}
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| INTEGER {(string_of_int $1)}
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title_list:
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| { "" }
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| title_list text { $1 ^ $2 }
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atoms:
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| atoms_list EOL { List.rev $1 }
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| atoms_list EOF { List.rev $1 }
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atoms_list:
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| { [] }
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| atoms_list WORD SPACE FLOAT SPACE FLOAT SPACE FLOAT EOL { ($2, [| $4;$6;$8 |]) :: $1 }
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| atoms_list WORD SPACE FLOAT SPACE FLOAT SPACE FLOAT SPACE EOL { ($2, [| $4;$6;$8 |]) :: $1 }
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