Scripts/gamess.rb

   1 # coding: utf-8
   2 #
   3 #  gamess.rb
   4 #
   5 #  Created by Toshi Nagata on 2009/11/22.
   6 #  Copyright 2009 Toshi Nagata. All rights reserved.
   7 #
   8 # This program is free software; you can redistribute it and/or modify
   9 # it under the terms of the GNU General Public License as published by
  10 # the Free Software Foundation version 2 of the License.
  11 #
  12 # This program is distributed in the hope that it will be useful,
  13 # but WITHOUT ANY WARRANTY; without even the implied warranty of
  14 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  15 # GNU General Public License for more details.
  16
  17 class MemoryIO < IO
  18   def initialize
  19     @buffer = ""
  20   end
  21   def write(s)
  22         @buffer << s
  23   end
  24   def buffer
  25     @buffer
  26   end
  27   def empty
  28     @buffer = ""
  29   end
  30 end
  31
  32 class Molecule
  33
  34   #  Import nbo log.  The argument is either an array of Strings
  35   #  or an IO object.
  36   def import_nbo_log(lines)
  37     if lines.is_a?(IO)
  38           getline = lambda { lines.gets }
  39         else
  40           getline = lambda { lines.shift }
  41     end
  42     nbo = Hash.new
  43         while (ln = getline.call) != nil
  44           if ln =~ /done with NBO analysis/
  45             break
  46           end
  47           if ln =~ /NATURAL POPULATIONS:  Natural atomic orbital occupancies/
  48             #  List of Natural AOs
  49                 getline.call
  50                 getline.call
  51                 getline.call
  52                 nbo["nao"] = []
  53                 while (ln = getline.call) != nil
  54                   if ln =~ /^\s*$/
  55                     #  Skip a blank line
  56                     ln = getline.call
  57                         if ln =~ /^\s*$/
  58                           #  Double blank lines indicates the end of the table
  59                           break
  60                         end
  61                   end
  62                   ln.chomp!
  63                   next unless ln =~ /^ *(\d+) *([A-Za-z]+) *(\d+) *([a-z]+) +([A-Za-z]+)\( *(\d+)([a-z]+)\)/
  64                   i = $1.to_i - 1
  65                   an = $3.to_i - 1
  66                   atom_label = $2 + $3.to_s
  67                   label = $4
  68                   type = $5
  69                   pn = $6
  70                   vals = $~.post_match.split.map { |e| e.to_f }
  71                   #  atom_index, type, pn+label, occupancy[, energy]
  72                   nbo["nao"].push([atom_label, type, pn + label] + vals)
  73                 end
  74           elsif ln =~ / NATURAL BOND ORBITALS \(Summary\):/
  75             nbo["nbo"] = []
  76                 getline.call
  77             while (ln = getline.call) != nil
  78                   break if ln =~ /Total Lewis/
  79                   if ln =~ /^\s*$/
  80                         #  Skip a blank line
  81                         ln = getline.call
  82                         if ln =~ /^\s*$/
  83                           #  Double blank lines indicates the end of the table
  84                           break
  85                         end
  86                   end
  87                   if ln =~ /^\s*(\d+)\. *([A-Za-z]+\*?) *\( *(\d+)\) *([A-Za-z]+) *(\d+)(- *([A-Za-z]+) *(\d+))? *(\d\.\d+)/
  88                         idx = $1.to_i
  89                         orb_kind = $2
  90                         orb_idx = $3
  91                         atom_label = $4 + ($5.to_i - 1).to_s
  92                         if $6 != nil
  93                           atom_label += "-" + $7 + ($8.to_i - 1).to_s
  94                         end
  95                         occ = $9.to_f
  96                         nbo["nbo"].push([orb_kind + "_" + orb_idx, atom_label, occ])
  97                   end
  98                 end
  99           elsif ln =~ /([A-Z]+)s in the ([A-Z]+) basis:/ || ln =~ /([A-Z]+) Fock matrix:/
 100             #  Read matrix
 101             dst = $1
 102                 src = $2
 103                 if src == nil
 104                   src = "F"   #  Fock
 105                 end
 106                 key = src + "/" + dst
 107                 getline.call
 108                 getline.call
 109                 getline.call
 110                 elements = []
 111                 labels = []
 112                 idx = 0
 113                 block = 0
 114                 while (ln = getline.call) != nil
 115                   if ln =~ /^\s*$/
 116                     #  Blank line: end of one block
 117                     ln = getline.call
 118                         if ln =~ /^\s*$/
 119                           #  Double blank lines indicates the end of the table
 120                           break
 121                         else
 122                           #  Begin next section
 123                           ln = getline.call
 124                           idx = 0
 125                           block += 1
 126                           next
 127                         end
 128                   end
 129                   ln.chomp!
 130                   ln =~ /-?\d+\.\d+/
 131                   lab = $~.pre_match.strip
 132                   a = ([$~[0]] + $~.post_match.split).map { |e| e.to_f }
 133                   if block == 0
 134                     lab =~ /^[0-9]+\. *(.*)$/
 135                     labels.push($1)
 136                   end
 137                   (elements[idx] ||= []).concat(a)
 138                   idx += 1
 139                 end
 140                 nbo[key] = LAMatrix.new(elements).transpose!
 141                 key2 = (src == "F" ? dst : src) + "_L"
 142                 if nbo[key2] == nil
 143                   nbo[key2] = labels
 144                 end
 145           end
 146         end
 147         @nbo = nbo
 148         if @nbo["AO/NAO"]
 149           #  Convert NAO based matrix into AO based matrix
 150           @nbo.keys.each { |key|
 151             if key[0..3] == "NAO/"
 152                   key2 = "AO/" + key[4..-1]
 153                   @nbo[key2] = @nbo["AO/NAO"] * @nbo[key]
 154                 end
 155           }
 156         end
 157         # puts @nbo.inspect
 158   end
 159
 160   def Molecule.read_gamess_basis_sets(fname)
 161     # $gamess_basis = Hash.new unless $gamess_basis
 162         $gamess_ecp = Hash.new unless $gamess_ecp
 163         # $gamess_basis_desc = Hash.new unless $gamess_basis_desc
 164         # $gamess_basis_keys = [] unless $gamess_basis_keys
 165         basename = File.basename(fname, ".*")
 166         keys = []
 167         descname = nil
 168     File.open(fname, "r") { |fp|
 169           while (s = fp.gets)
 170             if s =~ /^\s*!\s*/ && descname == nil
 171               #  Get the descriptive name from the first comment line
 172                   s = Regexp.last_match.post_match
 173                   if s =~ /  EMSL/
 174                     descname = Regexp.last_match.pre_match
 175                   else
 176                     descname = (s.split)[0]
 177                   end
 178                   $gamess_basis_desc[basename] = descname
 179                   next
 180                 end
 181                 ss, bas = (s.split)[0..1]     #  Tokens delimited by whitespaces
 182                 next if ss == nil || ss == ""
 183                 if ss == "$ECP"
 184                 #  Read the ECP section
 185                   ecp = $gamess_ecp[basename]
 186                   if !ecp
 187                     ecp = []
 188                         $gamess_ecp[basename] = ecp
 189                   end
 190                   keys << basename unless keys.include?(basename)
 191                   while (s = fp.gets)
 192                     break if s=~ /\$END/
 193                         ary = s.split  #  (PNAME, PTYPE, IZCORE, LMAX+1)
 194                         elem = ary[0].match(/\w{1,2}/).to_a[0]  #  ary[0] should begin with an element name
 195                         ap = Parameter.builtin.elements.find { |p| p.name.casecmp(elem) == 0 }
 196                         raise MolbyError, "the ECP definition does not begin with an element name: #{s}" if !ap
 197                         ecpdef = s
 198                         ln = 1
 199                         (0..Integer(ary[3])).each {
 200                           s = fp.gets
 201                           raise MolbyError, "the ECP definition ends unexpectedly at line #{ln} for: #{s}" if !s
 202                           ln += 1
 203                           ary = s.split  #  (NGPOT, comment)
 204                           ecpdef += s
 205                           (1..Integer(ary[0])).each {
 206                             s = fp.gets
 207                                 raise MolbyError, "the ECP definition ends unexpectedly at line #{ln} for: #{s}" if !s
 208                                 ln += 1
 209                                 ecpdef += s
 210                           }
 211                         }
 212                     ecp[ap.index] = ecpdef
 213                   end
 214                 elsif ss =~ /\W/
 215                   #  Comments or other unrecognizable lines
 216                   next
 217                 elsif (ap = Parameter.builtin.elements.find { |p| p.name.casecmp(ss) == 0 || p.fullname.casecmp(ss) == 0 })
 218                   #  Valid basis definition
 219                   if bas == nil || bas =~ /\W/
 220                     bas = basename
 221                   end
 222                   basis = $gamess_basis[bas]
 223                   if !basis
 224                     basis = []
 225                         $gamess_basis[bas] = basis
 226                   end
 227                   keys << bas unless keys.include?(bas)
 228                   basdef = ""
 229                   while (s = fp.gets) && s =~ /\S/
 230                     basdef += s
 231                   end
 232                   basis[ap.index] = basdef
 233                 else
 234                   raise MolbyError, "ss is not a valid element symbol or name: #{s}"
 235                 end
 236           end
 237     }
 238         unless $gamess_basis_keys.include?(basename)
 239           $gamess_basis_keys.push(basename)
 240         end
 241   end
 242
 243   #  Execute GAMESS (inferior copy of rungms script)
 244   #  inpname is the input file
 245   #  mol (optional) is the molecule from which the GAMESS input was built.
 246   #  If mol is specified and RUNTYP=OPTIMIZE, then the intermediate structures are
 247   #  displayed real-time.
 248   def Molecule.execute_gamess(inpname, mol = nil)
 249     gmsname = get_global_settings("gamess.executable_path")
 250     gmsdir = nil
 251     gmsvers = nil
 252
 253         cygwin_version = false  #  For windows: old cygwin version
 254
 255     while 1
 256       if gmsname == nil || !File.exist?(gmsname)
 257         gmsname = Dialog.open_panel("Please locate the GAMESS executable")
 258         exit if gmsname == nil
 259       end
 260       gmsbase = File.basename(gmsname)
 261       gmsdir = File.dirname(gmsname)
 262       if gmsbase =~ /gamess\.(.*)\.(exe|x)$/i
 263         gmsvers = $1
 264         break
 265       else
 266         gmsname = nil
 267         error_message_box(gmsbase + " does not look like a GAMESS executable!")
 268       end
 269     end
 270
 271 #       if mol == nil
 272 #               mol = Molecule.open(inpname)
 273 #               if mol == nil
 274 #                       error_message_box("Cannot open #{inpname} as GAMESS input")
 275 #                       return
 276 #               end
 277 #       end
 278
 279     inpbase = File.basename(inpname)
 280     inpdir = File.dirname(inpname)
 281     inpbody = inpbase.sub(/\.inp$/, "")
 282     logbase = inpbody + ".log"
 283
 284     set_global_settings("gamess.executable_path", gmsname)
 285
 286     ncpus = get_global_settings("gamess.ncpus").to_i
 287         if ncpus == 0
 288           ncpus = 1
 289         end
 290
 291     #  Prepare the scratch directory
 292         begin
 293           scrdir = create_temp_dir("gamess", inpbody)
 294         rescue
 295           error_message_box($!.to_s)
 296           return
 297         end
 298 #    scrdir = $home_directory + "/Molby/gamess"
 299 #       begin
 300 #         mkdir_recursive(scrdir)
 301 #       rescue
 302 #         error_message_box("Cannot create directory #{scrdir}: " + $!.to_s)
 303 #         return
 304 #       end
 305
 306 #    scrdir = scrdir + "/" + inpbody + "." + $$.to_s + ".0"
 307 #    n = 0
 308 #    while File.exist?(scrdir)
 309 #      scrdir = scrdir.sub(".#{n}", ".#{n + 1}")
 310 #      n += 1
 311 #    end
 312 #    Dir.mkdir(scrdir)
 313
 314     if $platform == "win"
 315       sep = "\\"
 316       scrdir.gsub!("/", sep)
 317       gmsdir.gsub!("/", sep)
 318     else
 319       sep = "/"
 320     end
 321
 322         #  Old (obsolete) cygwin version, using ddikick
 323     if $platform == "win"
 324           if gmsvers == "11"
 325             cygwin_version = true
 326           end
 327         end
 328
 329     #  Get the host name etc.
 330     hostname = backquote("hostname").chomp
 331     if $platform == "win"
 332           s = backquote("cmd.exe /c dir \"#{scrdir}\"")
 333       freebytes = s.split("\n").pop.match(/([0-9,]+)[^0-9]*$/).to_a[1]
 334       if freebytes
 335         freebytes = (freebytes.gsub(",","").to_i / 1024).to_s + " Kbytes"
 336       else
 337         freebytes = "(unknown)"
 338       end
 339       uname = backquote("cmd.exe /c ver").to_s.gsub("\n", "")
 340     else
 341       freebytes = `df -k "#{scrdir}"`
 342       uname = `uname`.chomp
 343     end
 344
 345     #  Redirect standard output to the log file
 346     logname = scrdir + sep + logbase
 347     fpout = File.open(logname, "w")
 348         if cygwin_version
 349           #  The cygwin version uses LF as the eol character
 350           fpout.binmode
 351         end
 352     fpout.print "----- GAMESS execution script -----\n"
 353     fpout.print "This job is running on host #{hostname}\n"
 354     fpout.print "under operating system #{uname} at #{Time.now.to_s}\n"
 355     fpout.print "Available scratch disk space (Kbyte units) at beginning of the job is\n"
 356     fpout.print freebytes + "\n"
 357
 358     #  Copy the input file
 359         scrprefix = scrdir + sep + inpbody
 360         if $platform == "win"
 361           scrbody = inpbody
 362         else
 363       scrbody = scrprefix
 364         end
 365     filecopy(inpname, scrprefix + ".F05")
 366     File.open("#{scrdir}/.in_use", "w") { |fp| }
 367
 368     #  Prepare environmental variables
 369     auxdir = "#{gmsdir}#{sep}auxdata"
 370     ENV["ERICFMT"] = "#{auxdir}#{sep}ericfmt.dat"
 371     ENV["MCPPATH"] = "#{auxdir}#{sep}MCP"
 372     ENV["BASPATH"] = "#{auxdir}#{sep}BASES"
 373     ENV["QUANPOL"] = "#{auxdir}#{sep}QUANPOL"
 374     ENV["EXTBAS"] = "/dev/null"
 375     ENV["IRCDATA"] = "#{scrbody}.irc"
 376         ENV["RESTART"] = "#{scrbody}.rst"
 377         ENV["TRAJECT"] = "#{scrbody}.trj"
 378     ENV["PUNCH"] = "#{scrbody}.dat"
 379     ENV["INPUT"] = "#{scrbody}.F05"
 380     ENV["AOINTS"] = "#{scrbody}.F08"
 381     ENV["MOINTS"] = "#{scrbody}.F09"
 382     ENV["DICTNRY"] = "#{scrbody}.F10"
 383     ENV["DRTFILE"] = "#{scrbody}.F11"
 384     ENV["CIVECTR"] = "#{scrbody}.F12"
 385     ENV["CASINTS"] = "#{scrbody}.F13"
 386     ENV["CIINTS"] = "#{scrbody}.F14"
 387     ENV["WORK15"] = "#{scrbody}.F15"
 388     ENV["WORK16"] = "#{scrbody}.F16"
 389     ENV["CSFSAVE"] = "#{scrbody}.F17"
 390     ENV["FOCKDER"] = "#{scrbody}.F18"
 391     ENV["WORK19"] = "#{scrbody}.F19"
 392     ENV["DASORT"] = "#{scrbody}.F20"
 393     ENV["DFTINTS"] = "#{scrbody}.F21"
 394     ENV["DFTGRID"] = "#{scrbody}.F22"
 395     ENV["JKFILE"] = "#{scrbody}.F23"
 396     ENV["ORDINT"] = "#{scrbody}.F24"
 397     ENV["EFPIND"] = "#{scrbody}.F25"
 398     ENV["PCMDATA"] = "#{scrbody}.F26"
 399     ENV["PCMINTS"] = "#{scrbody}.F27"
 400     ENV["MLTPL"] = "#{scrbody}.F28"
 401     ENV["MLTPLT"] = "#{scrbody}.F29"
 402     ENV["DAFL30"] = "#{scrbody}.F30"
 403     ENV["SOINTX"] = "#{scrbody}.F31"
 404     ENV["SOINTY"] = "#{scrbody}.F32"
 405     ENV["SOINTZ"] = "#{scrbody}.F33"
 406     ENV["SORESC"] = "#{scrbody}.F34"
 407     ENV["SIMEN"] = "#{scrbody}.simen"
 408     ENV["SIMCOR"] = "#{scrbody}.simcor"
 409     ENV["GCILIST"] = "#{scrbody}.F37"
 410     ENV["HESSIAN"] = "#{scrbody}.F38"
 411     ENV["SOCCDAT"] = "#{scrbody}.F40"
 412     ENV["AABB41"] = "#{scrbody}.F41"
 413     ENV["BBAA42"] = "#{scrbody}.F42"
 414     ENV["BBBB43"] = "#{scrbody}.F43"
 415     ENV["MCQD50"] = "#{scrbody}.F50"
 416     ENV["MCQD51"] = "#{scrbody}.F51"
 417     ENV["MCQD52"] = "#{scrbody}.F52"
 418     ENV["MCQD53"] = "#{scrbody}.F53"
 419     ENV["MCQD54"] = "#{scrbody}.F54"
 420     ENV["MCQD55"] = "#{scrbody}.F55"
 421     ENV["MCQD56"] = "#{scrbody}.F56"
 422     ENV["MCQD57"] = "#{scrbody}.F57"
 423     ENV["MCQD58"] = "#{scrbody}.F58"
 424     ENV["MCQD59"] = "#{scrbody}.F59"
 425     ENV["MCQD60"] = "#{scrbody}.F60"
 426     ENV["MCQD61"] = "#{scrbody}.F61"
 427     ENV["MCQD62"] = "#{scrbody}.F62"
 428     ENV["MCQD63"] = "#{scrbody}.F63"
 429     ENV["MCQD64"] = "#{scrbody}.F64"
 430     ENV["NMRINT1"] = "#{scrbody}.F61"
 431     ENV["NMRINT2"] = "#{scrbody}.F62"
 432     ENV["NMRINT3"] = "#{scrbody}.F63"
 433     ENV["NMRINT4"] = "#{scrbody}.F64"
 434     ENV["NMRINT5"] = "#{scrbody}.F65"
 435     ENV["NMRINT6"] = "#{scrbody}.F66"
 436     ENV["DCPHFH2"] = "#{scrbody}.F67"
 437     ENV["DCPHF21"] = "#{scrbody}.F68"
 438     ENV["GVVPT"] = "#{scrbody}.F69"
 439
 440     #    next files are used only during coupled cluster runs, so let's
 441     #    display the numerous definitions only if they are to be used.
 442         #    Don't set these variables on windows, where the memory for environmental variables
 443         #    is limited.
 444         if $platform != "win"
 445     ENV["CCREST"] = "#{scrbody}.F70"
 446     ENV["CCDIIS"] = "#{scrbody}.F71"
 447     ENV["CCINTS"] = "#{scrbody}.F72"
 448     ENV["CCT1AMP"] = "#{scrbody}.F73"
 449     ENV["CCT2AMP"] = "#{scrbody}.F74"
 450     ENV["CCT3AMP"] = "#{scrbody}.F75"
 451     ENV["CCVM"] = "#{scrbody}.F76"
 452     ENV["CCVE"] = "#{scrbody}.F77"
 453     ENV["EOMSTAR"] = "#{scrbody}.F80"
 454     ENV["EOMVEC1"] = "#{scrbody}.F81"
 455     ENV["EOMVEC2"] = "#{scrbody}.F82"
 456     ENV["EOMHC1"] = "#{scrbody}.F83"
 457     ENV["EOMHC2"] = "#{scrbody}.F84"
 458     ENV["EOMHHHH"] = "#{scrbody}.F85"
 459     ENV["EOMPPPP"] = "#{scrbody}.F86"
 460     ENV["EOMRAMP"] = "#{scrbody}.F87"
 461     ENV["EOMRTMP"] = "#{scrbody}.F88"
 462     ENV["EOMDG12"] = "#{scrbody}.F89"
 463     ENV["MMPP"] = "#{scrbody}.F90"
 464     ENV["MMHPP"] = "#{scrbody}.F91"
 465     ENV["MMCIVEC"] = "#{scrbody}.F92"
 466     ENV["MMCIVC1"] = "#{scrbody}.F93"
 467     ENV["MMCIITR"] = "#{scrbody}.F94"
 468     ENV["MMNEXM"] = "#{scrbody}.F95"
 469     ENV["MMNEXE"] = "#{scrbody}.F96"
 470     ENV["MMNREXM"] = "#{scrbody}.F97"
 471     ENV["MMNREXE"] = "#{scrbody}.F98"
 472         end
 473     #
 474     #     next are for TDHFX code, not used by current GAMESS
 475     #
 476         if false
 477     ENV["OLI201"] = "#{scrbody}.F201"
 478     ENV["OLI202"] = "#{scrbody}.F202"
 479     ENV["OLI203"] = "#{scrbody}.F203"
 480     ENV["OLI204"] = "#{scrbody}.F204"
 481     ENV["OLI205"] = "#{scrbody}.F205"
 482     ENV["OLI206"] = "#{scrbody}.F206"
 483     ENV["OLI207"] = "#{scrbody}.F207"
 484     ENV["OLI208"] = "#{scrbody}.F208"
 485     ENV["OLI209"] = "#{scrbody}.F209"
 486     ENV["OLI210"] = "#{scrbody}.F210"
 487     ENV["OLI211"] = "#{scrbody}.F211"
 488     ENV["OLI212"] = "#{scrbody}.F212"
 489     ENV["OLI213"] = "#{scrbody}.F213"
 490     ENV["OLI214"] = "#{scrbody}.F214"
 491     ENV["OLI215"] = "#{scrbody}.F215"
 492     ENV["OLI216"] = "#{scrbody}.F216"
 493     ENV["OLI217"] = "#{scrbody}.F217"
 494     ENV["OLI218"] = "#{scrbody}.F218"
 495     ENV["OLI219"] = "#{scrbody}.F219"
 496     ENV["OLI220"] = "#{scrbody}.F220"
 497     ENV["OLI221"] = "#{scrbody}.F221"
 498     ENV["OLI222"] = "#{scrbody}.F222"
 499     ENV["OLI223"] = "#{scrbody}.F223"
 500     ENV["OLI224"] = "#{scrbody}.F224"
 501     ENV["OLI225"] = "#{scrbody}.F225"
 502     ENV["OLI226"] = "#{scrbody}.F226"
 503     ENV["OLI227"] = "#{scrbody}.F227"
 504     ENV["OLI228"] = "#{scrbody}.F228"
 505     ENV["OLI229"] = "#{scrbody}.F229"
 506     ENV["OLI230"] = "#{scrbody}.F230"
 507     ENV["OLI231"] = "#{scrbody}.F231"
 508     ENV["OLI232"] = "#{scrbody}.F232"
 509     ENV["OLI233"] = "#{scrbody}.F233"
 510     ENV["OLI234"] = "#{scrbody}.F234"
 511     ENV["OLI235"] = "#{scrbody}.F235"
 512     ENV["OLI236"] = "#{scrbody}.F236"
 513     ENV["OLI237"] = "#{scrbody}.F237"
 514     ENV["OLI238"] = "#{scrbody}.F238"
 515     ENV["OLI239"] = "#{scrbody}.F239"
 516     end
 517
 518     if $platform == "win"
 519         #  if ncpus < 2
 520         #    ncpus = 2
 521         #  end
 522           if cygwin_version
 523             #  Old (obsolete) cygwin version, using ddikick
 524         fpout.print "ddikick will run #{ncpus} compute process\n"
 525                 ENV["CYGWIN"] = "nodosfilewarning"
 526           else
 527         fpout.print "Microsoft MPI will be running GAMESS on 1 node.\n"
 528         fpout.print "The binary kicked off by 'mpiexec' is gamess.#{gmsvers}.exe\n"
 529         fpout.print "MS-MPI will run #{ncpus*2} compute process\n"
 530         #  File containing environmental variables
 531         envfil = "#{scrprefix}.GMS.ENV"
 532         fp = File.open(envfil, "w")
 533         ENV.each { |k, v| fp.print "#{k}=#{v}\n" }
 534         fp.close
 535         #  File containing arguments to mpiexec
 536         procfil = "#{scrprefix}.processes.mpd"
 537         fp = File.open(procfil, "w")
 538         fp.print "-env ENVFIL \"#{envfil}\" -wdir \"#{scrdir}\" -n #{ncpus*2} \"#{gmsdir}#{sep}gamess.#{gmsvers}.exe\"\n"
 539         fp.close
 540           end
 541     end
 542
 543     fpout.close
 544     fplog = File.open(logname, "r")
 545     size = 0
 546     lines = []
 547         lineno = 0
 548     last_line = ""
 549     search_mode = 0
 550         nserch = -1
 551         rflag = 0
 552         ne_alpha = ne_beta = 0
 553         mo_count = 0
 554         ncomps = 0
 555
 556     #  Callback procs
 557         term_callback = lambda { |m, n|
 558           msg = "GAMESS execution on #{inpbase} "
 559           hmsg = "GAMESS "
 560           if n == 0
 561             msg += "succeeded."
 562                 hmsg += "Completed"
 563                 icon = :info
 564           else
 565             msg += "failed with status #{n}."
 566                 hmsg += "Failed"
 567                 icon = :error
 568           end
 569           msg += "\n(In directory #{inpdir})"
 570
 571           File.delete("#{scrdir}/.in_use")
 572
 573           ext_to_keep = [".dat", ".rst", ".trj", ".efp", ".gamma", ".log"]
 574           ext_to_keep.each { |ex|
 575             if File.exists?("#{scrprefix}#{ex}")
 576                   filecopy("#{scrprefix}#{ex}", "#{inpdir}#{sep}#{inpbody}#{ex}")
 577             end
 578           }
 579           Dir.foreach(scrdir) { |file|
 580             if file != "." && file != ".." && !ext_to_keep.include?(File.extname(file))
 581                   File.delete("#{scrdir}#{sep}#{file}")
 582             end
 583           }
 584
 585           begin
 586             erase_old_logs(scrdir, "latest", 5)
 587           rescue
 588             error_message_box($!.to_s)
 589                 return
 590           end
 591
 592           if (script = get_global_settings("gamess.postfix_script")) != nil && script != ""
 593             eval(script)
 594           end
 595
 596           if mol != nil
 597             message_box(msg, hmsg, :ok, icon)
 598       end
 599     }
 600
 601     timer_callback = lambda { |m, n|
 602       fplog.seek(0, IO::SEEK_END)
 603       sizec = fplog.tell
 604       if sizec > size
 605         #  Read new lines
 606         fplog.seek(size, IO::SEEK_SET)
 607         fplog.each_line { |line|
 608           if line[-1, 1] == "\n"
 609             lines.push(last_line + line)
 610             last_line = ""
 611           else
 612             last_line += line
 613             break
 614           end
 615         }
 616         size = fplog.tell
 617         last_i = nil
 618         i = 0
 619         while i < lines.count
 620           line = lines[i]
 621           if line =~ /GEOMETRY SEARCH POINT NSERCH= *(\d+)/
 622             nserch = $1.to_i
 623             last_i = i
 624                         search_mode = 1
 625                         energy = nil
 626                   elsif line =~ /START OF DRC CALCULATION/
 627                     search_mode = 3
 628                         nserch = 1
 629                         energy = nil
 630                   elsif line =~ /CONSTRAINED OPTIMIZATION POINT/
 631                     search_mode = 2
 632                         energy = nil
 633                   elsif line =~ /POINT *([0-9]+) *ON THE REACTION PATH/
 634                     nserch = $1.to_i
 635                         last_i = i
 636                   elsif line =~ /ATOMIC BASIS SET/
 637                         j = i
 638                         while j < lines.count
 639                           line = lines[j]
 640                           break if line =~ /TOTAL NUMBER OF BASIS SET/
 641                           j += 1
 642                         end
 643                         if j < lines.count
 644                           #  Found
 645                           bs_lines = []
 646                           ii = i
 647                           while ii <= j
 648                             bs_lines.push(lines[ii].chomp)
 649                                 ii += 1
 650                           end
 651                           begin
 652                             if mol
 653                                   ncomps = mol.sub_load_gamess_log_basis_set(bs_lines, lineno + i)
 654                                 end
 655                           rescue
 656                             puts $!.to_s
 657                             puts $!.backtrace.inspect
 658                           end
 659                           last_i = j
 660                         else
 661                           break  #  Wait until all basis set lines are read
 662                         end
 663                   elsif line =~ /NUMBER OF OCCUPIED ORBITALS/
 664                         line =~ /=\s*(\d+)/
 665                         n = Integer($1)
 666                         if line =~ /ALPHA/
 667                           ne_alpha = n
 668                         else
 669                           ne_beta = n
 670                         end
 671                   elsif line =~ /SCFTYP=(\w+)/
 672                         scftyp = $1
 673                         if ne_alpha > 0 || ne_beta > 0
 674                           rflag = 0
 675                           case scftyp
 676                           when "RHF"
 677                                 rflag = 1
 678                           when "ROHF"
 679                                 rflag = 2
 680                           end
 681                         end
 682                   elsif line =~ /^\s*(EIGENVECTORS|MOLECULAR ORBITALS)\s*$/
 683                         if mo_count == 0 && mol
 684                           mol.clear_mo_coefficients
 685                           mol.set_mo_info(:type=>["UHF", "RHF", "ROHF"][rflag], :alpha=>ne_alpha, :beta=>ne_beta)
 686                         end
 687                         i += 2
 688                         j = i
 689                         mo_count += 1
 690                         while j < lines.count
 691                           line = lines[j]
 692                           break if line =~ /\.\.\.\.\.\./ || line =~ /----------------/
 693                           j += 1
 694                         end
 695                         if j == lines.count
 696                           break  #  Wait until complete MO info are read
 697                         end
 698                         ii = i
 699                         mo_lines = []
 700                         while ii < j
 701                           mo_lines.push(lines[ii].chomp)
 702                           ii += 1
 703                         end
 704                         begin
 705                           if mol
 706                             mol.sub_load_gamess_log_mo_coefficients(mo_lines, lineno + i, ncomps)
 707                           end
 708                         rescue
 709                           puts $!.to_s
 710                           puts $!.backtrace.inspect
 711                         end
 712                         last_i = j
 713           elsif line =~ /NSERCH: *([0-9]+)/
 714           #  print line
 715                         if mol
 716                           n = $1
 717                           line =~ /E= +([-.0-9]+)/
 718                           energy = $1.to_f
 719                           line =~ /GRAD\. MAX= +([-.0-9]+)/
 720                           grad = $1
 721                           mol.show_text("Search: #{n}\nGradient: #{grad}")
 722                           # mol.set_property("energy", energy)
 723                         end
 724                         last_i = i
 725                   elsif line =~ /TOTAL ENERGY += *([-.0-9]+)/
 726                     energy = $1
 727                         if mol && search_mode == 2
 728                           mol.show_text("Point: #{nserch}\nEnergy: #{energy}")
 729                         end
 730                         energy = energy.to_f
 731                   elsif line =~ /FINAL .* ENERGY IS +([-.0-9]+) *AFTER/
 732                     energy = $1.to_f
 733                         if mol && search_mode == 0
 734                           mol.set_property("energy", energy)
 735                         end
 736           elsif nserch > 0 && line =~ /ddikick\.x/
 737             last_i = -1
 738             break
 739           elsif mol && nserch > 0 && (line =~ /COORDINATES OF ALL ATOMS/ || line =~ /COORDINATES \(IN ANGSTROM\) FOR \$DATA GROUP ARE/)
 740             #  There should be (natoms) lines
 741                         if line =~ /COORDINATES OF ALL ATOMS/
 742                           #  Skip header lines
 743                           i += 2
 744                     end
 745             if i + mol.natoms + 1 <= lines.count
 746               coords = []
 747               (i + 1...i + 1 + mol.natoms).each { |j|
 748                 name, charge, x, y, z = lines[j].split
 749                 coords.push(Vector3D[x.to_f, y.to_f, z.to_f])
 750               }
 751               mol.create_frame([coords])
 752                           if search_mode == 1 && energy
 753                             mol.set_property("energy", energy)
 754                           end
 755               mol.display
 756               last_i = i + mol.natoms
 757               i = last_i   #  Skip the processed lines
 758             end
 759                   elsif line =~ /N A T U R A L   B O N D   O R B I T A L   A N A L Y S I S/
 760                     #  NBO output
 761                     j = i + 1
 762                         while j < lines.count
 763                           break if lines[j] =~ /done with NBO analysis/
 764                           j += 1
 765                         end
 766                         if j < lines.count
 767                           nbo_lines = lines[i..j]
 768                           mol.import_nbo_log(nbo_lines) rescue puts "Error: #{$!}, #{$!.backtrace.inspect}"
 769                           last_i = j
 770                           i = last_i  #  Skip the processed lines
 771                         else
 772                           break  #  Wait until NBO is done
 773                         end
 774           end
 775           i += 1
 776         end
 777         if last_i == -1
 778           lines.clear
 779           break
 780         elsif last_i
 781           lines[0..last_i] = nil
 782                   lineno += last_i + 1
 783         end
 784       end
 785       true
 786     }
 787
 788     if (script = get_global_settings("gamess.prefix_script")) != nil && script != ""
 789           eval(script)
 790         end
 791
 792     if $platform == "win"
 793           if gmsvers == "11"
 794             hosts = "localhost " * ncpus
 795             cmdline = "cmd.exe /c \"#{gmsdir}/ddikick.exe #{gmsdir}/gamess.#{gmsvers}.exe #{inpbody} -ddi #{ncpus} #{ncpus} #{hosts} -scr #{scrdir} < NUL >>#{logname}"
 796           else
 797             cmdline = "cmd.exe /c \"mpiexec -configfile #{procfil} >>#{logname}"
 798           end
 799         else
 800           hosts = "localhost " * ncpus
 801           cmdline = "/bin/sh -c '#{gmsdir}/ddikick.x #{gmsdir}/gamess.#{gmsvers}.x #{inpbody} -ddi #{ncpus} #{ncpus} #{hosts} -scr #{scrdir} < /dev/null >>#{logname}'"
 802         end
 803
 804         if mol
 805           pid = mol.call_subprocess_async(cmdline, term_callback, timer_callback)
 806           if pid < 0
 807             error_message_box("GAMESS failed to start. Please examine GAMESS installation.")
 808             return
 809           end
 810         else
 811           pid = call_subprocess(cmdline, "Running GAMESS")
 812           term_callback.call(nil, pid)
 813           return pid
 814         end
 815
 816   end
 817
 818   def export_gamess(fname, hash)
 819
 820     def reorder_array(ary, ordered_sub_ary)
 821           return (ordered_sub_ary & ary) + (ary - ordered_sub_ary)
 822         end
 823
 824         now = Time.now.to_s
 825         if fname
 826           basename = File.basename(fname, ".*")
 827         else
 828           basename = File.basename(self.name, ".*")
 829         end
 830
 831         #  Various settings
 832         icharg = hash["charge"]
 833         mult = hash["mult"]
 834         runtyp = ["ENERGY", "PROP", "OPTIMIZE"][hash["runtype"].to_i]
 835         scftyp = ["RHF", "ROHF", "UHF"][hash["scftype"].to_i]
 836         bssname = hash["basis"]
 837         bssname2 = hash["secondary_basis"]
 838         if hash["use_secondary_basis"].to_i != 0 && bssname2 != bssname
 839           use_2nd = true
 840           element2 = hash["secondary_elements"].split(/[\s,]+/).map { |name| name.capitalize }
 841         else
 842           use_2nd = false
 843           bssname2 = bssname
 844         end
 845         basis = $gamess_basis[bssname]
 846         basis2 = $gamess_basis[bssname2]
 847
 848         #  Use effective core potentials?
 849         ecp = $gamess_ecp[bssname]
 850         ecp2 = $gamess_ecp[bssname2]
 851         ecp_read = (ecp || ecp2 ? "ECP=READ " : "")
 852
 853         #  Use only one built-in basis set?
 854         gbasis = nil
 855         if !use_2nd
 856           case bssname
 857           when "PM3"
 858                 gbasis = "PM3 NGAUSS=3"
 859           when "STO3G"
 860                 gbasis = "STO NGAUSS=3"
 861           when "321G"
 862                 gbasis = "N21 NGAUSS=3"
 863           when "631G"
 864                 gbasis = "N31 NGAUSS=6"
 865           when "631Gd"
 866                 gbasis = "N31 NGAUSS=6 NDFUNC=1"
 867           when "631Gdp"
 868                 gbasis = "N31 NGAUSS=6 NDFUNC=1 NPFUNC=1"
 869           when "6311G"
 870                 gbasis = "N311 NGAUSS=6"
 871           when "6311Gdp"
 872                 gbasis = "N311 NGAUSS=6 NDFUNC=1 NPFUNC=1"
 873           end
 874         end
 875
 876         #  Count non-dummy atoms
 877         natoms = 0
 878         each_atom { |ap|
 879           natoms += 1 if ap.atomic_number != 0
 880         }
 881
 882         #  Fill hash with default values
 883         h = (hash["CONTRL"] ||= Hash.new)
 884         h["COORD"] ||= "UNIQUE"
 885         h["EXETYP"] ||= "RUN"
 886         h["ICHARG"] ||= (icharg || 0).to_s
 887         h["ICUT"] ||= "20"
 888         h["INTTYP"] ||= "HONDO"
 889         h["ITOL"] ||= "30"
 890         h["MAXIT"] ||= "200"
 891         h["MOLPLT"] ||= ".T."
 892         h["MPLEVL"] ||= "0"
 893         h["MULT"] ||= mult.to_s
 894         h["QMTTOL"] ||= "1e-08"
 895         h["RUNTYP"] ||= runtyp
 896         if (hash["dft"] || 0) != 0 && hash["dfttype"]
 897           h["DFTTYP"] ||= hash["dfttype"]
 898         end
 899         if (hash["use_internal"] || 0) != 0 && (hash["runtype"] == 2 || h["RUNTYP"] == "OPTIMIZE")
 900           nzvar = natoms * 3 - 6  #  TODO: 3N-5 for linear molecules
 901           h["NZVAR"] ||= nzvar.to_s
 902         else
 903           nzvar = 0
 904         end
 905         h["SCFTYP"] ||= scftyp
 906         if ecp_read != ""
 907           h["ECP"] ||= "READ"
 908         end
 909         h["UNITS"] ||= "ANGS"
 910
 911         h = (hash["SCF"] ||= Hash.new)
 912         h["CONV"] ||= "1.0E-06"
 913         h["DIRSCF"] ||= ".T."
 914         h["FDIFF"] ||= ".T."
 915         h["DAMP"] ||= ".T."
 916
 917         h = (hash["STATPT"] ||= Hash.new)
 918         h["NSTEP"] ||= "400"
 919         h["OPTTOL"] ||= "1.0E-06"
 920     if hash["eliminate_freedom"] == 0
 921       h["PROJCT"] ||= ".F."
 922     end
 923
 924         h = (hash["SYSTEM"] ||= Hash.new)
 925         h["MEMDDI"] ||= "0"
 926         h["MWORDS"] ||= "16"
 927         h["TIMLIM"] ||= "50000"
 928
 929         h = (hash["GUESS"] ||= Hash.new)
 930         h["GUESS"] ||= "HUCKEL"
 931
 932         if gbasis
 933           h = (hash["BASIS"] ||= Hash.new)
 934           h["GBASIS"] ||= gbasis
 935         end
 936
 937         if nzvar > 0
 938           h = (hash["ZMAT"] ||= Hash.new)
 939           h["DLC"] ||= ".T."
 940           h["AUTO"] ||= ".T."
 941         end
 942
 943         if (hash["esp"] || 0) != 0
 944           h = (hash["ELPOT"] ||= Hash.new)
 945           h["IEPOT"] ||= "1"
 946           h["OUTPUT"] ||= "PUNCH"
 947           h["WHERE"] ||= "PDC"
 948           h = (hash["PDC"] ||= Hash.new)
 949           h["CONSTR"] ||= "NONE"
 950           h["PTSEL"] ||= "CONNOLLY"
 951         end
 952
 953     if (hash["include_nbo"] || 0) != 0
 954       h = (hash["NBO"] ||= Hash.new)
 955       s = ""
 956       ["nao", "nbo", "nho", "nlmo", "pnao", "pnbo", "pnho", "pnlmo"].each { |nao|
 957         if (hash[nao] || 0) != 0
 958           s += " f" + nao + " ao" + nao
 959         end
 960       }
 961       h[s] = ""
 962     end
 963
 964         if fname
 965           fp = File.open(fname, "wb")
 966         else
 967           fp = MemoryIO.new
 968         end
 969     if fp
 970           fp.print "!  GAMESS input\n"
 971           fp.print "!  Generated by Molby at #{now}\n"
 972           fp.print "!  Basis set: " + ($gamess_basis_desc[bssname] || "(not specified)") + "\n"
 973           if use_2nd
 974             fp.print "!  [" + element2.join(", ") + "]: " + ($gamess_basis_desc[bssname2] || "(not specified)") + "\n"
 975           end
 976           ordered = ["CONTRL", "SCF", "STATPT", "SYSTEM", "GUESS", "BASIS", "ZMAT", "ELPOT", "PDC"]
 977           controls = reorder_array(hash.keys.select { |k| k != "key_order" && hash[k].is_a?(Hash) },
 978                 hash["key_order"] || ordered)
 979           controls.each { |k|
 980             h = hash[k]
 981                 next if h == nil || h.size == 0 || (h["key_order"] && h.size == 1)
 982                 if k == "CONTRL"
 983                   ordered = ["COORD", "EXETYP", "ICHARG", "ICUT", "INTTYP", "ITOL", "MAXIT", "MOLPLT", "MPLEVL",
 984                              "MULT", "QMTTOL", "RUNTYP", "SCFTYP", "ECP", "UNITS", "DFTTYP", "NZVAR"]
 985                 elsif k == "SCF"
 986                   ordered = ["CONV", "DIRSCF", "FDIFF", "DAMP"]
 987                 elsif k == "STATPT"
 988                   ordered = ["NSTEP", "OPTTOL"]
 989                 elsif k == "SYSTEM"
 990                   ordered = ["MEMDDI", "MWORDS", "TIMLIM"]
 991                 elsif k == "GUESS"
 992                   ordered = ["GUESS"]
 993                 elsif k == "BASIS"
 994                   ordered = ["GBASIS"]
 995                 elsif k == "ZMAT"
 996                   ordered = ["DLC", "AUTO"]
 997                 elsif k == "ELPOT"
 998                   ordered = ["IEPOT", "OUTPUT", "WHERE"]
 999                 elsif k == "PDC"
1000                   ordered = ["CONSTR", "PTSEL"]
1001                 else
1002                   ordered = []
1003                 end
1004             keys = reorder_array(h.keys, h["key_order"] || ordered)
1005                 n = 0
1006                 keys.each_with_index { |kk, i|
1007                   v = h[kk]
1008                   if n == 0
1009                     fp.printf " $%-6s", k
1010                   elsif n % 3 == 0
1011                     fp.print "\n        "
1012                   end
1013                   if v == nil || v == ""
1014                     #  No value
1015                         fp.print " " + kk
1016                   else
1017                     fp.printf " %s=%s", kk, h[kk].to_s
1018                   end
1019                   n += 1
1020                 }
1021                 if n > 0
1022                   fp.print " $END\n"
1023                 end
1024           }
1025           fp.print " $DATA\n#{basename}\nC1 0\n"
1026           secondary = []
1027           each_atom { |ap|
1028             next if ap.atomic_number == 0
1029                 fp.printf "%-6s %4d %10.6f %10.6f %10.6f\n", ap.name, ap.atomic_number, ap.r.x, ap.r.y, ap.r.z
1030                 if use_2nd && element2.include?(ap.element)
1031                   secondary[ap.index] = true
1032                 end
1033             if !gbasis
1034                   #  Basis specification followed by a blank line
1035                   bas = (secondary[ap.index] ? basis2 : basis)
1036                   if bas.is_a?(Array)
1037                     bas = bas[ap.atomic_number]
1038                   end
1039                   if bas
1040                     fp.print bas
1041                     fp.print "\n"
1042                   else
1043                     puts "Warning: basis set is not defined for atom #{ap.index}, element #{ap.element}"
1044                   end
1045                 end
1046           }
1047           fp.print " $END\n"
1048           ecp_ary = []
1049           if ecp || ecp2
1050             fp.print " $ECP\n"
1051                 each_atom { |ap|
1052                   an = ap.atomic_number
1053                   next if an == 0
1054                   ecpp = (secondary[ap.index] ? ecp2 : ecp)
1055                   e = ecp_ary[an] || (ecpp && ecpp[an])
1056                   if e
1057                     #  Cache the PNAME of the $ECP entry and re-use it
1058                     ecp_ary[an] ||= (e.split)[0] + "\n"
1059                   else
1060                     e = ap.element.upcase + "-ECP NONE\n"
1061                   end
1062                   fp.print e
1063                 }
1064             fp.print " $END\n"
1065           end
1066         end
1067         if fname == nil
1068           s = fp.buffer
1069       fp.empty
1070           return s
1071         else
1072           fp.close
1073           return fname
1074         end
1075   end
1076
1077   def cmd_edit_gamess_input(s)
1078     h = Dialog.run("Edit GAMESS Input", "OK", "Cancel", :resizable=>true) {
1079           layout(1,
1080             item(:textview, :value=>s, :tag=>"edit", :width=>400, :height=>400, :flex=>[0,0,0,0,1,1]),
1081             :flex=>[0,0,0,0,1,1]
1082           )
1083           set_min_size(300, 300)
1084         }
1085         if h[:status] == 0
1086           return h["edit"]
1087         else
1088           return nil
1089         end
1090   end
1091
1092   def cmd_create_gamess_input
1093
1094     mol = self
1095
1096     if natoms == 0
1097       raise MolbyError, "cannot create GAMESS input; the molecule is empty"
1098     end
1099
1100         #  Descriptive text and internal string for popup menus
1101 #    bset_desc = ["PM3", "STO-3G", "3-21G", "6-31G", "6-31G(d)", "6-31G(d,p)", "6-311G", "6-311G(d,p)", "LanL2DZ"]
1102 #       bset_internal = ["PM3", "STO3G", "321G", "631G", "631Gd", "631Gdp", "6311G", "6311Gdp", "LanL2DZ"]
1103     bset_desc = $gamess_basis_keys.map { |key| $gamess_basis_desc[key] }
1104         dft_desc = ["B3LYP"]
1105         dft_internal = ["B3LYP"]
1106
1107         defaults = {"scftype"=>0, "runtype"=>0, "use_internal"=>1, "eliminate_freedom"=>1, "charge"=>"0", "mult"=>"1",
1108           "basis"=>4, "use_secondary_basis"=>0, "secondary_elements"=>"",
1109           "secondary_basis"=>8, "esp"=>0, "ncpus"=>"1"}
1110
1111         gamess_input_direct = nil
1112
1113     user_input = Hash.new
1114         ["CONTRL", "SCF", "STATPT", "SYSTEM", "GUESS", "BASIS"].each { |k|
1115           user_input[k] = Hash.new
1116         }
1117     if ".inp".casecmp(self.name[-4, 4]) == 0
1118           #  Read input and analyze commands
1119           fp = open(self.path, "r")
1120           key = hh = nil
1121           if fp
1122             while ln = fp.gets
1123                   ln.strip!
1124                   break if "$DATA".casecmp(ln[0, 5]) == 0
1125                   ln.split.each { |s|
1126                     if s[0] == "$"
1127                           #  New key
1128                           key = s[1..-1].upcase
1129                           hh = user_input[key] = Hash.new
1130                           (user_input["key_order"] ||= []).push(key)
1131                         else
1132                           k, v = s.split("=")
1133                           if key && hh
1134                             k.upcase!
1135                             hh[k] = v
1136                                 (hh["key_order"] ||= []).push(k)
1137                           end
1138                         end
1139                   }
1140                 end  #  end while
1141                 fp.close
1142                 user_input["charge"] = user_input["CONTRL"]["ICHARG"]
1143                 user_input["mult"] = user_input["CONTRL"]["MULT"]
1144                 user_input["runtype"] = ((i = ["ENERGY", "PROP", "OPTIMIZE"].find_index(user_input["CONTRL"]["RUNTYP"])) ? i.to_s : nil)
1145                 user_input["scftype"] = ((i = ["RHF", "ROHF", "UHF"].find_index(user_input["CONTRL"]["SCFTYP"])) ? i.to_s : nil)
1146                 dft_type = dft_internal.find_index(user_input["CONTRL"]["DFTTYP"])
1147                 if dft_type
1148                   user_input["dfttype"] = dft_type.to_s
1149                   user_input["dft"] = 1
1150                 end
1151                 bssname = nil
1152                 user_input["basis"] = "-1"
1153                 case user_input["BASIS"]["GBASIS"]
1154                 when "PM3"
1155                   bssname = "PM3"
1156                 when "STO"
1157                   bssname = "STO3G"
1158                 when "N21"
1159                   bssname = "321G"
1160                 when "N31"
1161                   if user_input["NDFUNC"] == "1"
1162                     if user_input["NPFUNC"] == "1"
1163                           bssname = "631Gdp"
1164                         else
1165                           bssname = "631Gd"
1166                         end
1167                   else
1168                     bssname = "631G"
1169                   end
1170                 when "N311"
1171                   if user_input["NDFUNC"] == "1" && user_input["NPFUNC"] == "1"
1172                     bssname = "6311Gdp"
1173                   else
1174                     bssname = "6311G"
1175                   end
1176                 end
1177                 if bssname
1178                   user_input["basis"] = $gamess_basis_keys.find_index(bssname).to_s
1179                 end
1180           #  puts user_input.inspect
1181           end
1182         end
1183
1184     hash = Dialog.run("GAMESS Export") {
1185       def load_basis_set_sub(item)
1186             fname = Dialog.open_panel("Select a file containing GAMESS basis set:")
1187                 if fname
1188                   Molecule.read_gamess_basis_sets(fname)
1189                   bset_desc_new = $gamess_basis_keys.map { |key| $gamess_basis_desc[key] }
1190                   sel1 = attr("basis", :value)
1191                   sel2 = attr("secondary_basis", :value)
1192                   set_attr("basis", :subitems=>bset_desc_new)
1193                   set_attr("basis", :value=>sel1)
1194                   set_attr("secondary_basis", :subitems=>bset_desc_new)
1195                   set_attr("secondary_basis", :value=>sel2)
1196                 end
1197       end
1198           def select_gamess_path(item)
1199             while 1
1200               fname = Dialog.open_panel("Locate GAMESS executable:")
1201                   return if fname == nil
1202                   bname = File.basename(fname)
1203                   if bname =~ /gamess\.(.*)\.(exe|x)$/i
1204                     set_attr("executable_path", :value=>fname)
1205                     return
1206                   else
1207                     error_message_box("\"#{bname}\" does not look like a GAMESS executable!  Please try again.")
1208                   end
1209                 end
1210           end
1211           def set_optional_scripts(item)
1212             h = Dialog.run("GAMESS Optional Scripts") {
1213                   s_pre = get_global_settings("gamess.prefix_script")
1214                   s_post = get_global_settings("gamess.postfix_script")
1215                   layout(1,
1216                     item(:text, :title=>"Script to run before GAMESS execution:"),
1217                         item(:textview, :width=>400, :height=>200, :value=>s_pre, :tag=>"prefix"),
1218                     item(:text, :title=>"Script to run after GAMESS execution:"),
1219                         item(:textview, :width=>400, :height=>200, :value=>s_post, :tag=>"postfix"))
1220                 }
1221                 if h[:status] == 0
1222                   set_global_settings("gamess.prefix_script", h["prefix"])
1223                   set_global_settings("gamess.postfix_script", h["postfix"])
1224                 end
1225           end
1226       nbos = ["nao", "nbo", "nho", "nlmo", "pnao", "pnbo", "pnho", "pnlmo"]
1227           layout(4,
1228                 item(:text, :title=>"SCF type"),
1229                 item(:popup, :subitems=>["RHF", "ROHF", "UHF"], :tag=>"scftype"),
1230             item(:text, :title=>"Run type"),
1231                 item(:popup, :subitems=>["Energy", "Property", "Optimize"], :tag=>"runtype",
1232                   :action=>lambda { |it| set_attr("use_internal", :enabled=>(it[:value] == 2)) } ),
1233         item(:checkbox, :title=>"Use internal coordinates for structure optimization", :tag=>"use_internal"),
1234         -1, -1, -1,
1235                 item(:checkbox, :title=>"Eliminate translation and rotational degrees of freedom", :tag=>"eliminate_freedom"),
1236                 -1, -1, -1,
1237
1238                 item(:text, :title=>"Charge"),
1239                 item(:textfield, :width=>80, :tag=>"charge"),
1240                 item(:text, :title=>"Multiplicity"),
1241                 item(:textfield, :width=>80, :tag=>"mult"),
1242
1243                 item(:checkbox, :title=>"Use DFT", :tag=>"dft",
1244                   :action=>lambda { |it| set_attr("dfttype", :enabled=>(it[:value] != 0)) } ),
1245                 -1,
1246                 item(:text, :title=>"DFT type"),
1247                 item(:popup, :subitems=>dft_desc, :tag=>"dfttype"),
1248
1249                 item(:line),
1250                 -1, -1, -1,
1251
1252                 item(:text, :title=>"Basis set"),
1253                 item(:popup, :subitems=>bset_desc + ["(no select)"], :tag=>"basis"),
1254                 -1,
1255                 -1,
1256
1257                 item(:button, :title=>"Load Basis Set...", :action=>:load_basis_set_sub),
1258                 -1, -1, -1,
1259
1260                 item(:checkbox, :title=>"Use secondary basis set", :tag=>"use_secondary_basis",
1261                   :action=>lambda { |it|
1262                     flag = (it[:value] != 0)
1263                         set_attr("secondary_elements", :enabled=>flag)
1264                         set_attr("secondary_basis", :enabled=>flag)
1265                   }),
1266                 -1, -1, -1,
1267
1268                 item(:text, :title=>"   Elements"),
1269                 item(:textfield, :width=>80, :tag=>"secondary_elements"),
1270                 item(:text, :title=>"Basis set"),
1271                 item(:popup, :subitems=>bset_desc, :tag=>"secondary_basis"),
1272
1273                 item(:line),
1274                 -1, -1, -1,
1275
1276                 item(:checkbox, :title=>"Calculate electrostatic potential (ESP)", :tag=>"esp"),
1277                 -1, -1, -1,
1278
1279         item(:line),
1280         -1, -1, -1,
1281
1282         item(:checkbox, :title=>"Include NBO instructions", :tag=>"include_nbo",
1283              :action=>lambda { |it|
1284                flag = (it[:value] != 0)
1285                nbos.each { |nbo| set_attr(nbo, :enabled=>flag) }
1286              }),
1287         -1, -1, -1,
1288         item(:checkbox, :title=>"NAO", :tag=>"nao"),
1289         item(:checkbox, :title=>"NBO", :tag=>"nbo"),
1290         item(:checkbox, :title=>"NHO", :tag=>"nho"),
1291         item(:checkbox, :title=>"NLMO", :tag=>"nlmo"),
1292         item(:checkbox, :title=>"PNAO", :tag=>"pnao"),
1293         item(:checkbox, :title=>"PNBO", :tag=>"pnbo"),
1294         item(:checkbox, :title=>"PNHO", :tag=>"pnho"),
1295         item(:checkbox, :title=>"PNLMO", :tag=>"pnlmo"),
1296
1297         item(:line),
1298                 -1, -1, -1,
1299
1300                 item(:checkbox, :title=>"Execute GAMESS on this machine", :tag=>"execute_local",
1301                   :action=>lambda { |it|
1302                     flag = (it[:value] != 0)
1303                         set_attr("executable_path", :enabled=>flag)
1304                         set_attr("select_path", :enabled=>flag)
1305                         set_attr("ncpus", :enabled=>flag)
1306                   }),
1307                 -1, -1, -1,
1308
1309                 item(:text, :title=>"   Path"),
1310                 item(:textfield, :width=>300, :tag=>"executable_path"),
1311                 -1, -1,
1312
1313                 -1,
1314                 item(:button, :title=>"Select Path...", :tag=>"select_path", :action=>:select_gamess_path),
1315                 -1,
1316                 item(:button, :title=>"Optional Scripts...", :action=>:set_optional_scripts),
1317
1318                 item(:text, :title=>"   N of CPUs"),
1319                 item(:textfield, :width=>80, :tag=>"ncpus"),
1320                 -1, -1,
1321
1322                 item(:line),
1323                 -1, -1, -1,
1324
1325                 item(:button, :title=>"Edit GAMESS Input and Go", :action=>lambda { |it|
1326                   h = Hash.new
1327                   each_item { |it2|
1328                     if (tag = it2[:tag]) != nil
1329                           h[tag] = it2[:value]
1330                         end
1331                   }
1332                   h["basis"] = $gamess_basis_keys[h["basis"]]
1333                   h["secondary_basis"] = $gamess_basis_keys[h["secondary_basis"]]
1334                   h["dfttype"] = dft_internal[h["dfttype"]]
1335                   gamess_input_direct = mol.cmd_edit_gamess_input(mol.export_gamess(nil, h))
1336                   if gamess_input_direct
1337                         end_modal(0)
1338                   end
1339                 }),
1340                 -1, -1, -1
1341           )
1342           values = Hash.new
1343           each_item { |it|
1344             tag = it[:tag]
1345                 if tag
1346                   values[tag] = (user_input[tag] || get_global_settings("gamess.#{tag}") || defaults[tag])
1347                   if tag == "basis" && values[tag] == "-1"
1348                     values[tag] = (bset_desc.count).to_s
1349                   end
1350                   it[:value] = values[tag]
1351                 end
1352           }
1353           set_attr("secondary_elements", :enabled=>(values["use_secondary_basis"] == 1))
1354           set_attr("secondary_basis", :enabled=>(values["use_secondary_basis"] == 1))
1355           set_attr("dfttype", :enabled=>(values["dft"] == 1))
1356           set_attr("use_internal", :enabled=>(values["runtype"] == 2))
1357           set_attr("executable_path", :enabled=>(values["execute_local"] == 1))
1358           set_attr("select_path", :enabled=>(values["execute_local"] == 1))
1359           set_attr("ncpus", :enabled=>(values["execute_local"] == 1))
1360       nbos.each { |nao|
1361         set_attr(nao, :enabled=>(values["include_nbo"] == 1))
1362       }
1363         }
1364         hash.each_pair { |key, value|
1365           next if key == :status
1366           set_global_settings("gamess.#{key}", value)
1367         }
1368         if hash[:status] == 0
1369           #  Specify basis by internal keys
1370           hash["basis"] = $gamess_basis_keys[hash["basis"]]
1371           hash["secondary_basis"] = $gamess_basis_keys[hash["secondary_basis"]]
1372           hash["dfttype"] = dft_internal[hash["dfttype"]]
1373           basename = (self.path ? File.basename(self.path, ".*") : self.name)
1374           fname = Dialog.save_panel("Export GAMESS input file:", self.dir, basename + ".inp", "GAMESS input file (*.inp)|*.inp|All files|*.*")
1375           return nil if !fname
1376           if gamess_input_direct
1377           #  puts "gamess_input_direct = \"#{gamess_input_direct}\""
1378             File.open(fname, "w") { |fp| fp.print(gamess_input_direct) }
1379           else
1380             export_gamess(fname, hash)
1381           end
1382           if hash["execute_local"] == 1
1383             Molecule.execute_gamess(fname, self)
1384           end
1385         else
1386           nil
1387         end
1388
1389   end
1390
1391   def cmd_create_cube
1392     grid = default_MO_grid
1393         if grid == nil
1394           Dialog.run {
1395             layout(1,
1396                   item(:text, :title=>"This molecule does not contain MO information."))
1397           }
1398           return
1399         end
1400
1401     mos = selected_MO
1402         if mos == nil || mos.length == 0
1403       Dialog.run {
1404             layout(1,
1405                   item(:text, :title=>"Please select MO(s) in the MO Info table."))
1406       }
1407           return
1408         end
1409         hash = Dialog.run {
1410           layout(1,
1411             item(:text, :title=>"Please specify cube dimensions (in angstrom units):"),
1412             layout(4,
1413                   item(:text, :title=>"Origin"),
1414                   item(:textfield, :width=>100, :height=>20, :tag=>"originx", :value=>sprintf("%.6f", grid[0].x)),
1415                   item(:textfield, :width=>100, :height=>20, :tag=>"originy", :value=>sprintf("%.6f", grid[0].y)),
1416                   item(:textfield, :width=>100, :height=>20, :tag=>"originz", :value=>sprintf("%.6f", grid[0].z)),
1417                   item(:text, :title=>"Delta"),
1418                   item(:textfield, :width=>100, :height=>20, :tag=>"deltax", :value=>sprintf("%.6f", grid[1])),
1419                   item(:textfield, :width=>100, :height=>20, :tag=>"deltay", :value=>sprintf("%.6f", grid[2])),
1420                   item(:textfield, :width=>100, :height=>20, :tag=>"deltaz", :value=>sprintf("%.6f", grid[3])),
1421                   item(:text, :title=>"Step"),
1422                   item(:textfield, :width=>100, :height=>20, :tag=>"stepx", :value=>grid[4].to_s),
1423                   item(:textfield, :width=>100, :height=>20, :tag=>"stepy", :value=>grid[5].to_s),
1424                   item(:textfield, :width=>100, :height=>20, :tag=>"stepz", :value=>grid[6].to_s)))
1425         }
1426         if hash[:status] == 0
1427           path = self.path || self.name
1428           dir = self.dir || Dir.pwd
1429           origin = Vector3D[hash["originx"], hash["originy"], hash["originz"]]
1430           dx = hash["deltax"]
1431           dy = hash["deltay"]
1432           dz = hash["deltaz"]
1433           nx = hash["stepx"]
1434           ny = hash["stepy"]
1435           nz = hash["stepz"]
1436           basename = File.basename(path, ".*")
1437           filenames = []
1438           mo_type = self.mo_type
1439           mos.each { |n|
1440             fname1 = fname2 = nil
1441             alpha = (mo_type != "UHF" ? "" : "alpha ")
1442                 a = (mo_type != "UHF" ? "" : "a")
1443             fname1 = Dialog.save_panel("Cube file name for #{alpha}MO #{n}", dir, basename + "_#{n}#{a}.cube", "Gaussian cube file (*.cube)|*.cube")
1444                 if (mo_type == "UHF")
1445                   fname2 = Dialog.save_panel("Cube file name for beta MO #{n}", dir, basename + "_#{n}b.cube", "Gaussian cube file (*.cube)|*.cube")
1446                 end
1447                 filenames.push([n, fname1, fname2])
1448           }
1449           filenames.each { |pair|
1450             n = pair[0]
1451                 alpha = (mo_type != "UHF" ? "" : "alpha ")
1452             show_progress_panel("Creating cube file for #{alpha}MO #{n}...")
1453                 if pair[1]
1454                   cubegen(pair[1], n, origin, dx, dy, dz, nx, ny, nz, true)
1455                 end
1456                 if pair[2] && mo_type == "UHF"
1457                   set_progress_message("Creating cube file for beta MO #{n}...")
1458                   cubegen(pair[2], n, origin, dx, dy, dz, nx, ny, nz, true, true)
1459                 end
1460             hide_progress_panel
1461           }
1462         end
1463   end
1464
1465 end
1466
1467 $gamess_basis = {
1468   "PM3"   => " PM3 0\n",
1469   "STO3G" => " STO 3\n",
1470   "321G"  => " N21 3\n",
1471   "631G"  => " N31 6\n" }
1472 $gamess_basis_desc = {
1473   "PM3"   => "PM3",
1474   "STO3G" => "STO-3G",
1475   "321G"  => "3-21G",
1476   "631G"  => "6-31G" }
1477 $gamess_basis_keys = ["PM3", "STO3G", "321G", "631G"]
1478
1479 ["631Gd", "631Gdp", "631+Gd", "631++Gdp", "6311Gdp", "6311+Gd", "6311++Gdp", "6311++G2d2p", "6311++G3df3pd", "LanL2DZ"].each { |n|
1480   Molecule.read_gamess_basis_sets("basis_sets/#{n}.txt")
1481 }
1482
1483 register_menu("QChem\tCreate GAMESS Input...",
1484   :cmd_create_gamess_input, :non_empty)
1485 register_menu("QChem\tCreate MOPAC6 Input...",
1486   :cmd_create_mopac_input, :non_empty)    # mopac6.rb
1487 register_menu("QChem\tCreate MO Cube...",
1488   :cmd_create_cube, lambda { |m| m && m.mo_type } )