$gamess_basis_keys.push(basename)
end
end
+
+ # Execute GAMESS (inferior copy of rungms script)
+ # inpname is the input file
+ # mol (optional) is the molecule from which the GAMESS input was built.
+ # If mol is specified and RUNTYP=OPTIMIZE, then the intermediate structures are
+ # displayed real-time.
+ def Molecule.execute_gamess(inpname, mol = nil)
+ gmsname = get_global_settings("gamess.executable_path")
+ gmsdir = nil
+ gmsvers = nil
+ while 1
+ if gmsname == nil || !File.exist?(gmsname)
+ gmsname = Dialog.open_panel("Please locate the GAMESS executable")
+ exit if gmsname == nil
+ end
+ gmsbase = File.basename(gmsname)
+ gmsdir = File.dirname(gmsname)
+ if gmsbase =~ /gamess\.(.*)\.(exe|x)$/i
+ gmsvers = $1
+ break
+ else
+ gmsname = nil
+ error_message_box(gmsbase + " does not look like a GAMESS executable!")
+ end
+ end
+
+ inpbase = File.basename(inpname)
+ inpdir = File.dirname(inpname)
+ inpbody = inpbase.sub(/\.inp$/, "")
+ logbase = inpbody + ".log"
+
+ set_global_settings("gamess.executable_path", gmsname)
+
+ # Prepare the scratch directory in the home directory
+ # (Not in the document home to avoid space-containing path in Windows)
+ scrdir = document_home.sub(/\/My Documents/, "") + "/gamess"
+ n = 0
+ while File.exist?(scrdir) && !File.directory?(scrdir)
+ if n == 0
+ scrdir += ".1"
+ else
+ scrdir = scrdir.sub(".#{n}", ".#{n + 1}")
+ end
+ n += 1
+ end
+ if !File.exist?(scrdir)
+ Dir.mkdir(scrdir)
+ end
+ scrdir = scrdir + "/" + inpbody + "." + $$.to_s + ".0"
+ n = 0
+ while File.exist?(scrdir)
+ scrdir = scrdir.sub(".#{n}", ".#{n + 1}")
+ n += 1
+ end
+ Dir.mkdir(scrdir)
+
+ if $platform == "win"
+ sep = "\\"
+ scrdir.gsub!("/", sep)
+ gmsdir.gsub!("/", sep)
+ else
+ sep = "/"
+ end
+
+ # Get the host name etc.
+ hostname = `hostname`.chomp
+ if $platform == "win"
+ freebytes = `dir #{scrdir}`.split("\n").pop.match(/([0-9,]+)[^0-9]*$/).to_a[1]
+ if freebytes
+ freebytes = (freebytes.gsub(",","").to_i / 1024).to_s + " Kbytes"
+ else
+ freebytes = "(unknown)"
+ end
+ uname = `ver`.to_s.gsub("\n", "")
+ else
+ freebytes = `df -k #{scrdir}`
+ uname = `uname`.chomp
+ end
+
+ # Redirect standard output to the log file
+ logname = scrdir + sep + logbase
+ fpout = File.open(logname, "w")
+ fpout.print "----- GAMESS execution script -----\n"
+ fpout.print "This job is running on host #{hostname}\n"
+ fpout.print "under operating system #{uname} at #{Time.now.to_s}\n"
+ fpout.print "Available scratch disk space (Kbyte units) at beginning of the job is\n"
+ fpout.print freebytes
+
+ # Copy the input file
+ scrprefix = scrdir + sep + inpbody
+ filecopy(inpname, scrprefix + ".F05")
+
+ # Prepare environmental variables
+ auxdir = "#{gmsdir}#{sep}auxdata"
+ ENV["ERICFMT"] = "#{auxdir}#{sep}ericfmt.dat"
+ ENV["MCPPATH"] = "#{auxdir}#{sep}MCP"
+ ENV["BASPATH"] = "#{auxdir}#{sep}BASES"
+ ENV["QUANPOL"] = "#{auxdir}#{sep}QUANPOL"
+ ENV["EXTBAS"] = "/dev/null"
+ ENV["IRCDATA"] = "#{scrprefix}.irc"
+ ENV["PUNCH"] = "#{scrprefix}.dat"
+ ENV["INPUT"] = "#{scrprefix}.F05"
+ ENV["AOINTS"] = "#{scrprefix}.F08"
+ ENV["MOINTS"] = "#{scrprefix}.F09"
+ ENV["DICTNRY"] = "#{scrprefix}.F10"
+ ENV["DRTFILE"] = "#{scrprefix}.F11"
+ ENV["CIVECTR"] = "#{scrprefix}.F12"
+ ENV["CASINTS"] = "#{scrprefix}.F13"
+ ENV["CIINTS"] = "#{scrprefix}.F14"
+ ENV["WORK15"] = "#{scrprefix}.F15"
+ ENV["WORK16"] = "#{scrprefix}.F16"
+ ENV["CSFSAVE"] = "#{scrprefix}.F17"
+ ENV["FOCKDER"] = "#{scrprefix}.F18"
+ ENV["WORK19"] = "#{scrprefix}.F19"
+ ENV["DASORT"] = "#{scrprefix}.F20"
+ ENV["DFTINTS"] = "#{scrprefix}.F21"
+ ENV["DFTGRID"] = "#{scrprefix}.F22"
+ ENV["JKFILE"] = "#{scrprefix}.F23"
+ ENV["ORDINT"] = "#{scrprefix}.F24"
+ ENV["EFPIND"] = "#{scrprefix}.F25"
+ ENV["PCMDATA"] = "#{scrprefix}.F26"
+ ENV["PCMINTS"] = "#{scrprefix}.F27"
+ ENV["MLTPL"] = "#{scrprefix}.F28"
+ ENV["MLTPLT"] = "#{scrprefix}.F29"
+ ENV["DAFL30"] = "#{scrprefix}.F30"
+ ENV["SOINTX"] = "#{scrprefix}.F31"
+ ENV["SOINTY"] = "#{scrprefix}.F32"
+ ENV["SOINTZ"] = "#{scrprefix}.F33"
+ ENV["SORESC"] = "#{scrprefix}.F34"
+ ENV["SIMEN"] = "#{scrprefix}.simen"
+ ENV["SIMCOR"] = "#{scrprefix}.simcor"
+ ENV["GCILIST"] = "#{scrprefix}.F37"
+ ENV["HESSIAN"] = "#{scrprefix}.F38"
+ ENV["SOCCDAT"] = "#{scrprefix}.F40"
+ ENV["AABB41"] = "#{scrprefix}.F41"
+ ENV["BBAA42"] = "#{scrprefix}.F42"
+ ENV["BBBB43"] = "#{scrprefix}.F43"
+ ENV["MCQD50"] = "#{scrprefix}.F50"
+ ENV["MCQD51"] = "#{scrprefix}.F51"
+ ENV["MCQD52"] = "#{scrprefix}.F52"
+ ENV["MCQD53"] = "#{scrprefix}.F53"
+ ENV["MCQD54"] = "#{scrprefix}.F54"
+ ENV["MCQD55"] = "#{scrprefix}.F55"
+ ENV["MCQD56"] = "#{scrprefix}.F56"
+ ENV["MCQD57"] = "#{scrprefix}.F57"
+ ENV["MCQD58"] = "#{scrprefix}.F58"
+ ENV["MCQD59"] = "#{scrprefix}.F59"
+ ENV["MCQD60"] = "#{scrprefix}.F60"
+ ENV["MCQD61"] = "#{scrprefix}.F61"
+ ENV["MCQD62"] = "#{scrprefix}.F62"
+ ENV["MCQD63"] = "#{scrprefix}.F63"
+ ENV["MCQD64"] = "#{scrprefix}.F64"
+ ENV["NMRINT1"] = "#{scrprefix}.F61"
+ ENV["NMRINT2"] = "#{scrprefix}.F62"
+ ENV["NMRINT3"] = "#{scrprefix}.F63"
+ ENV["NMRINT4"] = "#{scrprefix}.F64"
+ ENV["NMRINT5"] = "#{scrprefix}.F65"
+ ENV["NMRINT6"] = "#{scrprefix}.F66"
+ ENV["DCPHFH2"] = "#{scrprefix}.F67"
+ ENV["DCPHF21"] = "#{scrprefix}.F68"
+ ENV["GVVPT"] = "#{scrprefix}.F69"
+
+ # next files are used only during coupled cluster runs, so let's
+ # display the numerous definitions only if they are to be used.
+ ENV["CCREST"] = "#{scrprefix}.F70"
+ ENV["CCDIIS"] = "#{scrprefix}.F71"
+ ENV["CCINTS"] = "#{scrprefix}.F72"
+ ENV["CCT1AMP"] = "#{scrprefix}.F73"
+ ENV["CCT2AMP"] = "#{scrprefix}.F74"
+ ENV["CCT3AMP"] = "#{scrprefix}.F75"
+ ENV["CCVM"] = "#{scrprefix}.F76"
+ ENV["CCVE"] = "#{scrprefix}.F77"
+ ENV["EOMSTAR"] = "#{scrprefix}.F80"
+ ENV["EOMVEC1"] = "#{scrprefix}.F81"
+ ENV["EOMVEC2"] = "#{scrprefix}.F82"
+ ENV["EOMHC1"] = "#{scrprefix}.F83"
+ ENV["EOMHC2"] = "#{scrprefix}.F84"
+ ENV["EOMHHHH"] = "#{scrprefix}.F85"
+ ENV["EOMPPPP"] = "#{scrprefix}.F86"
+ ENV["EOMRAMP"] = "#{scrprefix}.F87"
+ ENV["EOMRTMP"] = "#{scrprefix}.F88"
+ ENV["EOMDG12"] = "#{scrprefix}.F89"
+ ENV["MMPP"] = "#{scrprefix}.F90"
+ ENV["MMHPP"] = "#{scrprefix}.F91"
+ ENV["MMCIVEC"] = "#{scrprefix}.F92"
+ ENV["MMCIVC1"] = "#{scrprefix}.F93"
+ ENV["MMCIITR"] = "#{scrprefix}.F94"
+ ENV["MMNEXM"] = "#{scrprefix}.F95"
+ ENV["MMNEXE"] = "#{scrprefix}.F96"
+ ENV["MMNREXM"] = "#{scrprefix}.F97"
+ ENV["MMNREXE"] = "#{scrprefix}.F98 "
+ #
+ # next are for TDHFX code, not used by current GAMESS
+ #
+ ENV["OLI201"] = "#{scrprefix}.F201"
+ ENV["OLI202"] = "#{scrprefix}.F202"
+ ENV["OLI203"] = "#{scrprefix}.F203"
+ ENV["OLI204"] = "#{scrprefix}.F204"
+ ENV["OLI205"] = "#{scrprefix}.F205"
+ ENV["OLI206"] = "#{scrprefix}.F206"
+ ENV["OLI207"] = "#{scrprefix}.F207"
+ ENV["OLI208"] = "#{scrprefix}.F208"
+ ENV["OLI209"] = "#{scrprefix}.F209"
+ ENV["OLI210"] = "#{scrprefix}.F210"
+ ENV["OLI211"] = "#{scrprefix}.F211"
+ ENV["OLI212"] = "#{scrprefix}.F212"
+ ENV["OLI213"] = "#{scrprefix}.F213"
+ ENV["OLI214"] = "#{scrprefix}.F214"
+ ENV["OLI215"] = "#{scrprefix}.F215"
+ ENV["OLI216"] = "#{scrprefix}.F216"
+ ENV["OLI217"] = "#{scrprefix}.F217"
+ ENV["OLI218"] = "#{scrprefix}.F218"
+ ENV["OLI219"] = "#{scrprefix}.F219"
+ ENV["OLI220"] = "#{scrprefix}.F220"
+ ENV["OLI221"] = "#{scrprefix}.F221"
+ ENV["OLI222"] = "#{scrprefix}.F222"
+ ENV["OLI223"] = "#{scrprefix}.F223"
+ ENV["OLI224"] = "#{scrprefix}.F224"
+ ENV["OLI225"] = "#{scrprefix}.F225"
+ ENV["OLI226"] = "#{scrprefix}.F226"
+ ENV["OLI227"] = "#{scrprefix}.F227"
+ ENV["OLI228"] = "#{scrprefix}.F228"
+ ENV["OLI229"] = "#{scrprefix}.F229"
+ ENV["OLI230"] = "#{scrprefix}.F230"
+ ENV["OLI231"] = "#{scrprefix}.F231"
+ ENV["OLI232"] = "#{scrprefix}.F232"
+ ENV["OLI233"] = "#{scrprefix}.F233"
+ ENV["OLI234"] = "#{scrprefix}.F234"
+ ENV["OLI235"] = "#{scrprefix}.F235"
+ ENV["OLI236"] = "#{scrprefix}.F236"
+ ENV["OLI237"] = "#{scrprefix}.F237"
+ ENV["OLI238"] = "#{scrprefix}.F238"
+ ENV["OLI239"] = "#{scrprefix}.F239"
+
+ if $platform == "win"
+ fpout.print "Microsoft MPI will be running GAMESS on 1 node.\n"
+ fpout.print "The binary kicked off by 'mpiexec' is gamess.#{gmsvers}.exe\n"
+ fpout.print "MS-MPI will run 1 compute process\n"
+ # File containing environmental variables
+ envfil = "#{scrprefix}.GMS.ENV"
+ fp = File.open(envfil, "w")
+ ENV.each { |k, v| fp.print "#{k}=#{v}\n" }
+ fp.close
+ # File containing arguments to mpiexec
+ procfil = "#{scrprefix}.processes.mpd"
+ fp = File.open(procfil, "w")
+ fp.print "-env ENVFIL #{envfil} -n 2 #{gmsdir}#{sep}gamess.#{gmsvers}.exe\n"
+ fp.close
+ end
+
+ fpout.close
+ fplog = File.open(logname, "r")
+ size = 0
+ lines = []
+ last_line = ""
+
+ # Callback proc
+ callback = proc {
+ fplog.seek(0, IO::SEEK_END)
+ sizec = fplog.tell
+ if sizec > size
+ # Read new lines
+ fplog.seek(size, IO::SEEK_SET)
+ fplog.each_line { |line|
+ if line[-1, 1] == "\n"
+ lines.push(last_line + line)
+ last_line = ""
+ else
+ last_line += line
+ break
+ end
+ }
+ size = fplog.tell
+ last_i = nil
+ i = 0
+ nserch = -1
+ while i < lines.count
+ line = lines[i]
+ if line =~ /GEOMETRY SEARCH POINT NSERCH= *(\d+)/
+ nserch = $1.to_i
+ last_i = i
+ elsif line =~ /NSERCH:/
+ print line
+ if mol
+ dummy, n, grad = line.match(/NSERCH:[^0-9]*([0-9]+).*GRAD[^0-9]*([-.0-9]+)/).to_a
+ mol.show_text("Search: #{n}\nGradient: #{grad}")
+ end
+ elsif nserch > 0 && line =~ /ddikick\.x/
+ last_i = -1
+ break
+ elsif mol && nserch > 0 && line =~ /COORDINATES OF ALL ATOMS/
+ # There should be (natoms + 2) lines
+ if i + mol.natoms + 3 <= lines.count
+ coords = []
+ (i + 3...i + 3 + mol.natoms).each { |j|
+ name, charge, x, y, z = lines[j].split
+ coords.push(Vector3D[x.to_f, y.to_f, z.to_f])
+ }
+ mol.create_frame([coords])
+ mol.display
+ last_i = i + mol.natoms + 2
+ i = last_i # Skip the processed lines
+ end
+ end
+ i += 1
+ end
+ if last_i == -1
+ lines.clear
+ break
+ elsif last_i
+ lines[0..last_i] = nil
+ end
+ end
+ true
+ }
+
+ show_console_window
+ if mol
+ mol.make_front
+ end
+
+ if $platform == "win"
+ status = call_subprocess("cmd.exe /c \"mpiexec -configfile #{procfil} >>#{logname}\"", "GAMESS")
+ else
+ status = call_subprocess("/bin/sh -c '#{gmsdir}/ddikick.x #{gmsdir}/gamess.#{gmsvers}.x #{inpbody} -ddi 1 1 localhost -scr #{scrdir} < /dev/null >>#{logname}'", "GAMESS", callback)
+ end
+
+ if status != 0
+ if status == -1
+ error_message_box("GAMESS failed to start. Please examine GAMESS installation.")
+ exit
+ elsif status == -2
+ error_message_box("GAMESS execution interrupted.")
+ else
+ error_message_box("GAMESS failed with exit status #{status}.")
+ end
+ end
+
+ ext_to_keep = [".dat", ".rst", ".trj", ".efp", ".gamma", ".log"]
+ ext_to_keep.each { |ex|
+ if File.exists?("#{scrprefix}#{ex}")
+ filecopy("#{scrprefix}#{ex}", "#{inpdir}#{sep}#{inpbody}#{ex}")
+ end
+ }
+ Dir.foreach(scrdir) { |file|
+ if file != "." && file != ".." && !ext_to_keep.include?(File.extname(file))
+ File.delete("#{scrdir}#{sep}#{file}")
+ end
+ }
+
+ end
def export_gamess(fname, hash)
defaults = {"scftype"=>0, "runtype"=>0, "charge"=>"0", "mult"=>"1",
"basis"=>4, "use_secondary_basis"=>0, "secondary_elements"=>"",
- "secondary_basis"=>8, "esp"=>0}
+ "secondary_basis"=>8, "esp"=>0, "ncpus"=>"1"}
hash = Dialog.run("GAMESS Export") {
def load_basis_set_sub(item)
set_attr("secondary_basis", :value=>sel2)
end
end
+ def select_gamess_path(item)
+ while 1
+ fname = Dialog.open_panel("Locate GAMESS executable:")
+ return if fname == nil
+ bname = File.basename(fname)
+ if bname =~ /gamess\.(.*)\.(exe|x)$/i
+ set_attr("executable_path", :value=>fname)
+ return
+ else
+ error_message_box("\"#{bname}\" does not look like a GAMESS executable! Please try again.")
+ end
+ end
+ end
layout(4,
item(:text, :title=>"SCF type"),
item(:popup, :subitems=>["RHF", "ROHF", "UHF"], :tag=>"scftype"),
-1, -1, -1,
item(:line),
+ -1, -1, -1,
+
+ item(:checkbox, :title=>"Execute GAMESS on this machine", :tag=>"execute_local",
+ :action=>proc { |it|
+ flag = (it[:value] != 0)
+ set_attr("executable_path", :enabled=>flag)
+ set_attr("select_path", :enabled=>flag)
+ set_attr("ncpus", :enabled=>flag)
+ }),
+ -1, -1, -1,
+
+ item(:text, :title=>" Path"),
+ item(:textfield, :width=>300, :tag=>"executable_path"),
+ -1, -1,
+
+ -1,
+ item(:button, :title=>"Select Path...", :tag=>"select_path", :action=>:select_gamess_path),
+ -1, -1,
+
+ item(:text, :title=>" N of CPUs"),
+ item(:textfield, :width=>80, :tag=>"ncpus"),
+ -1, -1,
+
+ item(:line),
-1, -1, -1
)
values = Hash.new
set_attr("secondary_basis", :enabled=>(values["use_secondary_basis"] == 1))
set_attr("dfttype", :enabled=>(values["dft"] == 1))
set_attr("use_internal", :enabled=>(values["runtype"] == 2))
+ set_attr("executable_path", :enabled=>(values["execute_local"] == 1))
+ set_attr("select_path", :enabled=>(values["execute_local"] == 1))
+ set_attr("ncpus", :enabled=>(values["execute_local"] == 1))
}
hash.each_pair { |key, value|
next if key == :status
hash["secondary_basis"] = $gamess_basis_keys[hash["secondary_basis"]]
hash["dfttype"] = dft_internal[hash["dfttype"]]
basename = (self.path ? File.basename(self.path, ".*") : self.name)
- fname = Dialog.save_panel("GAMESS input file name", self.dir, basename + ".inp", "GAMESS input file (*.inp)|*.inp|All files|*.*")
+ fname = Dialog.save_panel("Export GAMESS input file:", self.dir, basename + ".inp", "GAMESS input file (*.inp)|*.inp|All files|*.*")
return nil if !fname
export_gamess(fname, hash)
+ if hash["execute_local"] == 1
+ Molecule.execute_gamess(fname, self)
+ end
else
nil
end
OSDN Git Service
