set_global_settings("gamess.executable_path", gmsname)
+ ncpus = get_global_settings("gamess.ncpus").to_i
+ if ncpus == 0
+ ncpus = 1
+ end
+
# 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"
ENV["OLI239"] = "#{scrprefix}.F239"
if $platform == "win"
+ if ncpus < 2
+ ncpus = 2
+ end
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"
+ fpout.print "MS-MPI will run #{ncpus} compute process\n"
# File containing environmental variables
envfil = "#{scrprefix}.GMS.ENV"
fp = File.open(envfil, "w")
# 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.print "-env ENVFIL #{envfil} -n #{ncpus} #{gmsdir}#{sep}gamess.#{gmsvers}.exe\n"
fp.close
end
end
if $platform == "win"
- status = call_subprocess("cmd.exe /c \"mpiexec -configfile #{procfil} >>#{logname}\"", "GAMESS")
+ status = call_subprocess("cmd.exe /c \"mpiexec -configfile #{procfil} >>#{logname}\"", "GAMESS", callback)
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)
+ hosts = "localhost " * ncpus
+ status = call_subprocess("/bin/sh -c '#{gmsdir}/ddikick.x #{gmsdir}/gamess.#{gmsvers}.x #{inpbody} -ddi #{ncpus} #{ncpus} #{hosts} -scr #{scrdir} < /dev/null >>#{logname}'", "GAMESS", callback)
end
if status != 0
# Get the MDArena
arena = self.md_arena
if !arena.prepare(true) # Parameter check only
- Dialog.run("MD Error") {
+ mol = self
+ h = Dialog.run("MM/MD Parameter Missing", nil, nil) {
layout(1,
- item(:text, :title=>"Some parameters are missing. Please open\nthe 'parameters' table and examine."))
- set_attr(1, :hidden=>true) # Hide the cancel button
+ item(:text, :title=>"Some MM/MD parameters are missing.\nPlease select one of the following options."),
+ item(:button, :title=>"Auto Guess", :align=>:center,
+ :action=>proc { |it| end_modal(2) } ),
+ item(:button, :title=>"Run Antechamber Manually...", :align=>:center,
+ :action=>proc { |it| end_modal(3) } ),
+ item(:button, :title=>"Cancel", :align=>:center,
+ :action=>proc { |it| end_modal(1) } ))
}
- return nil
+ status = h[:status]
+ if status == 2
+ n = invoke_antechamber(false)
+ return nil if n != 0
+ elsif status == 3
+ n = invoke_antechamber(true)
+ return nil if n != 0
+ else
+ return nil
+ end
end
# Initialize some fields at first invocation
suffix = ""
end
log_level = (get_global_settings("antechamber.log_level") || "none")
- hash = Dialog.run("Run " + tool.capitalize) {
+ if tool == "antechamber"
+ msg = "Auto Guess MM/MD Parameters (Antechamber)"
+ else
+ msg = "Run " + tool.capitalize
+ end
+ hash = Dialog.run(msg) {
@toolname = tool + suffix
def valid_antechamber_dir(s)
FileTest.exist?(s + "/" + @toolname)
return ambertools_dialog("antechamber")
end
+ def remove_dir(dir)
+ entries = Dir.entries(dir)
+ entries.each { |en|
+ next if en == "." || en == ".."
+ fname = "#{dir}/#{en}"
+ if File.directory?(fname)
+ remove_dir(fname)
+ else
+ File.unlink(fname)
+ end
+ }
+ Dir.unlink(dir)
+ end
+
+ def erase_old_logs(tdir, level, keep_number)
+ log_dir = File.dirname(tdir)
+ if level == nil || level == "none"
+ remove_dir(tdir)
+ elsif level == "latest"
+ if keep_number == nil
+ keep_number = 5
+ else
+ keep_number = keep_number.to_i
+ end
+ entries = Dir.entries(log_dir).select { |en| en != "." && en != ".." && File.directory?("#{log_dir}/#{en}") }
+ # Sort by modification date
+ entries = entries.sort_by { |en| File.mtime("#{log_dir}/#{en}").to_i }
+ (0...entries.count - keep_number).each { |i|
+ remove_dir("#{log_dir}/#{entries[i]}")
+ }
+ end
+ end
+
+ def invoke_antechamber(ask_options = true)
+ # Find the ambertool directory
+ ante_dir = "#{ResourcePath}/amber11/bin"
+ # Ask for antechamber options and log directory
+ if ask_options
+ n = cmd_antechamber()
+ return 1 if n == 0
+ end
+ nc = get_global_settings("antechamber.nc").to_i
+ calc_charge = get_global_settings("antechamber.calc_charge").to_i
+ use_residue = get_global_settings("antechamber.use_residue").to_i
+ # Create log directory
+ name = self.name.sub(/\.\w*$/, "") # Remove the extension
+ log_dir = get_global_settings("antechamber.log_dir")
+ if log_dir == nil
+ log_dir = document_home + "/antechamber"
+ end
+ if !File.directory?(log_dir)
+ Dir.mkdir(log_dir)
+ end
+ tdir = nil
+ 1000.times { |i|
+ tdir = sprintf("%s/%s.%04d", log_dir, name, i)
+ if !File.exists?(tdir) && (Dir.mkdir(tdir) == 0)
+ break
+ end
+ tdir = nil
+ }
+ if tdir == nil
+ error_message_box("Cannot create log directory in #{log_dir}.")
+ return -1
+ end
+ cwd = Dir.pwd
+ Dir.chdir(tdir)
+ if use_residue == 0
+ mol2 = self.dup
+ mol2.assign_residue(mol2.all, 1)
+ else
+ mol2 = self
+ end
+ mol2.savepdb("./mol.pdb")
+ # Set environmental variable
+ p = ENV["AMBERHOME"]
+ if p == nil
+ amberhome = "#{ResourcePath}/amber11"
+ if $platform == "win"
+ amberhome.gsub!("/", "\\")
+ end
+ ENV["AMBERHOME"] = amberhome
+ end
+ if calc_charge != 0
+ opt = "-nc #{net_charge} -c bcc"
+ else
+ opt = ""
+ end
+ n = call_subprocess("#{ante_dir}/antechamber -i mol.pdb -fi pdb -o mol.ac -fo ac #{opt}", "Antechamber")
+ if n != 0
+ error_message_box("Antechamber failed: status = #{n}.")
+ Dir.chdir(cwd)
+ return n
+ else
+ n = call_subprocess("#{ante_dir}/parmchk -i mol.ac -f ac -o frcmod", "Parmchk")
+ if n != 0
+ error_message_box("Parmchk failed: status = #{n}.")
+ Dir.chdir(cwd)
+ return n
+ end
+ end
+ Dir.chdir(cwd)
+ n = import_ac("#{tdir}/mol.ac")
+ if n != 0
+ error_message_box("Cannot import antechamber output.")
+ return n
+ end
+ if calc_charge != 0
+ n = import_sqmout("#{tdir}/sqm.out")
+ if n != 0
+ error_message_box("Cannot import sqm output.")
+ return n
+ end
+ end
+ n = import_frcmod("#{tdir}/frcmod")
+ if n != 0
+ error_message_box("Cannot import parmchk output.")
+ return n
+ end
+ log_level = get_global_settings("antechamber.log_level")
+ log_keep_number = get_global_settings("antechamber.log_keep_number")
+ erase_old_logs(tdir, log_level, log_keep_number)
+ return 0
+
+ end
+
def import_ac(acfile)
open(acfile, "r") { |fp|
while (s = fp.gets)
ap.atom_type = type
end
}
+ return 0
end
def import_sqmout(file)
break
end
}
+ return 0
end
def import_frcmod(file)
end
end
}
+ return 0
end
def cmd_import_frcmod
md_menu->Append(myMenuID_Minimize, _T("Minimize..."));
md_menu->Append(myMenuID_StopMDRun, _T("Stop\tCtrl-."));
md_menu->AppendSeparator();
-// md_menu->Append(myMenuID_ReadParameters, _T("Read Parameters..."));
+// md_menu->Append(myMenuID_ReadParameters, _T("Read Parameters..."));
+ md_menu->Append(myMenuID_RunAntechamber, _T("Auto Guess MM/MD Parameters..."));
md_menu->Append(myMenuID_ViewGlobalParameters, _T("View Global Parameters..."));
md_menu->Append(myMenuID_ViewParameterFilesList, _T("Load/Unload Global Parameters..."));
md_menu->AppendSeparator();
md_menu->AppendSeparator();
wxMenu *md_tools_menu = new wxMenu;
- md_tools_menu->Append(myMenuID_RunAntechamber, _T("Antechamber/parmchk..."));
+/* md_tools_menu->Append(myMenuID_RunAntechamber, _T("Antechamber/parmchk...")); */
md_tools_menu->Append(myMenuID_RunResp, _T("GAMESS/RESP..."));
md_tools_menu->Append(myMenuID_CreateSanderInput, _T("Create SANDER input..."));
md_tools_menu->Append(myMenuID_ImportAmberLib, _T("Import AMBER Lib..."));
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