fp.print "# Generated by Molby at #{now}\n"
fp.print "import sys\n"
fp.print "import re\n"
+ fp.print "base = re.sub('\\.\\w*$', '', sys.argv[1]) # Basename of the input file\n"
fp.print "molecule mol {\n"
charge = Integer(hash["charge"])
mult = Integer(hash["mult"])
end
runtype = hash['runtype'].downcase
fp.print "energy, wfn = #{runtype}('scf', #{options})\n"
- fp.print "wfn.write_molden(re.sub('\\.\\w*$', '.molden', sys.argv[1]))\n"
+ fp.print "wfn.write_molden(f'{base}.molden')\n"
+ if hash['run_junpa'] != 0
+ fp.print "\n"
+ fp.print "# Interface for JANPA\n"
+ fp.print "# cf. https://sourceforge.net/p/janpa/wiki/psi4Examples/\n"
+ fp.print "d = wfn.Da().to_array()\n"
+ fp.print "s = wfn.S().to_array()\n"
+ fp.print "c = wfn.Ca().to_array()\n"
+ fp.print "occs = c.T.dot(s.dot(d).dot(s).dot(c))\n"
+ fp.print "molden(wfn, f'{base}.da.molden', density_a = psi4.core.Matrix.from_array(occs))\n"
+ end
end
if fname == nil
s = fp.buffer
end
end
+ # Execute JUNPA
+ # inppath is the input file minus extention
+ # mol is the molecule (may be nil)
+ def Molecule.execute_janpa(inppath, mol, spherical)
+ # nbo_desc = # JANPA
+ janpa_dir = "#{ResourcePath}/JANPA"
+ status = 0
+ if spherical
+ cmd1 = "java -jar #{janpa_dir}/molden2molden.jar -NormalizeBF -i #{inppath}.da.molden -o #{inppath}.in.molden >#{inppath}.janpa.log"
+ else
+ cmd1 = "java -jar #{janpa_dir}/molden2molden.jar -frompsi4v1mo -NormalizeBF -cart2pure -i #{inppath}.da.molden -o #{inppath}.in.molden >#{inppath}.janpa.log"
+ end
+ flag = system(cmd1)
+ if flag
+ cmd2 = "java -jar #{janpa_dir}/janpa.jar -i #{inppath}.in.molden"
+ ["nao", "pnao", "aho", "lho", "lpo", "clpo"].each { |type|
+ if (get_global_settings("psi4.#{type}").to_i != 0)
+ cmd2 += " -#{type.upcase}_Molden_File #{inppath}.#{type.upcase}.molden"
+ end
+ }
+ cmd2 += " >>#{inppath}.janpa.log"
+ flag = system(cmd2)
+ end
+ if flag
+ if mol
+ # import JANPA log and molden output
+ # Files: inppath.japa.log, inppath.{NAO,PNAO,AHO,LHO,LPO,CLPO}.molden
+ mol.sub_load_janpa_log(inppath)
+ end
+ else
+ status = $?.exitstatus
+ message_box("Execution of #{procname} failed with status #{status}.", "JANPA Failed")
+ end
+ return status
+ end
+
# Execute Psi4
# inpname is the input file
# mol (optional) is the molecule from which the Psi4 input was built.
hf_type = nil
nalpha = nil
nbeta = nil
+ spherical = false
outfile = inpdir + "/" + inpbody + ".out"
if File.exists?(outfile)
nalpha = Integer($1)
elsif line =~ /^ *Nbeta *= *(\d+)/
nbeta = Integer($1)
+ elsif line =~ /^ *Spherical Harmonics\?: *(\w+)/
+ spherical = ($1 == "true")
end
end
if next_index > 0
# Terminate callback
term_callback = lambda { |m, n|
+ do_janpa = false
begin
msg = "Psi4 execution of #{inpbase} "
hmsg = "Psi4 "
$stderr.write("#{e.backtrace.inspect}\n")
end
end
+ if (get_global_settings("psi4.run_janpa").to_i == 1)
+ do_janpa = true
+ end
elsif n == -1
# The child process actually did not start
# Restore the old file if outbackfile is not nil
if outbackfile && File.exists?(outbackfile)
File.delete(outbackfile)
end
+ if do_janpa
+ Molecule.execute_janpa(inpdir + "/" + inpbody, mol, spherical)
+ end
rescue => e
$stderr.write("#{e.message}\n")
$stderr.write("#{e.backtrace.inspect}\n")
dfttype_desc = ["B3LYP"]
runtype_desc = ["Energy", "Optimize"]
scftype_desc = ["RHF", "ROHF", "UHF"]
-# nbo_desc = ["nao", "nbo", "nho", "nlmo", "pnao", "pnbo", "pnho", "pnlmo"]
+ nbo_desc = ["nao", "pnao", "aho", "lho", "lpo", "clpo"] # JANPA
user_input = Hash.new
defaults = {"scftype"=>0, "runtype"=>0, "move_to_com"=>0, "do_reorient"=>0,
"use_symmetry"=>0, "charge"=>"0", "mult"=>"1",
#item(:line),
#-1, -1, -1,
# ------
- #item(:checkbox, :title=>"Include NBO instructions", :tag=>"include_nbo",
- # :action=>lambda { |it|
- # flag = (it[:value] != 0)
- # nbos.each { |nbo| set_attr(nbo, :enabled=>flag) }
- # }),
- #-1, -1, -1,
+ item(:checkbox, :title=>"Run JANPA after Psi4", :tag=>"run_janpa",
+ :action=>lambda { |it|
+ flag = (it[:value] != 0)
+ nbo_desc.each { |nbo| set_attr(nbo, :enabled=>flag) }
+ }),
+ -1, -1, -1,
# ------
- #item(:checkbox, :title=>"NAO", :tag=>"nao"),
- #item(:checkbox, :title=>"NBO", :tag=>"nbo"),
- #item(:checkbox, :title=>"NHO", :tag=>"nho"),
- #item(:checkbox, :title=>"NLMO", :tag=>"nlmo"),
+ item(:checkbox, :title=>"NAO", :tag=>"nao"),
+ item(:checkbox, :title=>"PNAO", :tag=>"pnao"),
+ item(:checkbox, :title=>"AHO", :tag=>"aho"),
+ item(:checkbox, :title=>"LHO", :tag=>"lho"),
# ------
- #item(:checkbox, :title=>"PNAO", :tag=>"pnao"),
- #item(:checkbox, :title=>"PNBO", :tag=>"pnbo"),
- #item(:checkbox, :title=>"PNHO", :tag=>"pnho"),
- #item(:checkbox, :title=>"PNLMO", :tag=>"pnlmo"),
+ item(:checkbox, :title=>"LPO", :tag=>"lpo"),
+ item(:checkbox, :title=>"CLPO", :tag=>"clpo"),
+ -1, -1,
# ------
item(:line),
-1, -1, -1,
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