end
# mol.set_mo_info should be set before calling this function
- def sub_load_molden(fp)
+ # Optional label is for importing JANPA output: "NAO" or "CPLO"
+ # If label is not nil, then returns a hash containing the following key/value pairs:
+ # :atoms => an array of [element_symbol, seq_num, atomic_num, x, y, z] (angstrom)
+ # :gto => an array of an array of [sym, [ex0, c0, ex1, c1, ...]]
+ # :moinfo => an array of [sym, energy, spin (0 or 1), occ]
+ # :mo => an array of [c0, c1, ...]
+ def sub_load_molden(fp, label = nil)
getline = lambda { @lineno += 1; return fp.gets }
bohr = 0.529177210903
errmsg = nil
ncomps = 0 # Number of components (AOs)
occ_alpha = 0 # Number of occupied alpha orbitals
occ_beta = 0 # Number of occupied beta orbitals
+ if label
+ hash = Hash.new
+ end
catch :ignore do
while line = getline.call
if line =~ /^\[Atoms\]/
if line =~ /^[A-Z]/
# element, index, atomic_number, x, y, z (in AU)
a = line.split(' ')
- if atoms[i].atomic_number != Integer(a[2]) ||
- (atoms[i].x - Float(a[3]) * bohr).abs > 1e-4 ||
- (atoms[i].y - Float(a[4]) * bohr).abs > 1e-4 ||
- (atoms[i].z - Float(a[5]) * bohr).abs > 1e-4
- errmsg = "The atom list does not match the current molecule."
- throw :ignore
+ if label
+ (hash[:atoms] ||= []).push([a[0], Integer(a[1]), Integer(a[2]), Float(a[3]) * bohr, Float(a[4]) * bohr, Float(a[5]) * bohr])
+ else
+ if atoms[i].atomic_number != Integer(a[2]) ||
+ (atoms[i].x - Float(a[3]) * bohr).abs > 1e-4 ||
+ (atoms[i].y - Float(a[4]) * bohr).abs > 1e-4 ||
+ (atoms[i].z - Float(a[5]) * bohr).abs > 1e-4
+ errmsg = "The atom list does not match the current molecule."
+ throw :ignore
+ end
end
i += 1
else
elsif line =~ /^\[GTO\]/
shell = 0
atom_index = 0
+ if label
+ gtos = []
+ hash[:gto] = []
+ end
while line = getline.call
# index, 0?
a = line.split(' ')
raise MolbyError, "Unknown gaussian shell type '#{a[0]}' at line #{@lineno} in MOLDEN file"
end
nprimitives = Integer(a[1])
+ if label
+ gtoline = [sym, []]
+ gtos.push(gtoline)
+ end
nprimitives.times { |i|
line = getline.call # exponent, contraction
b = line.split(' ')
+ if label
+ gtoline[1].push(Float(b[0]), Float(b[1]))
+ end
add_gaussian_primitive_coefficients(Float(b[0]), Float(b[1]), 0.0)
}
# end of one shell
- add_gaussian_orbital_shell(atom_index, sym, nprimitives)
+ if label == nil
+ add_gaussian_orbital_shell(atom_index, sym, nprimitives)
+ end
shell += 1
ncomps += n
end
# end of one atom
atom_index += 1
+ if label
+ hash[:gto].push(gtos)
+ end
end
redo # The next line will be the beginning of the next block
elsif line =~ /^\[MO\]/
m = []
idx_alpha = 1 # set_mo_coefficients() accepts 1-based index of MO
idx_beta = 1
+ if label
+ hash[:mo] = []
+ hash[:moinfo] = []
+ end
while true
# Loop for each MO
m.clear
occ_beta += 1
end
end
+ if label
+ hash[:moinfo].push([sym, ene, (spin == "Alpha" ? 0 : 1), occ])
+ end
elsif line =~ /^ *([0-9]+) +([-+.0-9e]+)/
m[i] = Float($2)
i += 1
idx_beta += 1
end
set_mo_coefficients(idx, ene, m)
+ if label
+ hash[:mo].push(m.dup)
+ end
break
end
else
end # end catch
if errmsg
message_box("The MOLDEN file was found but not imported. " + errmsg, "Psi4 import info", :ok)
- return false
+ return (label ? nil : false)
end
- return true
+ return (label ? hash : true)
end
-
+
+ # Import the JANPA log and related molden files
+ # Files: inppath.{NAO.molden,CLPO.molden,janpa.log}
+ def sub_load_janpa_log(inppath)
+ begin
+ fp = File.open(inppath + ".janpa.log", "rt") rescue fp = nil
+ if fp == nil
+ message_box("Cannot open JANPA log file #{inppath + '.janpa.log'}: " + $!.to_s)
+ return false
+ end
+ print("Importing #{inppath}.janpa.log.\n")
+ lineno = 0
+ getline = lambda { lineno += 1; return fp.gets }
+ h = Hash.new
+ mfiles = Hash.new
+ while line = getline.call
+ if line =~ /^NAO \#/
+ h["NAO"] = []
+ while line = getline.call
+ break if line !~ /^\s*[1-9]/
+ num = Integer(line[0, 5])
+ name = line[5, 21]
+ occ = Float(line[26, 11])
+ # like A1*: R1*s(0)
+ # atom_number, occupied?, shell_number, orb_sym, angular_number
+ name =~ /\s*[A-Z]+([0-9]+)(\*?):\s* R([0-9]+)\*([a-z]+)\(([-0-9]+)\)/
+ anum = Integer($1)
+ occupied = $2
+ shell_num = Integer($3)
+ orb_sym = $4
+ ang_num = Integer($5)
+ h["NAO"].push([num, anum, occupied, shell_num, orb_sym, ang_num, occ])
+ end
+ elsif line =~ /^\s*CLPO\s+D e s c r i p t i o n\s+Occupancy\s+Composition/
+ h["CLPO"] = []
+ while line = getline.call
+ break if line =~ /^\s*$/
+ num = Integer(line[0, 5])
+ label1 = line[5, 6].strip
+ desc = line[11, 30].strip
+ desc =~ /\s*([-A-Za-z0-9]+)(,\s*(.*$))?/
+ desc1 = $1
+ desc2 = ($3 || "")
+ if desc2 =~ /^(.*)*\(NB\)\s*$/ && label1 == ""
+ label1 = "(NB)"
+ desc2 = $1.strip
+ end
+ # like ["(BD)", "C1-H3", "Io = 0.2237"]
+ h["CLPO"][num - 1] = [label1, desc1, desc2]
+ end
+ elsif line =~ /^ -NAO_Molden_File: (\S*)/
+ mfiles["NAO"] = $1
+ elsif line =~ /^ -LHO_Molden_File: (\S*)/
+ mfiles["LHO"] = $1
+ elsif line =~ /^ -CLPO_Molden_File: (\S*)/
+ mfiles["CLPO"] = $1
+ elsif line =~ /^ -PNAO_Molden_File: (\S*)/
+ mfiles["PNAO"] = $1
+ elsif line =~ /^ -AHO_Molden_File: (\S*)/
+ mfiles["AHO"] = $1
+ elsif line =~ /^ -LPO_Molden_File: (\S*)/
+ mfiles["LPO"] = $1
+ end
+ end
+ fp.close
+ # Read molden files
+ mfiles.each { |key, value|
+ fp = Kernel.open(value, "rt") rescue fp = nil
+ if fp
+ print("Importing #{value}.\n")
+ res = sub_load_molden(fp, key)
+ if res
+ # Some kind of orbital based on AO
+ h["AO/#{key}"] = LAMatrix.new(res[:mo])
+ end
+ fp.close
+ end
+ }
+ @nbo = h
+ return true
+ rescue => e
+ $stderr.write(e.message + "\n")
+ $stderr.write(e.backtrace.inspect + "\n")
+ end
+ end
+
def loadout(filename)
retval = false
fp = open(filename, "rb")
retval = sub_load_psi4_log(fp)
if retval
# If .molden file exists, then try to read it
- mname = filename.gsub(/\.\w*$/, ".molden")
+ namepath = filename.gsub(/\.\w*$/, "")
+ mname = "#{namepath}.molden"
if File.exists?(mname)
fp2 = open(mname, "rb")
if fp2
flag = sub_load_molden(fp2)
fp2.close
+ status = (flag ? 0 : -1)
end
end
+ if File.exists?("#{namepath}.janpa.log")
+ flag = sub_load_janpa_log(namepath)
+ status = (flag ? 0 : -1)
+ end
end
break
end
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