end
break if i < ncomps # no MO info was found
end
- # TODO: reorder D, F, G coefficients for Molby order
next
end # end if
end # end while
# and load from it (i.e. use the basis set converted by molden2molden)
def sub_load_janpa_log(inppath)
begin
+ m2name_p = {0=>"x", 1=>"y", -1=>"z"}
+ m2name_d = {0=>"zz-rr", 1=>"xz", -1=>"yz", 2=>"xx-yy", -2=>"xy"}
+ m2name_f = {0=>"z3-zr2", 1=>"xz2-xr2", -1=>"yz2-yr2", 2=>"x2z-y2z", -2=>"xyz", 3=>"x3-xy2", -3=>"x2y-y3"}
+ m2name_g = {0=>"z4-z2r2+r4", 1=>"xz3-xzr2", -1=>"yz3-yzr2", 2=>"(x2-y2)(z2-r2)", -2=>"xyz2-xyr2", 3=>"x3z-xy2z", -3=>"x2yz-y3z", 4=>"x4-x2y2+y4", -4=>"x3y-xy3"}
fp = File.open(inppath + ".janpa.log", "rt") rescue fp = nil
if fp == nil
hide_progress_panel # Close if it is open
ang_num = Integer($5)
orb_desc = orb_sym
if orb_desc == "p"
- orb_desc += ["z", "x", "y"][ang_num + 1]
+ orb_desc += m2name_p[ang_num]
elsif orb_desc == "d"
- # TODO: handle d, f, g orbitals
+ orb_desc += m2name_d[ang_num]
+ elsif orb_desc == "f"
+ orb_desc += m2name_f[ang_num]
+ elsif orb_desc == "g"
+ orb_desc += m2name_g[ang_num]
end
h["NAO"].push([num, anum, occupied, group_num, orb_desc, occ])
nao_num = h["NAO"].length
((nao_infos[anum - 1] ||= Hash.new)[orb_desc] ||= []).unshift([nao_num, occ])
end
- # Create labels
+ # Create labels and reorder
+ # h["NAOold2new"][i] = j, h["NAOnew2old"][j] = i
+ # where i is the original NAO number, and j is reordered NAO number (0-based)
+ # NAOs are ordered by (1) atom, (2) principle, (3) orbital, (4) original index
h["NAO_L"] = []
+ reorder = []
nao_infos.each_with_index { |value, atom_index|
aname = self.atoms[atom_index].name
value.each { |orb_desc, ar|
end
principle = group_index + 1
orb_sym = orb_desc[0]
+ orb = 0
if orb_sym == "p"
principle += 1
+ orb = 1
elsif orb_sym == "d"
principle += 2
+ orb = 2
elsif orb_sym == "f"
principle += 3
+ orb = 3
elsif orb_sym == "g"
principle += 4
+ orb = 4
end
- h["NAO_L"][v[0] - 1] = "#{aname} (#{principle}#{orb_desc}) (#{label})"
+ h["NAO_L"][v[0] - 1] = "#{aname} (#{principle}#{orb_desc}) (#{label}, \##{v[0]})"
+ reorder[v[0] - 1] = [atom_index, principle, orb, v[0] - 1]
}
}
}
+ reorder = reorder.sort { |a, b| a[0] != b[0] ? a[0] <=> b[0] : (a[1] != b[1] ? a[1] <=> b[1] : (a[2] != b[2] ? a[2] <=> b[2] : a[3] <=> b[3])) }
+ h["NAOnew2old"] = []
+ h["NAOold2new"] = []
+ reorder.each_with_index { |a, i|
+ j = a[3]
+ h["NAOnew2old"][i] = j
+ h["NAOold2new"][j] = i
+ }
elsif line =~ /^\s*(C?)LPO\s+D e s c r i p t i o n\s+Occupancy\s+Composition/
if $1 == "C"
key = "CLPO"
key = "LPO"
end
h[key] = []
+ reorder = []
+ reorder_h = [] # Reorder of LHO (for key == "CLPO")
while line = getline.call
break if line =~ /^\s*$/
num = Integer(line[0, 5])
label1 = "(NB)"
desc2 = $1.strip
end
+ label1.gsub!(/[\(\)]/, "") # Strip parens
atoms = desc1.scan(/[A-Za-z]+(\d+)/) # "C1-H3" -> [["1"], ["3"]]
atoms = atoms.map { |a| Integer(a[0]) } # [1, 3]
hybrids_a = comp.scan(/h(\d+)@[A-Za-z]+(\d+)/) # "h8@C1...h13@H3" -> "[["8", "1"], ["13", "3"]]
hybrids[i] = Integer(a[0])
end
} # [8, 13]
- # like ["(BD)", [1, 3], "Io = 0.2237", occ, [8, 13]]
+ # like ["BD", [1, 3], "Io = 0.2237", occ, [8, 13]]
# 1, 3 are the atom indices (1-based)
# 8, 13 are the number of hybrid orbitals (1-based)
h[key][num - 1] = [label1, atoms, desc2, Float(occ), hybrids]
end
nao_num.times { |i|
val = h[key][i]
+ r = [100, nil, nil, i] # reorder elements
+ rh = [] # reorder elements for LHOs
if val == nil
label = "" # The labels for Rydberg orbitals may be replaced later
+ r[0] = 100 # Rydberg orbitals are sorted in the back
else
aname1 = self.atoms[val[1][0] - 1].name rescue aname1 = ""
aname2 = self.atoms[val[1][1] - 1].name rescue aname2 = ""
if aname2 == ""
- label = "#{aname1} #{val[0]}"
+ label = "#{aname1} (#{val[0]}, \##{i + 1})"
else
- label = "#{aname1}(#{aname2}) #{val[0]}"
+ label = "#{aname1}(#{aname2}) (#{val[0]}, \##{i + 1})"
end
+ r[0] = (val[0] == "LP" ? 1 : (val[0] == "BD" ? 2 : 3))
+ r[1] = val[1][0]
+ r[2] = val[1][1] or -1
end
h[key + "_L"][i] = label
- if key == "CLPO" && val != nil && val[0] != "(NB)"
+ reorder[i] = r
+ if key == "CLPO" && val != nil && val[0] != "NB"
hybrids = val[4]
- kind = (val[0] == "(BD)" ? "(val)" : "(lp)")
+ kind = (val[0] == "BD" ? "val" : "lp")
+ rh[0] = (val[0] == "BD" ? 2 : 1)
+ rh[1] = val[1][0]
+ rh[2] = val[1][1] or -1
if aname2 == ""
- label = "#{aname1} #{kind}"
+ label = "#{aname1} (#{kind}, \##{hybrids[0]})"
else
- label = "#{aname1}(#{aname2}) #{kind}"
+ label = "#{aname1}(#{aname2}) (#{kind}, \##{hybrids[0]})"
end
h["LHO_L"][hybrids[0] - 1] = label
+ rh[3] = hybrids[0] - 1
+ reorder_h[hybrids[0] - 1] = rh
if hybrids[1] != nil
# aname2 should be non-empty
- label = "#{aname2}(#{aname1}) #{kind}"
+ label = "#{aname2}(#{aname1}) (#{kind}, \##{hybrids[1]})"
h["LHO_L"][hybrids[1] - 1] = label
+ reorder_h[hybrids[1] - 1] = [rh[0], rh[2], rh[1], hybrids[1] - 1]
end
end
}
+ reorder = reorder.sort { |a, b| a[0] != b[0] ? a[0] <=> b[0] : (a[1] != b[1] ? a[1] <=> b[1] : (a[2] != b[2] ? a[2] <=> b[2] : a[3] <=> b[3])) }
+ h[key + "new2old"] = []
+ h[key + "old2new"] = []
+ reorder.each_with_index { |a, i|
+ j = a[3]
+ h[key + "new2old"][i] = j
+ h[key + "old2new"][j] = i
+ }
+ if key == "CLPO"
+ nao_num.times { |i|
+ if reorder_h[i] == nil
+ reorder_h[i] = [100, 0, 0, i]
+ end
+ }
+ reorder_h = reorder_h.sort { |a, b| a[0] != b[0] ? a[0] <=> b[0] : (a[1] != b[1] ? a[1] <=> b[1] : (a[2] != b[2] ? a[2] <=> b[2] : a[3] <=> b[3])) }
+ h["LHOnew2old"] = []
+ h["LHOold2new"] = []
+ reorder_h.each_with_index { |a, i|
+ j = a[3]
+ h["LHOnew2old"][i] = j
+ h["LHOold2new"][j] = i
+ }
+ end
elsif line =~ /^ -NAO_Molden_File: (\S*)/
mfiles["NAO"] = $1
elsif line =~ /^ -LHO_Molden_File: (\S*)/
res = sub_load_molden(fp, key)
if res
# Some kind of orbital based on AO
+ # Reorder the orbitals and labels
+ if key == "NAO" || key == "PNAO"
+ old2new = h["NAOold2new"]
+ elsif key == "LPO"
+ old2new = h["LPOold2new"]
+ elsif key == "CLPO"
+ old2new = h["CLPOold2new"]
+ elsif key == "AHO" || key == "LHO"
+ old2new = h["LHOold2new"]
+ end
+ if old2new
+ mo = []
+ nao_num.times { |i|
+ mo[old2new[i]] = res[:mo][i]
+ }
+ res[:mo] = mo
+ if h[key + "_L"]
+ labels = h[key + "_L"]
+ newlabels = []
+ nao_num.times { |i|
+ newlabels[old2new[i]] = labels[i]
+ }
+ h[key + "_L"] = newlabels
+ end
+ end
h["AO/#{key}"] = LAMatrix.new(res[:mo])
end
fp.close
# Set the label of Rydberg orbitals if possible
if h[key + "_L"] != nil
a = h["AO/#{key}"]
+ new2old = h[key + "new2old"]
nao_num.times { |i|
label = h[key + "_L"][i]
if label == ""
+ # Sum for all orbitals belonging to each atom
+ # and look for the 'most significant' atom
max_idx = nil
max_val = -1.0
+ old2new = h["NAOold2new"]
nao_infos.each_with_index { |inf, atom_index|
atomic_contrib = 0.0
inf.each { |k, v| # k is "s", "px" etc, v is array of [nao_num, occupancy]
# Sum for all naos belonging to this atom
v.each { |num_occ|
- atomic_contrib += a[i, num_occ[0] - 1] ** 2
+ n = num_occ[0] - 1
+ n = old2new[n] if old2new
+ atomic_contrib += a[i, n] ** 2
}
}
if atomic_contrib > max_val
max_idx = atom_index
end
}
- label = self.atoms[max_idx].name + " (ry)"
+ j = (new2old ? new2old[i] : i)
+ label = self.atoms[max_idx].name + " (ryd, \##{j + 1})"
h[key + "_L"][i] = label
end
}
@nbo["AO/PLHO"] = nil
end
end
+ if @nbo["AO/AHO"] && @nbo["LHO_L"]
+ # Copy labels from LHO
+ @nbo["AHO_L"] = @nbo["LHO_L"].dup
+ end
return true
rescue => e
$stderr.write(e.message + "\n")
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