surface_dialog_attr = @surface_dialog_attr
mol = self
mol.open_auxiliary_window("MO Surface", :resizable=>true, :has_close_box=>true) {
- tags = ["mo_ao", "mo", "color", "opacity", "threshold", "expand", "grid"]
+ tags = ["mo_ao", "mo", "color", "opacity", "threshold", "expand", "grid", "reverse", "basis"]
motype = mol.get_mo_info(:type)
alpha = mol.get_mo_info(:alpha)
beta = mol.get_mo_info(:beta)
ncomps = mol.get_mo_info(:ncomps)
- mo_index = 1
+ mo_index = 0
mo_ao = nil
coltable = [[0,0,1], [1,0,0], [0,1,0], [1,1,0], [0,1,1], [1,0,1], [0,0,0], [1,1,1]]
mo_ao_items = ["Molecular Orbitals", "Atomic Orbitals"]
mo_ao_keys = ["MO", "AO"]
- if (nbo = mol.instance_eval { @nbo }) != nil
+ if (nbo = mol.instance_eval { @nbo }) != nil
nbo.keys.each { |key|
- if key[0..2] == "AO/"
- key2 = key[3..-1]
- name2 = key2
- if key2 == "NAO"
- name2 = "Natural Atomic Orbitals"
- elsif key2 == "NBO"
- name2 = "Natural Bond Orbitals"
- elsif key2 == "NHO"
- name2 = "Natural Hybrid Orbitals"
- elsif key2 == "NLMO"
- name2 = "Natural Localized Molecular Orbitals"
- elsif key2 == "PNAO"
- name2 = "Pre-orthogonal Natural Atomic Orbitals"
- elsif key2 == "PNHO"
- name2 = "Pre-orthogonal Natural Hybrid Orbitals"
- elsif key2 == "PNBO"
- name2 = "Pre-orthogonal Natural Bond Orbitals"
- elsif key2 == "AHO"
- name2 = "Atomic Hybrid Orbitals"
- elsif key2 == "LHO"
- name2 = "Lewis Hybrid Orbitals"
- elsif key2 == "PLHO"
- name2 = "Pre-orthogonal Lewis Hybrid Orbitals"
- elsif key2 == "LPO"
- name2 = "Localized Property-optimized Orbitals"
- elsif key2 == "CLPO"
- name2 = "Chemist's Localized Property-optimized Orbitals"
- end
- mo_ao_items.push(name2)
- mo_ao_keys.push(key2)
- end
- }
+ if key[0..2] == "AO/"
+ key2 = key[3..-1]
+ name2 = key2
+ if key2 == "NAO"
+ name2 = "Natural Atomic Orbitals"
+ elsif key2 == "NBO"
+ name2 = "Natural Bond Orbitals"
+ elsif key2 == "NHO"
+ name2 = "Natural Hybrid Orbitals"
+ elsif key2 == "NLMO"
+ name2 = "Natural Localized Molecular Orbitals"
+ elsif key2 == "PNAO"
+ name2 = "Pre-orthogonal Natural Atomic Orbitals"
+ elsif key2 == "PNHO"
+ name2 = "Pre-orthogonal Natural Hybrid Orbitals"
+ elsif key2 == "PNBO"
+ name2 = "Pre-orthogonal Natural Bond Orbitals"
+ elsif key2 == "AHO"
+ name2 = "Atomic Hybrid Orbitals"
+ elsif key2 == "LHO"
+ name2 = "Lewis Hybrid Orbitals"
+ elsif key2 == "PLHO"
+ name2 = "Pre-orthogonal Lewis Hybrid Orbitals"
+ elsif key2 == "LPO"
+ name2 = "Localized Property-optimized Orbitals"
+ elsif key2 == "CLPO"
+ name2 = "Chemist's Localized Property-optimized Orbitals"
+ end
+ mo_ao_items.push(name2)
+ mo_ao_keys.push(key2)
+ end
+ }
end
mult = (motype == "UHF" ? 2 : 1)
mo_menu = ["1000 (-00.00000000)"] # Dummy entry; create later
tabvals = []
- coeffs = nil
+ coeffs_matrix = nil # Coefficient matrix for showing surface
+ coeffs = nil # Coefficient array for showing surface
+ table_coeffs_matrix = nil # Coefficient matrix for table (based on "basis")
a_idx_old = -1
occ = nil
- ncomps.times { |i|
- a_idx, s_idx, label = mol.get_gaussian_component_info(i)
- if a_idx_old != a_idx
- a_idx_old = a_idx
- a = a_idx.to_s
- n = mol.atoms[a_idx].name
- else
- a = n = ""
- end
- tabvals.push([a, n, label, a_idx])
- }
on_update_attr = lambda {
tags.each { |tag|
surface_dialog_attr[tag] = item_with_tag(tag)[:value]
it[:enabled] = true
end
}
+ update_mo_labels = lambda { |mo_ao_index|
+ m = []
+ if mo_ao_index == 0
+ m = (1..(ncomps * mult)).map { |n|
+ if motype == "UHF"
+ i1 = (n - 1) / 2 + 1
+ i2 = n % 2
+ c1 = (i2 == 0 ? "B" : "A")
+ c2 = (i1 > (i2 == 0 ? beta : alpha) ? "*" : "")
+ else
+ i1 = n
+ i2 = 1
+ c1 = ""
+ if i1 > beta && i1 > alpha
+ c2 = "*"
+ elsif i1 > beta || i1 > alpha
+ c2 = "S"
+ else
+ c2 = ""
+ end
+ end
+ en = mol.get_mo_energy(i1 + (i2 == 0 ? ncomps : 0))
+ sprintf("%d%s%s (%.8f)", i1, c1, c2, en)
+ }
+ elsif mo_ao_index == 1
+ m = []
+ ncomps.times { |i|
+ m[i] = sprintf("%d: %s (%s)", i + 1, tabvals[i][2], mol.atoms[tabvals[i][3]].name)
+ }
+ else
+ m = []
+ key = mo_ao_keys[mo_ao_index]
+ labels = nbo[key + "_L"]
+ if labels == nil && key[0] == ?P
+ labels = nbo[key[1..-1] + "_L"]
+ end
+ ncomps.times { |i|
+ if labels
+ lab = sprintf("%d: %s", i + 1, labels[i])
+ else
+ lab = sprintf("%s%d", key, i + 1)
+ end
+ m[i] = lab
+ }
+ end
+ return m
+ }
on_get_value = lambda { |it, row, col|
- if col < 3
- tabvals[row][col]
- else
- if coeffs == nil
- if mo_ao == 0
- coeffs = mol.get_mo_coefficients(mo_index)
- elsif mo_ao == 1
- coeffs = (0...ncomps).map { |i| (i == mo_index ? 1.0 : 0.0) }
- else
- coeffs = nbo["AO/" + mo_ao_keys[mo_ao]].column(mo_index).to_a[0]
- end
- end
- sprintf("%.6f", coeffs[row])
- end
+ begin
+ if !table_coeffs_matrix || !coeffs_matrix
+ # Update tabvals
+ tabvals = []
+ bs = value("basis")
+ if bs == 0 # AO
+ ncomps.times { |i|
+ a_idx, s_idx, label = mol.get_gaussian_component_info(i)
+ if a_idx_old != a_idx
+ a_idx_old = a_idx
+ a = a_idx.to_s
+ n = mol.atoms[a_idx].name
+ else
+ a = n = ""
+ end
+ tabvals.push([a, n, label, a_idx])
+ }
+ else
+ labels = update_mo_labels.call(bs + 1)
+ ncomps.times { |i|
+ label = labels[i]
+ label = label.gsub(/^\d+: /, "")
+ tabvals.push([(i + 1).to_s, "", label, i])
+ }
+ end
+ # Update coeffs_matrix
+ if !coeffs_matrix
+ # coeffs_matrix = AO/(orbitals_to_display)
+ if mo_ao == 0
+ m = []
+ ncomps.times { |i|
+ mult.times { |j|
+ m.push(mol.get_mo_coefficients(i * mult + j + 1))
+ }
+ }
+ coeffs_matrix = LAMatrix.new(m) # Matrix AO/MO
+ elsif mo_ao == 1
+ coeffs_matrix = LAMatrix.identity(ncomps) # Matrix AO/AO (identity)
+ else
+ coeffs_matrix = nbo["AO/" + mo_ao_keys[mo_ao]]
+ end
+ end
+ # m2 = AO/(basis)
+ if bs == 0 # AO
+ m2 = LAMatrix.identity(ncomps)
+ else
+ m2 = nbo["AO/" + mo_ao_keys[bs + 1]]
+ end
+ # (basis)/(orbitals_to_display)
+ table_coeffs_matrix = m2.inverse * coeffs_matrix
+ end
+ # Update coefficient array
+ if !coeffs
+ coeffs = coeffs_matrix.column(mo_index).to_a[0]
+ end
+ if col < 3
+ tabvals[row][col]
+ else
+ sprintf("%.6f", table_coeffs_matrix[mo_index, row])
+ end
+ rescue => e
+ $stderr.write(e.to_s + "\n")
+ $stderr.write(e.backtrace.inspect + "\n")
+ end
}
- h = {"mo"=>nil, "color"=>nil, "opacity"=>nil, "threshold"=>nil, "expand"=>nil, "grid"=>nil}
+ h = {"mo"=>nil, "color"=>nil, "opacity"=>nil, "threshold"=>nil, "expand"=>nil, "grid"=>nil, "reverse"=>nil, "basis"=>nil }
should_update = true
on_action = lambda { |it|
tag = it[:tag]
color0 = [1,1,1,opac]
mol.set_surface_attr(:color=>color, :color0=>color0)
h[tag] = value
- elsif tag == "threshold"
- thres = it[:value].to_f
+ elsif tag == "threshold" || tag == "reverse"
+ thres = item_with_tag("threshold")[:value].to_f
thres = 0.001 if thres >= 0.0 && thres < 0.001
thres = -0.001 if thres <= 0.0 && thres > -0.001
+ if item_with_tag("reverse")[:value] == 1
+ thres = -thres
+ end
mol.set_surface_attr(:thres=>thres)
h[tag] = value
else
mo = it[:value]
if mo_ao == 0
if motype == "UHF"
- mo_index = (mo / 2) + (mo % 2 == 1 ? ncomps : 0) + 1
- if mo_index <= alpha || (mo_index > ncomps && mo_index <= ncomps + beta)
+ mo_index = (mo / 2) + (mo % 2 == 1 ? ncomps : 0)
+ if mo_index < alpha || (mo_index >= ncomps && mo_index < ncomps + beta)
occ_new = 1
else
occ_new = 0
end
else
- mo_index = mo + 1
- if mo_index <= alpha && mo_index <= beta
+ mo_index = mo
+ if mo_index < alpha && mo_index < beta
occ_new = 1
- elsif mo_index <= alpha || mo_index <= beta
+ elsif mo_index < alpha || mo_index < beta
occ_new = -1
else
occ_new = 0
}
on_set_action = lambda { |it|
if mo_ao != it[:value]
- mo_ao = it[:value]
- if mo_ao == 0
- mo_menu = (1..(ncomps * mult)).map { |n|
- if motype == "UHF"
- i1 = (n - 1) / 2 + 1
- i2 = n % 2
- c1 = (i2 == 0 ? "B" : "A")
- c2 = (i1 > (i2 == 0 ? beta : alpha) ? "*" : "")
- else
- i1 = n
- i2 = 1
- c1 = ""
- if i1 > beta && i1 > alpha
- c2 = "*"
- elsif i1 > beta || i1 > alpha
- c2 = "S"
- else
- c2 = ""
- end
- end
- en = mol.get_mo_energy(i1 + (i2 == 0 ? ncomps : 0))
- sprintf("%d%s%s (%.8f)", i1, c1, c2, en)
- }
- elsif mo_ao == 1
- mo_menu = []
- ncomps.times { |i|
- mo_menu[i] = sprintf("%d: %s (%s)", i + 1, tabvals[i][2], mol.atoms[tabvals[i][3]].name)
- }
- else
- mo_menu = []
- key = mo_ao_keys[mo_ao]
- labels = nbo[key + "_L"]
- if labels == nil && key[0] == ?P
- labels = nbo[key[1..-1] + "_L"]
- end
- ncomps.times { |i|
- if labels
- lab = sprintf("%d: %s", i + 1, labels[i])
- else
- lab = sprintf("%s%d", key, i + 1)
- end
- mo_menu[i] = lab
- }
- end
- it0 = item_with_tag("mo")
- it0[:subitems] = mo_menu
- #it0[:value] = 0 # Keep the mo number invariant
- h["mo"] = nil # "Update" button is forced to be enabled
- on_mo_action.call(it0)
- end
- on_update_attr.call
+ mo_ao = it[:value]
+ mo_menu = update_mo_labels.call(mo_ao)
+ it0 = item_with_tag("mo")
+ val = it0[:value]
+ it0[:subitems] = mo_menu
+ it0[:value] = val # Keep the mo number invariant
+ h["mo"] = nil # "Update" button is forced to be enabled
+ coeffs = nil
+ coeffs_matrix = nil # Matrix needs update
+ on_mo_action.call(it0)
+ end
+ on_update_attr.call
}
+ on_basis_action = lambda { |it|
+ if h["basis"] != value("basis")
+ table_coeffs_matrix = nil
+ item_with_tag("table")[:refresh] = true
+ end
+ }
on_update = lambda { |it|
h.each_key { |key|
h[key] = value(key)
thres = h["threshold"].to_f
thres = 0.001 if thres >= 0.0 && thres < 0.001
thres = -0.001 if thres <= 0.0 && thres > -0.001
+ if h["reverse"] == 1
+ thres = -thres
+ end
expand = h["expand"].to_f
expand = 0.01 if expand < 0.01
expand = 10.0 if expand > 10.0
grid = 10000000
end
if mo_ao == 0
- idx = mo_index
+ idx = mo_index + 1
else
idx = 0
mol.set_mo_coefficients(0, 0.0, coeffs)
item(:textfield, :tag=>"opacity", :width=>80, :value=>"0.8", :action=>on_action),
item(:text, :title=>"Threshold"),
item(:textfield, :tag=>"threshold", :width=>80, :value=>"0.05", :action=>on_action),
- item(:text, :title=>"Box Limit"),
- item(:textfield, :tag=>"expand", :width=>80, :value=>"1.4", :action=>on_action)),
- layout(2,
+ item(:checkbox, :tag=>"reverse", :title=>"Reverse Phase", :action=>on_action),
+ -1),
+ layout(4,
item(:text, :title=>"Number of Grid Points"),
- item(:textfield, :tag=>"grid", :width=>120, :value=>"512000", :action=>on_action)),
- item(:table, :width=>300, :height=>300, :tag=>"table",
- :columns=>[["Atom", 60], ["Name", 60], ["Label", 60], ["Coeff", 120]],
- :on_count=> lambda { |it| tabvals.count },
+ item(:textfield, :tag=>"grid", :width=>80, :value=>"512000", :action=>on_action),
+ item(:text, :title=>"Box Limit"),
+ item(:textfield, :tag=>"expand", :width=>80, :value=>"1.4", :action=>on_action)),
+ # table coefficients are based on "basis" (AO, NAO, etc.)
+ # MO is not allowed as basis, so the "basis" menu begins with "AO"
+ layout(2,
+ item(:text, :title=>"Coeffs based on:"),
+ item(:popup, :tag=>"basis", :subitems=>mo_ao_keys[1..-1], :value=>1, :action=>on_basis_action)),
+ item(:table, :width=>380, :height=>300, :tag=>"table",
+ :columns=>[["Atom", 40], ["Name", 60], ["Label", 140], ["Coeff", 120]],
+ :on_count=> lambda { |it| ncomps },
:on_get_value=>on_get_value,
:flex=>[0,0,0,0,1,1]),
layout(3,
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