Class: Chem::G98::Link
- Inherits:
-
Object
- Object
- Chem::G98::Link
- Defined in:
- lib/chem/db/g98.rb
Instance Attribute Summary collapse
-
#default_link ⇒ Object
Returns the value of attribute default_link.
-
#goto ⇒ Object
readonly
Returns the value of attribute goto.
-
#jump_link ⇒ Object
Returns the value of attribute jump_link.
-
#major_number ⇒ Object
readonly
Returns the value of attribute major_number.
-
#minor_number ⇒ Object
readonly
Returns the value of attribute minor_number.
-
#next_link ⇒ Object
Returns the value of attribute next_link.
-
#parameters ⇒ Object
readonly
Returns the value of attribute parameters.
-
#stop ⇒ Object
Returns the value of attribute stop.
Instance Method Summary collapse
-
#initialize(major, minor, parameters, goto, gr) ⇒ Link
constructor
A new instance of Link.
- #parameter_to_s ⇒ Object
- #process(lines) ⇒ Object
- #to_s ⇒ Object
Constructor Details
#initialize(major, minor, parameters, goto, gr) ⇒ Link
Returns a new instance of Link.
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# File 'lib/chem/db/g98.rb', line 30 def initialize major, minor, parameters, goto, gr @major_number = major @minor_number = minor @parameters = parameters @goto = goto @gaussian_result = gr end |
Instance Attribute Details
#default_link ⇒ Object
Returns the value of attribute default_link.
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# File 'lib/chem/db/g98.rb', line 29 def default_link @default_link end |
#goto ⇒ Object (readonly)
Returns the value of attribute goto.
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# File 'lib/chem/db/g98.rb', line 29 def goto @goto end |
#jump_link ⇒ Object
Returns the value of attribute jump_link.
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# File 'lib/chem/db/g98.rb', line 28 def jump_link @jump_link end |
#major_number ⇒ Object (readonly)
Returns the value of attribute major_number.
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# File 'lib/chem/db/g98.rb', line 29 def major_number @major_number end |
#minor_number ⇒ Object (readonly)
Returns the value of attribute minor_number.
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# File 'lib/chem/db/g98.rb', line 29 def minor_number @minor_number end |
#next_link ⇒ Object
Returns the value of attribute next_link.
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# File 'lib/chem/db/g98.rb', line 28 def next_link @next_link end |
#parameters ⇒ Object (readonly)
Returns the value of attribute parameters.
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# File 'lib/chem/db/g98.rb', line 29 def parameters @parameters end |
#stop ⇒ Object
Returns the value of attribute stop.
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# File 'lib/chem/db/g98.rb', line 28 def stop @stop end |
Instance Method Details
#parameter_to_s ⇒ Object
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# File 'lib/chem/db/g98.rb', line 44 def parameter_to_s s = '' @parameters.each do |key, value| s = s + key.to_s + '(' + value.to_s + ') ' end return s end |
#process(lines) ⇒ Object
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# File 'lib/chem/db/g98.rb', line 51 def process lines case (@major_number * 100 + @minor_number) when 101 # Initializes program and controls overlaying lines.proceed 3 n_atoms = 0 @gaussian_result.atoms = atoms = Hash.new if lines.next_line.split.length < 2 # Z-Matrix @gaussian_result.has_z_matrix_coordinate = true var = Hash.new atoms_tmp = Array.new while /^ \w+/ =~ lines.next_line lines.proceed atoms_tmp.push lines.now n_atoms = n_atoms + 1 if lines.now.split[0] != 'X' end lines.proceed if /Variables:/ =~ lines.now lines.proceed while /^ \w+/ =~ lines.now sp = lines.now.split var[sp[0]] = sp[1].to_f lines.proceed end end n = 1 atoms_tmp.each do |atom_line| atom = G98Atom.new n_atoms, @gaussian_result atom_array = atom_line.split atom.element = atom_array[0] if atom_array.length >= 2 if /\d/ !~ atom_array[2] length = var[atom_array[2]] else length = atom_array[2].to_f end atom.distance(atoms[atom_array[1].to_i], length) end if atom_array.length >= 4 if /\d/ !~ atom_array[4] angle = var[atom_array[4]] else angle = atom_array[4].to_f end atom.angle(atoms[atom_array[3].to_i], angle) end if atom_array.length >= 7 if /\d/ !~ atom_array[6] angle_a = var[atom_array[6]] else angle_a = atom_array[6].to_f end if /\d/ !~ atom_array[7] angle_b = var[atom_array[7]] else angle_b = atom_array[7].to_f end atom.dihedral(atoms[atom_array[5].to_i], angle_a, angle_b) end atoms[n] = atom n = n + 1 end else # Cartessian Matrix @gaussian_result.has_cartessian_coordinate = true while /^ \w+/ =~ lines.next_line && / The following ModRedundant/ !~ lines.next_line lines.proceed atom_array = lines.now.split atom = G98Atom.new n_atoms + 1, @gaussian_result atom.element, atom.x, atom.y, atom.z = atom_array atoms[n_atoms + 1] = atom n_atoms = n_atoms + 1 if lines.now.split[0] != 'X' end end @gaussian_result.n_atoms = n_atoms @gaussian_result.atoms = atoms lines.proceed # @stop = true when 103 # Berny optimization to minima and TS, STQN transition state searches @next_link = @jump_link if @jump_link lines.proceed 2 while /GradGradGrad/ !~ lines.now if(/ Optimization completed./ =~ lines.now) # if(/ Predicted change in Energy=/ =~ lines.now && / Optimization completed./ =~ lines.next_line) @next_link = @default_link end lines.proceed end # lines.proceed 2 # lines.proceed while / Predicted change in Energy=/ !~ lines.now # puts lines.now # is_loop = true if / Optimization completed./ =~ lines.now # # lines.proceed while /^ Predicted change in Energy=/ !~ lines.now # # lines.proceed # # is_loop = true if / Optimization completed./ =~ lines.now # lines.proceed while /GradGradGrad/ !~ lines.now lines.proceed when 105 # MS optimization when 106 # Numerical differentiation of forces/dipoles to obtain polarizability/hyperpolarizability when 107 # Linear-synchronous-transit (LST) transition state search when 108 # Potential energy surface scan when 109 # Newton-Raphson optimization when 110 # Double numerical differentiation of energies to produce frequencies when 111 # Double num. diff. of energies to compute polarizabilities & hyperpolarizabilities when 113 # EF optimization using analytic gradients when 114 # EF numerical optimization (using only energies) when 115 # Follows reaction path using the intrinsic reaction coordinate (IRC) when 116 # Numerical self-consistent reaction field (SCRF) when 117 # Post-SCF SCRF when 118 # Trajectory calculations when 120 # Controls ONIOM calculations when 202 # Reorients coordinates, calculates symmetry, and checks variable # IOp(15) : Symmetry control. # 1: Unconditionally turn symmetry off. Note that Symm is still called, and will determine the # framework group. However, the molecule is not oriented. while / Stoichiometry/ !~ lines.now && /Error/ !~ lines.now lines.proceed end if /Error/ =~ lines.now lines.proceed 6 return end @gaussian_result.stoichiometry = lines.now.split[1] lines.proceed @gaussian_result.symmetricity = lines.now.split[2] if /KH/ !~ @gaussian_result.symmetricity unless @parameters.has_key?(15) && @parameters[15] == 1 lines.proceed while /Standard orientation:/ !~ lines.now lines.proceed 5 1.upto @gaussian_result.n_atoms do |num| o_array = lines.now.split @gaussian_result.atoms[o_array[0].to_i].x = o_array[3].to_f @gaussian_result.atoms[o_array[0].to_i].y = o_array[4].to_f @gaussian_result.atoms[o_array[0].to_i].z = o_array[5].to_f lines.proceed end lines.proceed end while(/^ Isotopes:/ !~ lines.now) lines.proceed end while /-$/ =~ lines.now || /,\D+-\d/ =~ lines.next_line lines.proceed end lines.proceed else lines.proceed 3 end when 301 # Generate basis set information @gaussian_result.standard_basis = lines.now.split(':')[1].chop # Standard basis: VSTO-3G (5D, 7F) lines.proceed if / Basis set in the form of general basis input:/ =~ lines.now # with GFINPUT Keyword (24=10) while /^$/ !~ lines.next_line lines.proceed # 1 0 end lines.proceed 2#^$ end while / There are/ =~ lines.now lines.proceed end lines.proceed while /\d+ basis functions/ !~ lines.now @gaussian_result.n_orbitals = lines.now.split[0].to_i lines.proceed @gaussian_result.n_electron = lines.now.split[0].to_i lines.proceed @gaussian_result.nuclear_repulsion_energy = lines.now.split[3].to_f lines.proceed when 302 # Calculates overlap, kinetic, and potential integrals lines.proceed 3 # No discrimination between 302 and 303. More Gaussian results needed! when 303 # Calculates multipole integrals ; when 308 # Computes dipole velocity and RxD integrals when 309 # Computes ECP integrals when 310 # Computes spdf 2-electron integrals in a primitive fashion when 311 # Computes sp 2-electron integrals when 314 # Computes spdf 2-electron integrals when 316 # Prints 2-electron integrals when 319 # Computes 1-electron integrals for approximate spin orbital coupling when 401 # Forms the initial MO guess @gaussian_result.guess = lines.now.chop if @gaussian_result.guess == nil# Projected INDO Guess. lines.proceed if / Initial guess orbital symmetries:/ =~ lines.now lines.proceed 2 while /\(A.\)/ =~ lines.now lines.proceed end end when 402 # Performs semi-empirical and molecular mechanics calculations while / Dipole moment=/ !~ lines.now lines.proceed end lines.now.split[4].to_f# Assertive Programming lines.proceed when 405 # Initializes an MCSCF calculation when 502 # Iteratively solves the SCF equations (conven. UHF & ROHF, all direct methods, SCRF) lines.proceed while / SCF Done:/ !~ lines.now @gaussian_result.energy = lines.now.split[4].to_f lines.proceed lines.now.split[5].to_f lines.proceed 2 # lines.proceed if / Axes restored/ =~ lines.now if / Annihilation of the first spin contaminant:/ =~ lines.now lines.proceed 2 end if / Final SCRF E-Field is:/ =~ lines.now lines.proceed 15 end if /---------/ =~ lines.now && /DeltaG/ =~ lines.next_line # if /---------/ =~ lines.now while /DeltaG/ !~ lines.now lines.proceed end @gaussian_result.scrf_delta_g = lines.now.split[4].to_f lines.proceed 2 end # lines.proceed when 503 # Iteratively solves the SCF equations using direct minimization when 506 # Performs an ROHF or GVB-PP calculation when 508 # Quadratically convergent SCF program when 510 # MC-SCF when 601 # Population and related analyses (including multipole moments) # puts 'l601 : '+ lines.now # lines.proceed # puts 'l601 : '+ lines.now # lines.proceed # puts 'l601 : '+ lines.now # lines.proceed # puts 'l601 : '+ lines.now # lines.proceed 4 lines.proceed 7 if / Orbital Symmetries:/ =~ lines.now lines.proceed while / electronic state/ !~ lines.now lines.proceed end lines.proceed while / Alpha / =~ lines.now || / Beta / =~ lines.now if / Molecular Orbital Coefficients/ =~ lines.now if(@parameters.has_key?(7))# Population = Full n = @gaussian_result.n_orbitals / 5.0 n_orbital_col = n.ceil else n_orbital_col = 2 end lines.proceed # Molecular Orbital Coefficients last_occupy_or_virtual = '' 1.upto(n_orbital_col) do |cycle| lines.proceed # 1 2 3 4 5 mo_array = lines.now.split 0.upto( mo_array.length - 1 ) do |n_mo| /\((.+)\)/ =~ mo_array[n_mo] ; sym = $+ /\)--(.)/ =~ mo_array[n_mo] occupy_or_virtual = ($+ != nil ? $+ : mo_array[n_mo]) @gaussian_result.mo[(cycle - 1) * 5 + n_mo] = MolecularOrbital.new(((cycle - 1) * 5 + n_mo), sym, occupy_or_virtual) if last_occupy_or_virtual == 'O' && occupy_or_virtual == 'V' @gaussian_result.homo = @gaussian_result.mo[(cycle - 1) * 5 + n_mo - 1] @gaussian_result.lumo = @gaussian_result.mo[(cycle - 1) * 5 + n_mo] elsif(@gaussian_result.homo == nil && n_orbital_col == cycle && mo_array.length - 1 == n_mo) # No LUMO ! Example Br- @gaussian_result.homo = @gaussian_result.mo[(cycle - 1) * 5 + n_mo - 1] @gaussian_result.lumo = nil end last_occupy_or_virtual = occupy_or_virtual end lines.proceed ev_array = lines.now.split 0.upto (ev_array.length - 3) do |n_ev| @gaussian_result.mo[(cycle - 1) * 5 + n_ev].eigen_value = ev_array[n_ev + 2].to_f end lines.proceed 1.upto(@gaussian_result.n_orbitals) do | num | coef_array = [lines.now[0..3].strip, lines.now[5..8].strip, lines.now[9..10].strip, lines.now[11..21].strip] 0.upto (mo_array.length - 1) do |n_mo| coef_array << lines.now[(21 + n_mo*10)..(31 + n_mo*10)] end plus = 0 # if /^[[:alpha:]]+/ =~ coef_array[2] if coef_array[1] != '' atom = @gaussian_result.atoms[coef_array[1].to_i] end 1.upto( mo_array.length ) do |n_ao| atom.ao(coef_array[3]).push(coef_array[n_ao + 2].to_i) @gaussian_result.mo[(cycle - 1) * 5 + n_ao - 1].push([atom.index, coef_array[3]], coef_array[3 + n_ao].to_f) # @gaussian_result.mo[(cycle - 1) * 5 + n_ao].push(coef_array[n_ao + plus + 2].to_f) end lines.proceed end end lines.proceed # DENSITY MATRIX. density_time = @gaussian_result.n_orbitals while(density_time >0) lines.proceed # 1 2 3 4 5 lines.proceed density_time density_time = density_time - 5 end lines.proceed # Full Mulliken population analysis: mulliken_time = @gaussian_result.n_orbitals while(mulliken_time > 0) lines.proceed # 1 2 3 4 5 lines.proceed mulliken_time mulliken_time = mulliken_time - 5 end lines.proceed # Gross orbital populations: 1.upto(@gaussian_result.n_orbitals) do |num| lines.proceed end lines.proceed # Condensed to atoms (all electrons): end n = (@gaussian_result.n_atoms) / 6.0 if /Condensed to / =~ lines.now lines.proceed if / 1/ =~ lines.now # BUG of Gaussian98 !? 1.upto(n.ceil) do |num| @gaussian_result.exist_condensed_to_atom = true lines.proceed 1.upto(@gaussian_result.n_atoms) do |nn| array = lines.now.split 1.upto(array.length - 2) do |col| @gaussian_result.atoms[array[0].to_i].density[(num - 1)* 6 + col] = array[col + 1].to_f end lines.proceed end end end end lines.proceed 2 1.upto(@gaussian_result.n_atoms) do | num | @gaussian_result.atoms[lines.now.split[0].to_i].total_atomic_charge = lines.now.split[2].to_f lines.proceed end @gaussian_result.sum_of_mulliken_charge = lines.now.split[4].to_f lines.proceed lines.proceed # Atomic charges with hydrogens summed into heavy atoms: lines.proceed # 1 1.upto(@gaussian_result.n_atoms) do |num| @gaussian_result.atoms[lines.now.split[0].to_i].heavy_charge = lines.now.split[2].to_f lines.proceed end lines.proceed if /Atomic-Atomic Spin Densities./ =~ lines.now lines.proceed n = @gaussian_result.n_atoms / 6.0 1.upto n.ceil do |num| lines.proceed @gaussian_result.n_atoms end lines.proceed lines.proceed # Total atomic spin densities: lines.proceed # 1 lines.proceed @gaussian_result.n_atoms lines.proceed if /Isotropic Fermi / =~ lines.now lines.proceed 1.upto(@gaussian_result.n_atoms) do |num| lines.proceed end end lines.proceed end # if(@parameters.has_key?(7) && (@parameters[7] == 3 || @parameters[7] == 2)) if/ Electronic spatial extent/ =~ lines.now # if(@parameters.has_key?(28)) @gaussian_result.electronic_spatial_extent = lines.now.split[5].to_f lines.proceed 3 @gaussian_result.dipole_moment_total = lines.now.split[7].to_f lines.proceed while / N-N=/ !~ lines.now lines.proceed if / Symmetry/ =~ lines.now lines.proceed while / Symmetry/ =~ lines.now end end if /Exact polarizability/ =~ lines.now lines.now.split[7].to_f #Assertive programming ;) lines.proceed while /Thermochemistry/ != lines.now lines.proceed while / TOTAL BOT/ !~ lines.now lines.proceed while / ROTATIONAL/ !~ lines.now lines.proceed end # @stop = true when 602 # 1-electron properties (potential, field, and field gradient) when 604 # Evaluates MOs or density over a grid of points lines.proceed while / LenV=/ !~ lines.now when 607 # Performs NBO analyses when 608 # Non-iterative DFT energies when 609 # Atoms in Molecules properties when 701 # 1-electron integral first or second derivatives lines.proceed if /solvent charges in/ =~ lines.now when 702 # 2-electron integral first or second derivatives (sp) lines.proceed if /Density matrix is not symmetric/ =~ lines.now when 703 # 2-electron integral first or second derivatives (spdf) when 709 # Forms the ECP integral derivative contribution to gradients when 716 # Processes information for optimizations and frequencies # ***** Axes restored to original set ***** lines.proceed if /Axes restored/ =~ lines.now if /Rotating electric field/ =~ lines.now lines.proceed while /Axes restored/ !~ lines.now lines.proceed end lines.proceed # ------------------------------------------------------------------- lines.proceed # Center Atomic Forces (Hartrees/Bohr) lines.proceed # Number Number X Y Z lines.proceed # ------------------------------------------------------------------- 1.upto(@gaussian_result.n_atoms) do |num| lines.now.split[4].to_f #Assertive Programming ;) lines.proceed end lines.proceed # ------------------------------------------------------------------- lines.proceed # Cartesian Forces: Max 2.919256220 RMS 1.058248881 when 801 # Initializes transformation of 2-electron integrals lines.proceed 2 when 802 # Performs integral transformation (N3 in-core) when 803 # Complete basis set (CBS) extrapolation when 804 # Integral transformation # if /^$/ =~ lines.now # lines.proceed 3 # **** Warning!!: The largest alpha MO coefficient is 0.39613240D+02 # else # lines.proceed # Estimate disk for full transformation 8758468 words. # end while !(/ANorm/ =~ lines.now && /^ E2=/ =~ lines.next_line) lines.proceed end lines.proceed 2 when 811 # Transforms integral derivatives & computes their contributions to MP2 2nd derivatives lines.proceed # Form MO integral derivatives with frozen-active canonical formalism. lines.proceed # MDV= 6291456. lines.proceed # Discarding MO integrals. lines.proceed # Reordered first order wavefunction length = 176418 lines.proceed if /In DefCFB/ =~ lines.now lines.proceed if /Large arrays: / =~ lines.now when 901 # Anti-symmetrizes 2-electron integrals when 902 # Determines the stability of the Hartree-Fock wavefunction when 903 # Old in-core MP2 when 905 # Complex MP2 when 906 # Semi-direct MP2 # puts 'l906 : ' + lines.now # lines.proceed 12 lines.proceed while / E2 =/ !~ lines.now lines.proceed when 908 # OVGF (closed shell) when 909 # OVGF (open shell) when 913 # Calculates post-SCF energies and gradient terms while /^ QCISD\(T\)=/ !~ lines.now lines.proceed end lines.proceed 1 when 914 # CI-Single, RPA and Zindo excited states; SCF stability lines.proceed while / state/ !~ lines.now lines.proceed n_state = 0 while / Ground to excited state/ !~ lines.now n_state = n_state + 1 lines.proceed end while / Excitation energies and oscillator strengths:/ !~ lines.now lines.proceed end 1.upto n_state do |num| lines.proceed while / Excited State / !~ lines.now lines.proceed lines.proceed while /\d+ ->/ =~ lines.now end when 915 # Computes fifth order quantities (for MP5, QCISD (TQ) and BD (TQ)) when 918 # Reoptimizes the wavefunction when 1002 # Iteratively solves the CPHF equations; computes various properteis # lines.proceed while /degrees of freedom in the / !~ lines.now # lines.proceed # Petite list used in FoFDir. # lines.proceed #MinBra= 0 MaxBra= 2 Meth= 1. # lines.proceed #IRaf= 0 NMat= 1 IRICut= 1 DoRegI=T DoRafI=F ISym2E= 1 JSym2E=1. # lines.proceed while /vectors were produced by pass/ =~ lines.now while /Inverted reduced A of dimension/ !~ lines.now lines.proceed end lines.proceed if / Calculating GIAO nuclear magnetic shielding tensors./ =~ lines.now 1.upto @gaussian_result.n_atoms do |num| lines.proceed while /Eigenvalues:/ !~ lines.now lines.proceed end end # while /^$/ !~ lines.now # lines.proceed # end # end # lines.proceed when 1003 # Iteratively solves the CP-MCSCF equations when 1014 # Computes analytic CI-Single second derivatives when 1101 # Computes 1-electron integral derivatives when 1102 # Computes dipole derivative integrals when 1110 # 2-electron integral derivative condition to F lines.proceed if /G2DrvN: will do/ =~ lines.now lines.proceed if /FoFDir used for/ =~ lines.now when 1111 # 2 PDM and post-SCF derivatives when 1112 # MP2 second derivatives lines.proceed if /R2 and R3 integrals will be/ =~ lines.now lines.proceed while / Incrementing Polarizabilities/ !~ lines.now lines.proceed 2 when 9999 # Finalizes calculation and output while !lines.eof? if / Normal termination/ =~ lines.now # puts ' ****** Normal termination ****** ' end lines.proceed end @stop = true else puts 'Not implemented Link Number!!' printf " major : %d minor : %d\n", @major_number, @minor_number,to_s end rescue puts 'exception at ' + (@major_number * 100 + @minor_number).to_s raise end |
#to_s ⇒ Object
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# File 'lib/chem/db/g98.rb', line 41 def to_s sprintf("%2d%02d %2s ", @major_number, @minor_number, @goto.to_s) + parameter_to_s end |