pygauss.tests.test_molecule module

Created on Thu May 14 18:55:52 2015

@author: cjs14

class pygauss.tests.test_molecule.MockFolder[source]

Bases: object

write_file(*arg, **kwargs)[source]
class pygauss.tests.test_molecule.Test_Combine_Molecules[source]

Bases: object

setUp()[source]
test_combine_all()[source]
test_combine_part()[source]
test_combine_to_file()[source]
test_combine_transform()[source]
class pygauss.tests.test_molecule.Test_Freq[source]

Bases: object

setUp()[source]
test_is_conformer()[source]
test_plot_freq()[source]
test_zpe_correction()[source]

zero-point error correction

File extract: Zero-point correction= 0.168038 (Hartree/Particle)

class pygauss.tests.test_molecule.Test_Images[source]

Bases: object

setUp()[source]
test_returns_init()[source]
test_returns_init_with_axes()[source]
test_returns_init_with_ball_stick()[source]
test_returns_init_with_rotations()[source]
test_returns_init_with_wire()[source]
test_returns_nbo_charges()[source]
test_returns_opt()[source]
class pygauss.tests.test_molecule.Test_Init[source]

Bases: object

class pygauss.tests.test_molecule.Test_NBO[source]

Bases: object

File Extracts:

Second Order Perturbation Theory Analysis of Fock Matrix in NBO Basis

Threshold for printing: 0.50 kcal/mol
(Intermolecular threshold: 0.05 kcal/mol)
E(2) E(j)-E(i) F(i,j)

Donor NBO (i) Acceptor NBO (j) kcal/mol a.u. a.u.

within unit 1
  1. CR ( 1) O 1 / 20. RY*( 1) H 2 0.75 19.70 0.108
  1. LP ( 2) O 1 / 21. RY*( 1) H 3 0.62 1.41 0.026
from unit 1 to unit 2
1. BD ( 1) O 1 - H 2 / 23. RY*( 2) O 4 0.05 2.35 0.010 1. BD ( 1) O 1 - H 2 / 27. RY*( 1) H 6 0.07 1.43 0.009 1. BD ( 1) O 1 - H 2 / 36. BD*( 1) O 4 - H 5 0.52 0.95 0.020 1. BD ( 1) O 1 - H 2 / 37. BD*( 1) O 4 - H 6 0.05 0.95 0.006 2. BD ( 1) O 1 - H 3 / 27. RY*( 1) H 6 0.07 1.41 0.009 2. BD ( 1) O 1 - H 3 / 37. BD*( 1) O 4 - H 6 0.08 0.93 0.008

11. LP ( 2) O 1 / 27. RY*( 1) H 6 0.07 1.36 0.009 11. LP ( 2) O 1 / 36. BD*( 1) O 4 - H 5 0.20 0.88 0.012 11. LP ( 2) O 1 / 37. BD*( 1) O 4 - H 6 0.10 0.88 0.008

from unit 1 to unit 3
  1. BD ( 1) O 1 - H 2 / 39. BD*( 1) O 7 - H 9 0.11 1.04 0.010
from unit 2 to unit 1
3. BD ( 1) O 4 - H 5 / 20. RY*( 1) H 2 0.06 1.66 0.009 3. BD ( 1) O 4 - H 5 / 34. BD*( 1) O 1 - H 2 0.36 1.11 0.018 4. BD ( 1) O 4 - H 6 / 16. RY*( 1) O 1 0.08 3.32 0.015 4. BD ( 1) O 4 - H 6 / 20. RY*( 1) H 2 0.27 1.66 0.019 4. BD ( 1) O 4 - H 6 / 34. BD*( 1) O 1 - H 2 0.91 1.11 0.029 8. CR ( 1) O 4 / 20. RY*( 1) H 2 0.06 19.82 0.031 8. CR ( 1) O 4 / 34. BD*( 1) O 1 - H 2 0.26 19.27 0.064
  1. LP ( 2) O 4 / 34. BD*( 1) O 1 - H 2 9.59 1.06 0.091
within unit 2
13. LP ( 2) O 4 / 26. RY*( 1) H 5 0.63 1.45 0.027 13. LP ( 2) O 4 / 27. RY*( 1) H 6 0.63 1.45 0.027
from unit 2 to unit 3
3. BD ( 1) O 4 - H 5 / 28. RY*( 1) O 7 0.08 3.32 0.015 3. BD ( 1) O 4 - H 5 / 33. RY*( 1) H 9 0.27 1.66 0.019 3. BD ( 1) O 4 - H 5 / 39. BD*( 1) O 7 - H 9 0.91 1.11 0.029 4. BD ( 1) O 4 - H 6 / 33. RY*( 1) H 9 0.06 1.66 0.009 4. BD ( 1) O 4 - H 6 / 39. BD*( 1) O 7 - H 9 0.36 1.11 0.018 8. CR ( 1) O 4 / 33. RY*( 1) H 9 0.06 19.82 0.031 8. CR ( 1) O 4 / 39. BD*( 1) O 7 - H 9 0.26 19.27 0.063
  1. LP ( 2) O 4 / 39. BD*( 1) O 7 - H 9 9.49 1.06 0.090
from unit 3 to unit 1
  1. BD ( 1) O 7 - H 9 / 34. BD*( 1) O 1 - H 2 0.11 1.04 0.010
from unit 3 to unit 2
5. BD ( 1) O 7 - H 8 / 26. RY*( 1) H 5 0.08 1.41 0.009 5. BD ( 1) O 7 - H 8 / 36. BD*( 1) O 4 - H 5 0.08 0.93 0.008 6. BD ( 1) O 7 - H 9 / 23. RY*( 2) O 4 0.05 2.35 0.010 6. BD ( 1) O 7 - H 9 / 26. RY*( 1) H 5 0.07 1.43 0.009 6. BD ( 1) O 7 - H 9 / 36. BD*( 1) O 4 - H 5 0.06 0.95 0.006 6. BD ( 1) O 7 - H 9 / 37. BD*( 1) O 4 - H 6 0.52 0.95 0.020

15. LP ( 2) O 7 / 26. RY*( 1) H 5 0.07 1.36 0.009 15. LP ( 2) O 7 / 36. BD*( 1) O 4 - H 5 0.10 0.88 0.009 15. LP ( 2) O 7 / 37. BD*( 1) O 4 - H 6 0.20 0.88 0.012

within unit 3
  1. CR ( 1) O 7 / 33. RY*( 1) H 9 0.75 19.70 0.108
  1. LP ( 2) O 7 / 32. RY*( 1) H 8 0.62 1.41 0.026
setUp()[source]
test_group_energy()[source]
File lines to filter:
  1. CR ( 1) O 7 / 33. RY*( 1) H 9 0.75 19.70 0.108
  1. LP ( 2) O 7 / 32. RY*( 1) H 8 0.62 1.41 0.026
test_hbond_energy()[source]

File lines to filter: 11. LP ( 2) O 1 / 36. BD*( 1) O 4 - H 5 0.20 0.88 0.012

11. LP ( 2) O 1 / 37. BD*( 1) O 4 - H 6 0.10 0.88 0.008 13. LP ( 2) O 4 / 34. BD*( 1) O 1 - H 2 9.59 1.06 0.091 13. LP ( 2) O 4 / 39. BD*( 1) O 7 - H 9 9.49 1.06 0.090 15. LP ( 2) O 7 / 36. BD*( 1) O 4 - H 5 0.10 0.88 0.009 15. LP ( 2) O 7 / 37. BD*( 1) O 4 - H 6 0.20 0.88 0.012
test_no_hbond_energy()[source]
test_total_energy()[source]
class pygauss.tests.test_molecule.Test_Opt[source]

Bases: object

File Extracts:

Standard basis: 6-311+G(d,p) (5D, 7F)
272 basis functions, 429 primitive gaussians, 281 cartesian basis functions

SCF Done: E(RB3LYP) = -805.105260336 A.U. after 11 cycles

Item Value Threshold Converged? Maximum Force 0.000070 0.000450 YES RMS Force 0.000016 0.000300 YES Maximum Displacement 0.001604 0.001800 YES RMS Displacement 0.000326 0.001200 YES

setUp()[source]
test_basis_descript()[source]
test_basis_funcs()[source]
test_is_optimised()[source]
test_optimisation_energy()[source]
test_plot_optimisation()[source]
class pygauss.tests.test_molecule.Test_Orbitals[source]

Bases: object

setUp()[source]
test_orbital_count()[source]
test_orbital_energies
test_orbital_homo_lumo()[source]
test_plot_dos()[source]
test_yield_orbital_images_no_isos()[source]
class pygauss.tests.test_molecule.Test_PES[source]

Bases: object

test_plot_pes
class pygauss.tests.test_molecule.Test_Start[source]

Bases: object

setUp()[source]
test_bad_fname
test_good_fname()[source]
test_wildcard_fname()[source]
pygauss.tests.test_molecule.mock_isosurface(*args, **kwargs)[source]