Différences entre les versions de « VBTutorial1 »

De Workshops
Aller à la navigation Aller à la recherche
Ligne 13 : Ligne 13 :
  
 
= '''Basics of VB theory and XMVB program''' =
 
= '''Basics of VB theory and XMVB program''' =
 +
 +
 +
 +
{| class="collapsible collapsed wikitable"
 +
|-
 +
!<big><big><big>'''Computer exercises'''</big></big></big>
 +
|-
 +
|
 +
== Exercise 1 : Starting up with the H<math>{}_2</math> molecule ==
 +
 +
<big><big><center><font color=orange> '''***** INPUT FILES TO BE FINALIZED *****''' </font></center></big></big>
 +
 +
Two Gamess and XMVB input files for the H<math>{}_2</math> molecule are provided in the ''Exercise'' folder on the tutorial machines :
 +
* the file ''h2-atom.xmi'' input uses the fragment specification in terms of atoms (''frgtyp=atom'') ;
 +
* the file ''h2-sao.xmi'' input uses the fragment specification in terms of symmetry-adapted orbitals (''frgtyp=sao'').
 +
 +
There are VBSCF calculations with the 6-31G(d,p) basis set. Just inspect these inputs, run the gamess-xmvb program (using : ''vbrun h2-atom'' and : ''vbrun h2-sao'', and analyze the outputs.
 +
 +
Then these input files could serve you as templates for the next exercises.
 +
 +
== Exercise 2 : HF molecule : weights and bond energy ==
 +
 +
<big><big><center><font color=orange> '''***** INPUT FILES TO BE FINALIZED *****''' </font></center></big></big>
 +
 +
# Compute a VBSCF three structure wave function for the HF molecule, using the ''frgtyp=sao'' specification and automatic guess (''guess=auto''). Which structure(s) should be kept in further BOVB calculations ?
 +
# Using VBSCF orbitals as guess orbitals :
 +
## Compute a L-BOVB wave function on a selected subset of structures ;
 +
## Compute a VBCISD wave function for the multi-structure wave function
 +
## Compare structure weights at the VBSCF, L-BOVB and VBCI levels
 +
# Compute bond energies at the L-BOVB and VBCISD levels.
 +
 +
{| class="collapsible collapsed wikitable"
 +
|-
 +
!'''Remark'''
 +
|-
 +
|
 +
We do not recommend to use the ''frgtyp=atom'' specification together with the automatic guess (''guess=auto''). With ''frgtyp=atom'' you should specify orbital guess from HF MOs through an extra $gus section (see manual, and next exercises).
 +
|}
 +
 +
{| class="collapsible collapsed wikitable"
 +
|-
 +
!'''Hints'''
 +
|-
 +
|
 +
* To compute the bond energy at the BOVB level, you can simply use the ROHF energies computed with Gamess for the separate H and F atoms, as the L-BOVB wave function dissociate to uncorrelated H+F fragments.
 +
* To compute the bond energy at the VBCISD level, you should however compute the separate fragments at this level of theory.
 +
|}
 +
 +
== Exercise 3 : F<math>{}_2</math> molecule and charge-shift resonance energy ==
 +
 +
<big><big><center><font color=orange> '''***** INPUT FILES TO BE FINALIZED *****''' </font></center></big></big>
 +
 +
# Compute a VBSCF wave function for the F<math>{}_2</math> molecule, using the cc-pvtz basis set, and with inactive orbitals localized on only one of the fluorine atoms ;
 +
## first the ''frgtyp=sao'' specification and automatic guess (''guess=auto'') ;
 +
## second the ''frgtyp=atom'' specification and providing HF MOs as guess orbital through an extra $Gus section in the xmvb input
 +
# D-BOVB level :
 +
## Compute a L-BOVB wave function using VBSCF orbitals as guess orbitals ;
 +
## Starting from the previous solution, compute a D-BOVB solution, by allowing only the inactive to delocalize onto the two atoms, while the active orbitals are kept frozen. Compare total energy with the previous level.
 +
# π-D-BOVB level :
 +
## Recompute a π-D-BOVB solution for the F<math>{}_2</math> molecule (see : [[General_guidelines_for_BOVB_calculations#High_symmetry_case:| >> see "high symmetry case" in the "general guidelines for BOVB calculations"]].
 +
## Compare the total energy and weights with the previous level.
 +
# We want to calculate the charge-shift resonance energy (RE_<sub>CS</sub>) for the F<math>{}_2</math> molecule. For that, we have to compute a VB wave-function corresponding to a single covalent structure, and take the energy difference with the full (covalent+ionic) wave-function.
 +
## Compute a purely covalent wave function for F<math>{}_2</math> at the VBSCF level. What would be the L-BOVB solution ?
 +
## Compute a purely covalent wave function for F<math>{}_2</math> at the D-BOVB level.
 +
## Deduce the RE_<sub>CS</sub> at the VBSCF, L-BOVB and D-BOVB. Compare it with the experimental bond energy : ~40 kcal/mol).
 +
 +
 +
<big>[[General_guidelines_for_BOVB_calculations| >> general guidelines for BOVB calculations]]</big>
 +
 +
 +
<font color=red>'''If you have not finished these first three exercises by the end of tutorial session 1, we recommend that after having completed them you move directly to [[VBTutorial2|tutorial 2]]'''</font>
 +
 +
 +
== Exercice 4 (optional) : Solvent effect on C(Me)<math>{}_3</math>-Cl weights ==
 +
 +
<big><big><center><font color=red> '''***** INPUT FILES TO BE WRITTEN *****''' </font></center></big></big>
 +
 +
# C(Me)<math>{}_3</math>-Cl at equilibrium geometry :
 +
## Compute a VBSCF wave function using ''frgtyp=atom'' and a $Gus section to specify guess orbitals. The active electron pair will be the C-Cl bond, and all inactive orbitals should be localized either on Cl or on the C(Me3) fragment. Which structures should be kept in further BOVB calculations ?
 +
## Redo the VBSCF calculation reading the orbital file obtained at the previous step as guess file, and now requesting a boys localization (keyword : ''boys''). Compare the VBSCF orbitals obtained with and without the ''boys'' keyword (you can use the ''moldendat'' utility and them ''molden'' to display them).
 +
## Compute a L-BOVB wave function.
 +
## Compute a D-BOVB wave function, by freezing the active orbitals, and delocalizing all inactive orbitals onto the whole molecule (see also : [[General_guidelines_for_BOVB_calculations| >> general guidelines for BOVB calculations]]).
 +
# Starting from guess orbitals obtained at equilibrium geometry, redo the D-BOVB calculation for the large inter fragment distance. How does the weights of the different structures evolve when the molecule is stretched ?
 +
# Redo the D-BOVB calculations at equilibrium geometry and large distance using VBPCM for water. How does the weights change with solvation effects ?
 +
 +
{| class="collapsible collapsed wikitable"
 +
|-
 +
!''Hints and remarks''
 +
|-
 +
|
 +
* It is strongly advisable to use the ''boys'' keyword at the VBSCF step, as it will provide more physically meaningful orbitals for the next BOVB calculations (the same remark would hold with VBCI)
 +
* To reperform D-BOVB at large interatomic distances (question n°2), you have to proceed in two steps :
 +
** starting from the orbitals converged at equilibrium distances (question n°1.3) as a guess : reperform a L-BOVB first at large interatomic distances ;
 +
** then, starting from the orbitals just obtained as a guess do a D-BOVB calculation.
 +
* Same remark for solvent calculations : you can start from converged gas phase L-BOVB orbitals as guess, but you'll have first to reperform L-BOVB and then D-BOVB.
 +
|}
 +
 +
|}
  
  
Ligne 21 : Ligne 119 :
 
|  
 
|  
  
 
+
==Exercise 5 : '''The lone pairs of H<sub>2</sub>O'''==
==Exercise 1 : '''The lone pairs of H<sub>2</sub>O'''==
 
  
  
Ligne 151 : Ligne 248 :
  
 
|}
 
|}
 
 
{| class="collapsible collapsed wikitable"
 
|-
 
!<big><big><big>'''Computer exercises'''</big></big></big>
 
|-
 
|
 
== Exercise 2 : Starting up with the H<math>{}_2</math> molecule ==
 
 
<big><big><center><font color=orange> '''***** INPUT FILES TO BE FINALIZED *****''' </font></center></big></big>
 
 
Two Gamess and XMVB input files for the H<math>{}_2</math> molecule are provided in the ''Exercise'' folder on the tutorial machines :
 
* the file ''h2-atom.xmi'' input uses the fragment specification in terms of atoms (''frgtyp=atom'') ;
 
* the file ''h2-sao.xmi'' input uses the fragment specification in terms of symmetry-adapted orbitals (''frgtyp=sao'').
 
 
There are VBSCF calculations with the 6-31G(d,p) basis set. Just inspect these inputs, run the gamess-xmvb program (using : ''vbrun h2-atom'' and : ''vbrun h2-sao'', and analyze the outputs.
 
 
Then these input files could serve you as templates for the next exercises.
 
 
== Exercise 3 : HF molecule : weights and bond energy ==
 
 
<big><big><center><font color=orange> '''***** INPUT FILES TO BE FINALIZED *****''' </font></center></big></big>
 
 
# Compute a VBSCF three structure wave function for the HF molecule, using the ''frgtyp=sao'' specification and automatic guess (''guess=auto''). Which structure(s) should be kept in further BOVB calculations ?
 
# Using VBSCF orbitals as guess orbitals :
 
## Compute a L-BOVB wave function on a selected subset of structures ;
 
## Compute a VBCISD wave function for the multi-structure wave function
 
## Compare structure weights at the VBSCF, L-BOVB and VBCI levels
 
# Compute bond energies at the L-BOVB and VBCISD levels.
 
 
{| class="collapsible collapsed wikitable"
 
|-
 
!'''Remark'''
 
|-
 
|
 
We do not recommend to use the ''frgtyp=atom'' specification together with the automatic guess (''guess=auto''). With ''frgtyp=atom'' you should specify orbital guess from HF MOs through an extra $gus section (see manual, and next exercises).
 
|}
 
 
{| class="collapsible collapsed wikitable"
 
|-
 
!'''Hints'''
 
|-
 
|
 
* To compute the bond energy at the BOVB level, you can simply use the ROHF energies computed with Gamess for the separate H and F atoms, as the L-BOVB wave function dissociate to uncorrelated H+F fragments.
 
* To compute the bond energy at the VBCISD level, you should however compute the separate fragments at this level of theory.
 
|}
 
 
== Exercise 4 : F<math>{}_2</math> molecule and charge-shift resonance energy ==
 
 
<big><big><center><font color=orange> '''***** INPUT FILES TO BE FINALIZED *****''' </font></center></big></big>
 
 
# Compute a VBSCF wave function for the F<math>{}_2</math> molecule, using the cc-pvtz basis set, and with inactive orbitals localized on only one of the fluorine atoms ;
 
## first the ''frgtyp=sao'' specification and automatic guess (''guess=auto'') ;
 
## second the ''frgtyp=atom'' specification and providing HF MOs as guess orbital through an extra $Gus section in the xmvb input
 
# D-BOVB level :
 
## Compute a L-BOVB wave function using VBSCF orbitals as guess orbitals ;
 
## Starting from the previous solution, compute a D-BOVB solution, by allowing only the inactive to delocalize onto the two atoms, while the active orbitals are kept frozen. Compare total energy with the previous level.
 
# π-D-BOVB level :
 
## Recompute a π-D-BOVB solution for the F<math>{}_2</math> molecule (see : [[General_guidelines_for_BOVB_calculations#High_symmetry_case:| >> see "high symmetry case" in the "general guidelines for BOVB calculations"]].
 
## Compare the total energy and weights with the previous level.
 
# We want to calculate the charge-shift resonance energy (RE_<sub>CS</sub>) for the F<math>{}_2</math> molecule. For that, we have to compute a VB wave-function corresponding to a single covalent structure, and take the energy difference with the full (covalent+ionic) wave-function.
 
## Compute a purely covalent wave function for F<math>{}_2</math> at the VBSCF level. What would be the L-BOVB solution ?
 
## Compute a purely covalent wave function for F<math>{}_2</math> at the D-BOVB level.
 
## Deduce the RE_<sub>CS</sub> at the VBSCF, L-BOVB and D-BOVB. Compare its value computed at the D-BOVB level with the bond energy (Experimental : ~40 kcal/mol).
 
 
== Exercice 5 : Solvent effect on C(Me)<math>{}_3</math>-Cl weights ==
 
 
<big><big><center><font color=red> '''***** INPUT FILES TO BE WRITTEN *****''' </font></center></big></big>
 
 
# C(Me)<math>{}_3</math>-Cl at equilibrium geometry :
 
## Compute a VBSCF wave function using ''frgtyp=atom'' and a $Gus section to specify guess orbitals. The active electron pair will be the C-Cl bond, and all inactive orbitals should be localized either on Cl or on the C(Me3) fragment. Which structures should be kept in further BOVB calculations ?
 
## Redo the VBSCF calculation reading the orbital file obtained at the previous step as guess file, and now requesting a boys localization (keyword : ''boys''). Compare the VBSCF orbitals obtained with and without the ''boys'' keyword (you can use the ''moldendat'' utility and them ''molden'' to display them).
 
## Compute a L-BOVB wave function.
 
## Compute a D-BOVB wave function, by freezing the active orbitals, and delocalizing all inactive orbitals onto the whole molecule (see also : [[General_guidelines_for_BOVB_calculations| >> general guidelines for BOVB calculations]]).
 
# Starting from guess orbitals obtained at equilibrium geometry, redo the D-BOVB calculation for the large inter fragment distance. How does the weights of the different structures evolve when the molecule is stretched ?
 
# Redo the D-BOVB calculations at equilibrium geometry and large distance using VBPCM for water. How does the weights change with solvation effects ?
 
 
{| class="collapsible collapsed wikitable"
 
|-
 
!''Hints and remarks''
 
|-
 
|
 
* It is strongly advisable to use the ''boys'' keyword at the VBSCF step, as it will provide more physically meaningful orbitals for the next BOVB calculations (the same remark would hold with VBCI)
 
* To reperform D-BOVB at large interatomic distances (question n°2), you have to proceed in two steps :
 
** starting from the orbitals converged at equilibrium distances (question n°1.3) as a guess : reperform a L-BOVB first at large interatomic distances ;
 
** then, starting from the orbitals just obtained as a guess do a D-BOVB calculation.
 
* Same remark for solvent calculations : you can start from converged gas phase L-BOVB orbitals as guess, but you'll have first to reperform L-BOVB and then D-BOVB.
 
|}
 
 
|}
 
 
 
<big>[[General_guidelines_for_BOVB_calculations| >> general guidelines for BOVB calculations]]</big>
 

Version du 3 juillet 2012 à 19:12

<< Return to the program


How to modify this page :

  • first : log in (top right of this page) ;
  • click on [edit] (far right) to edit a section of the page ;
  • write your text directly in the wiki page, and click on the "Save page" button (bottom left) to save your modifications

Pictures : how to insert a picture in your text

See also this page for an introduction to the basics of the wiki syntax


Basics of VB theory and XMVB program