https://sourceforge.net/p/janpa/wiki/clpoExample/Recent changes to clpoExampleenSun, 13 Jan 2019 12:37:44 -0000https://sourceforge.net/p/janpa/wiki/clpoExample/<div class="markdown_content"><pre>--- v16 +++ v17 @@ -78,12 +78,11 @@ #### Step 3: running JANPA To analyze the electronic structure of the molecule with JANPA we now run -`java -jar janpa.jar -i input.molden -ignorefock -CLPO_Molden_File CLPO.molden &gt; janpa.log` +`java -jar janpa.jar -i input.molden -CLPO_Molden_File CLPO.molden &gt; janpa.log` This will produce two files: `janpa.log` containing the general output of the program and `CLPO.molden` suitable for orbitals visualization with JMOL. Note: -i) although using the `-ignorefock` key is not mandatory, it is highly recommended for analyzing the orbitals obtained -from a correlated wavefunction, since in this case no 'energies' of the orbitals are available. +i) there was `-ignorefock` option in JANPA versions prior to 2.02. Using this option was highly recommended for analyzing the orbitals obtained from a correlated wavefunction, since in this case no 'energies' of the orbitals are available. For the same reason the default behaviour has been changed in JANPA v. 2.02, so that the Fock matrix is ignored by default. In case if for some reason the Fock matrix analysis is still needed, the option `-doFock` should be used. ii) the `CLPO.molden` file is produced in a correct MOLDEN format and can readily be used for further CLPO orbital visualization. #### Step 4: analyzing the output file </pre> </div>TimNSun, 13 Jan 2019 12:37:44 -0000https://sourceforge.net2abf2a6dc97b0fea74eca5b9405d6457b7b721cahttps://sourceforge.net/p/janpa/wiki/clpoExample/<div class="markdown_content"><pre>--- v15 +++ v16 @@ -87,7 +87,7 @@ ii) the `CLPO.molden` file is produced in a correct MOLDEN format and can readily be used for further CLPO orbital visualization. #### Step 4: analyzing the output file -Lets look into the most essential parts of the [`janpa.log`](http://janpa.sourceforge.net/page_files/clpoExample/janpa.log) log file. +Lets look into the most essential parts of [the `janpa.log` log file](http://janpa.sourceforge.net/page_files/clpoExample/janpa.log). The first thing we need to ensure is that there were no errors in the input file. For that we check the few last lines of the log: ~~~ 0 warning(s) @@ -221,7 +221,7 @@ The `CLPO.molden` file generated by JANPA during the previous step can now be used to visualize the localized orbitals. To this end, [JMOL](https://sourceforge.net/projects/jmol/) program can be used. JMOL can read MOLDEN files -produced by JANPA directly: just use the File -&gt; Open command and chose the [`CLPO.molden`](http://janpa.sourceforge.net/page_files/clpoExample/CLPO.molden). One can then +produced by JANPA directly: just use the File -&gt; Open command and choose [the `CLPO.molden` file](http://janpa.sourceforge.net/page_files/clpoExample/CLPO.molden). One can then proceed with orbital visualization using ContextMenu -&gt; Surfaces -&gt; Molecular orbitals menu. Alternatively, the following commands can be used in JMOL console (ContextMenu -&gt; Console) to plot orbitals: `mo list` </pre> </div>TimNTue, 16 Oct 2018 17:54:40 -0000https://sourceforge.net2f2a9a1ca3740279636468d7faf4cc14c33eb3fbhttps://sourceforge.net/p/janpa/wiki/clpoExample/<div class="markdown_content"><pre>--- v14 +++ v15 @@ -24,6 +24,13 @@ * ~~~ In this example we used B3LYP-D3/def2-TZVP level of theory to obtain the optimized geometry of the molecule and compute its normal vibration frequencies to ensure that the optimized geometry is stable (not a transition state). The ORCA results for this input is [available for download](http://janpa.sourceforge.net/page_files/clpoExample/opt.zip). + +The optimized geometry of the molecule looks like this: + +(note that this visualization uses XYZ Cartesian coordinates of the atoms as the only source of information. +Therefore, it is of no importance whether or not any of the 'sticks' are drawn between the atoms, as well as the number of these 'sticks'. In contrast to that, the bonding analysis involving the localized orbotals performed below does have a relation +to the true pattern of covalent bonding) + *Note however, that we do **not recommended** using the 'orbitals' produced by DFT calculations for bonding analysis - because it is a feature of the most commonly used Kohn-Sham formulation of DFT that these orbitals correspond to an @@ -80,7 +87,7 @@ ii) the `CLPO.molden` file is produced in a correct MOLDEN format and can readily be used for further CLPO orbital visualization. #### Step 4: analyzing the output file -Lets look into the most essential parts of the `janpa.log` log file. +Lets look into the most essential parts of the [`janpa.log`](http://janpa.sourceforge.net/page_files/clpoExample/janpa.log) log file. The first thing we need to ensure is that there were no errors in the input file. For that we check the few last lines of the log: ~~~ 0 warning(s) @@ -214,7 +221,7 @@ The `CLPO.molden` file generated by JANPA during the previous step can now be used to visualize the localized orbitals. To this end, [JMOL](https://sourceforge.net/projects/jmol/) program can be used. JMOL can read MOLDEN files -produced by JANPA directly: just use the File -&gt; Open command and chose the `CLPO.molden`. One can then +produced by JANPA directly: just use the File -&gt; Open command and chose the [`CLPO.molden`](http://janpa.sourceforge.net/page_files/clpoExample/CLPO.molden). One can then proceed with orbital visualization using ContextMenu -&gt; Surfaces -&gt; Molecular orbitals menu. Alternatively, the following commands can be used in JMOL console (ContextMenu -&gt; Console) to plot orbitals: `mo list` </pre> </div>TimNTue, 16 Oct 2018 17:52:43 -0000https://sourceforge.netd3cd4ff4f75989fbdc6511e117091e827c4c4f16https://sourceforge.net/p/janpa/wiki/clpoExample/<div class="markdown_content"><pre>--- v13 +++ v14 @@ -238,8 +238,10 @@ to adjust the contour value to which the isosurface should correspond (the value of 0.1 a.u. was used to produce the isosurfaces shown below). It is also possible to use the `isosurface` command to plot orbitals, e.g., -`` -For more details about these and the other orbital plotting commands, see the JMOL documentation. +`isosurface color yellow dodgerblue cutoff 0.1 resolution 15 mo 15 translucent 0.45` +(some nice-looking [colors ](http://jmol.sourceforge.net/jscolors/)combinations are `[250,187,13] skyblue` , `[255,255,0] [102,204,255]`, `[247,255,71] [113,168,254]`, `[250,187,13] [185,214,248]`, `[250,187,13] blue`, `darkorange skyblue`). In this example the `translucent 0.45` produces 'semi-transparent' isosurfaces and +can be replaced with, e.g., `mesh nofill` to make the 'wireframe' representation as used in the illustrations below. +For more details about these and the other orbital plotting commands, see the [JMOL documentation](https://chemapps.stolaf.edu/jmol/docs/). </pre> </div>TimNTue, 16 Oct 2018 17:39:53 -0000https://sourceforge.netfa9f04138d13c7e149e235e8ca179b9c7c530c88https://sourceforge.net/p/janpa/wiki/clpoExample/<div class="markdown_content"><pre>--- v12 +++ v13 @@ -1,4 +1,4 @@ -#A quick introduction to LPO/CLPO analysis +#A quick practical guide through LPO/CLPO analysis This page presents an example of using LPO/CLPO methods of JANPA to investigate covalent bonding in cyanamide (IUPAC name aminoformonitrile). The structural formula of the molecule is shown below:  @@ -211,6 +211,38 @@ #### Step 5: visualizing the localized orbitals + +The `CLPO.molden` file generated by JANPA during the previous step can now be used to visualize the localized orbitals. +To this end, [JMOL](https://sourceforge.net/projects/jmol/) program can be used. JMOL can read MOLDEN files +produced by JANPA directly: just use the File -&gt; Open command and chose the `CLPO.molden`. One can then +proceed with orbital visualization using ContextMenu -&gt; Surfaces -&gt; Molecular orbitals menu. +Alternatively, the following commands can be used in JMOL console (ContextMenu -&gt; Console) to plot orbitals: +`mo list` +to show the full list of the orbitals, e.g., +~~~ +.............. +model 1.1; mo 8 # energy 7.000 occupancy 6.5700006E-4 beta1a +model 1.1; mo 7 # energy 6.000 occupancy 2.8900002E-4 beta1a +model 1.1; mo 6 # energy 5.000 occupancy 1.998445 beta1a +model 1.1; mo 5 # energy 4.000 occupancy 0.045001 beta1a +model 1.1; mo 4 # energy 3.000 occupancy 1.963944 beta1a +model 1.1; mo 3 # energy 2.000 occupancy 0.004084 beta1a +model 1.1; mo 2 # energy 1.000 occupancy 3.3300003E-4 beta1a +model 1.1; mo 1 # energy 0.000 occupancy 5.5999997E-5 beta1a +~~~ +(note that the occupancies and the orbital numbering here is exactly the same as in the `*** Summary of CLPO results` +table above). +The command +`mo 4` +can then be used to plot the selected orbital (in this case, CLPO 4), while the `mo cutoff 0.1` command can be used +to adjust the contour value to which the isosurface should correspond (the value of 0.1 a.u. was used to produce +the isosurfaces shown below). +It is also possible to use the `isosurface` command to plot orbitals, e.g., +`` +For more details about these and the other orbital plotting commands, see the JMOL documentation. + + + Bonding orbital | Antibonding orbital | Pair of atoms ---------- | ---------- | ------ CLPO 4  | CLPO 5  | C1 - N2 ('sigma') @@ -220,13 +252,28 @@ CLPO 46  | CLPO 47  | N2 - H3 ('sigma') CLPO 48  | CLPO 49  | N2 - H4 ('sigma') -CLPO 6 - -CLPO 39 - -CLPO 50 - -CLPO 97 - -CLPO 98 - +It follows from these bonding orbital isosurfaces that each single bond anticipated from a structural formula +of the molecule is accompained by a localized bonding orbital of 'sigma' symmetry, while the triple +bond (which is usually modeled as a family of one 'sigma' and two 'pi' bonds) between N5 and C1 +additionally includes two bonding orbitals of 'pi' symmetry. +Note that according to the `*** Summary of CLPO results` table given above, occupancies of +all bonding orbitals are very close to 2.0 (they fall in the range between 1.91 to 1.97 electrons), +which agrees with the classical Lewis picture anticipating the bond to formed by the pair of electrons. +Occupancies of antibonding orbitals are, on the other hand, quite low: mainly less than 0.1 electrons, +with the exception of CLPO 17 corresponding to one of N5-C1 'pi' bonds which has occupancy of almost 0.2 electrons +due to a possible conjugation with the lone pair of N2 (represented by CLPO 50, see below). + +Orbital | Comments +---------- | ---------- +CLPO 6  | Core orbital of C1 +CLPO 39  | Core orbital of N2 +CLPO 50  | **Lone pair of N2** +CLPO 97  | **Lone pair of N5** +CLPO 98  | Core orbital of N5 + +It can be seen that there are indeed two ('valence') lone pairs, one per each of the nitrogen atoms in the molecule. +What is more, the spatial orientation of these lone pairs is in good agreement with the hybridization models +of N2 (sp³) and N5 (sp¹) atoms expected from chemical intuition: the lone pair +at N5 is oriented along the same line as N5-C1 bond, while lone pair at N2 follows a 'tetrahedral' direction +along with N2-C1, N2-H3 and N2-H4 bonds. + </pre> </div>TimNTue, 16 Oct 2018 17:07:51 -0000https://sourceforge.neta01f82eee08b21f1dbf52b361d38eb83a7fc4712https://sourceforge.net/p/janpa/wiki/clpoExample/<div class="markdown_content"><pre>--- v11 +++ v12 @@ -213,36 +213,12 @@ #### Step 5: visualizing the localized orbitals Bonding orbital | Antibonding orbital | Pair of atoms ---------- | ---------- | ------ -CLPO 4  | CLPO 5  | C1 -- N2 -Cell | Cell | Cell - - - - -CLPO 13 - -CLPO 14 - - -CLPO 15 - -CLPO 16 - - -CLPO 17 - -CLPO 18 - - -CLPO 46 - -CLPO 47 - - -CLPO 48 - -CLPO 49 - +CLPO 4  | CLPO 5  | C1 - N2 ('sigma') +CLPO 13  | CLPO 14  | C1 - N5 ('sigma') +CLPO 15  | CLPO 16  | C1 - N5 ('first pi') +CLPO 17  | CLPO 18  | C1 - N5 ('second pi') +CLPO 46  | CLPO 47  | N2 - H3 ('sigma') +CLPO 48  | CLPO 49  | N2 - H4 ('sigma') CLPO 6  </pre> </div>TimNTue, 16 Oct 2018 15:50:57 -0000https://sourceforge.net079ce3a4511fa8e1b5f76d8ad20c369125606c99https://sourceforge.net/p/janpa/wiki/clpoExample/<div class="markdown_content"><pre>--- v10 +++ v11 @@ -1,9 +1,11 @@ #A quick introduction to LPO/CLPO analysis -This page presents an example of using LPO/CLPO methods of JANPA to investigate covalent bonding in cyanamide (IUPAC name aminoformonitrile) - - -**1** +This page presents an example of using LPO/CLPO methods of JANPA to investigate covalent bonding in cyanamide (IUPAC name aminoformonitrile). The structural formula of the molecule is shown below: + +It is worth noting that each nitrogen atom typically possesses a so-called 'lone pair' (also callen ['nonbonding electron pair'](https://goldbook.iupac.org/html/L/L03618.html)) commonly designated with two dots: + + +#### Step 1: geometry Above all, we need to obtain the 3D geometry of the molecule. This can be done, for example, by DFT geometry optimization in ORCA ~~~ @@ -30,7 +32,7 @@ In order to generate the true orbitals for subsequent localization we can use MP2 method. -**2** +#### Step 2: the density matrix The following example presents the input file for PSI4 (version 1.2) and uses the optimized geometry from the previous run ~~~ memory 4200 mb @@ -63,11 +65,11 @@ For more information on the structure of this file, see [using Janpa with PSI4](/p/janpa/wiki/psi4Examples) In this example we used MP2(full)/def2-TZVPP level of theory to produce relaxed density matrix and save it as `mp2.molden` file, which can be easily converted to a format appropriate for JANPA input (see below). The PSI4 results for this input is [available for download](http://janpa.sourceforge.net/page_files/clpoExample/mp2.zip). Alternatively, the natural MP2 orbitals corresponding to a relaxed density can be produced with ORCA as well. However, PSI4 is capable of being generalizable to other correlated methods (like CCSD) more straightforwardly, and tharefore was considered to be more appropriate for illustrative purposes here. -**3** - We now need to convert the `mp2.molden` file into the correct MOLDEN format. This can be done by a `molden2molden` program from Janpa package by running a command + +We now need to convert the `mp2.molden` file into the correct MOLDEN format. This can be done by a `molden2molden` program from Janpa package by running a command `java -jar molden2molden.jar -i mp2.molden -o input.molden -normalizebf` -**4** +#### Step 3: running JANPA To analyze the electronic structure of the molecule with JANPA we now run `java -jar janpa.jar -i input.molden -ignorefock -CLPO_Molden_File CLPO.molden &gt; janpa.log` This will produce two files: `janpa.log` containing the general output of the program and `CLPO.molden` suitable @@ -77,7 +79,7 @@ from a correlated wavefunction, since in this case no 'energies' of the orbitals are available. ii) the `CLPO.molden` file is produced in a correct MOLDEN format and can readily be used for further CLPO orbital visualization. -**5** +#### Step 4: analyzing the output file Lets look into the most essential parts of the `janpa.log` log file. The first thing we need to ensure is that there were no errors in the input file. For that we check the few last lines of the log: ~~~ @@ -208,12 +210,14 @@ chemical valencies of the H, C and N atoms constituting the molecule under study. - - -CLPO 4 - -CLPO 5 - +#### Step 5: visualizing the localized orbitals +Bonding orbital | Antibonding orbital | Pair of atoms +---------- | ---------- | ------ +CLPO 4  | CLPO 5  | C1 -- N2 +Cell | Cell | Cell + + + CLPO 13  </pre> </div>TimNTue, 16 Oct 2018 15:43:30 -0000https://sourceforge.net7cff45bbb0f1df73044acb46892d900abb54e737https://sourceforge.net/p/janpa/wiki/clpoExample/<div class="markdown_content"><pre>--- v9 +++ v10 @@ -210,5 +210,43 @@ - - +CLPO 4 + +CLPO 5 + + +CLPO 13 + +CLPO 14 + + +CLPO 15 + +CLPO 16 + + +CLPO 17 + +CLPO 18 + + +CLPO 46 + +CLPO 47 + + +CLPO 48 + +CLPO 49 + + +CLPO 6 + +CLPO 39 + +CLPO 50 + +CLPO 97 + +CLPO 98 + </pre> </div>TimNTue, 16 Oct 2018 11:20:19 -0000https://sourceforge.net0a4a082919f76923db36c15d33ff8c7abf942ce7https://sourceforge.net/p/janpa/wiki/clpoExample/<div class="markdown_content"><pre>--- v8 +++ v9 @@ -199,6 +199,14 @@ That means that CLPOs 4, 13, 15, 17, 46 and 48 describe the covalent bonds connecting the atoms C1-N2, C1-N5, C1-N5, C1-N5, N2-H3 and N2-H4 respectively. In other words, there are some single bods, and a triple bond between C1 and N5 -- in exact agreement with the structural formula of the molecule given above! +In addition to that, CLPOs 6, 39, 50, 97 and 98 are the non-bonding (or 'lone') pairs. As will be evident from the below +visualization of these orbitals, CLPOs 6, 39 and 98 correspond to the 'inner shells' (commonly denoted as 1s²), while +CLPOs 50 and 97 are the lone pairs belonging to the 'valence shells' of nitrogen atoms. This is again in agreement +with our expectations! +Finally, the total number of bonds formed by each atom of the molecule (fiven as the diagonal elements of the +`Number of two-center(2C) orbitals for each pair of atoms` table) agree with the well-known +chemical valencies of the H, C and N atoms constituting the molecule under study. + </pre> </div>TimNTue, 16 Oct 2018 11:17:16 -0000https://sourceforge.net7d32bf0f17c557c8c1940b57e13cad76bf953605https://sourceforge.net/p/janpa/wiki/clpoExample/<div class="markdown_content"><pre>--- v7 +++ v8 @@ -115,9 +115,92 @@ ~~~ reporting the bond orders computed accordign to K.Wiberg definition from the density matrix in NAO basis. - -~~~ - -~~~ +The most essential part of bonding analysis (actually, the CLPO analysis), however, is contained in the lines +~~~ +*** Summary of CLPO results + + CLPO D e s c r i p t i o n Occupancy Composition + 3 C1 (RY) 0.00408 1.0 * h3@C1 + 4 (BD) C1-N2, Io = 0.1950 1.96394 h4@C1 * ( 0.6344) + h35@N2 * ( 0.7730) + 5 C1-N2, antibonding (NB) 0.04500 h4@C1 * (-0.7730) + h35@N2 * ( 0.6344) + 6 (LP) C1 1.99844 1.0 * h5@C1 + 10 C1 (RY) 0.00230 1.0 * h9@C1 + 11 C1 (RY) 0.02158 1.0 * h10@C1 + 12 C1 (RY) 0.00487 1.0 * h11@C1 + 13 (BD) C1-N5, Io = 0.1268 1.96923 h12@C1 * (-0.6608) + h102@N5 * ( 0.7506) + 14 C1-N5, antibonding (NB) 0.02785 h12@C1 * (-0.7506) + h102@N5 * (-0.6608) + 15 (BD) C1-N5, Io = 0.0777 1.91413 h13@C1 * ( 0.6791) + h103@N5 * ( 0.7341) + 16 C1-N5, antibonding (NB) 0.08438 h13@C1 * (-0.7341) + h103@N5 * ( 0.6791) + 17 (BD) C1-N5, Io = 0.1397 1.93044 h14@C1 * ( 0.6559) + h104@N5 * ( 0.7549) + 18 C1-N5, antibonding (NB) 0.18407 h14@C1 * (-0.7549) + h104@N5 * ( 0.6559) + 24 C1 (RY) 0.00385 1.0 * h20@C1 + 25 C1 (RY) 0.00379 1.0 * h21@C1 + 26 C1 (RY) 0.00388 1.0 * h22@C1 + 27 C1 (RY) 0.00515 1.0 * h23@C1 + 38 N2 (RY) 0.00651 1.0 * h34@N2 + 39 (LP) N2 1.99867 1.0 * h36@N2 + 40 N2 (RY) 0.00235 1.0 * h37@N2 + 43 N2 (RY) 0.00181 1.0 * h40@N2 + 44 N2 (RY) 0.00241 1.0 * h41@N2 + 45 N2 (RY) 0.01609 1.0 * h42@N2 + 46 (BD) N2-H3, Io = 0.4098 1.94850 h43@N2 * ( 0.8396) + h65@H3 * ( 0.5432) + 47 N2-H3, antibonding (NB) 0.02417 h43@N2 * ( 0.5432) + h65@H3 * (-0.8396) + 48 (BD) N2-H4, Io = 0.4098 1.94850 h44@N2 * ( 0.8396) + h79@H4 * ( 0.5432) + 49 N2-H4, antibonding (NB) 0.02417 h44@N2 * ( 0.5432) + h79@H4 * (-0.8396) + 50 (LP) N2 1.82926 1.0 * h45@N2 + 56 N2 (RY) 0.00648 1.0 * h51@N2 + 58 N2 (RY) 0.00664 1.0 * h53@N2 + 59 N2 (RY) 0.00554 1.0 * h54@N2 + 60 N2 (RY) 0.00554 1.0 * h55@N2 + 69 H3 (RY) 0.00177 1.0 * h64@H3 + 75 H3 (RY) 0.00174 1.0 * h71@H3 + 82 H4 (RY) 0.00180 1.0 * h78@H4 + 88 H4 (RY) 0.00175 1.0 * h85@H4 + 96 N5 (RY) 0.01168 1.0 * h93@N5 + 97 (LP) N5 1.93003 1.0 * h94@N5 + 98 (LP) N5 1.99866 1.0 * h95@N5 + 100 N5 (RY) 0.00114 1.0 * h97@N5 + 102 N5 (RY) 0.00585 1.0 * h99@N5 + 103 N5 (RY) 0.00564 1.0 * h100@N5 + 104 N5 (RY) 0.00738 1.0 * h101@N5 + 110 N5 (RY) 0.00510 1.0 * h110@N5 + 111 N5 (RY) 0.00514 1.0 * h111@N5 + 112 N5 (RY) 0.00394 1.0 * h112@N5 + 113 N5 (RY) 0.00249 1.0 * h113@N5 + +Note: 74 one-center RY orbitals, each having occupancy below 1.00e-03, + were not printed (use the program option -RyOccPrintThreshold to change this behavior) + Total occupancy of these RY orbitals is 0.02212 + + +Number of two-center(2C) orbitals for each pair of atoms +Centr. A/B 1 2 3 4 5 + 1 ( 4) 1 0 0 3 + 2 ( 3) 1 1 0 + 3 ( 1) 0 0 + 4 ( 1) 0 + 5 ( 3) +VAL: C 4 +VAL: N 3 +VAL: H 1 +VAL: H 1 +VAL: N 3 + +&gt;&gt; CLPO occupancy summary &gt;&gt; + bonding (BD): 11.67473 in 6 oribtals + anti-bonding (NB): 0.38964 in 6 oribtals + 1c-lone pairs (LP): 9.75506 in 5 oribtals + 1c-unoccupied (RY): 0.18037 in 104 oribtals + +Method BD+LP....in NB+RY BD+NB+LP BD+NB+LP+RY trace(D) Sum[Bd^2+Lp^2] ||D||^2 + CLPO 21.42979 11 0.57001 21.81943 21.99980 22.000 41.7730 42.6760 +~~~ + +That means that CLPOs 4, 13, 15, 17, 46 and 48 describe the covalent bonds connecting the atoms C1-N2, +C1-N5, C1-N5, C1-N5, N2-H3 and N2-H4 respectively. In other words, there are some single bods, +and a triple bond between C1 and N5 -- in exact agreement with the structural formula of the molecule given above! + + +  </pre> </div>TimNTue, 16 Oct 2018 11:11:57 -0000https://sourceforge.netd0479a12c20e5ef13ee3f5089303e03a47edb4cc