wiki - User contributions [en]

Ibarramyes

2026-05-22T08:43:21Z

Wikiadmin:

==lab marking==
You have a good working wiki. It would be good if you round off reported values to correct significant figures and report values of wavenumber in your answers as well. If you have any specific questions, do email Prof. Hunt

==NH3 Molecule==
===calculation data===
{| class="wikitable"
|Name of submitted log file|| NH3_OPTF_POP_MI_CHEM307.LOG
|-
|Molecule|| NH3
|-
|Method|| RB3LYP
|-
|Basis set|| 6-31G(d,p)
|-
|Final energy||-56.557769
|-
|RMS gradient|| 1.53e-07
|-
|Point group|| C3v
|}

===Item Table===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000015 YES
RMS Force 0.000000 0.000010 YES
Maximum Displacement 0.000003 0.000060 YES
RMS Displacement 0.000001 0.000040 YES

</pre>

===Optimized molecule image===
[[File:MI_nh3smaller.png]]

===Jmol rotatable molecule===
logfile: [[Media:NH3_OPTF_POP_MI_CHEM307.LOG]]
<jmol><jmolApplet>
<title>Optimized NH3 molecule</title>
<color>#d5b3ff</color>
<size>200</size>
<uploadedFileContents>NH3_OPTF_POP_MI_CHEM307.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Important geometric parameters===
Optimized bond distance and angle for NH3 
r(N-H)=1.018Â 
θ (H-N-H)=106°

===Logfile Information===
<pre>
Low frequencies --- -5.6864 -3.6131 -3.6124 -0.0014 0.0045 0.0162
Low frequencies --- 1089.3674 1693.9284 1693.9284
</pre>

{| class="wikitable"
|Mode || 1|| 2|| 3|| 4|| 5|| 6
|-
|wavenumber(cm-1)||1089 || 1693|| 1693 || 3461|| 3589|| 3589
|-
|Symmetry || A1|| E|| E|| A1|| E|| E
|-
|intensity(arbitrary units)|| 145|| 14|| 14|| 1|| 0.3|| 0.3
|-
|}

===IR Spectrum of NH3===
[[File:MI_IRspectra_nh3.PNG]]

===Charge Analysis of NH3===
[[File:MI_nh3ChargeAnalysisFull.PNG ]]

{| class="wikitable"
| Atom ||charge
|-
| N|| 0.375
|-
| H|| -1.125
|-
|}

==N2F2 Molecule==
===Calculation Data===
{| class="wikitable"
|Name of submitted log file||MI_N2F2_OPTF_POP_CHEM307.LOG
|-
|Molecule|| N2F2
|-
|Method|| RB3LYP
|-
|Basis set|| 6-31G(d,p)
|-
|Final energy||-309.01241
|-
|RMS gradient|| 3.17e-07
|-
|Point group|| C2v
|}

===Item Table and Low Frequencies===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000001 0.000015 YES
RMS Force 0.000000 0.000010 YES
Maximum Displacement 0.000001 0.000060 YES
RMS Displacement 0.000001 0.000040 YES

</pre>

<pre>
Low frequencies --- 0.0005 0.0005 0.0013 3.2233 4.3533 5.0998
Low frequencies --- 347.8772 561.2472 771.6105
</pre>

===Optimized molecule image===
[[File:MI_N2F2image.png]]

===Jmol rotatable molecule===
logfile: [[Media:MI_N2F2_OPTF_POP_CHEM307.LOG]]
<jmol><jmolApplet>
<title>Optimized N2F2 molecule</title>
<color>#edd1ff</color>
<size>200</size>
<uploadedFileContents>MI_N2F2_OPTF_POP_CHEM307.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Important geometric parameters===
Optimized bond distance and angle for N2F2 
r(N-F)=1.391Â 
r(N=N)1.220Â 
θ (F-N=N)=35°

===Logfile Information===

{| class="wikitable"
|Mode || 1|| 2|| 3|| 4|| 5|| 6
|-
|wavenumber(cm-1)||348 || 561|| 772 || 949|| 987|| 1637
|-
|Symmetry || A1|| A2|| B2|| A1|| B2|| A1
|-
|intensity(arbitrary units)|| 0.6|| 0|| 75|| 75|| 81|| 21
|-
|}

===IR Spectrum of N2F2===
[[File:MI_N2F2_IRspectra.PNG]]

===Charge Analysis of N2F2===

[[File:MI_N2F2_ChargeAnalysis.PNG ]]

{| class="wikitable"
| Atom ||charge
|-
| N|| 0.215
|-
| F|| -0.215
|-
|}

===Molecular Orbitals===
[[File:MI_N2F2_MO9.PNG |350px ]] [[File:MI_n2f2_LCAO.jpg |350px ]]

=== Additional Questions about N2F2===

Q. How many vibrations are expected from the 3N-6 rule? 
A. N2F2 has 4 atoms, therefore 3(4)-6=6; so 6 vibrations are expected. 
 
Q. Why are there only 4 peaks in the IR spectrum? 
A. There are 6 vibrational modes but due to its symmetry, some modes have 0 intensity. Only the modes that can change the dipole moment will appear visible on the IR spectrum. 
 
Q. Which vibration is the asymmetric N-F stretch? 
A. The vibration at 949cm-1 
 
Q. What is the nature of the highest energy vibration 
A. The N=N stretch 
 
Q. Which MOs are core orbital MOs? 
A. MO 1 and MO 2 are for the S orbitals for the F, and MO 3 and MO 4 for the S orbitals for the N 

==Computational Lab 2==

==BH3 Molecule==
===calculation data===
{| class="wikitable"
|Name of submitted log file|| NH3_OPTF_POP_MI_CHEM307.LOG
|-
|Molecule|| BH3
|-
|Method|| RB3LYP
|-
|Basis set|| 6-31G(d,p)
|-
|Final energy||-26.615324
|-
|RMS gradient|| 0.000002
|-
|Point group|| D3H
|}

===Item Table===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000015 YES
RMS Force 0.000003 0.000010 YES
Maximum Displacement 0.000017 0.000060 YES
RMS Displacement 0.000011 0.000040 YES

1 2 3
A2" ?A ?A
Frequencies -- 1162.9745 1213.1390 1213.1392
Red. masses -- 1.2531 1.1072 1.1072
Frc consts -- 0.9986 0.9600 0.9600
IR Inten -- 92.5682 14.0550 14.0544
Atom AN X Y Z X Y Z X Y Z
1 5 0.00 0.00 -0.16 -0.10 0.00 0.00 0.00 -0.10 0.00
2 1 0.00 0.00 0.57 0.81 0.00 0.00 0.00 -0.08 0.00
3 1 0.00 0.00 0.57 0.14 -0.39 0.00 -0.39 0.59 0.00
4 1 0.00 0.00 0.57 0.14 0.39 0.00 0.39 0.59 0.00
4 5 6
?B ?A ?A
Frequencies -- 2582.5813 2715.7180 2715.7189
Red. masses -- 1.0078 1.1273 1.1273
Frc consts -- 3.9604 4.8987 4.8987
IR Inten -- 0.0000 126.3320 126.3260
Atom AN X Y Z X Y Z X Y Z
1 5 0.00 0.00 0.00 -0.11 0.00 0.00 0.00 -0.11 0.00
2 1 0.00 0.58 0.00 -0.02 0.00 0.00 0.00 0.81 0.00
3 1 -0.50 -0.29 0.00 0.60 0.36 0.00 0.36 0.19 0.00
4 1 0.50 -0.29 0.00 0.60 -0.36 0.00 -0.36 0.19 0.00

</pre>

==NH3BH<ub>3 Molecule==
===calculation data===
{| class="wikitable"
|Name of submitted log file|| MI_NH3BH3_opt.LOG
|-
|Molecule|| NH3BH3
|-
|Method|| RB3LYP
|-
|Basis set|| 6-31G(d,p)
|-
|Final energy|| -
|-
|RMS gradient|| -
|-
|Point group|| -
|}

===Item Table===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000002 0.000015 YES
RMS Force 0.000001 0.000010 YES
Maximum Displacement 0.000021 0.000060 YES
RMS Displacement 0.000009 0.000040 YES

1 2 3
A A A
Frequencies -- 263.3534 632.9708 638.4420
Red. masses -- 1.0078 5.0021 1.0452
Frc consts -- 0.0412 1.1808 0.2510
IR Inten -- 0.0000 14.0108 3.5497
Atom AN X Y Z X Y Z X Y Z
1 1 0.00 0.01 0.36 0.29 -0.03 0.00 0.44 0.10 0.04
2 1 0.00 0.31 -0.19 0.29 0.02 0.03 -0.33 0.13 0.01
3 1 0.00 -0.32 -0.18 0.29 0.02 -0.03 -0.10 0.14 0.05
4 1 0.00 0.01 0.45 -0.36 0.00 0.00 0.56 0.17 0.06
5 1 0.00 -0.39 -0.22 -0.36 0.00 0.00 -0.13 0.20 0.07
6 1 0.00 0.38 -0.23 -0.36 0.00 0.00 -0.43 0.19 0.03
7 5 0.00 0.00 0.00 0.48 0.00 0.00 0.00 -0.03 -0.01
8 7 0.00 0.00 0.00 -0.36 0.00 0.00 0.00 -0.05 -0.01
4 5 6
A A A
Frequencies -- 638.5038 1069.1625 1069.1794
Red. masses -- 1.0452 1.3347 1.3347
Frc consts -- 0.2511 0.8989 0.8989
IR Inten -- 3.5466 40.5061 40.5107
Atom AN X Y Z X Y Z X Y Z
1 1 -0.13 -0.03 0.15 0.58 0.04 0.07 -0.26 -0.01 0.15
2 1 -0.31 -0.06 0.12 -0.51 0.10 -0.02 -0.37 -0.10 0.09
3 1 0.45 -0.02 0.11 -0.07 0.15 0.08 0.63 0.00 0.04
4 1 -0.17 -0.05 0.20 -0.41 -0.06 -0.05 0.18 0.03 -0.12
5 1 0.57 -0.04 0.17 0.05 -0.11 -0.06 -0.44 0.02 -0.07
6 1 -0.40 -0.07 0.18 0.36 -0.09 -0.01 0.26 0.07 -0.09
7 5 0.00 0.01 -0.03 0.00 -0.12 -0.05 0.00 0.05 -0.12
8 7 0.00 0.01 -0.05 0.00 0.10 0.04 0.00 -0.04 0.10
7 8 9
A A A
Frequencies -- 1196.1906 1203.5375 1203.5588
Red. masses -- 1.1451 1.0608 1.0608
Frc consts -- 0.9654 0.9053 0.9053
IR Inten -- 108.9560 3.4683 3.4681
Atom AN X Y Z X Y Z X Y Z
1 1 0.55 0.17 0.00 -0.18 -0.10 -0.57 -0.21 -0.09 0.49
2 1 0.55 -0.09 -0.15 -0.09 0.63 -0.33 0.27 0.15 -0.24
3 1 0.55 -0.08 0.15 0.28 0.06 0.18 -0.05 0.66 0.33
4 1 -0.02 0.00 0.00 0.01 0.00 0.01 0.02 0.00 -0.01
5 1 -0.02 0.00 0.00 -0.02 0.00 0.00 0.00 -0.01 -0.01
6 1 -0.02 0.00 0.00 0.01 -0.01 0.01 -0.02 0.00 0.00
7 5 -0.11 0.00 0.00 0.00 -0.05 0.06 0.00 -0.06 -0.05
8 7 -0.02 0.00 0.00 0.00 -0.01 0.01 0.00 -0.01 -0.01
10 11 12
A A A
Frequencies -- 1328.8294 1676.0351 1676.0418
Red. masses -- 1.1792 1.0555 1.0555
Frc consts -- 1.2268 1.7470 1.7470
IR Inten -- 113.6263 27.5647 27.5648
Atom AN X Y Z X Y Z X Y Z
1 1 0.00 0.00 0.00 0.01 0.00 0.01 0.01 0.00 -0.01
2 1 0.00 0.00 0.00 -0.01 0.00 -0.01 0.00 0.01 -0.01
3 1 0.00 0.00 0.00 0.00 0.01 0.01 -0.01 0.00 0.00
4 1 0.53 0.21 0.00 -0.23 -0.11 0.46 -0.17 -0.10 -0.59
5 1 0.53 -0.10 0.19 -0.04 0.66 0.34 0.28 0.01 0.18
6 1 0.53 -0.11 -0.18 0.26 0.18 -0.27 -0.11 0.62 -0.31
7 5 0.00 0.00 0.00 0.00 -0.01 0.00 0.00 0.00 0.01
8 7 -0.11 0.00 0.00 0.00 -0.05 -0.04 0.00 -0.04 0.05
13 14 15
A A A
Frequencies -- 2471.9755 2532.0644 2532.0918
Red. masses -- 1.0218 1.1176 1.1176
Frc consts -- 3.6789 4.2217 4.2218
IR Inten -- 67.2020 231.2493 231.2395
Atom AN X Y Z X Y Z X Y Z
1 1 -0.15 0.56 -0.01 0.01 -0.04 -0.01 -0.21 0.78 -0.02
2 1 -0.15 -0.29 -0.48 0.18 0.35 0.56 0.12 0.21 0.37
3 1 -0.15 -0.27 0.49 -0.19 -0.34 0.61 0.10 0.16 -0.32
4 1 0.01 0.00 0.00 0.00 0.00 0.00 -0.01 -0.01 0.00
5 1 0.01 0.00 0.00 0.00 0.00 -0.01 0.00 0.00 0.00
6 1 0.01 0.00 0.00 0.00 0.00 -0.01 0.00 -0.01 0.00
7 5 0.04 0.00 0.00 0.00 0.00 -0.10 0.00 -0.10 0.00
8 7 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
16 17 18
A A A
Frequencies -- 3464.0944 3581.1221 3581.1454
Red. masses -- 1.0270 1.0921 1.0921
Frc consts -- 7.2611 8.2518 8.2519
IR Inten -- 2.5107 27.9530 27.9537
Atom AN X Y Z X Y Z X Y Z
1 1 0.00 0.00 0.00 0.00 0.01 0.00 0.00 0.00 0.00
2 1 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.01
3 1 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.01
4 1 -0.18 0.55 -0.01 -0.28 0.76 -0.01 0.00 0.01 -0.02
5 1 -0.18 -0.26 0.48 0.15 0.18 -0.35 -0.24 -0.32 0.57
6 1 -0.18 -0.28 -0.47 0.14 0.18 0.33 0.25 0.35 0.57
7 5 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
8 7 0.04 0.00 0.00 0.00 -0.08 0.00 0.00 0.00 -0.08

</pre>

Clauseluke

2026-05-22T08:42:09Z

Wikiadmin:

==lab marking==
It would be good if you round off reported values to correct significant figures and report values of wavenumber in your answers as well. Please pay a bit more attention to overall formatting. overall a decent attempt. Also, you have uploaded an incorrect file for N2F2. If you have any specific questions, do email Prof. Hunt

==NH3 Molecule==
===calculation data===
{| class="wikitable"
|name of submitted log file|| lukeclausenNH3optfpop.log
|-
|molecule|| NH3
|-
|method|| RB3LYP
|-
|basis set||| 6-31G(d,p)
|-
|final energy|| -56.557769
|-
|RMS gradient|| 0.000000153
|-
|point group|| C3v
|}
===Item Table===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000015 YES
RMS Force 0.000000 0.000010 YES
Maximum Displacement 0.000003 0.000060 YES
RMS Displacement 0.000001 0.000040 YES
</pre>
===Optimised molecule image===
[[file:LdcoptfNH3.png|400px]]

[[media:LUKECLAUSENNH3OPTFPOP.LOG]]

<jmol><jmolApplet>
<title>3d model of my NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LUKECLAUSENNH3OPTFPOP.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Important geometric parameters===
Optimised bond distance and angle for NH3 
r(N-H)=1.018Â 
θ(H-N-H)106°

===IR NH2===
[[file:LUKECLAUSENNH3OPTFPOP ir.png|450px]]
{| class="wikitable"
|molecule|| NH3
|-
|mode||1||2||3||4||5||6
|-
|frequency(cm-1)||1089.37||1693.93||1693.93||3461.38||3589.93||3589.93
|-
|intensity||145.4277||13.5571||13.5572||1.0593||0.2699||0.2699
|-
|symmetry||A1||E||E||A1||E||E
|}
<pre>
Low frequencies --- -5.6864 -3.6131 -3.6124 0.0017 0.0048 0.0162
Low frequencies --- 1089.3674 1693.9284 1693.9284
</pre>

[[media:LUKECLAUSENNH3OPTFPOP.LOG]]

===charges and MO===
[[file:ChargesNH3ldc.png|400px]]

==Project Molecule==
{| class="wikitable"
|name of submitted log file|| lukeclausenN2F2optfpop.log
|-
|molecule|| N2F2
|-
|method|| RB3LYP
|-
|basis set||| 6-31G(d,p)
|-
|final energy|| -309.01241
|-
|RMS gradient|| 0.000000317
|-
|point group|| C2v
|}
===Item Table===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000001 0.000015 YES
RMS Force 0.000000 0.000010 YES
Maximum Displacement 0.000001 0.000060 YES
RMS Displacement 0.000001 0.000040 YES
</pre>

===Optimised molecule image===
[[file:LDCoptfN2F2.png|150px]]

[[media:LUKECLAUSENN2F2OPTFPOP.LOG]]

<jmol><jmolApplet>
<title>3d model of my N2F2</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LUKECLAUSENN2F2OPTFPOP.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Important geometric parameters===
Optimised bond distance and angle for N2F2 
r(N-F)=1.28Â 
r(N-N)=1.23Â 
θ(N-N-F)120.0°

===IR N2F2===
[[file:LUKECLAUSENN2F2OPTFPOP_ir.png|450px]]
{| class="wikitable"
|molecule|| N2F2
|-
|mode||1||2||3||4||5||6
|-
|frequency(cm-1)||347.8772||561.2472||771.6105||949.4548 || 987.2543||1636.6075
|-
|intensity||0.6108||0.000||74.7044||75.4125||81.1265||20.5391
|-
|symmetry||A1||A2||B2||A1||B2||A1
|}
<pre>
Low frequencies --- -0.0015 -0.0012 -0.0010 3.2225 4.3532 5.1001
Low frequencies --- 347.8772 561.2472 771.6105
</pre>
===IR questions===
How many vibrations are expected from the 3N-6 rule?

3N-6 -> (3*4)-6 = 6 vibrations

Why are there only 4 peaks in the IR spectrum?

Even though there being 6 vibrational modes only some of these are IR active such as symmetric vibrations because cis-N2F2 is small and highly symmetrical some of the movements have no or very little change in dipole moment, and do not appear. they might also just be too small

Which vibration is the asymmetric N-F stretch?

Vibration 3

What is the nature of the highest energy vibration?
N=N stretch, they move together and then pull apart

==MO and Charges==

[[file:LukeclausenN2F2Orbitlal9MO.png|450px]]

[[File:LDCoptfN2F2 charges.png|450px]]

[[File:Mo9 ldc.jpg|450px]]

[[File:Lcao ldc.jpg|450px]]

the F - N bonds are showing because they are long and weak and as a result the software doesnt visualise them

the core orbital is n= 1, s orbital

==charge range==
-0.197 to 0.197

=comp chem lab2=
==NH3 Molecule==
===calculation data===
{| class="wikitable"
|name of submitted log file|| lukeclausenNH3optfpop.log
|-
|molecule|| NH3
|-
|method|| RB3LYP
|-
|basis set||| 6-31G(d,p)
|-
|final energy|| -56.557769
|-
|RMS gradient|| 0.000000153
|-
|point group|| C3v
|}
===Item Table===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000015 YES
RMS Force 0.000000 0.000010 YES
Maximum Displacement 0.000003 0.000060 YES
RMS Displacement 0.000001 0.000040 YES
</pre>
===Optimised molecule image===
[[file:LdcoptfNH3.png|400px]]

[[media:LUKECLAUSENNH3OPTFPOP.LOG]]

<jmol><jmolApplet>
<title>3d model of my NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LUKECLAUSENNH3OPTFPOP.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Important geometric parameters===
Optimised bond distance and angle for NH3 
r(N-H)=1.018Â 
θ(H-N-H)106°

===IR NH3===
[[file:LUKECLAUSENNH3OPTFPOP ir.png|450px]]
{| class="wikitable"
|molecule|| NH3
|-
|mode||1||2||3||4||5||6
|-
|frequency(cm-1)||1089.37||1693.93||1693.93||3461.38||3589.93||3589.93
|-
|intensity||145.4277||13.5571||13.5572||1.0593||0.2699||0.2699
|-
|symmetry||A1||E||E||A1||E||E
|}
<pre>
Low frequencies --- -5.6864 -3.6131 -3.6124 0.0017 0.0048 0.0162
Low frequencies --- 1089.3674 1693.9284 1693.9284
</pre>

[[media:LUKECLAUSENNH3OPTFPOP.LOG]]

===charges and MO===
[[file:ChargesNH3ldc.png|400px]]

==BH3 molecule==
[[media:LDC_BH3_OPTF_REAL.LOG]]
<jmol><jmolApplet>
<title>3d model of my BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LDC_BH3_OPTF_REAL.LOG</uploadedFileContents>
</jmolApplet></jmol>
===Calculation Data===
{| class="wikitable"
|name of submitted log file|| :LDC_BH3_OPTF_REAL
|-
|molecule|| BH3
|-
|method|| RB3LYP
|-
|basis set|| 6-31G(d,p)
|-
|final energy|| -26.6153
|-
|RMS gradient|| 0.000000013
|-
|point group|| D3H
|}
===Item Table===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000015 YES
RMS Force 0.000000 0.000010 YES
Maximum Displacement 0.000000 0.000060 YES
RMS Displacement 0.000000 0.000040 YES
RMS Displacement 0.000033 0.000040 YES
</pre>
===Important Geometric Parameters===
Optimised bond distance and angle for BH3 
r(B-H)= 1.19Â 
θ(H-B-H)= 120°
===Vibrations===
Full mass-weighted force constant matrix:
<pre>
Low frequencies --- -9.3466 -9.3312 -0.0721 -0.0009 0.5366 2.5570
Low frequencies --- 1162.9903 1213.1496 1213.1498
</pre>

===NH3BH3 molecule==
[[media:LDC_H3NBH3_OPTF_REAL.LOG]]
<jmol><jmolApplet>
<title>3d model of my NH3BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LDC_H3NBH3_OPTF_REAL.LOG</uploadedFileContents>
</jmolApplet></jmol>
===Calculation Data===
{| class="wikitable"
|name of submitted log file|| :LDC_H3NBH3_OPTF_REAL
|-
|molecule|| BH3NH3
|-
|method|| RB3LYP
|-
|basis set|| 6-31G(d,p)
|-
|final energy|| -83.224689
|-
|RMS gradient|| 0.000001
|-
|point group|| C1
|}
===item table===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000001 0.000015 YES
RMS Force 0.000001 0.000010 YES
Maximum Displacement 0.000058 0.000060 YES
RMS Displacement 0.000026 0.000040 YES
</pre>
;energy
:Et=ENH3BH3- (ENH3+EBH3)
:Et=-83.224689-(-56.557769-26.615324)
:Et=-0.051596 hartree
:ENH3BH3 = -83.224689 (Electronice energy hartree) 46.384 (thermal energy kcal/mol)
:ENH3 = -56.557769 (Electronice energy hartree) 23.409 (thermal energy kcal/mol)
:EBH3 = -26.615324 (Electronice energy hartree) 18.397 (thermal energy kcal/mol)
:Et=46.384-(23.409+18.397)
:Et=-4.578 kcal/mol
===low frequency===
<pre>
Full mass-weighted force constant matrix:
Low frequencies --- -3.3373 -1.0989 -0.0008 0.0005 0.0007 3.6750
Low frequencies --- 263.3597 632.9816 638.4447
</pre>

===Me3NHCl molecule===
[[media:ME3NHC SCAN LDC NOTHF.LOG]]
<jmol><jmolApplet>
<title>3d model of my ME3NHCl molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ME3NHC SCAN LDC NOTHF.LOG</uploadedFileContents>
</jmolApplet></jmol>

Clauseluke

2026-05-22T05:54:33Z

Wikiadmin: Reverted edits by Clauseluke (talk) to last revision by Qurat

Ibarramyes

2026-05-22T05:53:57Z

Wikiadmin: Undo revision 31064 by Ibarramyes (talk)

Ibarramyes

2026-05-22T05:52:12Z

Wikiadmin: Undo revision 31065 by Ibarramyes (talk)

Ibarramyes

2026-05-22T05:51:49Z

Wikiadmin: Undo revision 31066 by Wikiadmin (talk)

Ibarramyes

2026-05-22T05:50:56Z

Wikiadmin: Reverted edits by Ibarramyes (talk) to last revision by Qurat

User talk:MergedUsers

2026-03-24T04:02:34Z

Wikiadmin: Wikiadmin moved page User talk:Nelsonsimo to User talk:MergedUsers: Automatically moved page while merging the account "Nelsonsimo" to "MergedUsers"

==NH3 Molecule==
===Method information===
NOTE: values of the energy and gradient will differ slightly for every calculation
{| class="wikitable"
|name of submitted log file|| NELSONSIMO_NH3_OPT_PT2.LOG
|-
|molecule|| NH3
|-
|method|| B3LYP
|-
|basis set|| 6-31G(d,p)
|-
|final energy|| -56.557769
|-
|RMS gradient|| 0.0000002
|-
|point group|| C3v
|}

===Item Table===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000015 YES
RMS Force 0.000000 0.000010 YES
Maximum Displacement 0.000003 0.000060 YES
RMS Displacement 0.000001 0.000040 YES
</pre>

<pre>
Low frequencies --- -5.6864 -3.6131 -3.6124 -0.0014 0.0045 0.0162
Low frequencies --- 1089.3674 1693.9284 1693.9284
</pre>

===Optimised molecule===
logfile: [[Media:NELSONSIMO_NH3_OPT_PT2.LOG]]

static image:
[[File:nelsonsimo_nh3_opt.png|300px]]

Jmol rotateable molecule

optimised NH3 molecule
<jmol><jmolApplet>
<color>cyan</color>
<size>300</size>
<uploadedFileContents>NELSONSIMO_NH3_OPT_PT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Geometric parameters===
Optimised bond distance and angle for NH3 
{| class="wikitable" style="text-align: center;
| coord || value
|-
|r(N-H)|| 1.02Â
|-
|θ|| 106°
|}

===Vibrations===

table of vibrations:
{| class="wikitable" style="text-align: center;
|mode || 1 || 2 || 3 || 4 || 5 || 6
|-
|wavenumber (cm-1)|| 1089 || 1694 || 1694 || 3461 || 3590 || 3590
|-
|symmetry|| A1 || E || E || A1 || E || E
|-
|intensity (arbitary units)|| 145 || 14 || 14 || 1 || 0 || 0
|}
IR spectrum: 
[[File:NELSONSIMO NH3 OPT PT1 ir.png|600px]]

===Charges===
image of NBO charges colour coded red for negative and green for positive the charge range is ±1.125e
 
[[File:Nelsonsimo_nh3_opt_charge.png|300px]]
[[File:Nelsonsimo_nh3_opt_charge_data.png |300px]]

table of NH3 charges:
{| class="wikitable" style="text-align: center;
!atom|| charge
|-
|N|| -1.13
|-
|H|| +0.38
|}

==Project Molecule==
===Method information===
NOTE: values of the energy and gradient will differ slightly for every calculation
{| class="wikitable"
|name of submitted log file|| NELSONSIMO_N2F2_OPT2.LOG
|-
|molecule|| N2F2
|-
|method|| B3LYP
|-
|basis set|| 6-31G(d,p)
|-
|final energy|| -309.012413
|-
|RMS gradient|| 0.0000003
|-
|point group|| C2v
|}

===Item Table===
<pre>
Item Value Threshold Converged?
Maximum Force 0.000001 0.000015 YES
RMS Force 0.000000 0.000010 YES
Maximum Displacement 0.000001 0.000060 YES
RMS Displacement 0.000001 0.000040 YES
</pre>

<pre>
Low frequencies --- -0.0015 -0.0012 -0.0010 3.2225 4.3532 5.1001
Low frequencies --- 347.8772 561.2472 771.6105
</pre>

===Optimised molecule===
logfile: [[Media:NELSONSIMO_N2F2_OPT2.LOG]]

static image:
[[File:Nelsonsimo_n2f2_opt.png|500px]]

Jmol rotateable molecule

optimised N2F2 molecule
<jmol><jmolApplet>
<color>cyan</color>
<size>300</size>
<uploadedFileContents>NELSONSIMO_N2F2_OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Geometric parameters===
Optimised bond distance and angle for N2F2 
{| class="wikitable" style="text-align: center;
| coord || value
|-
|r(N=N)|| 1.22Â
|-
|r(N-F)|| 1.39Â
|-
|θ(F-N=N)|| 114°
|-
|D(F-N=N-F)|| 0°
|}

===Vibrations===

table of vibrations:
{| class="wikitable" style="text-align: center;
|mode || 1 || 2 || 3 || 4 || 5 || 6
|-
|wavenumber (cm-1)|| 348 || 561 || 772 || 950 || 987 || 1637
|-
|symmetry|| A1 || A2 || B2 || A1 || B2 || A1
|-
|intensity (arbitary units)|| 1 || 0 || 75 || 75 || 81 || 21
|}
IR spectrum: 
[[File:Nelsonsimo_n2f2_opt_ir.png|600px]]
===Charges===
image of NBO charges colour coded red for negative and green for positive the charge range is ±0.215e
 
[[File:Nelsonsimo_n2f2_opt_charge2.png|400px]]
[[File:Nelsonsimo_n2f2_opt_charge_data2.PNG |300px]]

table of N2F2 charges:
{| class="wikitable" style="text-align: center;
!atom|| charge
|-
|N|| +0.22
|-
|F|| -0.22
|}

'''answer these questions'''

*the molecule from the log file does not have bonds between the F and N atoms, what is going on here? 
::The bonds are still present, just not viewable in the log file (they are however there in the .chk file) as they exceed a predetermined value in length and gaussview does not show bonds that exceed this value

*how many vibrations are expected from the 3N-6 rule? 
::There are 6 vibrations, as 3(4)-6 = 12-6 = 6 and (N = 4)

*why are there only 4 peaks in the IR spectrum? 
::There are only 4 peaks as the intensity for two of them are too close to 0 to actually show up at the scale the spectra is.

*which vibration is the asymmetric N-F stretch? 
::Mode 3 is the asymmetric stretch of N-F as each side is stretching up and down at different times while the N=N stays the same

*what is the nature of the highest energy vibration? 
::the highest energy vibration is mode 6, where we see N=N stretching

===Molecular Orbitals===
'''more questions'''

*which MOs are core orbital MOs? 
::MOs 1, 2, 3, and 4 are the core orbitals as they have energy values close to -20eV, being -24.76eV for MOs 1 and 2 and -14.52 for MOs 3 and 4. they also hold onto the electron density very tightly

{| class="wikitable" style="text-align: center;
!MO 9 of N2F2|| the LCAO MO
|-
|[[File:Nelsonsimo_n2f2_opt2_MO9.png|300px]]|| [[File:Nelsonsimo_n2f2_MO9_LCAO2.PNG|300px]]
|}

Mod:Hunt Research Group/AdditionalFunctions.py

2025-12-10T07:43:35Z

Wikiadmin: /* Required arguments */

CubePy is under [https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode CC BY-NC-SA license]

<code>AdditionalFunctions.py</code> is a collection of functions that do not work directly with cube files, but with data produced by the other scripts.

=Requirements=
* Python
* Matplotlib

An easy way to obtain Python with the required modules is by installing [https://anaconda.org Anaconda].

Anaconda comes with Spyder, which is a Python editor that you can use to write and run Python codes (Applications <math>\rightarrow</math> Anaconda Navigator <math>\rightarrow</math> spyder <math>\rightarrow</math> Launch)

=Instructions=
==Running the code==
The plotting functions can be run from the terminal window by typing:

<pre>python AdditionalFunctions.py function_name file_path1 file_path2... arg1=val1 arg2=val2...</pre>

=Functions=
==OverlapKDEs==
[[File:ia2514_fig10.png|400px|right|thumb|Figure 1. Plot generated by OverlapKDEs]]
This function plots overlapping KDEs as read from _kde.out files written by [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/PlotCube.py#PlotHistogram <code>PlotHistogram</code>] from [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/PlotCube.py <code>PlotCube.py</code>] (when <code>save</code> is True).

===Required arguments===

* <code>fpaths</code> (string) = paths for _kde.out files

===Optional arguments===
* <code>value_type</code> (string, default='esp') = can be ‘esp’/’potential’ or ‘dens’/’density’ (or any uppercase version of the aforementioned); used in conjunction with the keywords <code>au</code> and <code>units</code> in order to convert the values to the appropriate units
* <code>xlim</code> (list, default=None) = x axis limits
* <code>ylim</code> (list, default=None) = y axis limits
* <code>log</code> (boolean, default=True) = if True, it saves a .log file of the command used to run the functions (the command is tidied-up before saving i.e. unnecessary spaces are removed, argument values are converted to their usual uppercase/lowercase versions, file lists are explicit - instead of using wildcard symbols such as *)
* <code>logfile</code> (string, default=None) = the name of the log file (if <code>log</code> is True); by default the file name is the input file name followed by the function name

===Observations===
* if you only want to specify one limit for either of the axis, use None for the other (e.g. xlim=[None,3.5])

===Example===
<pre>python AdditionalFunctions.py OverlapKDEs NH3CH2Cl_esp_kde.out NH3CH2OH_esp_kde.out NH3CH2BH2_esp_kde.out xlim=[2,10]</pre>
The resulting plot is shown in figure 1.

==PlotHistogram==
This function plots one KDE and/or one histogram as read from _kde.out and _hist.out files written by [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/PlotCube.py#PlotHistogram <code>PlotHistogram</code>] from [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/PlotCube.py <code>PlotCube.py</code>] (when <code>save</code> is True).

===Required arguments===
[[File:ia2514_fig5.png|right|thumb|Figure 2. Plot generated by PlotHistogram]]
* <code>fpaths</code> (string) = paths for _kde.out and _hist.out files (should be one of each at most)

===Optional arguments===
* <code>value_type</code> (string, default='esp') = can be ‘esp’/’potential’ or ‘dens’/’density’ (or any uppercase version of the aforementioned); used in conjunction with the keywords <code>au</code> and <code>units</code> in order to convert the values to the appropriate units
* <code>colour</code> (string, default='rainbow') = colour scheme ('rainbow' by default, change it to 'bwr' for blue-white-red) - full list [https://matplotlib.org/users/colormaps.html here]
* <code>cb_lim</code> (list, default=None) = limits for the colour bar (list of two floats; if not specified, the limits will be the min and max of the values; if the limits do not cover the whole range of values, a warning is printed)
* <code>xlim</code> (list, default=None) = x axis limits
* <code>ylim</code> (list, default=None) = y axis limits
* <code>log</code> (boolean, default=True) = if True, it saves a .log file of the command used to run the functions (the command is tidied-up before saving i.e. unnecessary spaces are removed, argument values are converted to their usual uppercase/lowercase versions, file lists are explicit - instead of using wildcard symbols such as *)
* <code>logfile</code> (string, default=None) = the name of the log file (if <code>log</code> is True); by default the file name is the input file name followed by the function name
* <code>cb_sym</code> (boolean, default=False) = if True, the colour bar limits are chosen to be symmetric around 0 (<code>cb_lim</code>, if specified, overrides <code>cb_sym</code>)

===Observations===
* if you only want to specify one limit for either of the axis, use None for the other (e.g. xlim=[None,3.5])
* the function only works for one histogram file and/or one KDE file. If multiple files of either type are specified as arguments, the execution of the program is stopped and a warning is printed.
* the data in the files specified as arguments must be in the same units. If that is not the case, the execution of the program is stopped and a warning is printed.

===Example===
<pre>python AdditionalFunctions.py PlotHistogram test_emim_oac_esp_kde.out test_emim_oac_esp_hist.out</pre>
The resulting plot is shown in figure 2.

Mod:Hunt Research Group/AdditionalFunctions.py

2025-12-10T07:42:53Z

Wikiadmin:

CubePy is under [https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode CC BY-NC-SA license]

<code>AdditionalFunctions.py</code> is a collection of functions that do not work directly with cube files, but with data produced by the other scripts.

=Requirements=
* Python
* Matplotlib

An easy way to obtain Python with the required modules is by installing [https://anaconda.org Anaconda].

Anaconda comes with Spyder, which is a Python editor that you can use to write and run Python codes (Applications <math>\rightarrow</math> Anaconda Navigator <math>\rightarrow</math> spyder <math>\rightarrow</math> Launch)

=Instructions=
==Running the code==
The plotting functions can be run from the terminal window by typing:

<pre>python AdditionalFunctions.py function_name file_path1 file_path2... arg1=val1 arg2=val2...</pre>

=Functions=
==OverlapKDEs==
[[File:ia2514_fig10.png|400px|right|thumb|Figure 1. Plot generated by OverlapKDEs]]
This function plots overlapping KDEs as read from _kde.out files written by [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/PlotCube.py#PlotHistogram <code>PlotHistogram</code>] from [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/PlotCube.py <code>PlotCube.py</code>] (when <code>save</code> is True).

===Required arguments===

* <code>fpaths</code> (string) = paths for _kde.out files

===Optional arguments===
* <code>value_type</code> (string, default='esp') = can be ‘esp’/’potential’ or ‘dens’/’density’ (or any uppercase version of the aforementioned); used in conjunction with the keywords <code>au</code> and <code>units</code> in order to convert the values to the appropriate units
* <code>xlim</code> (list, default=None) = x axis limits
* <code>ylim</code> (list, default=None) = y axis limits
* <code>log</code> (boolean, default=True) = if True, it saves a .log file of the command used to run the functions (the command is tidied-up before saving i.e. unnecessary spaces are removed, argument values are converted to their usual uppercase/lowercase versions, file lists are explicit - instead of using wildcard symbols such as *)
* <code>logfile</code> (string, default=None) = the name of the log file (if <code>log</code> is True); by default the file name is the input file name followed by the function name

===Observations===
* if you only want to specify one limit for either of the axis, use None for the other (e.g. xlim=[None,3.5])

===Example===
<pre>python AdditionalFunctions.py OverlapKDEs NH3CH2Cl_esp_kde.out NH3CH2OH_esp_kde.out NH3CH2BH2_esp_kde.out xlim=[2,10]</pre>
The resulting plot is shown in figure 1.

==PlotHistogram==
This function plots one KDE and/or one histogram as read from _kde.out and _hist.out files written by [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/PlotCube.py#PlotHistogram <code>PlotHistogram</code>] from [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/PlotCube.py <code>PlotCube.py</code>] (when <code>save</code> is True).

===Required arguments===
[[File:la2514_fig5.png|400px|right|thumb|Figure 2. Plot generated by PlotHistogram]]
* <code>fpaths</code> (string) = paths for _kde.out and _hist.out files (should be one of each at most)

===Optional arguments===
* <code>value_type</code> (string, default='esp') = can be ‘esp’/’potential’ or ‘dens’/’density’ (or any uppercase version of the aforementioned); used in conjunction with the keywords <code>au</code> and <code>units</code> in order to convert the values to the appropriate units
* <code>colour</code> (string, default='rainbow') = colour scheme ('rainbow' by default, change it to 'bwr' for blue-white-red) - full list [https://matplotlib.org/users/colormaps.html here]
* <code>cb_lim</code> (list, default=None) = limits for the colour bar (list of two floats; if not specified, the limits will be the min and max of the values; if the limits do not cover the whole range of values, a warning is printed)
* <code>xlim</code> (list, default=None) = x axis limits
* <code>ylim</code> (list, default=None) = y axis limits
* <code>log</code> (boolean, default=True) = if True, it saves a .log file of the command used to run the functions (the command is tidied-up before saving i.e. unnecessary spaces are removed, argument values are converted to their usual uppercase/lowercase versions, file lists are explicit - instead of using wildcard symbols such as *)
* <code>logfile</code> (string, default=None) = the name of the log file (if <code>log</code> is True); by default the file name is the input file name followed by the function name
* <code>cb_sym</code> (boolean, default=False) = if True, the colour bar limits are chosen to be symmetric around 0 (<code>cb_lim</code>, if specified, overrides <code>cb_sym</code>)

===Observations===
* if you only want to specify one limit for either of the axis, use None for the other (e.g. xlim=[None,3.5])
* the function only works for one histogram file and/or one KDE file. If multiple files of either type are specified as arguments, the execution of the program is stopped and a warning is printed.
* the data in the files specified as arguments must be in the same units. If that is not the case, the execution of the program is stopped and a warning is printed.

===Example===
<pre>python AdditionalFunctions.py PlotHistogram test_emim_oac_esp_kde.out test_emim_oac_esp_hist.out</pre>
The resulting plot is shown in figure 2.

File:Ia2514 fig5.png

2025-12-10T07:41:36Z

Wikiadmin:

File:Ia2514 fig10.png

2025-12-10T07:39:03Z

Wikiadmin:

Mod:Hunt Research Group/report writing

2025-12-10T04:23:54Z

Wikiadmin: /* "have been" or "were"? */

=Report Instructions=
===written work is NOT a conversation===
::*many students are far too too colloquial
::*use a more developed and higher level of language, replace simple generic terms with specific terms
::*avoid using the following terms: done, even though, although, a lot, meaning, owing, that is, ...
::*for example, replace done with "carried out", "executed", "investigated", "implemented", "performed"
::*carry out a search on your document for the above words, and ensure you eliminate these from your document unless absolutely essential
===avoid personal pronouns===
::* personal pronouns are: I, you, he, she, it, we, they, me, him, her, us, and them
::* in papers avoid personal pronouns
::* in a thesis they can be used apringly to emphasise work you did
::* NOT "we analysed X"
::* YES "X was analysed"

===science is SPECIFIC===
::*avoid using the following terms: this, their, these, them, it
::*all students are expected to have used the "find" feature for the above and to have eliminated these words (there are a few cases where use is appropriate)
::*never use general extensions such as "and so on", "etc", "so on and so forth"
::*it is OK to repeat a term if it allows you to be specific

===is it LARGER or HIGHER?===
::*use larger for preference over higher or bigger (and smaller over lower)
::*options
:::you can use higher when its a quantity, its positive, and the quantity is normally pictured like a "ladder" or vertical ruler
:::you can use greater when it refers to a group of things "a greater number of X"
:::larger is good for sizes, volumes, areas, distances etc
::*when referring to negative numbers NEVER use larger or bigger or higher
:::the problem is does larger mean less negative or a larger absolute quantity even though its negative
:::use "X is more negative" and "X is less negative"

===avoid the use of RUBBISH words===
::*rubbish words add no knew knowledge or content
::::"the fact that"
::::"an interesting point"
::::"it is worth noting"
::::"due to the fact"
::::"it is important to consider"

::*words that are colloquial and typical of oral but not written statements
::::"on the other hand"
::::"some would say"
::::"in other words"
::::"in reality"
::::"this is indeed"
::::"when looking at"

::*avoid words that mention earlier statements, the reader is intelligent, they know what you have written previously
::::"as discussed above"
::::"as noted earlier"
::::"as mentioned earlier"

::*avoid explicitly mentioning data shown in figures and graphs
::::we are intelligent we can see your graph, do NOT describe graphs or figures in the text
::::rather make a statement and then just add "..., Figure X" at the end of the sentence
::::do not use "as shown in Figure X", "it can be seen in Figure X"

===use proper sentence construction===
::*SVO=subject-verb-object
::*example "The graph shows that X is larger than Y." subject=the graph, verb=shows, object=x and y
::*the subject can be a noun, pronoun, adjectives or descriptive phrases that go with these
::*a pronoun refers to people, I, you, he, she, we, they
::*an adjective qualifies, defines, modifies a noun, for example: big, unique, old
::*adverbs (consequently, clearly) apply to a whole sentence or clause and can be used to start a sentence
::*conjunctions or connectors link two elements (clauses) in a sentence, there are two types
::*ones that cannot come at the start of a sentence (for, and, nor, but, or , yet, that)
::*ones that can come at the start of a sentence, but please avoid doing so (if, unless, also, provided, as, because, since, therefor, although, though, after, before, while)
::*the above preface a subordinating clause, ie a clause that clarifies, expands or explains the meaning of the main clause
::*do NOT start sentences with: as, although, while, because
::*you can start sentences with: nevertheless, therefor, however
::*of course, this is English, the rules can-be and are broken at times, but not by you!

===avoid "old" English===
:do not use old, non modern English, avoid the following ... and related
::hereby, herein, heretofore, herewith
::therein, thereby
::wherein, whereby, whereupon, whereon
::hitherto, whence

==="have been" or "were"?===
::Consider the following example
:::"X have been computed" is choosing to treat this as an event extending to the present.
:::"X were computed" is choosing to treat this as an event in the past.
::the numbers we generate in computational chemistry don’t change from the past to the present (if they do there is a problem!) we use “have been”
::experimentalists, on the other hand, who measure something at a given time in the past, but cannot guarantee it is the same now (in the present) must use “were"

===plurals!===
::a surprising number of students have problems with plurals
::if there is more than one, make it plural
::if you have grouped entities, and then refer to the group, using a singular reference
::Consider the following example
:::"the ESP of all molecules has been evaluated"
:::: there are multiple molecules
:::: but the whole group (of all molecules) is a single entity and we use "has" and not "have" the plural

===all statements must be TRUE===
::*read your sentences carefully, in isolation, is it true?
::*for example a common mistake is "ILs exhibit unique properties" this is NOT true there is no single property that is unique to ILs, but "ILs exhibit a unique combination of properties" is true.

===do not anthropomorphise===
::* that is do make human an inhuman entity, avoid "their" "themselves"

===your LOGIC must be good===
::*make sure that when you say "A therefore B" in a sentence that A and B are EXPLICITLY connected
::*sentence construction NOT "due to B, A" but YES to "A due to B"

===SET-UP the problem===
::*students have a tendency to start in the middle of an explanation and not set up the problem
::*start from the beginning explain the problem or concept from scratch
::*it might be helpful to imagine you are explaining the concept to an UG, who knows nothing about the problem

===ONE sentence ONE idea===
::*students can have a tendency to produce long rambling sentences
::*scientific writing is short and to the point
::*don't be overly wordy, don't try to "sound good" state it as it is.

===use PARAGRAPHS appropriately===
::*organise your sentences that are about the same point together

===referring to Figures===
::*do not write "comment ... as shown in Figure X", rather format this as "comment, Figure X"

===notation and ACRONYMS===
::*clearly define all notation at the first use e.g. define what N1124 means
::*avoid the use acronyms if at all possible, only use very COMMON acronyms

Mod:Hunt Research Group/Python scripts for cube files

2025-12-09T00:23:16Z

Wikiadmin: /* Getting started */

[[File:ia2514_small_gif.gif|right]]

=Processing Cube Files=
===Python Codes===
The latest version of <code>CubePy</code>, along with a test cube file can be found [[:Media:CubePy_v1.1.zip|here]].

CubePy is under [https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode CC BY-NC-SA license]

CubePy encompasses six modules that can be used to read, save, manipulate and visualise data from cube files:
* [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group/ReadCube.py ReadCube.py] - used to extract data from cube files and return it in convenient python formats
* [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group/SaveCube.py SaveCube.py] - used to save data from cube files in convenient formats
* [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group/CalculateCube.py CalculateCube.py] - used to manipulate data from cube files
* [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group/PlotCube.py PlotCube.py] - used to plot data from cube files (using [https://matplotlib.org Matplotlib])
* [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group/PlotCube_mayavi.py PlotCube_mayavi.py] - used to plot data from cube files (using [http://docs.enthought.com/mayavi/mayavi/ Mayavi])
* [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group/AdditionalFunctions.py AdditionalFunctions.py] - used to manipulate data not from cube files, but from files produced by the scripts above

===Getting started===
*you will need to have installed
:matplotlib
:numpy
:scipy
:mayavi
:pandas
 
to run the modules a python script is needed

The Python script can be written and run in different ways:
* as a new .py file using Spyder (Spyder -> File -> New file... -> [write the file] -> Save As... [make sure you save the file in the same directory as <code>CalculateCube.py</code> -> Run -> Run [the file will be run in the iPython console]
* in the IPython console in Spyder: write the Python commands directly in the console, but make sure that the current working directory is the one containing <code>CalculateCube.py</code>
* in the terminal window: type <code>ipython</code>, then write the Python commands directly in the terminal, but make sure that the current working directory is the one containing <code>CalculateCube.py</code>

===If you want to save data from cube files===
* for saving the values from the cube files, use the functions from SaveCube.py
* for saving histogram data, use the function <code>PlotHistogram</code> from PlotCube.py with <code>save=True</code>
* for saving a short summary file of the minimum, maximum and lowest curvature points on the van der Waals surface, use <code>save=True</code> when running <code>PlotSurface</code> from PlotCube_mayavi.py

===If you want to plot surfaces, isosurfaces, slices===
* use the functions from [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/PlotCube_mayavi.py PlotCube_mayavi.py]. They are faster and better at 3D plotting than the equivalent functions from [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/PlotCube.py PlotCube.py]

If you want to generate static figures you can also consider using the 3D plotting functions from PlotCube.py. These are especially recommended when wanting to display atoms as they look better than their PlotCube_mayavi.py equivalents. However, keep in mind that Matplotlib sometimes fails at 3D rendering, which generates "incorrect" plots (i.e. elements that should be behind the rest of the plot appear at the front). Therefore, plots created using function from PlotCube.py should be double-checked (by comparing them with plots from PlotCube_mayavi.py, by example).

===If you want to plot histograms and KDEs===
* use <code>PlotHistogram</code> from PlotCube.py to plot a histogram and/or KDE directly from cube files
* use <code>OverlapKDEs</code> and <code>PlotHistogram</code> from AdditionalFunctions.py to plot histograms and KDEs from files written by <code>PlotHistogram</code> from PlotCube.py when <code>save=True</code>

Mod:Hunt Research Group/Python scripts for cube files

2025-12-09T00:22:57Z

Wikiadmin: /* Getting started */

[[File:ia2514_small_gif.gif|right]]

=Processing Cube Files=
===Python Codes===
The latest version of <code>CubePy</code>, along with a test cube file can be found [[:Media:CubePy_v1.1.zip|here]].

CubePy is under [https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode CC BY-NC-SA license]

CubePy encompasses six modules that can be used to read, save, manipulate and visualise data from cube files:
* [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group/ReadCube.py ReadCube.py] - used to extract data from cube files and return it in convenient python formats
* [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group/SaveCube.py SaveCube.py] - used to save data from cube files in convenient formats
* [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group/CalculateCube.py CalculateCube.py] - used to manipulate data from cube files
* [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group/PlotCube.py PlotCube.py] - used to plot data from cube files (using [https://matplotlib.org Matplotlib])
* [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group/PlotCube_mayavi.py PlotCube_mayavi.py] - used to plot data from cube files (using [http://docs.enthought.com/mayavi/mayavi/ Mayavi])
* [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group/AdditionalFunctions.py AdditionalFunctions.py] - used to manipulate data not from cube files, but from files produced by the scripts above

===Getting started===
*you will need to have installed
:matplotlib
:numpy
:scipy
:mayavi
:pandas
*old initial set-up [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group/CubePy_setup getting started]
 
to run the modules a python script is needed

The Python script can be written and run in different ways:
* as a new .py file using Spyder (Spyder -> File -> New file... -> [write the file] -> Save As... [make sure you save the file in the same directory as <code>CalculateCube.py</code> -> Run -> Run [the file will be run in the iPython console]
* in the IPython console in Spyder: write the Python commands directly in the console, but make sure that the current working directory is the one containing <code>CalculateCube.py</code>
* in the terminal window: type <code>ipython</code>, then write the Python commands directly in the terminal, but make sure that the current working directory is the one containing <code>CalculateCube.py</code>

===If you want to save data from cube files===
* for saving the values from the cube files, use the functions from SaveCube.py
* for saving histogram data, use the function <code>PlotHistogram</code> from PlotCube.py with <code>save=True</code>
* for saving a short summary file of the minimum, maximum and lowest curvature points on the van der Waals surface, use <code>save=True</code> when running <code>PlotSurface</code> from PlotCube_mayavi.py

===If you want to plot surfaces, isosurfaces, slices===
* use the functions from [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/PlotCube_mayavi.py PlotCube_mayavi.py]. They are faster and better at 3D plotting than the equivalent functions from [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/PlotCube.py PlotCube.py]

If you want to generate static figures you can also consider using the 3D plotting functions from PlotCube.py. These are especially recommended when wanting to display atoms as they look better than their PlotCube_mayavi.py equivalents. However, keep in mind that Matplotlib sometimes fails at 3D rendering, which generates "incorrect" plots (i.e. elements that should be behind the rest of the plot appear at the front). Therefore, plots created using function from PlotCube.py should be double-checked (by comparing them with plots from PlotCube_mayavi.py, by example).

===If you want to plot histograms and KDEs===
* use <code>PlotHistogram</code> from PlotCube.py to plot a histogram and/or KDE directly from cube files
* use <code>OverlapKDEs</code> and <code>PlotHistogram</code> from AdditionalFunctions.py to plot histograms and KDEs from files written by <code>PlotHistogram</code> from PlotCube.py when <code>save=True</code>

Mod:Hunt Research Group/SAPT

2025-12-07T18:59:54Z

Wikiadmin: /* Run interactively */

==Run SAPT calculations using Psi4==

Psi4 website https://psicode.org/psi4manual/master/index.html

===PBS submission script===
:copy the submission script below into a file called runpsi4.sh
:copy your input file to testb.inp
:submit with
<pre>
sbatch runpsi4.sh
</pre>
<pre>
#!/bin/bash
#SBATCH --job-name=testb
#SBATCH --cpus-per-task=16
#SBATCH --mem=32GB
#SBATCH --partition=quicktest
#SBATCH --time=4:59:00
#SBATCH -o /nfs/scratch/huntpa/testb.out
#SBATCH -e /nfs/scratch/huntpa/testb.err

cp /nfs/home/huntpa/julian/testb.inp /nfs/scratch/huntpa/testb.inp
export PSI_SCRATCH='/nfs/scratch/huntpa/'

cd /nfs/scratch/huntpa/
module --quiet purge
module load foss/2024a GCC/13.3.0 OpenMPI/5.0.3
module load Miniconda3/23.9.0-0
export PIP_NO_CACHE_DIR=1
export PYTHONNOUSERSITE=1
source $(conda info --base)/etc/profile.d/conda.sh
conda activate psi4env
psi4 -i testb.inp

test -r testb.out
if [ $? -eq 0 ]
then
cp /nfs/scratch/huntpa/testb.out /nfs/home/huntpa/julian/testb.out
cp /nfs/scratch/huntpa/testb.log /nfs/home/huntpa/julian/testb.log
cp /nfs/scratch/huntpa/timer.dat /nfs/home/huntpa/julian/testb.time
fi
</pre>

===Run a test job===

Here is an examplpe input file for the SAPT(2) calculation of the H3N-HCl dimer. Copy the content into a file called testa.inp

<pre>
memory 14 GB

molecule mol {
0 1
N 1.876377 0.000001 -0.000006
H 2.237648 0.661745 -0.680615
H 2.237486 0.258575 0.913443
H 2.237570 -0.920339 -0.232740
--
0 1
Cl -1.177795 0.000000 -0.000001
H 0.175168 0.000012 -0.000026

units angstrom
symmetry c1
no_reorient
}

set basis 6-311+G(d,p)

energy('sapt2')
</pre>

Run the file

you will get the following files
:test.out has your output
:test.log has runtime info
:timer.dat has info on timing
check against the output below for the SAPT section
<pre>
SAPT Results
--------------------------------------------------------------------------------------------------------
Electrostatics -36.32899016 [mEh] -22.79678645 [kcal/mol] -95.38176366 [kJ/mol]
Elst10,r -36.63905676 [mEh] -22.99135619 [kcal/mol] -96.19584351 [kJ/mol]
Elst12,r 0.31006660 [mEh] 0.19456974 [kcal/mol] 0.81407985 [kJ/mol]

Exchange 51.13218109 [mEh] 32.08592939 [kcal/mol] 134.24754146 [kJ/mol]
Exch10 48.11718409 [mEh] 30.19399013 [kcal/mol] 126.33166682 [kJ/mol]
Exch10(S^2) 46.43751367 [mEh] 29.13998098 [kcal/mol] 121.92169213 [kJ/mol]
Exch11(S^2) 0.99070562 [mEh] 0.62167719 [kcal/mol] 2.60109761 [kJ/mol]
Exch12(S^2) 2.02429139 [mEh] 1.27026208 [kcal/mol] 5.31477704 [kJ/mol]

Induction -22.98775238 [mEh] -14.42503300 [kcal/mol] -60.35434386 [kJ/mol]
Ind20,r -25.00378267 [mEh] -15.69011116 [kcal/mol] -65.64743140 [kJ/mol]
Ind22 -1.93327324 [mEh] -1.21314732 [kcal/mol] -5.07580888 [kJ/mol]
Exch-Ind20,r 14.66201899 [mEh] 9.20055621 [kcal/mol] 38.49513087 [kJ/mol]
Exch-Ind22 1.13365603 [mEh] 0.71137993 [kcal/mol] 2.97641390 [kJ/mol]
delta HF,r (2) -11.84637149 [mEh] -7.43371065 [kcal/mol] -31.10264835 [kJ/mol]

Dispersion -7.02240313 [mEh] -4.40662468 [kcal/mol] -18.43731942 [kJ/mol]
Disp20 -9.19384826 [mEh] -5.76922712 [kcal/mol] -24.13844860 [kJ/mol]
Exch-Disp20 2.17144513 [mEh] 1.36260245 [kcal/mol] 5.70112918 [kJ/mol]

Total HF -10.71000784 [mEh] -6.72063166 [kcal/mol] -28.11912557 [kJ/mol]
Total SAPT0 -17.73241096 [mEh] -11.12725634 [kcal/mol] -46.55644499 [kJ/mol]
Total SAPT2 -15.20696457 [mEh] -9.54251473 [kcal/mol] -39.92588548 [kJ/mol]

Special recipe for scaled SAPT0 (see Manual):
Electrostatics sSAPT0 -36.63905676 [mEh] -22.99135619 [kcal/mol] -96.19584351 [kJ/mol]
Exchange sSAPT0 48.11718409 [mEh] 30.19399013 [kcal/mol] 126.33166682 [kJ/mol]
Induction sSAPT0 -20.53889410 [mEh] -12.88835117 [kcal/mol] -53.92486646 [kJ/mol]
Dispersion sSAPT0 -6.77815052 [mEh] -4.25335384 [kcal/mol] -17.79603418 [kJ/mol]
Total sSAPT0 -15.83891729 [mEh] -9.93907107 [kcal/mol] -41.58507733 [kJ/mol]
--------------------------------------------------------------------------------------------------------
</pre>

===Run interactively===

Psi4 comes as a pyhton module, thus we can use conda to create personal versions of Psi4 on the HPC.

*Start an interactive session
<pre>
srun --cpus-per-task=16 --mem=16G --time=0-05:00:00 --pty bash
</pre>

*Check to see what has been loaded
<pre>
module list
</pre>
make sure python and GCC and OpenMPI are all present, if not
<pre>
module load foss/2024a GCC/13.3.0 OpenMPI/5.0.3
</pre>

*Load your personal conda
Check the latest version of Miniconda
<pre>
module spider Miniconda
</pre>
Then load the latest version *NOTE* currently 23.9.0 is NOT WORKING
load the previous version
<pre>
module load Miniconda3/23.9.0-0
conda --version
module load Miniconda3/22.11.1-1
conda --version
</pre>
prevent conda from trying to use the system python and pip
conda init is not recommended as it modifies your shell configuration files. This can cause problems with the module system and other software. Instead, use the source $(conda info --base)/etc/profile.d/conda.sh command to activate conda in your current shell session.
<pre>
export PIP_NO_CACHE_DIR=1
export PYTHONNOUSERSITE=1
source $(conda info --base)/etc/profile.d/conda.sh
</pre>

*Create and activate a Psi4 environment
Create a Psi4 environment, check its there and then activate it:
<pre>
conda create -n psi4env
conda env list
# conda environments:
#
base /home/software/EasyBuild/software/Miniconda3/23.9.0-0
psi4env /nfs/home/huntpa/.conda/envs/psi4env
conda activate psi4env
</pre>

*Install PSI4
Install and check psi4 version
<pre>
conda install -c conda-forge psi4
Collecting package metadata (current_repodata.json): done
Solving environment: done
...
The following packages will be downloaded:
...
Proceed ([y]/n)?
...
Downloading and Extracting Packages:
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
</pre>
then test the version
<pre>
psi4 --version
1.9.1
</pre>

Run the job interactively
<pre>
psi4 testa.inp -n 10
</pre>

Mod:Hunt Research Group/SAPT

2025-12-07T18:58:51Z

Wikiadmin: /* Run interactively */

==Run SAPT calculations using Psi4==

Psi4 website https://psicode.org/psi4manual/master/index.html

===PBS submission script===
:copy the submission script below into a file called runpsi4.sh
:copy your input file to testb.inp
:submit with
<pre>
sbatch runpsi4.sh
</pre>
<pre>
#!/bin/bash
#SBATCH --job-name=testb
#SBATCH --cpus-per-task=16
#SBATCH --mem=32GB
#SBATCH --partition=quicktest
#SBATCH --time=4:59:00
#SBATCH -o /nfs/scratch/huntpa/testb.out
#SBATCH -e /nfs/scratch/huntpa/testb.err

cp /nfs/home/huntpa/julian/testb.inp /nfs/scratch/huntpa/testb.inp
export PSI_SCRATCH='/nfs/scratch/huntpa/'

cd /nfs/scratch/huntpa/
module --quiet purge
module load foss/2024a GCC/13.3.0 OpenMPI/5.0.3
module load Miniconda3/23.9.0-0
export PIP_NO_CACHE_DIR=1
export PYTHONNOUSERSITE=1
source $(conda info --base)/etc/profile.d/conda.sh
conda activate psi4env
psi4 -i testb.inp

test -r testb.out
if [ $? -eq 0 ]
then
cp /nfs/scratch/huntpa/testb.out /nfs/home/huntpa/julian/testb.out
cp /nfs/scratch/huntpa/testb.log /nfs/home/huntpa/julian/testb.log
cp /nfs/scratch/huntpa/timer.dat /nfs/home/huntpa/julian/testb.time
fi
</pre>

===Run a test job===

Here is an examplpe input file for the SAPT(2) calculation of the H3N-HCl dimer. Copy the content into a file called testa.inp

<pre>
memory 14 GB

molecule mol {
0 1
N 1.876377 0.000001 -0.000006
H 2.237648 0.661745 -0.680615
H 2.237486 0.258575 0.913443
H 2.237570 -0.920339 -0.232740
--
0 1
Cl -1.177795 0.000000 -0.000001
H 0.175168 0.000012 -0.000026

units angstrom
symmetry c1
no_reorient
}

set basis 6-311+G(d,p)

energy('sapt2')
</pre>

Run the file

you will get the following files
:test.out has your output
:test.log has runtime info
:timer.dat has info on timing
check against the output below for the SAPT section
<pre>
SAPT Results
--------------------------------------------------------------------------------------------------------
Electrostatics -36.32899016 [mEh] -22.79678645 [kcal/mol] -95.38176366 [kJ/mol]
Elst10,r -36.63905676 [mEh] -22.99135619 [kcal/mol] -96.19584351 [kJ/mol]
Elst12,r 0.31006660 [mEh] 0.19456974 [kcal/mol] 0.81407985 [kJ/mol]

Exchange 51.13218109 [mEh] 32.08592939 [kcal/mol] 134.24754146 [kJ/mol]
Exch10 48.11718409 [mEh] 30.19399013 [kcal/mol] 126.33166682 [kJ/mol]
Exch10(S^2) 46.43751367 [mEh] 29.13998098 [kcal/mol] 121.92169213 [kJ/mol]
Exch11(S^2) 0.99070562 [mEh] 0.62167719 [kcal/mol] 2.60109761 [kJ/mol]
Exch12(S^2) 2.02429139 [mEh] 1.27026208 [kcal/mol] 5.31477704 [kJ/mol]

Induction -22.98775238 [mEh] -14.42503300 [kcal/mol] -60.35434386 [kJ/mol]
Ind20,r -25.00378267 [mEh] -15.69011116 [kcal/mol] -65.64743140 [kJ/mol]
Ind22 -1.93327324 [mEh] -1.21314732 [kcal/mol] -5.07580888 [kJ/mol]
Exch-Ind20,r 14.66201899 [mEh] 9.20055621 [kcal/mol] 38.49513087 [kJ/mol]
Exch-Ind22 1.13365603 [mEh] 0.71137993 [kcal/mol] 2.97641390 [kJ/mol]
delta HF,r (2) -11.84637149 [mEh] -7.43371065 [kcal/mol] -31.10264835 [kJ/mol]

Dispersion -7.02240313 [mEh] -4.40662468 [kcal/mol] -18.43731942 [kJ/mol]
Disp20 -9.19384826 [mEh] -5.76922712 [kcal/mol] -24.13844860 [kJ/mol]
Exch-Disp20 2.17144513 [mEh] 1.36260245 [kcal/mol] 5.70112918 [kJ/mol]

Total HF -10.71000784 [mEh] -6.72063166 [kcal/mol] -28.11912557 [kJ/mol]
Total SAPT0 -17.73241096 [mEh] -11.12725634 [kcal/mol] -46.55644499 [kJ/mol]
Total SAPT2 -15.20696457 [mEh] -9.54251473 [kcal/mol] -39.92588548 [kJ/mol]

Special recipe for scaled SAPT0 (see Manual):
Electrostatics sSAPT0 -36.63905676 [mEh] -22.99135619 [kcal/mol] -96.19584351 [kJ/mol]
Exchange sSAPT0 48.11718409 [mEh] 30.19399013 [kcal/mol] 126.33166682 [kJ/mol]
Induction sSAPT0 -20.53889410 [mEh] -12.88835117 [kcal/mol] -53.92486646 [kJ/mol]
Dispersion sSAPT0 -6.77815052 [mEh] -4.25335384 [kcal/mol] -17.79603418 [kJ/mol]
Total sSAPT0 -15.83891729 [mEh] -9.93907107 [kcal/mol] -41.58507733 [kJ/mol]
--------------------------------------------------------------------------------------------------------
</pre>

===Run interactively===

Psi4 comes as a pyhton module, thus we can use conda to create personal versions of Psi4 on the HPC.

*Start an interactive session
<pre>
srun --cpus-per-task=16 --mem=16G --time=0-05:00:00 --pty bash
</pre>

*Check to see what has been loaded
<pre>
module list
</pre>
make sure python and GCC and OpenMPI are all present, if not
<pre>
module load foss/2024a GCC/13.3.0 OpenMPI/5.0.3
</pre>

*Load your personal conda
Check the latest version of Miniconda
<pre>
module spider Miniconda
</pre>
Then load the latest version *NOTE* currently 23.9.0 is NOT WORKING
load the previous version
<pre>
module load Miniconda3/23.9.0-0
conda --version
module load Miniconda3/22.11.1-1
conda --version
</pre>
prevent conda from trying to use the system python and pip
conda init is not recommended as it modifies your shell configuration files. This can cause problems with the module system and other software. Instead, use the source $(conda info --base)/etc/profile.d/conda.sh command to activate conda in your current shell session.
<pre>
export PIP_NO_CACHE_DIR=1
export PYTHONNOUSERSITE=1
source $(conda info --base)/etc/profile.d/conda.sh
</pre>

*Create and activate a Psi4 environment
Create a Psi4 environment:
<pre>
conda create -n psi4env
conda env list
# conda environments:
#
base /home/software/EasyBuild/software/Miniconda3/23.9.0-0
psi4env /nfs/home/huntpa/.conda/envs/psi4env
conda activate psi4env
</pre>

*Install PSI4
Install and check psi4 version
<pre>
conda install -c conda-forge psi4
Collecting package metadata (current_repodata.json): done
Solving environment: done
...
The following packages will be downloaded:
...
Proceed ([y]/n)?
...
Downloading and Extracting Packages:
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
</pre>
then test the version
<pre>
psi4 --version
1.9.1
</pre>

Run the job interactively
<pre>
psi4 testa.inp -n 10
</pre>

Mod:Hunt Research Group/SAPT

2025-12-07T18:56:57Z

Wikiadmin: /* Run interactively */

==Run SAPT calculations using Psi4==

Psi4 website https://psicode.org/psi4manual/master/index.html

===PBS submission script===
:copy the submission script below into a file called runpsi4.sh
:copy your input file to testb.inp
:submit with
<pre>
sbatch runpsi4.sh
</pre>
<pre>
#!/bin/bash
#SBATCH --job-name=testb
#SBATCH --cpus-per-task=16
#SBATCH --mem=32GB
#SBATCH --partition=quicktest
#SBATCH --time=4:59:00
#SBATCH -o /nfs/scratch/huntpa/testb.out
#SBATCH -e /nfs/scratch/huntpa/testb.err

cp /nfs/home/huntpa/julian/testb.inp /nfs/scratch/huntpa/testb.inp
export PSI_SCRATCH='/nfs/scratch/huntpa/'

cd /nfs/scratch/huntpa/
module --quiet purge
module load foss/2024a GCC/13.3.0 OpenMPI/5.0.3
module load Miniconda3/23.9.0-0
export PIP_NO_CACHE_DIR=1
export PYTHONNOUSERSITE=1
source $(conda info --base)/etc/profile.d/conda.sh
conda activate psi4env
psi4 -i testb.inp

test -r testb.out
if [ $? -eq 0 ]
then
cp /nfs/scratch/huntpa/testb.out /nfs/home/huntpa/julian/testb.out
cp /nfs/scratch/huntpa/testb.log /nfs/home/huntpa/julian/testb.log
cp /nfs/scratch/huntpa/timer.dat /nfs/home/huntpa/julian/testb.time
fi
</pre>

===Run a test job===

Here is an examplpe input file for the SAPT(2) calculation of the H3N-HCl dimer. Copy the content into a file called testa.inp

<pre>
memory 14 GB

molecule mol {
0 1
N 1.876377 0.000001 -0.000006
H 2.237648 0.661745 -0.680615
H 2.237486 0.258575 0.913443
H 2.237570 -0.920339 -0.232740
--
0 1
Cl -1.177795 0.000000 -0.000001
H 0.175168 0.000012 -0.000026

units angstrom
symmetry c1
no_reorient
}

set basis 6-311+G(d,p)

energy('sapt2')
</pre>

Run the file

you will get the following files
:test.out has your output
:test.log has runtime info
:timer.dat has info on timing
check against the output below for the SAPT section
<pre>
SAPT Results
--------------------------------------------------------------------------------------------------------
Electrostatics -36.32899016 [mEh] -22.79678645 [kcal/mol] -95.38176366 [kJ/mol]
Elst10,r -36.63905676 [mEh] -22.99135619 [kcal/mol] -96.19584351 [kJ/mol]
Elst12,r 0.31006660 [mEh] 0.19456974 [kcal/mol] 0.81407985 [kJ/mol]

Exchange 51.13218109 [mEh] 32.08592939 [kcal/mol] 134.24754146 [kJ/mol]
Exch10 48.11718409 [mEh] 30.19399013 [kcal/mol] 126.33166682 [kJ/mol]
Exch10(S^2) 46.43751367 [mEh] 29.13998098 [kcal/mol] 121.92169213 [kJ/mol]
Exch11(S^2) 0.99070562 [mEh] 0.62167719 [kcal/mol] 2.60109761 [kJ/mol]
Exch12(S^2) 2.02429139 [mEh] 1.27026208 [kcal/mol] 5.31477704 [kJ/mol]

Induction -22.98775238 [mEh] -14.42503300 [kcal/mol] -60.35434386 [kJ/mol]
Ind20,r -25.00378267 [mEh] -15.69011116 [kcal/mol] -65.64743140 [kJ/mol]
Ind22 -1.93327324 [mEh] -1.21314732 [kcal/mol] -5.07580888 [kJ/mol]
Exch-Ind20,r 14.66201899 [mEh] 9.20055621 [kcal/mol] 38.49513087 [kJ/mol]
Exch-Ind22 1.13365603 [mEh] 0.71137993 [kcal/mol] 2.97641390 [kJ/mol]
delta HF,r (2) -11.84637149 [mEh] -7.43371065 [kcal/mol] -31.10264835 [kJ/mol]

Dispersion -7.02240313 [mEh] -4.40662468 [kcal/mol] -18.43731942 [kJ/mol]
Disp20 -9.19384826 [mEh] -5.76922712 [kcal/mol] -24.13844860 [kJ/mol]
Exch-Disp20 2.17144513 [mEh] 1.36260245 [kcal/mol] 5.70112918 [kJ/mol]

Total HF -10.71000784 [mEh] -6.72063166 [kcal/mol] -28.11912557 [kJ/mol]
Total SAPT0 -17.73241096 [mEh] -11.12725634 [kcal/mol] -46.55644499 [kJ/mol]
Total SAPT2 -15.20696457 [mEh] -9.54251473 [kcal/mol] -39.92588548 [kJ/mol]

Special recipe for scaled SAPT0 (see Manual):
Electrostatics sSAPT0 -36.63905676 [mEh] -22.99135619 [kcal/mol] -96.19584351 [kJ/mol]
Exchange sSAPT0 48.11718409 [mEh] 30.19399013 [kcal/mol] 126.33166682 [kJ/mol]
Induction sSAPT0 -20.53889410 [mEh] -12.88835117 [kcal/mol] -53.92486646 [kJ/mol]
Dispersion sSAPT0 -6.77815052 [mEh] -4.25335384 [kcal/mol] -17.79603418 [kJ/mol]
Total sSAPT0 -15.83891729 [mEh] -9.93907107 [kcal/mol] -41.58507733 [kJ/mol]
--------------------------------------------------------------------------------------------------------
</pre>

===Run interactively===

Psi4 comes as a pyhton module, thus we can use conda to create personal versions of Psi4 on the HPC.

*Start an interactive session
<pre>
srun --cpus-per-task=16 --mem=16G --time=0-05:00:00 --pty bash
</pre>

*Check to see what has been loaded
<pre>
module list
</pre>
make sure python and GCC and OpenMPI are all present, if not
<pre>
module load foss/2024a GCC/13.3.0 OpenMPI/5.0.3
</pre>

*Load your personal conda
Check the latest version of Miniconda
<pre>
module spider Miniconda
</pre>
Then load the latest version *NOTE* currently 23.9.0 is NOT WORKING
load the previous version
<pre>
module load Miniconda3/23.9.0-0
conda --version
module load Miniconda3/22.11.1-1
conda --version
</pre>
prevent conda from trying to use the system python and pip
<pre>
export PIP_NO_CACHE_DIR=1
export PYTHONNOUSERSITE=1
source $(conda info --base)/etc/profile.d/conda.sh
</pre>

*Create and activate a Psi4 environment
Create a Psi4 environment:
<pre>
conda create -n psi4env
conda env list
# conda environments:
#
base /home/software/EasyBuild/software/Miniconda3/23.9.0-0
psi4env /nfs/home/huntpa/.conda/envs/psi4env
</pre>

<pre>

conda activate psi4env
</pre>
conda init is not recommended as it modifies your shell configuration files. This can cause problems with the module system and other software. Instead, use the source $(conda info --base)/etc/profile.d/conda.sh command to activate conda in your current shell session.

*Install PSI4
Install and check psi4 version
<pre>
conda install -c conda-forge psi4
Collecting package metadata (current_repodata.json): done
Solving environment: done
...
The following packages will be downloaded:
...
Proceed ([y]/n)?
...
Downloading and Extracting Packages:
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
</pre>
then test the version
<pre>
psi4 --version
1.9.1
</pre>

Run the job interactively
<pre>
psi4 testa.inp -n 10
</pre>

Mod:Hunt Research Group/SAPT

2025-12-07T18:53:57Z

Wikiadmin: /* Run interactively */

==Run SAPT calculations using Psi4==

Psi4 website https://psicode.org/psi4manual/master/index.html

===PBS submission script===
:copy the submission script below into a file called runpsi4.sh
:copy your input file to testb.inp
:submit with
<pre>
sbatch runpsi4.sh
</pre>
<pre>
#!/bin/bash
#SBATCH --job-name=testb
#SBATCH --cpus-per-task=16
#SBATCH --mem=32GB
#SBATCH --partition=quicktest
#SBATCH --time=4:59:00
#SBATCH -o /nfs/scratch/huntpa/testb.out
#SBATCH -e /nfs/scratch/huntpa/testb.err

cp /nfs/home/huntpa/julian/testb.inp /nfs/scratch/huntpa/testb.inp
export PSI_SCRATCH='/nfs/scratch/huntpa/'

cd /nfs/scratch/huntpa/
module --quiet purge
module load foss/2024a GCC/13.3.0 OpenMPI/5.0.3
module load Miniconda3/23.9.0-0
export PIP_NO_CACHE_DIR=1
export PYTHONNOUSERSITE=1
source $(conda info --base)/etc/profile.d/conda.sh
conda activate psi4env
psi4 -i testb.inp

test -r testb.out
if [ $? -eq 0 ]
then
cp /nfs/scratch/huntpa/testb.out /nfs/home/huntpa/julian/testb.out
cp /nfs/scratch/huntpa/testb.log /nfs/home/huntpa/julian/testb.log
cp /nfs/scratch/huntpa/timer.dat /nfs/home/huntpa/julian/testb.time
fi
</pre>

===Run a test job===

Here is an examplpe input file for the SAPT(2) calculation of the H3N-HCl dimer. Copy the content into a file called testa.inp

<pre>
memory 14 GB

molecule mol {
0 1
N 1.876377 0.000001 -0.000006
H 2.237648 0.661745 -0.680615
H 2.237486 0.258575 0.913443
H 2.237570 -0.920339 -0.232740
--
0 1
Cl -1.177795 0.000000 -0.000001
H 0.175168 0.000012 -0.000026

units angstrom
symmetry c1
no_reorient
}

set basis 6-311+G(d,p)

energy('sapt2')
</pre>

Run the file

you will get the following files
:test.out has your output
:test.log has runtime info
:timer.dat has info on timing
check against the output below for the SAPT section
<pre>
SAPT Results
--------------------------------------------------------------------------------------------------------
Electrostatics -36.32899016 [mEh] -22.79678645 [kcal/mol] -95.38176366 [kJ/mol]
Elst10,r -36.63905676 [mEh] -22.99135619 [kcal/mol] -96.19584351 [kJ/mol]
Elst12,r 0.31006660 [mEh] 0.19456974 [kcal/mol] 0.81407985 [kJ/mol]

Exchange 51.13218109 [mEh] 32.08592939 [kcal/mol] 134.24754146 [kJ/mol]
Exch10 48.11718409 [mEh] 30.19399013 [kcal/mol] 126.33166682 [kJ/mol]
Exch10(S^2) 46.43751367 [mEh] 29.13998098 [kcal/mol] 121.92169213 [kJ/mol]
Exch11(S^2) 0.99070562 [mEh] 0.62167719 [kcal/mol] 2.60109761 [kJ/mol]
Exch12(S^2) 2.02429139 [mEh] 1.27026208 [kcal/mol] 5.31477704 [kJ/mol]

Induction -22.98775238 [mEh] -14.42503300 [kcal/mol] -60.35434386 [kJ/mol]
Ind20,r -25.00378267 [mEh] -15.69011116 [kcal/mol] -65.64743140 [kJ/mol]
Ind22 -1.93327324 [mEh] -1.21314732 [kcal/mol] -5.07580888 [kJ/mol]
Exch-Ind20,r 14.66201899 [mEh] 9.20055621 [kcal/mol] 38.49513087 [kJ/mol]
Exch-Ind22 1.13365603 [mEh] 0.71137993 [kcal/mol] 2.97641390 [kJ/mol]
delta HF,r (2) -11.84637149 [mEh] -7.43371065 [kcal/mol] -31.10264835 [kJ/mol]

Dispersion -7.02240313 [mEh] -4.40662468 [kcal/mol] -18.43731942 [kJ/mol]
Disp20 -9.19384826 [mEh] -5.76922712 [kcal/mol] -24.13844860 [kJ/mol]
Exch-Disp20 2.17144513 [mEh] 1.36260245 [kcal/mol] 5.70112918 [kJ/mol]

Total HF -10.71000784 [mEh] -6.72063166 [kcal/mol] -28.11912557 [kJ/mol]
Total SAPT0 -17.73241096 [mEh] -11.12725634 [kcal/mol] -46.55644499 [kJ/mol]
Total SAPT2 -15.20696457 [mEh] -9.54251473 [kcal/mol] -39.92588548 [kJ/mol]

Special recipe for scaled SAPT0 (see Manual):
Electrostatics sSAPT0 -36.63905676 [mEh] -22.99135619 [kcal/mol] -96.19584351 [kJ/mol]
Exchange sSAPT0 48.11718409 [mEh] 30.19399013 [kcal/mol] 126.33166682 [kJ/mol]
Induction sSAPT0 -20.53889410 [mEh] -12.88835117 [kcal/mol] -53.92486646 [kJ/mol]
Dispersion sSAPT0 -6.77815052 [mEh] -4.25335384 [kcal/mol] -17.79603418 [kJ/mol]
Total sSAPT0 -15.83891729 [mEh] -9.93907107 [kcal/mol] -41.58507733 [kJ/mol]
--------------------------------------------------------------------------------------------------------
</pre>

===Run interactively===

Psi4 comes as a pyhton module, thus we can use conda to create personal versions of Psi4 on the HPC.

*Start an interactive session
<pre>
srun --cpus-per-task=16 --mem=16G --time=0-05:00:00 --pty bash
</pre>

*Check to see what has been loaded
<pre>
module list
</pre>
make sure python and GCC and OpenMPI are all present, if not
<pre>
module load foss/2024a GCC/13.3.0 OpenMPI/5.0.3
</pre>

*Load your personal conda
Check the latest version of Miniconda
<pre>
module spider Miniconda
</pre>
Then load the latest version *NOTE* currently 23.9.0 is NOT WORKING
load the previous version
<pre>
module load Miniconda3/23.9.0-0
conda --version
module load Miniconda3/22.11.1-1
conda --version
</pre>
prevent conda from trying to use the system python and pip
<pre>
export PIP_NO_CACHE_DIR=1
export PYTHONNOUSERSITE=1
</pre>

*Create and activate a Psi4 environment
Create a Psi4 environment:
<pre>
conda create -n psi4env
conda env list
# conda environments:
#
base /home/software/EasyBuild/software/Miniconda3/23.9.0-0
psi4env /nfs/home/huntpa/.conda/envs/psi4env
</pre>

<pre>
source $(conda info --base)/etc/profile.d/conda.sh
conda activate psi4env
</pre>
conda init is not recommended as it modifies your shell configuration files. This can cause problems with the module system and other software. Instead, use the source $(conda info --base)/etc/profile.d/conda.sh command to activate conda in your current shell session.

*Install PSI4
Install and check psi4 version
<pre>
conda install -c conda-forge psi4
Collecting package metadata (current_repodata.json): done
Solving environment: done
...
The following packages will be downloaded:
...
Proceed ([y]/n)?
...
Downloading and Extracting Packages:
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
</pre>
then test the version
<pre>
psi4 --version
1.9.1
</pre>

Run the job interactively
<pre>
psi4 testa.inp -n 10
</pre>

Mod:Hunt Research Group/SAPT

2025-12-07T18:53:16Z

Wikiadmin: /* Run interactively */

==Run SAPT calculations using Psi4==

Psi4 website https://psicode.org/psi4manual/master/index.html

===PBS submission script===
:copy the submission script below into a file called runpsi4.sh
:copy your input file to testb.inp
:submit with
<pre>
sbatch runpsi4.sh
</pre>
<pre>
#!/bin/bash
#SBATCH --job-name=testb
#SBATCH --cpus-per-task=16
#SBATCH --mem=32GB
#SBATCH --partition=quicktest
#SBATCH --time=4:59:00
#SBATCH -o /nfs/scratch/huntpa/testb.out
#SBATCH -e /nfs/scratch/huntpa/testb.err

cp /nfs/home/huntpa/julian/testb.inp /nfs/scratch/huntpa/testb.inp
export PSI_SCRATCH='/nfs/scratch/huntpa/'

cd /nfs/scratch/huntpa/
module --quiet purge
module load foss/2024a GCC/13.3.0 OpenMPI/5.0.3
module load Miniconda3/23.9.0-0
export PIP_NO_CACHE_DIR=1
export PYTHONNOUSERSITE=1
source $(conda info --base)/etc/profile.d/conda.sh
conda activate psi4env
psi4 -i testb.inp

test -r testb.out
if [ $? -eq 0 ]
then
cp /nfs/scratch/huntpa/testb.out /nfs/home/huntpa/julian/testb.out
cp /nfs/scratch/huntpa/testb.log /nfs/home/huntpa/julian/testb.log
cp /nfs/scratch/huntpa/timer.dat /nfs/home/huntpa/julian/testb.time
fi
</pre>

===Run a test job===

Here is an examplpe input file for the SAPT(2) calculation of the H3N-HCl dimer. Copy the content into a file called testa.inp

<pre>
memory 14 GB

molecule mol {
0 1
N 1.876377 0.000001 -0.000006
H 2.237648 0.661745 -0.680615
H 2.237486 0.258575 0.913443
H 2.237570 -0.920339 -0.232740
--
0 1
Cl -1.177795 0.000000 -0.000001
H 0.175168 0.000012 -0.000026

units angstrom
symmetry c1
no_reorient
}

set basis 6-311+G(d,p)

energy('sapt2')
</pre>

Run the file

you will get the following files
:test.out has your output
:test.log has runtime info
:timer.dat has info on timing
check against the output below for the SAPT section
<pre>
SAPT Results
--------------------------------------------------------------------------------------------------------
Electrostatics -36.32899016 [mEh] -22.79678645 [kcal/mol] -95.38176366 [kJ/mol]
Elst10,r -36.63905676 [mEh] -22.99135619 [kcal/mol] -96.19584351 [kJ/mol]
Elst12,r 0.31006660 [mEh] 0.19456974 [kcal/mol] 0.81407985 [kJ/mol]

Exchange 51.13218109 [mEh] 32.08592939 [kcal/mol] 134.24754146 [kJ/mol]
Exch10 48.11718409 [mEh] 30.19399013 [kcal/mol] 126.33166682 [kJ/mol]
Exch10(S^2) 46.43751367 [mEh] 29.13998098 [kcal/mol] 121.92169213 [kJ/mol]
Exch11(S^2) 0.99070562 [mEh] 0.62167719 [kcal/mol] 2.60109761 [kJ/mol]
Exch12(S^2) 2.02429139 [mEh] 1.27026208 [kcal/mol] 5.31477704 [kJ/mol]

Induction -22.98775238 [mEh] -14.42503300 [kcal/mol] -60.35434386 [kJ/mol]
Ind20,r -25.00378267 [mEh] -15.69011116 [kcal/mol] -65.64743140 [kJ/mol]
Ind22 -1.93327324 [mEh] -1.21314732 [kcal/mol] -5.07580888 [kJ/mol]
Exch-Ind20,r 14.66201899 [mEh] 9.20055621 [kcal/mol] 38.49513087 [kJ/mol]
Exch-Ind22 1.13365603 [mEh] 0.71137993 [kcal/mol] 2.97641390 [kJ/mol]
delta HF,r (2) -11.84637149 [mEh] -7.43371065 [kcal/mol] -31.10264835 [kJ/mol]

Dispersion -7.02240313 [mEh] -4.40662468 [kcal/mol] -18.43731942 [kJ/mol]
Disp20 -9.19384826 [mEh] -5.76922712 [kcal/mol] -24.13844860 [kJ/mol]
Exch-Disp20 2.17144513 [mEh] 1.36260245 [kcal/mol] 5.70112918 [kJ/mol]

Total HF -10.71000784 [mEh] -6.72063166 [kcal/mol] -28.11912557 [kJ/mol]
Total SAPT0 -17.73241096 [mEh] -11.12725634 [kcal/mol] -46.55644499 [kJ/mol]
Total SAPT2 -15.20696457 [mEh] -9.54251473 [kcal/mol] -39.92588548 [kJ/mol]

Special recipe for scaled SAPT0 (see Manual):
Electrostatics sSAPT0 -36.63905676 [mEh] -22.99135619 [kcal/mol] -96.19584351 [kJ/mol]
Exchange sSAPT0 48.11718409 [mEh] 30.19399013 [kcal/mol] 126.33166682 [kJ/mol]
Induction sSAPT0 -20.53889410 [mEh] -12.88835117 [kcal/mol] -53.92486646 [kJ/mol]
Dispersion sSAPT0 -6.77815052 [mEh] -4.25335384 [kcal/mol] -17.79603418 [kJ/mol]
Total sSAPT0 -15.83891729 [mEh] -9.93907107 [kcal/mol] -41.58507733 [kJ/mol]
--------------------------------------------------------------------------------------------------------
</pre>

===Run interactively===

Psi4 comes as a pyhton module, thus we can use conda to create personal versions of Psi4 on the HPC.

*Start an interactive session
<pre>
srun --cpus-per-task=16 --mem=16G --time=0-05:00:00 --pty bash
</pre>

*Check to see what has been loaded
<pre>
module list
</pre>
make sure python and GCC and OpenMPI are all present, if not
<pre>
module load foss/2024a GCC/13.3.0 OpenMPI/5.0.3
</pre>

*Load your personal conda
Check the latest version of Miniconda
<pre>
module spider Miniconda
</pre>
Then load the latest version *NOTE* currently 23.9.0 is NOT WORKING
load the previous version
<pre>
module load Miniconda3/23.9.0-0
conda --version
module load Miniconda3/22.11.1-1
conda --version
</pre>
conda 23.9.0
<pre>
export PIP_NO_CACHE_DIR=1
export PYTHONNOUSERSITE=1
</pre>
prevents conda from trying to use the system python and pip

*Create and activate a Psi4 environment
Create a Psi4 environment:
<pre>
conda create -n psi4env
conda env list
# conda environments:
#
base /home/software/EasyBuild/software/Miniconda3/23.9.0-0
psi4env /nfs/home/huntpa/.conda/envs/psi4env
</pre>

<pre>
source $(conda info --base)/etc/profile.d/conda.sh
conda activate psi4env
</pre>
conda init is not recommended as it modifies your shell configuration files. This can cause problems with the module system and other software. Instead, use the source $(conda info --base)/etc/profile.d/conda.sh command to activate conda in your current shell session.

*Install PSI4
Install and check psi4 version
<pre>
conda install -c conda-forge psi4
Collecting package metadata (current_repodata.json): done
Solving environment: done
...
The following packages will be downloaded:
...
Proceed ([y]/n)?
...
Downloading and Extracting Packages:
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
</pre>
then test the version
<pre>
psi4 --version
1.9.1
</pre>

Run the job interactively
<pre>
psi4 testa.inp -n 10
</pre>

Mod:Hunt Research Group/SAPT

2025-12-07T18:50:42Z

Wikiadmin: /* Run interactively */

==Run SAPT calculations using Psi4==

Psi4 website https://psicode.org/psi4manual/master/index.html

===PBS submission script===
:copy the submission script below into a file called runpsi4.sh
:copy your input file to testb.inp
:submit with
<pre>
sbatch runpsi4.sh
</pre>
<pre>
#!/bin/bash
#SBATCH --job-name=testb
#SBATCH --cpus-per-task=16
#SBATCH --mem=32GB
#SBATCH --partition=quicktest
#SBATCH --time=4:59:00
#SBATCH -o /nfs/scratch/huntpa/testb.out
#SBATCH -e /nfs/scratch/huntpa/testb.err

cp /nfs/home/huntpa/julian/testb.inp /nfs/scratch/huntpa/testb.inp
export PSI_SCRATCH='/nfs/scratch/huntpa/'

cd /nfs/scratch/huntpa/
module --quiet purge
module load foss/2024a GCC/13.3.0 OpenMPI/5.0.3
module load Miniconda3/23.9.0-0
export PIP_NO_CACHE_DIR=1
export PYTHONNOUSERSITE=1
source $(conda info --base)/etc/profile.d/conda.sh
conda activate psi4env
psi4 -i testb.inp

test -r testb.out
if [ $? -eq 0 ]
then
cp /nfs/scratch/huntpa/testb.out /nfs/home/huntpa/julian/testb.out
cp /nfs/scratch/huntpa/testb.log /nfs/home/huntpa/julian/testb.log
cp /nfs/scratch/huntpa/timer.dat /nfs/home/huntpa/julian/testb.time
fi
</pre>

===Run a test job===

Here is an examplpe input file for the SAPT(2) calculation of the H3N-HCl dimer. Copy the content into a file called testa.inp

<pre>
memory 14 GB

molecule mol {
0 1
N 1.876377 0.000001 -0.000006
H 2.237648 0.661745 -0.680615
H 2.237486 0.258575 0.913443
H 2.237570 -0.920339 -0.232740
--
0 1
Cl -1.177795 0.000000 -0.000001
H 0.175168 0.000012 -0.000026

units angstrom
symmetry c1
no_reorient
}

set basis 6-311+G(d,p)

energy('sapt2')
</pre>

Run the file

you will get the following files
:test.out has your output
:test.log has runtime info
:timer.dat has info on timing
check against the output below for the SAPT section
<pre>
SAPT Results
--------------------------------------------------------------------------------------------------------
Electrostatics -36.32899016 [mEh] -22.79678645 [kcal/mol] -95.38176366 [kJ/mol]
Elst10,r -36.63905676 [mEh] -22.99135619 [kcal/mol] -96.19584351 [kJ/mol]
Elst12,r 0.31006660 [mEh] 0.19456974 [kcal/mol] 0.81407985 [kJ/mol]

Exchange 51.13218109 [mEh] 32.08592939 [kcal/mol] 134.24754146 [kJ/mol]
Exch10 48.11718409 [mEh] 30.19399013 [kcal/mol] 126.33166682 [kJ/mol]
Exch10(S^2) 46.43751367 [mEh] 29.13998098 [kcal/mol] 121.92169213 [kJ/mol]
Exch11(S^2) 0.99070562 [mEh] 0.62167719 [kcal/mol] 2.60109761 [kJ/mol]
Exch12(S^2) 2.02429139 [mEh] 1.27026208 [kcal/mol] 5.31477704 [kJ/mol]

Induction -22.98775238 [mEh] -14.42503300 [kcal/mol] -60.35434386 [kJ/mol]
Ind20,r -25.00378267 [mEh] -15.69011116 [kcal/mol] -65.64743140 [kJ/mol]
Ind22 -1.93327324 [mEh] -1.21314732 [kcal/mol] -5.07580888 [kJ/mol]
Exch-Ind20,r 14.66201899 [mEh] 9.20055621 [kcal/mol] 38.49513087 [kJ/mol]
Exch-Ind22 1.13365603 [mEh] 0.71137993 [kcal/mol] 2.97641390 [kJ/mol]
delta HF,r (2) -11.84637149 [mEh] -7.43371065 [kcal/mol] -31.10264835 [kJ/mol]

Dispersion -7.02240313 [mEh] -4.40662468 [kcal/mol] -18.43731942 [kJ/mol]
Disp20 -9.19384826 [mEh] -5.76922712 [kcal/mol] -24.13844860 [kJ/mol]
Exch-Disp20 2.17144513 [mEh] 1.36260245 [kcal/mol] 5.70112918 [kJ/mol]

Total HF -10.71000784 [mEh] -6.72063166 [kcal/mol] -28.11912557 [kJ/mol]
Total SAPT0 -17.73241096 [mEh] -11.12725634 [kcal/mol] -46.55644499 [kJ/mol]
Total SAPT2 -15.20696457 [mEh] -9.54251473 [kcal/mol] -39.92588548 [kJ/mol]

Special recipe for scaled SAPT0 (see Manual):
Electrostatics sSAPT0 -36.63905676 [mEh] -22.99135619 [kcal/mol] -96.19584351 [kJ/mol]
Exchange sSAPT0 48.11718409 [mEh] 30.19399013 [kcal/mol] 126.33166682 [kJ/mol]
Induction sSAPT0 -20.53889410 [mEh] -12.88835117 [kcal/mol] -53.92486646 [kJ/mol]
Dispersion sSAPT0 -6.77815052 [mEh] -4.25335384 [kcal/mol] -17.79603418 [kJ/mol]
Total sSAPT0 -15.83891729 [mEh] -9.93907107 [kcal/mol] -41.58507733 [kJ/mol]
--------------------------------------------------------------------------------------------------------
</pre>

===Run interactively===

Psi4 comes as a pyhton module, thus we can use conda to create personal versions of Psi4 on the HPC.

*Start an interactive session
<pre>
srun --cpus-per-task=16 --mem=16G --time=0-05:00:00 --pty bash
</pre>

*Check to see what has been loaded
<pre>
module list
</pre>
make sure python and GCC and OpenMPI are all present, if not
<pre>
module load foss/2024a GCC/13.3.0 OpenMPI/5.0.3
</pre>

*Load your personal conda
Check the latest version of Miniconda
<pre>
module spider Miniconda
</pre>
Then load the latest version
<pre>
module load Miniconda3/23.9.0-0
conda --version
</pre>
conda 23.9.0
<pre>
export PIP_NO_CACHE_DIR=1
export PYTHONNOUSERSITE=1
</pre>
prevents conda from trying to use the system python and pip

*Create and activate a Psi4 environment
Create a Psi4 environment:
<pre>
conda create -n psi4env
conda env list
# conda environments:
#
base /home/software/EasyBuild/software/Miniconda3/23.9.0-0
psi4env /nfs/home/huntpa/.conda/envs/psi4env
</pre>

<pre>
source $(conda info --base)/etc/profile.d/conda.sh
conda activate psi4env
</pre>
conda init is not recommended as it modifies your shell configuration files. This can cause problems with the module system and other software. Instead, use the source $(conda info --base)/etc/profile.d/conda.sh command to activate conda in your current shell session.

*Install PSI4
Install and check psi4 version
<pre>
conda install -c conda-forge psi4
Collecting package metadata (current_repodata.json): done
Solving environment: done
...
The following packages will be downloaded:
...
Proceed ([y]/n)?
...
Downloading and Extracting Packages:
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
</pre>
then test the version
<pre>
psi4 --version
1.9.1
</pre>

Run the job interactively
<pre>
psi4 testa.inp -n 10
</pre>

Mod:Hunt Research Group/SAPT

2025-12-04T18:54:39Z

Wikiadmin: /* Run interactively */

==Run SAPT calculations using Psi4==

Psi4 website https://psicode.org/psi4manual/master/index.html

===PBS submission script===
:copy the submission script below into a file called runpsi4.sh
:copy your input file to testb.inp
:submit with
<pre>
sbatch runpsi4.sh
</pre>
<pre>
#!/bin/bash
#SBATCH --job-name=testb
#SBATCH --cpus-per-task=16
#SBATCH --mem=32GB
#SBATCH --partition=quicktest
#SBATCH --time=4:59:00
#SBATCH -o /nfs/scratch/huntpa/testb.out
#SBATCH -e /nfs/scratch/huntpa/testb.err

cp /nfs/home/huntpa/julian/testb.inp /nfs/scratch/huntpa/testb.inp
export PSI_SCRATCH='/nfs/scratch/huntpa/'

cd /nfs/scratch/huntpa/
module --quiet purge
module load foss/2024a GCC/13.3.0 OpenMPI/5.0.3
module load Miniconda3/23.9.0-0
export PIP_NO_CACHE_DIR=1
export PYTHONNOUSERSITE=1
source $(conda info --base)/etc/profile.d/conda.sh
conda activate psi4env
psi4 -i testb.inp

test -r testb.out
if [ $? -eq 0 ]
then
cp /nfs/scratch/huntpa/testb.out /nfs/home/huntpa/julian/testb.out
cp /nfs/scratch/huntpa/testb.log /nfs/home/huntpa/julian/testb.log
cp /nfs/scratch/huntpa/timer.dat /nfs/home/huntpa/julian/testb.time
fi
</pre>

===Run a test job===

Here is an examplpe input file for the SAPT(2) calculation of the H3N-HCl dimer. Copy the content into a file called testa.inp

<pre>
memory 14 GB

molecule mol {
0 1
N 1.876377 0.000001 -0.000006
H 2.237648 0.661745 -0.680615
H 2.237486 0.258575 0.913443
H 2.237570 -0.920339 -0.232740
--
0 1
Cl -1.177795 0.000000 -0.000001
H 0.175168 0.000012 -0.000026

units angstrom
symmetry c1
no_reorient
}

set basis 6-311+G(d,p)

energy('sapt2')
</pre>

Run the file

you will get the following files
:test.out has your output
:test.log has runtime info
:timer.dat has info on timing
check against the output below for the SAPT section
<pre>
SAPT Results
--------------------------------------------------------------------------------------------------------
Electrostatics -36.32899016 [mEh] -22.79678645 [kcal/mol] -95.38176366 [kJ/mol]
Elst10,r -36.63905676 [mEh] -22.99135619 [kcal/mol] -96.19584351 [kJ/mol]
Elst12,r 0.31006660 [mEh] 0.19456974 [kcal/mol] 0.81407985 [kJ/mol]

Exchange 51.13218109 [mEh] 32.08592939 [kcal/mol] 134.24754146 [kJ/mol]
Exch10 48.11718409 [mEh] 30.19399013 [kcal/mol] 126.33166682 [kJ/mol]
Exch10(S^2) 46.43751367 [mEh] 29.13998098 [kcal/mol] 121.92169213 [kJ/mol]
Exch11(S^2) 0.99070562 [mEh] 0.62167719 [kcal/mol] 2.60109761 [kJ/mol]
Exch12(S^2) 2.02429139 [mEh] 1.27026208 [kcal/mol] 5.31477704 [kJ/mol]

Induction -22.98775238 [mEh] -14.42503300 [kcal/mol] -60.35434386 [kJ/mol]
Ind20,r -25.00378267 [mEh] -15.69011116 [kcal/mol] -65.64743140 [kJ/mol]
Ind22 -1.93327324 [mEh] -1.21314732 [kcal/mol] -5.07580888 [kJ/mol]
Exch-Ind20,r 14.66201899 [mEh] 9.20055621 [kcal/mol] 38.49513087 [kJ/mol]
Exch-Ind22 1.13365603 [mEh] 0.71137993 [kcal/mol] 2.97641390 [kJ/mol]
delta HF,r (2) -11.84637149 [mEh] -7.43371065 [kcal/mol] -31.10264835 [kJ/mol]

Dispersion -7.02240313 [mEh] -4.40662468 [kcal/mol] -18.43731942 [kJ/mol]
Disp20 -9.19384826 [mEh] -5.76922712 [kcal/mol] -24.13844860 [kJ/mol]
Exch-Disp20 2.17144513 [mEh] 1.36260245 [kcal/mol] 5.70112918 [kJ/mol]

Total HF -10.71000784 [mEh] -6.72063166 [kcal/mol] -28.11912557 [kJ/mol]
Total SAPT0 -17.73241096 [mEh] -11.12725634 [kcal/mol] -46.55644499 [kJ/mol]
Total SAPT2 -15.20696457 [mEh] -9.54251473 [kcal/mol] -39.92588548 [kJ/mol]

Special recipe for scaled SAPT0 (see Manual):
Electrostatics sSAPT0 -36.63905676 [mEh] -22.99135619 [kcal/mol] -96.19584351 [kJ/mol]
Exchange sSAPT0 48.11718409 [mEh] 30.19399013 [kcal/mol] 126.33166682 [kJ/mol]
Induction sSAPT0 -20.53889410 [mEh] -12.88835117 [kcal/mol] -53.92486646 [kJ/mol]
Dispersion sSAPT0 -6.77815052 [mEh] -4.25335384 [kcal/mol] -17.79603418 [kJ/mol]
Total sSAPT0 -15.83891729 [mEh] -9.93907107 [kcal/mol] -41.58507733 [kJ/mol]
--------------------------------------------------------------------------------------------------------
</pre>

===Run interactively===

Psi4 comes as a pyhton module, thus we can use conda to create personal versions of Psi4 on the HPC.

*Start an interactive session
<pre>
srun --cpus-per-task=16 --mem=16G --time=0-05:00:00 --pty bash
</pre>

*Load your personal conda
Check the latest version of Miniconda
<pre>
module spider Miniconda
</pre>
Then load the latest version
<pre>
module load Miniconda3/23.9.0-0
conda --version
</pre>
conda 23.9.0
<pre>
export PIP_NO_CACHE_DIR=1
export PYTHONNOUSERSITE=1
</pre>
prevents conda from trying to use the system python and pip

*Create and activate a Psi4 environment
Create a Psi4 environment:
<pre>
conda create -n psi4env
conda env list
# conda environments:
#
base /home/software/EasyBuild/software/Miniconda3/23.9.0-0
psi4env /nfs/home/huntpa/.conda/envs/psi4env
</pre>

<pre>
source $(conda info --base)/etc/profile.d/conda.sh
conda activate psi4env
</pre>
conda init is not recommended as it modifies your shell configuration files. This can cause problems with the module system and other software. Instead, use the source $(conda info --base)/etc/profile.d/conda.sh command to activate conda in your current shell session.

*Install PSI4
Install and check psi4 version
<pre>
conda install -c conda-forge psi4
Collecting package metadata (current_repodata.json): done
Solving environment: done
...
The following packages will be downloaded:
...
Proceed ([y]/n)?
...
Downloading and Extracting Packages:
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
</pre>
then test the version
<pre>
psi4 --version
1.9.1
</pre>

Run the job interactively
<pre>
psi4 testa.inp -n 10
</pre>

Mod:Hunt Research Group/SAPT

2025-12-04T18:53:55Z

Wikiadmin: /* Run a test job */

==Run SAPT calculations using Psi4==

Psi4 website https://psicode.org/psi4manual/master/index.html

===PBS submission script===
:copy the submission script below into a file called runpsi4.sh
:copy your input file to testb.inp
:submit with
<pre>
sbatch runpsi4.sh
</pre>
<pre>
#!/bin/bash
#SBATCH --job-name=testb
#SBATCH --cpus-per-task=16
#SBATCH --mem=32GB
#SBATCH --partition=quicktest
#SBATCH --time=4:59:00
#SBATCH -o /nfs/scratch/huntpa/testb.out
#SBATCH -e /nfs/scratch/huntpa/testb.err

cp /nfs/home/huntpa/julian/testb.inp /nfs/scratch/huntpa/testb.inp
export PSI_SCRATCH='/nfs/scratch/huntpa/'

cd /nfs/scratch/huntpa/
module --quiet purge
module load foss/2024a GCC/13.3.0 OpenMPI/5.0.3
module load Miniconda3/23.9.0-0
export PIP_NO_CACHE_DIR=1
export PYTHONNOUSERSITE=1
source $(conda info --base)/etc/profile.d/conda.sh
conda activate psi4env
psi4 -i testb.inp

test -r testb.out
if [ $? -eq 0 ]
then
cp /nfs/scratch/huntpa/testb.out /nfs/home/huntpa/julian/testb.out
cp /nfs/scratch/huntpa/testb.log /nfs/home/huntpa/julian/testb.log
cp /nfs/scratch/huntpa/timer.dat /nfs/home/huntpa/julian/testb.time
fi
</pre>

===Run a test job===

Here is an examplpe input file for the SAPT(2) calculation of the H3N-HCl dimer. Copy the content into a file called testa.inp

<pre>
memory 14 GB

molecule mol {
0 1
N 1.876377 0.000001 -0.000006
H 2.237648 0.661745 -0.680615
H 2.237486 0.258575 0.913443
H 2.237570 -0.920339 -0.232740
--
0 1
Cl -1.177795 0.000000 -0.000001
H 0.175168 0.000012 -0.000026

units angstrom
symmetry c1
no_reorient
}

set basis 6-311+G(d,p)

energy('sapt2')
</pre>

Run the file

you will get the following files
:test.out has your output
:test.log has runtime info
:timer.dat has info on timing
check against the output below for the SAPT section
<pre>
SAPT Results
--------------------------------------------------------------------------------------------------------
Electrostatics -36.32899016 [mEh] -22.79678645 [kcal/mol] -95.38176366 [kJ/mol]
Elst10,r -36.63905676 [mEh] -22.99135619 [kcal/mol] -96.19584351 [kJ/mol]
Elst12,r 0.31006660 [mEh] 0.19456974 [kcal/mol] 0.81407985 [kJ/mol]

Exchange 51.13218109 [mEh] 32.08592939 [kcal/mol] 134.24754146 [kJ/mol]
Exch10 48.11718409 [mEh] 30.19399013 [kcal/mol] 126.33166682 [kJ/mol]
Exch10(S^2) 46.43751367 [mEh] 29.13998098 [kcal/mol] 121.92169213 [kJ/mol]
Exch11(S^2) 0.99070562 [mEh] 0.62167719 [kcal/mol] 2.60109761 [kJ/mol]
Exch12(S^2) 2.02429139 [mEh] 1.27026208 [kcal/mol] 5.31477704 [kJ/mol]

Induction -22.98775238 [mEh] -14.42503300 [kcal/mol] -60.35434386 [kJ/mol]
Ind20,r -25.00378267 [mEh] -15.69011116 [kcal/mol] -65.64743140 [kJ/mol]
Ind22 -1.93327324 [mEh] -1.21314732 [kcal/mol] -5.07580888 [kJ/mol]
Exch-Ind20,r 14.66201899 [mEh] 9.20055621 [kcal/mol] 38.49513087 [kJ/mol]
Exch-Ind22 1.13365603 [mEh] 0.71137993 [kcal/mol] 2.97641390 [kJ/mol]
delta HF,r (2) -11.84637149 [mEh] -7.43371065 [kcal/mol] -31.10264835 [kJ/mol]

Dispersion -7.02240313 [mEh] -4.40662468 [kcal/mol] -18.43731942 [kJ/mol]
Disp20 -9.19384826 [mEh] -5.76922712 [kcal/mol] -24.13844860 [kJ/mol]
Exch-Disp20 2.17144513 [mEh] 1.36260245 [kcal/mol] 5.70112918 [kJ/mol]

Total HF -10.71000784 [mEh] -6.72063166 [kcal/mol] -28.11912557 [kJ/mol]
Total SAPT0 -17.73241096 [mEh] -11.12725634 [kcal/mol] -46.55644499 [kJ/mol]
Total SAPT2 -15.20696457 [mEh] -9.54251473 [kcal/mol] -39.92588548 [kJ/mol]

Special recipe for scaled SAPT0 (see Manual):
Electrostatics sSAPT0 -36.63905676 [mEh] -22.99135619 [kcal/mol] -96.19584351 [kJ/mol]
Exchange sSAPT0 48.11718409 [mEh] 30.19399013 [kcal/mol] 126.33166682 [kJ/mol]
Induction sSAPT0 -20.53889410 [mEh] -12.88835117 [kcal/mol] -53.92486646 [kJ/mol]
Dispersion sSAPT0 -6.77815052 [mEh] -4.25335384 [kcal/mol] -17.79603418 [kJ/mol]
Total sSAPT0 -15.83891729 [mEh] -9.93907107 [kcal/mol] -41.58507733 [kJ/mol]
--------------------------------------------------------------------------------------------------------
</pre>

===Run interactively===

Psi4 comes as a pyhton module, thus we can use conda to create personal versions of Psi4 on the HPC.

*Start an interactive session
<pre>
srun --cpus-per-task=16 --mem=16G --time=0-05:00:00 --pty bash
</pre>

*Load your personal conda
Check the latest version of Miniconda
<pre>
module spider Miniconda
</pre>
Then load the latest version
<pre>
module load Miniconda3/23.9.0-0
conda --version
</pre>
conda 23.9.0
<pre>
export PIP_NO_CACHE_DIR=1
export PYTHONNOUSERSITE=1
</pre>
prevents conda from trying to use the system python and pip

*Create and activate a Psi4 environment
Create a Psi4 environment:
<pre>
conda create -n psi4env
conda env list
# conda environments:
#
base /home/software/EasyBuild/software/Miniconda3/23.9.0-0
psi4env /nfs/home/huntpa/.conda/envs/psi4env
</pre>

<pre>
source $(conda info --base)/etc/profile.d/conda.sh
conda activate psi4env
</pre>
conda init is not recommended as it modifies your shell configuration files. This can cause problems with the module system and other software. Instead, use the source $(conda info --base)/etc/profile.d/conda.sh command to activate conda in your current shell session.

*Install PSI4
Install and check psi4 version
<pre>
conda install -c conda-forge psi4
Collecting package metadata (current_repodata.json): done
Solving environment: done
...
The following packages will be downloaded:
...
Proceed ([y]/n)?
...
Downloading and Extracting Packages:
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
</pre>
then test the version
<pre>
psi4 --version
1.9.1
</pre>

Mod:Hunt Research Group/SAPT

2025-12-04T18:53:16Z

Wikiadmin: /* Run SAPT calculations using Psi4 */

==Run SAPT calculations using Psi4==

Psi4 website https://psicode.org/psi4manual/master/index.html

===PBS submission script===
:copy the submission script below into a file called runpsi4.sh
:copy your input file to testb.inp
:submit with
<pre>
sbatch runpsi4.sh
</pre>
<pre>
#!/bin/bash
#SBATCH --job-name=testb
#SBATCH --cpus-per-task=16
#SBATCH --mem=32GB
#SBATCH --partition=quicktest
#SBATCH --time=4:59:00
#SBATCH -o /nfs/scratch/huntpa/testb.out
#SBATCH -e /nfs/scratch/huntpa/testb.err

cp /nfs/home/huntpa/julian/testb.inp /nfs/scratch/huntpa/testb.inp
export PSI_SCRATCH='/nfs/scratch/huntpa/'

cd /nfs/scratch/huntpa/
module --quiet purge
module load foss/2024a GCC/13.3.0 OpenMPI/5.0.3
module load Miniconda3/23.9.0-0
export PIP_NO_CACHE_DIR=1
export PYTHONNOUSERSITE=1
source $(conda info --base)/etc/profile.d/conda.sh
conda activate psi4env
psi4 -i testb.inp

test -r testb.out
if [ $? -eq 0 ]
then
cp /nfs/scratch/huntpa/testb.out /nfs/home/huntpa/julian/testb.out
cp /nfs/scratch/huntpa/testb.log /nfs/home/huntpa/julian/testb.log
cp /nfs/scratch/huntpa/timer.dat /nfs/home/huntpa/julian/testb.time
fi
</pre>

===Run a test job===

Here is an examplpe input file for the SAPT(2) calculation of the H3N-HCl dimer. Copy the content into a file called testa.inp

<pre>
memory 14 GB

molecule mol {
0 1
N 1.876377 0.000001 -0.000006
H 2.237648 0.661745 -0.680615
H 2.237486 0.258575 0.913443
H 2.237570 -0.920339 -0.232740
--
0 1
Cl -1.177795 0.000000 -0.000001
H 0.175168 0.000012 -0.000026

units angstrom
symmetry c1
no_reorient
}

set basis 6-311+G(d,p)

energy('sapt2')
</pre>

Run the file interactively as a test
Normally you will run via a PBS script!!
<pre>
psi4 testa.inp -n 10
</pre>
you will get the following files
:test.out has your output
:test.log has runtime info
:timer.dat has info on timing
check against the output below for the SAPT section
<pre>
SAPT Results
--------------------------------------------------------------------------------------------------------
Electrostatics -36.32899016 [mEh] -22.79678645 [kcal/mol] -95.38176366 [kJ/mol]
Elst10,r -36.63905676 [mEh] -22.99135619 [kcal/mol] -96.19584351 [kJ/mol]
Elst12,r 0.31006660 [mEh] 0.19456974 [kcal/mol] 0.81407985 [kJ/mol]

Exchange 51.13218109 [mEh] 32.08592939 [kcal/mol] 134.24754146 [kJ/mol]
Exch10 48.11718409 [mEh] 30.19399013 [kcal/mol] 126.33166682 [kJ/mol]
Exch10(S^2) 46.43751367 [mEh] 29.13998098 [kcal/mol] 121.92169213 [kJ/mol]
Exch11(S^2) 0.99070562 [mEh] 0.62167719 [kcal/mol] 2.60109761 [kJ/mol]
Exch12(S^2) 2.02429139 [mEh] 1.27026208 [kcal/mol] 5.31477704 [kJ/mol]

Induction -22.98775238 [mEh] -14.42503300 [kcal/mol] -60.35434386 [kJ/mol]
Ind20,r -25.00378267 [mEh] -15.69011116 [kcal/mol] -65.64743140 [kJ/mol]
Ind22 -1.93327324 [mEh] -1.21314732 [kcal/mol] -5.07580888 [kJ/mol]
Exch-Ind20,r 14.66201899 [mEh] 9.20055621 [kcal/mol] 38.49513087 [kJ/mol]
Exch-Ind22 1.13365603 [mEh] 0.71137993 [kcal/mol] 2.97641390 [kJ/mol]
delta HF,r (2) -11.84637149 [mEh] -7.43371065 [kcal/mol] -31.10264835 [kJ/mol]

Dispersion -7.02240313 [mEh] -4.40662468 [kcal/mol] -18.43731942 [kJ/mol]
Disp20 -9.19384826 [mEh] -5.76922712 [kcal/mol] -24.13844860 [kJ/mol]
Exch-Disp20 2.17144513 [mEh] 1.36260245 [kcal/mol] 5.70112918 [kJ/mol]

Total HF -10.71000784 [mEh] -6.72063166 [kcal/mol] -28.11912557 [kJ/mol]
Total SAPT0 -17.73241096 [mEh] -11.12725634 [kcal/mol] -46.55644499 [kJ/mol]
Total SAPT2 -15.20696457 [mEh] -9.54251473 [kcal/mol] -39.92588548 [kJ/mol]

Special recipe for scaled SAPT0 (see Manual):
Electrostatics sSAPT0 -36.63905676 [mEh] -22.99135619 [kcal/mol] -96.19584351 [kJ/mol]
Exchange sSAPT0 48.11718409 [mEh] 30.19399013 [kcal/mol] 126.33166682 [kJ/mol]
Induction sSAPT0 -20.53889410 [mEh] -12.88835117 [kcal/mol] -53.92486646 [kJ/mol]
Dispersion sSAPT0 -6.77815052 [mEh] -4.25335384 [kcal/mol] -17.79603418 [kJ/mol]
Total sSAPT0 -15.83891729 [mEh] -9.93907107 [kcal/mol] -41.58507733 [kJ/mol]
--------------------------------------------------------------------------------------------------------
</pre>

===Run interactively===

Psi4 comes as a pyhton module, thus we can use conda to create personal versions of Psi4 on the HPC.

*Start an interactive session
<pre>
srun --cpus-per-task=16 --mem=16G --time=0-05:00:00 --pty bash
</pre>

*Load your personal conda
Check the latest version of Miniconda
<pre>
module spider Miniconda
</pre>
Then load the latest version
<pre>
module load Miniconda3/23.9.0-0
conda --version
</pre>
conda 23.9.0
<pre>
export PIP_NO_CACHE_DIR=1
export PYTHONNOUSERSITE=1
</pre>
prevents conda from trying to use the system python and pip

*Create and activate a Psi4 environment
Create a Psi4 environment:
<pre>
conda create -n psi4env
conda env list
# conda environments:
#
base /home/software/EasyBuild/software/Miniconda3/23.9.0-0
psi4env /nfs/home/huntpa/.conda/envs/psi4env
</pre>

<pre>
source $(conda info --base)/etc/profile.d/conda.sh
conda activate psi4env
</pre>
conda init is not recommended as it modifies your shell configuration files. This can cause problems with the module system and other software. Instead, use the source $(conda info --base)/etc/profile.d/conda.sh command to activate conda in your current shell session.

*Install PSI4
Install and check psi4 version
<pre>
conda install -c conda-forge psi4
Collecting package metadata (current_repodata.json): done
Solving environment: done
...
The following packages will be downloaded:
...
Proceed ([y]/n)?
...
Downloading and Extracting Packages:
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
</pre>
then test the version
<pre>
psi4 --version
1.9.1
</pre>

Mod:Hunt Research Group/SAPT

2025-12-04T18:52:49Z

Wikiadmin:

==Run SAPT calculations using Psi4==

===Installing Psi4 locally for yourself on the HPC===

Psi4 website https://psicode.org/psi4manual/master/index.html

===PBS submission script===
:copy the submission script below into a file called runpsi4.sh
:copy your input file to testb.inp
:submit with
<pre>
sbatch runpsi4.sh
</pre>
<pre>
#!/bin/bash
#SBATCH --job-name=testb
#SBATCH --cpus-per-task=16
#SBATCH --mem=32GB
#SBATCH --partition=quicktest
#SBATCH --time=4:59:00
#SBATCH -o /nfs/scratch/huntpa/testb.out
#SBATCH -e /nfs/scratch/huntpa/testb.err

cp /nfs/home/huntpa/julian/testb.inp /nfs/scratch/huntpa/testb.inp
export PSI_SCRATCH='/nfs/scratch/huntpa/'

cd /nfs/scratch/huntpa/
module --quiet purge
module load foss/2024a GCC/13.3.0 OpenMPI/5.0.3
module load Miniconda3/23.9.0-0
export PIP_NO_CACHE_DIR=1
export PYTHONNOUSERSITE=1
source $(conda info --base)/etc/profile.d/conda.sh
conda activate psi4env
psi4 -i testb.inp

test -r testb.out
if [ $? -eq 0 ]
then
cp /nfs/scratch/huntpa/testb.out /nfs/home/huntpa/julian/testb.out
cp /nfs/scratch/huntpa/testb.log /nfs/home/huntpa/julian/testb.log
cp /nfs/scratch/huntpa/timer.dat /nfs/home/huntpa/julian/testb.time
fi
</pre>

===Run a test job===

Here is an examplpe input file for the SAPT(2) calculation of the H3N-HCl dimer. Copy the content into a file called testa.inp

<pre>
memory 14 GB

molecule mol {
0 1
N 1.876377 0.000001 -0.000006
H 2.237648 0.661745 -0.680615
H 2.237486 0.258575 0.913443
H 2.237570 -0.920339 -0.232740
--
0 1
Cl -1.177795 0.000000 -0.000001
H 0.175168 0.000012 -0.000026

units angstrom
symmetry c1
no_reorient
}

set basis 6-311+G(d,p)

energy('sapt2')
</pre>

Run the file interactively as a test
Normally you will run via a PBS script!!
<pre>
psi4 testa.inp -n 10
</pre>
you will get the following files
:test.out has your output
:test.log has runtime info
:timer.dat has info on timing
check against the output below for the SAPT section
<pre>
SAPT Results
--------------------------------------------------------------------------------------------------------
Electrostatics -36.32899016 [mEh] -22.79678645 [kcal/mol] -95.38176366 [kJ/mol]
Elst10,r -36.63905676 [mEh] -22.99135619 [kcal/mol] -96.19584351 [kJ/mol]
Elst12,r 0.31006660 [mEh] 0.19456974 [kcal/mol] 0.81407985 [kJ/mol]

Exchange 51.13218109 [mEh] 32.08592939 [kcal/mol] 134.24754146 [kJ/mol]
Exch10 48.11718409 [mEh] 30.19399013 [kcal/mol] 126.33166682 [kJ/mol]
Exch10(S^2) 46.43751367 [mEh] 29.13998098 [kcal/mol] 121.92169213 [kJ/mol]
Exch11(S^2) 0.99070562 [mEh] 0.62167719 [kcal/mol] 2.60109761 [kJ/mol]
Exch12(S^2) 2.02429139 [mEh] 1.27026208 [kcal/mol] 5.31477704 [kJ/mol]

Induction -22.98775238 [mEh] -14.42503300 [kcal/mol] -60.35434386 [kJ/mol]
Ind20,r -25.00378267 [mEh] -15.69011116 [kcal/mol] -65.64743140 [kJ/mol]
Ind22 -1.93327324 [mEh] -1.21314732 [kcal/mol] -5.07580888 [kJ/mol]
Exch-Ind20,r 14.66201899 [mEh] 9.20055621 [kcal/mol] 38.49513087 [kJ/mol]
Exch-Ind22 1.13365603 [mEh] 0.71137993 [kcal/mol] 2.97641390 [kJ/mol]
delta HF,r (2) -11.84637149 [mEh] -7.43371065 [kcal/mol] -31.10264835 [kJ/mol]

Dispersion -7.02240313 [mEh] -4.40662468 [kcal/mol] -18.43731942 [kJ/mol]
Disp20 -9.19384826 [mEh] -5.76922712 [kcal/mol] -24.13844860 [kJ/mol]
Exch-Disp20 2.17144513 [mEh] 1.36260245 [kcal/mol] 5.70112918 [kJ/mol]

Total HF -10.71000784 [mEh] -6.72063166 [kcal/mol] -28.11912557 [kJ/mol]
Total SAPT0 -17.73241096 [mEh] -11.12725634 [kcal/mol] -46.55644499 [kJ/mol]
Total SAPT2 -15.20696457 [mEh] -9.54251473 [kcal/mol] -39.92588548 [kJ/mol]

Special recipe for scaled SAPT0 (see Manual):
Electrostatics sSAPT0 -36.63905676 [mEh] -22.99135619 [kcal/mol] -96.19584351 [kJ/mol]
Exchange sSAPT0 48.11718409 [mEh] 30.19399013 [kcal/mol] 126.33166682 [kJ/mol]
Induction sSAPT0 -20.53889410 [mEh] -12.88835117 [kcal/mol] -53.92486646 [kJ/mol]
Dispersion sSAPT0 -6.77815052 [mEh] -4.25335384 [kcal/mol] -17.79603418 [kJ/mol]
Total sSAPT0 -15.83891729 [mEh] -9.93907107 [kcal/mol] -41.58507733 [kJ/mol]
--------------------------------------------------------------------------------------------------------
</pre>

===Run interactively===

Psi4 comes as a pyhton module, thus we can use conda to create personal versions of Psi4 on the HPC.

*Start an interactive session
<pre>
srun --cpus-per-task=16 --mem=16G --time=0-05:00:00 --pty bash
</pre>

*Load your personal conda
Check the latest version of Miniconda
<pre>
module spider Miniconda
</pre>
Then load the latest version
<pre>
module load Miniconda3/23.9.0-0
conda --version
</pre>
conda 23.9.0
<pre>
export PIP_NO_CACHE_DIR=1
export PYTHONNOUSERSITE=1
</pre>
prevents conda from trying to use the system python and pip

*Create and activate a Psi4 environment
Create a Psi4 environment:
<pre>
conda create -n psi4env
conda env list
# conda environments:
#
base /home/software/EasyBuild/software/Miniconda3/23.9.0-0
psi4env /nfs/home/huntpa/.conda/envs/psi4env
</pre>

<pre>
source $(conda info --base)/etc/profile.d/conda.sh
conda activate psi4env
</pre>
conda init is not recommended as it modifies your shell configuration files. This can cause problems with the module system and other software. Instead, use the source $(conda info --base)/etc/profile.d/conda.sh command to activate conda in your current shell session.

*Install PSI4
Install and check psi4 version
<pre>
conda install -c conda-forge psi4
Collecting package metadata (current_repodata.json): done
Solving environment: done
...
The following packages will be downloaded:
...
Proceed ([y]/n)?
...
Downloading and Extracting Packages:
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
</pre>
then test the version
<pre>
psi4 --version
1.9.1
</pre>

Mod:Hunt Research Group/SAPT

2025-12-04T18:48:39Z

Wikiadmin:

==Run SAPT calculations using Psi4==

===Installing Psi4 locally for yourself on the HPC===

Psi4 website https://psicode.org/psi4manual/master/index.html

===PBS submission script===
:copy the submission script below into a file called runpsi4.sh
:copy your input file to testb.inp
:submit with
<pre>
sbatch runpsi4.sh
</pre>
<pre>
#!/bin/bash
#SBATCH --job-name=testb
#SBATCH --cpus-per-task=16
#SBATCH --mem=32GB
#SBATCH --partition=quicktest
#SBATCH --time=4:59:00
#SBATCH -o /nfs/scratch/huntpa/testb.out
#SBATCH -e /nfs/scratch/huntpa/testb.err

cp /nfs/home/huntpa/julian/testb.inp /nfs/scratch/huntpa/testb.inp
export PSI_SCRATCH='/nfs/scratch/huntpa/'

cd /nfs/scratch/huntpa/
module --quiet purge
module load foss/2024a GCC/13.3.0 OpenMPI/5.0.3
module load Miniconda3/23.9.0-0
export PIP_NO_CACHE_DIR=1
export PYTHONNOUSERSITE=1
source $(conda info --base)/etc/profile.d/conda.sh
conda activate psi4env
psi4 -i testb.inp

test -r testb.out
if [ $? -eq 0 ]
then
cp /nfs/scratch/huntpa/testb.out /nfs/home/huntpa/julian/testb.out
cp /nfs/scratch/huntpa/testb.log /nfs/home/huntpa/julian/testb.log
cp /nfs/scratch/huntpa/timer.dat /nfs/home/huntpa/julian/testb.time
fi
</pre>

Psi4 comes as a pyhton module, thus we can use conda to create personal versions of Psi4 on the HPC.

====Start an interactive session====
<pre>
srun --cpus-per-task=16 --mem=16G --time=0-05:00:00 --pty bash
</pre>

====Create your personal conda====
Check the latest version of Miniconda
<pre>
module spider Miniconda
</pre>
Then load the latest version
<pre>
module load Miniconda3/23.9.0-0
conda --version
</pre>
conda 23.9.0
<pre>
export PIP_NO_CACHE_DIR=1
export PYTHONNOUSERSITE=1
</pre>
prevents conda from trying to use the system python and pip

====Create and activate a Psi4 environment====
Create a Psi4 environment:
<pre>
conda create -n psi4env
conda env list
# conda environments:
#
base /home/software/EasyBuild/software/Miniconda3/23.9.0-0
psi4env /nfs/home/huntpa/.conda/envs/psi4env
</pre>

<pre>
source $(conda info --base)/etc/profile.d/conda.sh
conda activate psi4env
</pre>
conda init is not recommended as it modifies your shell configuration files. This can cause problems with the module system and other software. Instead, use the source $(conda info --base)/etc/profile.d/conda.sh command to activate conda in your current shell session.

====Install PSI4====
Install and check psi4 version
<pre>
conda install -c conda-forge psi4
Collecting package metadata (current_repodata.json): done
Solving environment: done
...
The following packages will be downloaded:
...
Proceed ([y]/n)?
...
Downloading and Extracting Packages:
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
</pre>
then test the version
<pre>
psi4 --version
1.9.1
</pre>

===Run a test job===

Here is an examplpe input file for the SAPT(2) calculation of the H3N-HCl dimer. Copy the content into a file called testa.inp

<pre>
memory 14 GB

molecule mol {
0 1
N 1.876377 0.000001 -0.000006
H 2.237648 0.661745 -0.680615
H 2.237486 0.258575 0.913443
H 2.237570 -0.920339 -0.232740
--
0 1
Cl -1.177795 0.000000 -0.000001
H 0.175168 0.000012 -0.000026

units angstrom
symmetry c1
no_reorient
}

set basis 6-311+G(d,p)

energy('sapt2')
</pre>

Run the file interactively as a test
Normally you will run via a PBS script!!
<pre>
psi4 testa.inp -n 10
</pre>
you will get the following files
:test.out has your output
:test.log has runtime info
:timer.dat has info on timing
check against the output below for the SAPT section
<pre>
SAPT Results
--------------------------------------------------------------------------------------------------------
Electrostatics -36.32899016 [mEh] -22.79678645 [kcal/mol] -95.38176366 [kJ/mol]
Elst10,r -36.63905676 [mEh] -22.99135619 [kcal/mol] -96.19584351 [kJ/mol]
Elst12,r 0.31006660 [mEh] 0.19456974 [kcal/mol] 0.81407985 [kJ/mol]

Exchange 51.13218109 [mEh] 32.08592939 [kcal/mol] 134.24754146 [kJ/mol]
Exch10 48.11718409 [mEh] 30.19399013 [kcal/mol] 126.33166682 [kJ/mol]
Exch10(S^2) 46.43751367 [mEh] 29.13998098 [kcal/mol] 121.92169213 [kJ/mol]
Exch11(S^2) 0.99070562 [mEh] 0.62167719 [kcal/mol] 2.60109761 [kJ/mol]
Exch12(S^2) 2.02429139 [mEh] 1.27026208 [kcal/mol] 5.31477704 [kJ/mol]

Induction -22.98775238 [mEh] -14.42503300 [kcal/mol] -60.35434386 [kJ/mol]
Ind20,r -25.00378267 [mEh] -15.69011116 [kcal/mol] -65.64743140 [kJ/mol]
Ind22 -1.93327324 [mEh] -1.21314732 [kcal/mol] -5.07580888 [kJ/mol]
Exch-Ind20,r 14.66201899 [mEh] 9.20055621 [kcal/mol] 38.49513087 [kJ/mol]
Exch-Ind22 1.13365603 [mEh] 0.71137993 [kcal/mol] 2.97641390 [kJ/mol]
delta HF,r (2) -11.84637149 [mEh] -7.43371065 [kcal/mol] -31.10264835 [kJ/mol]

Dispersion -7.02240313 [mEh] -4.40662468 [kcal/mol] -18.43731942 [kJ/mol]
Disp20 -9.19384826 [mEh] -5.76922712 [kcal/mol] -24.13844860 [kJ/mol]
Exch-Disp20 2.17144513 [mEh] 1.36260245 [kcal/mol] 5.70112918 [kJ/mol]

Total HF -10.71000784 [mEh] -6.72063166 [kcal/mol] -28.11912557 [kJ/mol]
Total SAPT0 -17.73241096 [mEh] -11.12725634 [kcal/mol] -46.55644499 [kJ/mol]
Total SAPT2 -15.20696457 [mEh] -9.54251473 [kcal/mol] -39.92588548 [kJ/mol]

Special recipe for scaled SAPT0 (see Manual):
Electrostatics sSAPT0 -36.63905676 [mEh] -22.99135619 [kcal/mol] -96.19584351 [kJ/mol]
Exchange sSAPT0 48.11718409 [mEh] 30.19399013 [kcal/mol] 126.33166682 [kJ/mol]
Induction sSAPT0 -20.53889410 [mEh] -12.88835117 [kcal/mol] -53.92486646 [kJ/mol]
Dispersion sSAPT0 -6.77815052 [mEh] -4.25335384 [kcal/mol] -17.79603418 [kJ/mol]
Total sSAPT0 -15.83891729 [mEh] -9.93907107 [kcal/mol] -41.58507733 [kJ/mol]
--------------------------------------------------------------------------------------------------------
</pre>

Mod:Hunt Research Group:restart symbolic zmat

2025-11-13T16:53:23Z

Wikiadmin: /* run the job */

=create an input file=
*extract the final geometry from the optimisation log file first
:: extract_structure.py filename (on your log file with without the .log extension)
:: this will give you a file filename.xyz
:: copy this to filename.inp and add the following information to the top of the file
:: number of atoms
:: atom at 0,0,0
:the following example has 22 atoms and is centered at atom 16, then the coordinates follow
<pre>
22
16
7 -0.047020 -1.332546 0.137334
7 -1.252302 0.460618 -0.104654
6 -1.629750 1.865930 -0.321180
</pre>

=run the job=
<pre>
pos_restartzmat.py file.inp
</pre>
:output will look something like this
<pre>
input file is emim_yp50_opt.inp
symbolic z-matrix output file is emim_yp50_opt_1.com
YOU MUST UPDATE THE FIELD AND CHECK CHARGE
YOU MUST MAKE THE FIXED ATOM xyz CONSTANTS
total number of atoms 19
center at atom 16
</pre>
:this will produce a file_1.com
:CHECK THIS FILE
::change the field it is set to x+50 at the moment
::change the multiplicity and charge
::make constants the fixed atom and dummy atoms marking the axes

=altering the script=
:you may want to edit the lines in the script for the optimisation

=pos_restartzmat.py=
<pre>
#!/opt/local/bin/python3
#
# pos_restartzmat.py
#
# python script to take cartesian coords from an electric field run and
# produce a file to continue the run, ie no re-orientation
# in a FIRST step you will need to extract the last set of coordinates from your optimisation job
# use extract_structure.py
# to run the script type python pos_restartzmat.py input_file_name (without extension)
# input file has extension .inp and format
# no of atoms
# x where we center at atom x
# atomic symbol and coordinates
#
import sys
import os
import numpy as np
dir=os.getcwd()
#
if len(sys.argv) == 1:
print('to run the script please type: python symb_restartzmat.py input_file_name $without extension$')
sys.exit()
else:
base=str(sys.argv[1])
file=base+'.inp'
out1=base+'_1.com'
s='directory is '
print('{0:}{1:}'.format(s,dir))
s='input file is '
print('{0:}{1:}'.format(s,file))
s='symbolic z-matrix output file is '
print('{0:}{1:}'.format(s,out1))
s='YOU MUST UPDATE THE FIELD AND CHECK CHARGE'
print('{0:}'.format(s))
s='YOU MUST MAKE THE FIXED ATOM xyz CONSTANTS'
print('{0:}'.format(s))
#close if
#
# set some defaults
atomtotal=0
atomcenter=0
nz1=0
nz2=0
nz3=0
col_atom=[]
col_x=[]
col_y=[]
col_z=[]
p=4.0

# open file and read lines one by one
f=open(file,"r")

#total number of atoms
line =f.readline()
#print('{0:}'.format(line))
atomtotal=int(line.rstrip())
atomtotal=atomtotal-3
s='total number of atoms '
print('{0:}{1:}'.format(s,atomtotal))

#center at atom
line =f.readline()
#print('{0:}'.format(line))
atomcenter=int(line.rstrip())
s='center at atom '
print('{0:}{1:}'.format(s,atomcenter))

#read in atoms and coordinates
mx=np.zeros(atomtotal,dtype=float)
my=np.zeros(atomtotal,dtype=float)
mz=np.zeros(atomtotal,dtype=float)
n=0
while n < atomtotal :
line =f.readline()
# print('{0:}'.format(line))
a1,b1,c1,d1=line.rstrip().split()
col_atom.append(a1)
col_x.append(float(b1))
col_y.append(float(c1))
col_z.append(float(d1))
n=n+1
#close while
#turn list into a numpty array
mx=np.array(col_x)
my=np.array(col_y)
mz=np.array(col_z)
#print(ny)

# write to the _symb.xyz file
c=open(out1,"w")
s="%nprocshared=32\n%mem=58GB\n"
c.write('{0:}'.format(s))
s='%chk='+base+'_1.chk\n'
c.write('{0:}'.format(s))
s="#b3lyp/6-311+g(d,p) int=ultrafine scf=conver=10 empiricaldispersion=gd3bj \n "
c.write('{0:}'.format(s))
s1="opt=(z-matrix,notrust,maxstep=60) field=x+50 "
s2="nosymm pop=(full,nbo7,dipole,chelpg) prop \n \n "
c.write('{0:}{1:}'.format(s1,s2))
s="Title Card Required \n\n"
c.write('{0:}'.format(s))
charge=-1
multiplicity=1
c.write('{0:} {1:} \n'.format(charge,multiplicity))
#
#write out z-matrix
n=0
while n < atomtotal:
m=n+1
c.write('{0:} 0 x{1:<4} y{2:<4} z{3:<4} \n'.format(col_atom[n],m,m,m))
n=n+1
#close while
m=n+1
c.write('{0:} 0 x{1:<4} y{2:<4} z{3:<4} \n'.format('Xx',m,m,m))
m=n+2
c.write('{0:} 0 x{1:<4} y{2:<4} z{3:<4} \n'.format('Xy',m,m,m))
m=n+3
c.write('{0:} 0 x{1:<4} y{2:<4} z{3:<4} \n'.format('Xz',m,m,m))
c.write('\n'.format())

#write out variables
n=0
while n < atomtotal:
m=n+1
c.write(' x{0:<3}={1:>9.6f} \n y{2:<3}={3:9.6f} \n z{4:<3}={5:9.6f} \n'.format(m,mx[n],m,my[n],m,mz[n]))
n=n + 1
#close while
c.write('\n'.format())
m=n+1
c.write(' x{0:<3}={1:>9.6f} \n y{2:<3}={3:9.6f} \n z{4:<3}={5:9.6f} \n'.format(m,p,m,0.0,m,0.0))
m=n+2
c.write(' x{0:<3}={1:>9.6f} \n y{2:<3}={3:9.6f} \n z{4:<3}={5:9.6f} \n'.format(m,0.0,m,p,m,0.0))
m=n+3
c.write(' x{0:<3}={1:>9.6f} \n y{2:<3}={3:9.6f} \n z{4:<3}={5:9.6f} \n'.format(m,0.0,m,0.0,m,p))
c.write('\n\n'.format())

# close all open files
f.close()
c.close()
#
</pre>

Mod:Hunt Research Group:restart symbolic zmat

2025-11-13T16:52:56Z

Wikiadmin: /* run the job */

=create an input file=
*extract the final geometry from the optimisation log file first
:: extract_structure.py filename (on your log file with without the .log extension)
:: this will give you a file filename.xyz
:: copy this to filename.inp and add the following information to the top of the file
:: number of atoms
:: atom at 0,0,0
:the following example has 22 atoms and is centered at atom 16, then the coordinates follow
<pre>
22
16
7 -0.047020 -1.332546 0.137334
7 -1.252302 0.460618 -0.104654
6 -1.629750 1.865930 -0.321180
</pre>

=run the job=
<pre>
pos_restartzmat.py file.inp
</pre>
:output will look something like this
<pre>
input file is emim_yp50_opt.inp
symbolic z-matrix output file is emim_yp50_opt_1.com
YOU MUST UPDATE THE FIELD AND CHECK CHARGE
YOU MUST MAKE THE FIXED ATOM xyz CONSTANTS
total number of atoms 19
center at atom 16
</pre>
:this will produce a file_1.com
:CHECK THIS FILE
::change the field it is set to xp+50 at the moment
::change the multiplicity and charge
::make constants the fixed atom and dummy atoms marking the axes

=altering the script=
:you may want to edit the lines in the script for the optimisation

=pos_restartzmat.py=
<pre>
#!/opt/local/bin/python3
#
# pos_restartzmat.py
#
# python script to take cartesian coords from an electric field run and
# produce a file to continue the run, ie no re-orientation
# in a FIRST step you will need to extract the last set of coordinates from your optimisation job
# use extract_structure.py
# to run the script type python pos_restartzmat.py input_file_name (without extension)
# input file has extension .inp and format
# no of atoms
# x where we center at atom x
# atomic symbol and coordinates
#
import sys
import os
import numpy as np
dir=os.getcwd()
#
if len(sys.argv) == 1:
print('to run the script please type: python symb_restartzmat.py input_file_name $without extension$')
sys.exit()
else:
base=str(sys.argv[1])
file=base+'.inp'
out1=base+'_1.com'
s='directory is '
print('{0:}{1:}'.format(s,dir))
s='input file is '
print('{0:}{1:}'.format(s,file))
s='symbolic z-matrix output file is '
print('{0:}{1:}'.format(s,out1))
s='YOU MUST UPDATE THE FIELD AND CHECK CHARGE'
print('{0:}'.format(s))
s='YOU MUST MAKE THE FIXED ATOM xyz CONSTANTS'
print('{0:}'.format(s))
#close if
#
# set some defaults
atomtotal=0
atomcenter=0
nz1=0
nz2=0
nz3=0
col_atom=[]
col_x=[]
col_y=[]
col_z=[]
p=4.0

# open file and read lines one by one
f=open(file,"r")

#total number of atoms
line =f.readline()
#print('{0:}'.format(line))
atomtotal=int(line.rstrip())
atomtotal=atomtotal-3
s='total number of atoms '
print('{0:}{1:}'.format(s,atomtotal))

#center at atom
line =f.readline()
#print('{0:}'.format(line))
atomcenter=int(line.rstrip())
s='center at atom '
print('{0:}{1:}'.format(s,atomcenter))

#read in atoms and coordinates
mx=np.zeros(atomtotal,dtype=float)
my=np.zeros(atomtotal,dtype=float)
mz=np.zeros(atomtotal,dtype=float)
n=0
while n < atomtotal :
line =f.readline()
# print('{0:}'.format(line))
a1,b1,c1,d1=line.rstrip().split()
col_atom.append(a1)
col_x.append(float(b1))
col_y.append(float(c1))
col_z.append(float(d1))
n=n+1
#close while
#turn list into a numpty array
mx=np.array(col_x)
my=np.array(col_y)
mz=np.array(col_z)
#print(ny)

# write to the _symb.xyz file
c=open(out1,"w")
s="%nprocshared=32\n%mem=58GB\n"
c.write('{0:}'.format(s))
s='%chk='+base+'_1.chk\n'
c.write('{0:}'.format(s))
s="#b3lyp/6-311+g(d,p) int=ultrafine scf=conver=10 empiricaldispersion=gd3bj \n "
c.write('{0:}'.format(s))
s1="opt=(z-matrix,notrust,maxstep=60) field=x+50 "
s2="nosymm pop=(full,nbo7,dipole,chelpg) prop \n \n "
c.write('{0:}{1:}'.format(s1,s2))
s="Title Card Required \n\n"
c.write('{0:}'.format(s))
charge=-1
multiplicity=1
c.write('{0:} {1:} \n'.format(charge,multiplicity))
#
#write out z-matrix
n=0
while n < atomtotal:
m=n+1
c.write('{0:} 0 x{1:<4} y{2:<4} z{3:<4} \n'.format(col_atom[n],m,m,m))
n=n+1
#close while
m=n+1
c.write('{0:} 0 x{1:<4} y{2:<4} z{3:<4} \n'.format('Xx',m,m,m))
m=n+2
c.write('{0:} 0 x{1:<4} y{2:<4} z{3:<4} \n'.format('Xy',m,m,m))
m=n+3
c.write('{0:} 0 x{1:<4} y{2:<4} z{3:<4} \n'.format('Xz',m,m,m))
c.write('\n'.format())

#write out variables
n=0
while n < atomtotal:
m=n+1
c.write(' x{0:<3}={1:>9.6f} \n y{2:<3}={3:9.6f} \n z{4:<3}={5:9.6f} \n'.format(m,mx[n],m,my[n],m,mz[n]))
n=n + 1
#close while
c.write('\n'.format())
m=n+1
c.write(' x{0:<3}={1:>9.6f} \n y{2:<3}={3:9.6f} \n z{4:<3}={5:9.6f} \n'.format(m,p,m,0.0,m,0.0))
m=n+2
c.write(' x{0:<3}={1:>9.6f} \n y{2:<3}={3:9.6f} \n z{4:<3}={5:9.6f} \n'.format(m,0.0,m,p,m,0.0))
m=n+3
c.write(' x{0:<3}={1:>9.6f} \n y{2:<3}={3:9.6f} \n z{4:<3}={5:9.6f} \n'.format(m,0.0,m,0.0,m,p))
c.write('\n\n'.format())

# close all open files
f.close()
c.close()
#
</pre>

Mod:Hunt Research Group:restart symbolic zmat

2025-11-13T16:52:13Z

Wikiadmin: /* create an input file */

=create an input file=
*extract the final geometry from the optimisation log file first
:: extract_structure.py filename (on your log file with without the .log extension)
:: this will give you a file filename.xyz
:: copy this to filename.inp and add the following information to the top of the file
:: number of atoms
:: atom at 0,0,0
:the following example has 22 atoms and is centered at atom 16, then the coordinates follow
<pre>
22
16
7 -0.047020 -1.332546 0.137334
7 -1.252302 0.460618 -0.104654
6 -1.629750 1.865930 -0.321180
</pre>

=run the job=
<pre>
pos_restartzmat.py file.inp
</pre>
:output will look something like this
<pre>
input file is emim_yp50_opt.inp
symbolic z-matrix output file is emim_yp50_opt_1.com
YOU MUST UPDATE THE FIELD AND CHECK CHARGE
YOU MUST MAKE THE FIXED ATOM xyz CONSTANTS
total number of atoms 19
center at atom 16
</pre>
:this will produce a file_1.com
:CHECK THIS FILE
::change the multiplicity and charge
::make constants the fixed atom and dummy atoms marking the axes

=altering the script=
:you may want to edit the lines in the script for the optimisation

=pos_restartzmat.py=
<pre>
#!/opt/local/bin/python3
#
# pos_restartzmat.py
#
# python script to take cartesian coords from an electric field run and
# produce a file to continue the run, ie no re-orientation
# in a FIRST step you will need to extract the last set of coordinates from your optimisation job
# use extract_structure.py
# to run the script type python pos_restartzmat.py input_file_name (without extension)
# input file has extension .inp and format
# no of atoms
# x where we center at atom x
# atomic symbol and coordinates
#
import sys
import os
import numpy as np
dir=os.getcwd()
#
if len(sys.argv) == 1:
print('to run the script please type: python symb_restartzmat.py input_file_name $without extension$')
sys.exit()
else:
base=str(sys.argv[1])
file=base+'.inp'
out1=base+'_1.com'
s='directory is '
print('{0:}{1:}'.format(s,dir))
s='input file is '
print('{0:}{1:}'.format(s,file))
s='symbolic z-matrix output file is '
print('{0:}{1:}'.format(s,out1))
s='YOU MUST UPDATE THE FIELD AND CHECK CHARGE'
print('{0:}'.format(s))
s='YOU MUST MAKE THE FIXED ATOM xyz CONSTANTS'
print('{0:}'.format(s))
#close if
#
# set some defaults
atomtotal=0
atomcenter=0
nz1=0
nz2=0
nz3=0
col_atom=[]
col_x=[]
col_y=[]
col_z=[]
p=4.0

# open file and read lines one by one
f=open(file,"r")

#total number of atoms
line =f.readline()
#print('{0:}'.format(line))
atomtotal=int(line.rstrip())
atomtotal=atomtotal-3
s='total number of atoms '
print('{0:}{1:}'.format(s,atomtotal))

#center at atom
line =f.readline()
#print('{0:}'.format(line))
atomcenter=int(line.rstrip())
s='center at atom '
print('{0:}{1:}'.format(s,atomcenter))

#read in atoms and coordinates
mx=np.zeros(atomtotal,dtype=float)
my=np.zeros(atomtotal,dtype=float)
mz=np.zeros(atomtotal,dtype=float)
n=0
while n < atomtotal :
line =f.readline()
# print('{0:}'.format(line))
a1,b1,c1,d1=line.rstrip().split()
col_atom.append(a1)
col_x.append(float(b1))
col_y.append(float(c1))
col_z.append(float(d1))
n=n+1
#close while
#turn list into a numpty array
mx=np.array(col_x)
my=np.array(col_y)
mz=np.array(col_z)
#print(ny)

# write to the _symb.xyz file
c=open(out1,"w")
s="%nprocshared=32\n%mem=58GB\n"
c.write('{0:}'.format(s))
s='%chk='+base+'_1.chk\n'
c.write('{0:}'.format(s))
s="#b3lyp/6-311+g(d,p) int=ultrafine scf=conver=10 empiricaldispersion=gd3bj \n "
c.write('{0:}'.format(s))
s1="opt=(z-matrix,notrust,maxstep=60) field=x+50 "
s2="nosymm pop=(full,nbo7,dipole,chelpg) prop \n \n "
c.write('{0:}{1:}'.format(s1,s2))
s="Title Card Required \n\n"
c.write('{0:}'.format(s))
charge=-1
multiplicity=1
c.write('{0:} {1:} \n'.format(charge,multiplicity))
#
#write out z-matrix
n=0
while n < atomtotal:
m=n+1
c.write('{0:} 0 x{1:<4} y{2:<4} z{3:<4} \n'.format(col_atom[n],m,m,m))
n=n+1
#close while
m=n+1
c.write('{0:} 0 x{1:<4} y{2:<4} z{3:<4} \n'.format('Xx',m,m,m))
m=n+2
c.write('{0:} 0 x{1:<4} y{2:<4} z{3:<4} \n'.format('Xy',m,m,m))
m=n+3
c.write('{0:} 0 x{1:<4} y{2:<4} z{3:<4} \n'.format('Xz',m,m,m))
c.write('\n'.format())

#write out variables
n=0
while n < atomtotal:
m=n+1
c.write(' x{0:<3}={1:>9.6f} \n y{2:<3}={3:9.6f} \n z{4:<3}={5:9.6f} \n'.format(m,mx[n],m,my[n],m,mz[n]))
n=n + 1
#close while
c.write('\n'.format())
m=n+1
c.write(' x{0:<3}={1:>9.6f} \n y{2:<3}={3:9.6f} \n z{4:<3}={5:9.6f} \n'.format(m,p,m,0.0,m,0.0))
m=n+2
c.write(' x{0:<3}={1:>9.6f} \n y{2:<3}={3:9.6f} \n z{4:<3}={5:9.6f} \n'.format(m,0.0,m,p,m,0.0))
m=n+3
c.write(' x{0:<3}={1:>9.6f} \n y{2:<3}={3:9.6f} \n z{4:<3}={5:9.6f} \n'.format(m,0.0,m,0.0,m,p))
c.write('\n\n'.format())

# close all open files
f.close()
c.close()
#
</pre>

Mod:Hunt Research Group:restart symbolic zmat

2025-11-13T16:52:01Z

Wikiadmin: /* create an input file */

=create an input file=
*extract the final geometry from the optimisation log file first
:: extract_structure.py filename (on your log file with without the .log extension)
:: this will give you a file filename.xyz
:: copy this to filename.inp and add the following information to the top of the file
:: number of atoms
:: atom at 0,0,0
:example has 22 atoms and is centered at atom 16, then the coordinates follow
<pre>
22
16
7 -0.047020 -1.332546 0.137334
7 -1.252302 0.460618 -0.104654
6 -1.629750 1.865930 -0.321180
</pre>

=run the job=
<pre>
pos_restartzmat.py file.inp
</pre>
:output will look something like this
<pre>
input file is emim_yp50_opt.inp
symbolic z-matrix output file is emim_yp50_opt_1.com
YOU MUST UPDATE THE FIELD AND CHECK CHARGE
YOU MUST MAKE THE FIXED ATOM xyz CONSTANTS
total number of atoms 19
center at atom 16
</pre>
:this will produce a file_1.com
:CHECK THIS FILE
::change the multiplicity and charge
::make constants the fixed atom and dummy atoms marking the axes

=altering the script=
:you may want to edit the lines in the script for the optimisation

=pos_restartzmat.py=
<pre>
#!/opt/local/bin/python3
#
# pos_restartzmat.py
#
# python script to take cartesian coords from an electric field run and
# produce a file to continue the run, ie no re-orientation
# in a FIRST step you will need to extract the last set of coordinates from your optimisation job
# use extract_structure.py
# to run the script type python pos_restartzmat.py input_file_name (without extension)
# input file has extension .inp and format
# no of atoms
# x where we center at atom x
# atomic symbol and coordinates
#
import sys
import os
import numpy as np
dir=os.getcwd()
#
if len(sys.argv) == 1:
print('to run the script please type: python symb_restartzmat.py input_file_name $without extension$')
sys.exit()
else:
base=str(sys.argv[1])
file=base+'.inp'
out1=base+'_1.com'
s='directory is '
print('{0:}{1:}'.format(s,dir))
s='input file is '
print('{0:}{1:}'.format(s,file))
s='symbolic z-matrix output file is '
print('{0:}{1:}'.format(s,out1))
s='YOU MUST UPDATE THE FIELD AND CHECK CHARGE'
print('{0:}'.format(s))
s='YOU MUST MAKE THE FIXED ATOM xyz CONSTANTS'
print('{0:}'.format(s))
#close if
#
# set some defaults
atomtotal=0
atomcenter=0
nz1=0
nz2=0
nz3=0
col_atom=[]
col_x=[]
col_y=[]
col_z=[]
p=4.0

# open file and read lines one by one
f=open(file,"r")

#total number of atoms
line =f.readline()
#print('{0:}'.format(line))
atomtotal=int(line.rstrip())
atomtotal=atomtotal-3
s='total number of atoms '
print('{0:}{1:}'.format(s,atomtotal))

#center at atom
line =f.readline()
#print('{0:}'.format(line))
atomcenter=int(line.rstrip())
s='center at atom '
print('{0:}{1:}'.format(s,atomcenter))

#read in atoms and coordinates
mx=np.zeros(atomtotal,dtype=float)
my=np.zeros(atomtotal,dtype=float)
mz=np.zeros(atomtotal,dtype=float)
n=0
while n < atomtotal :
line =f.readline()
# print('{0:}'.format(line))
a1,b1,c1,d1=line.rstrip().split()
col_atom.append(a1)
col_x.append(float(b1))
col_y.append(float(c1))
col_z.append(float(d1))
n=n+1
#close while
#turn list into a numpty array
mx=np.array(col_x)
my=np.array(col_y)
mz=np.array(col_z)
#print(ny)

# write to the _symb.xyz file
c=open(out1,"w")
s="%nprocshared=32\n%mem=58GB\n"
c.write('{0:}'.format(s))
s='%chk='+base+'_1.chk\n'
c.write('{0:}'.format(s))
s="#b3lyp/6-311+g(d,p) int=ultrafine scf=conver=10 empiricaldispersion=gd3bj \n "
c.write('{0:}'.format(s))
s1="opt=(z-matrix,notrust,maxstep=60) field=x+50 "
s2="nosymm pop=(full,nbo7,dipole,chelpg) prop \n \n "
c.write('{0:}{1:}'.format(s1,s2))
s="Title Card Required \n\n"
c.write('{0:}'.format(s))
charge=-1
multiplicity=1
c.write('{0:} {1:} \n'.format(charge,multiplicity))
#
#write out z-matrix
n=0
while n < atomtotal:
m=n+1
c.write('{0:} 0 x{1:<4} y{2:<4} z{3:<4} \n'.format(col_atom[n],m,m,m))
n=n+1
#close while
m=n+1
c.write('{0:} 0 x{1:<4} y{2:<4} z{3:<4} \n'.format('Xx',m,m,m))
m=n+2
c.write('{0:} 0 x{1:<4} y{2:<4} z{3:<4} \n'.format('Xy',m,m,m))
m=n+3
c.write('{0:} 0 x{1:<4} y{2:<4} z{3:<4} \n'.format('Xz',m,m,m))
c.write('\n'.format())

#write out variables
n=0
while n < atomtotal:
m=n+1
c.write(' x{0:<3}={1:>9.6f} \n y{2:<3}={3:9.6f} \n z{4:<3}={5:9.6f} \n'.format(m,mx[n],m,my[n],m,mz[n]))
n=n + 1
#close while
c.write('\n'.format())
m=n+1
c.write(' x{0:<3}={1:>9.6f} \n y{2:<3}={3:9.6f} \n z{4:<3}={5:9.6f} \n'.format(m,p,m,0.0,m,0.0))
m=n+2
c.write(' x{0:<3}={1:>9.6f} \n y{2:<3}={3:9.6f} \n z{4:<3}={5:9.6f} \n'.format(m,0.0,m,p,m,0.0))
m=n+3
c.write(' x{0:<3}={1:>9.6f} \n y{2:<3}={3:9.6f} \n z{4:<3}={5:9.6f} \n'.format(m,0.0,m,0.0,m,p))
c.write('\n\n'.format())

# close all open files
f.close()
c.close()
#
</pre>

Mod:Hunt Research Group:restart symbolic zmat

2025-11-13T16:49:33Z

Wikiadmin: /* run the job */

=create an input file=
*extract the final geometry from the optimisation log file first
:: extract_structure.py filename (on your log file with without the .log extension)
:: this will give you a file filename.xyz
:: copy this to filename.inp and add the following information to the top of the file
:: number of atoms
:: atom at 0,0,0

=run the job=
<pre>
pos_restartzmat.py file.inp
</pre>
:output will look something like this
<pre>
input file is emim_yp50_opt.inp
symbolic z-matrix output file is emim_yp50_opt_1.com
YOU MUST UPDATE THE FIELD AND CHECK CHARGE
YOU MUST MAKE THE FIXED ATOM xyz CONSTANTS
total number of atoms 19
center at atom 16
</pre>
:this will produce a file_1.com
:CHECK THIS FILE
::change the multiplicity and charge
::make constants the fixed atom and dummy atoms marking the axes

=altering the script=
:you may want to edit the lines in the script for the optimisation

=pos_restartzmat.py=
<pre>
#!/opt/local/bin/python3
#
# pos_restartzmat.py
#
# python script to take cartesian coords from an electric field run and
# produce a file to continue the run, ie no re-orientation
# in a FIRST step you will need to extract the last set of coordinates from your optimisation job
# use extract_structure.py
# to run the script type python pos_restartzmat.py input_file_name (without extension)
# input file has extension .inp and format
# no of atoms
# x where we center at atom x
# atomic symbol and coordinates
#
import sys
import os
import numpy as np
dir=os.getcwd()
#
if len(sys.argv) == 1:
print('to run the script please type: python symb_restartzmat.py input_file_name $without extension$')
sys.exit()
else:
base=str(sys.argv[1])
file=base+'.inp'
out1=base+'_1.com'
s='directory is '
print('{0:}{1:}'.format(s,dir))
s='input file is '
print('{0:}{1:}'.format(s,file))
s='symbolic z-matrix output file is '
print('{0:}{1:}'.format(s,out1))
s='YOU MUST UPDATE THE FIELD AND CHECK CHARGE'
print('{0:}'.format(s))
s='YOU MUST MAKE THE FIXED ATOM xyz CONSTANTS'
print('{0:}'.format(s))
#close if
#
# set some defaults
atomtotal=0
atomcenter=0
nz1=0
nz2=0
nz3=0
col_atom=[]
col_x=[]
col_y=[]
col_z=[]
p=4.0

# open file and read lines one by one
f=open(file,"r")

#total number of atoms
line =f.readline()
#print('{0:}'.format(line))
atomtotal=int(line.rstrip())
atomtotal=atomtotal-3
s='total number of atoms '
print('{0:}{1:}'.format(s,atomtotal))

#center at atom
line =f.readline()
#print('{0:}'.format(line))
atomcenter=int(line.rstrip())
s='center at atom '
print('{0:}{1:}'.format(s,atomcenter))

#read in atoms and coordinates
mx=np.zeros(atomtotal,dtype=float)
my=np.zeros(atomtotal,dtype=float)
mz=np.zeros(atomtotal,dtype=float)
n=0
while n < atomtotal :
line =f.readline()
# print('{0:}'.format(line))
a1,b1,c1,d1=line.rstrip().split()
col_atom.append(a1)
col_x.append(float(b1))
col_y.append(float(c1))
col_z.append(float(d1))
n=n+1
#close while
#turn list into a numpty array
mx=np.array(col_x)
my=np.array(col_y)
mz=np.array(col_z)
#print(ny)

# write to the _symb.xyz file
c=open(out1,"w")
s="%nprocshared=32\n%mem=58GB\n"
c.write('{0:}'.format(s))
s='%chk='+base+'_1.chk\n'
c.write('{0:}'.format(s))
s="#b3lyp/6-311+g(d,p) int=ultrafine scf=conver=10 empiricaldispersion=gd3bj \n "
c.write('{0:}'.format(s))
s1="opt=(z-matrix,notrust,maxstep=60) field=x+50 "
s2="nosymm pop=(full,nbo7,dipole,chelpg) prop \n \n "
c.write('{0:}{1:}'.format(s1,s2))
s="Title Card Required \n\n"
c.write('{0:}'.format(s))
charge=-1
multiplicity=1
c.write('{0:} {1:} \n'.format(charge,multiplicity))
#
#write out z-matrix
n=0
while n < atomtotal:
m=n+1
c.write('{0:} 0 x{1:<4} y{2:<4} z{3:<4} \n'.format(col_atom[n],m,m,m))
n=n+1
#close while
m=n+1
c.write('{0:} 0 x{1:<4} y{2:<4} z{3:<4} \n'.format('Xx',m,m,m))
m=n+2
c.write('{0:} 0 x{1:<4} y{2:<4} z{3:<4} \n'.format('Xy',m,m,m))
m=n+3
c.write('{0:} 0 x{1:<4} y{2:<4} z{3:<4} \n'.format('Xz',m,m,m))
c.write('\n'.format())

#write out variables
n=0
while n < atomtotal:
m=n+1
c.write(' x{0:<3}={1:>9.6f} \n y{2:<3}={3:9.6f} \n z{4:<3}={5:9.6f} \n'.format(m,mx[n],m,my[n],m,mz[n]))
n=n + 1
#close while
c.write('\n'.format())
m=n+1
c.write(' x{0:<3}={1:>9.6f} \n y{2:<3}={3:9.6f} \n z{4:<3}={5:9.6f} \n'.format(m,p,m,0.0,m,0.0))
m=n+2
c.write(' x{0:<3}={1:>9.6f} \n y{2:<3}={3:9.6f} \n z{4:<3}={5:9.6f} \n'.format(m,0.0,m,p,m,0.0))
m=n+3
c.write(' x{0:<3}={1:>9.6f} \n y{2:<3}={3:9.6f} \n z{4:<3}={5:9.6f} \n'.format(m,0.0,m,0.0,m,p))
c.write('\n\n'.format())

# close all open files
f.close()
c.close()
#
</pre>

Mod:Hunt Research Group:restart symbolic zmat

2025-11-13T16:49:15Z

Wikiadmin:

=create an input file=
*extract the final geometry from the optimisation log file first
:: extract_structure.py filename (on your log file with without the .log extension)
:: this will give you a file filename.xyz
:: copy this to filename.inp and add the following information to the top of the file
:: number of atoms
:: atom at 0,0,0

=run the job=
<pre>
pos_restartzmat.py file.inp
</pre>
:output will look something like this
<pre>
input file is emim_yp50_opt.inp
symbolic z-matrix output file is emim_yp50_opt_1.com
YOU MUST UPDATE THE FIELD AND CHECK CHARGE
YOU MUST MAKE THE FIXED ATOM xyz CONSTANTS
total number of atoms 19
center at atom 16
</pre>
:this will produce a file_1.com
:CHECK THIS FILE
::change the multiplicity and charge
::make constants the fixed atom and dummy atoms marking the axes

=run the job=
:you may want to edit the lines in the script for the optimisation

=pos_restartzmat.py=
<pre>
#!/opt/local/bin/python3
#
# pos_restartzmat.py
#
# python script to take cartesian coords from an electric field run and
# produce a file to continue the run, ie no re-orientation
# in a FIRST step you will need to extract the last set of coordinates from your optimisation job
# use extract_structure.py
# to run the script type python pos_restartzmat.py input_file_name (without extension)
# input file has extension .inp and format
# no of atoms
# x where we center at atom x
# atomic symbol and coordinates
#
import sys
import os
import numpy as np
dir=os.getcwd()
#
if len(sys.argv) == 1:
print('to run the script please type: python symb_restartzmat.py input_file_name $without extension$')
sys.exit()
else:
base=str(sys.argv[1])
file=base+'.inp'
out1=base+'_1.com'
s='directory is '
print('{0:}{1:}'.format(s,dir))
s='input file is '
print('{0:}{1:}'.format(s,file))
s='symbolic z-matrix output file is '
print('{0:}{1:}'.format(s,out1))
s='YOU MUST UPDATE THE FIELD AND CHECK CHARGE'
print('{0:}'.format(s))
s='YOU MUST MAKE THE FIXED ATOM xyz CONSTANTS'
print('{0:}'.format(s))
#close if
#
# set some defaults
atomtotal=0
atomcenter=0
nz1=0
nz2=0
nz3=0
col_atom=[]
col_x=[]
col_y=[]
col_z=[]
p=4.0

# open file and read lines one by one
f=open(file,"r")

#total number of atoms
line =f.readline()
#print('{0:}'.format(line))
atomtotal=int(line.rstrip())
atomtotal=atomtotal-3
s='total number of atoms '
print('{0:}{1:}'.format(s,atomtotal))

#center at atom
line =f.readline()
#print('{0:}'.format(line))
atomcenter=int(line.rstrip())
s='center at atom '
print('{0:}{1:}'.format(s,atomcenter))

#read in atoms and coordinates
mx=np.zeros(atomtotal,dtype=float)
my=np.zeros(atomtotal,dtype=float)
mz=np.zeros(atomtotal,dtype=float)
n=0
while n < atomtotal :
line =f.readline()
# print('{0:}'.format(line))
a1,b1,c1,d1=line.rstrip().split()
col_atom.append(a1)
col_x.append(float(b1))
col_y.append(float(c1))
col_z.append(float(d1))
n=n+1
#close while
#turn list into a numpty array
mx=np.array(col_x)
my=np.array(col_y)
mz=np.array(col_z)
#print(ny)

# write to the _symb.xyz file
c=open(out1,"w")
s="%nprocshared=32\n%mem=58GB\n"
c.write('{0:}'.format(s))
s='%chk='+base+'_1.chk\n'
c.write('{0:}'.format(s))
s="#b3lyp/6-311+g(d,p) int=ultrafine scf=conver=10 empiricaldispersion=gd3bj \n "
c.write('{0:}'.format(s))
s1="opt=(z-matrix,notrust,maxstep=60) field=x+50 "
s2="nosymm pop=(full,nbo7,dipole,chelpg) prop \n \n "
c.write('{0:}{1:}'.format(s1,s2))
s="Title Card Required \n\n"
c.write('{0:}'.format(s))
charge=-1
multiplicity=1
c.write('{0:} {1:} \n'.format(charge,multiplicity))
#
#write out z-matrix
n=0
while n < atomtotal:
m=n+1
c.write('{0:} 0 x{1:<4} y{2:<4} z{3:<4} \n'.format(col_atom[n],m,m,m))
n=n+1
#close while
m=n+1
c.write('{0:} 0 x{1:<4} y{2:<4} z{3:<4} \n'.format('Xx',m,m,m))
m=n+2
c.write('{0:} 0 x{1:<4} y{2:<4} z{3:<4} \n'.format('Xy',m,m,m))
m=n+3
c.write('{0:} 0 x{1:<4} y{2:<4} z{3:<4} \n'.format('Xz',m,m,m))
c.write('\n'.format())

#write out variables
n=0
while n < atomtotal:
m=n+1
c.write(' x{0:<3}={1:>9.6f} \n y{2:<3}={3:9.6f} \n z{4:<3}={5:9.6f} \n'.format(m,mx[n],m,my[n],m,mz[n]))
n=n + 1
#close while
c.write('\n'.format())
m=n+1
c.write(' x{0:<3}={1:>9.6f} \n y{2:<3}={3:9.6f} \n z{4:<3}={5:9.6f} \n'.format(m,p,m,0.0,m,0.0))
m=n+2
c.write(' x{0:<3}={1:>9.6f} \n y{2:<3}={3:9.6f} \n z{4:<3}={5:9.6f} \n'.format(m,0.0,m,p,m,0.0))
m=n+3
c.write(' x{0:<3}={1:>9.6f} \n y{2:<3}={3:9.6f} \n z{4:<3}={5:9.6f} \n'.format(m,0.0,m,0.0,m,p))
c.write('\n\n'.format())

# close all open files
f.close()
c.close()
#
</pre>

Mod:Hunt Research Group:restart symbolic zmat

2025-11-13T16:47:56Z

Wikiadmin:

=create an input file=
*extract the final geometry from the optimisation log file first
:: extract_structure.py filename (on your log file with without the .log extension)
:: this will give you a file filename.xyz
:: copy this to filename.inp and add the following information to the top of the file
:: number of atoms
:: atom at 0,0,0

=run the job=
<pre>
pos_restartzmat.py file.inp
</pre>
:output will look something like this
<pre>
input file is emim_yp50_opt.inp
symbolic z-matrix output file is emim_yp50_opt_1.com
YOU MUST UPDATE THE FIELD AND CHECK CHARGE
YOU MUST MAKE THE FIXED ATOM xyz CONSTANTS
total number of atoms 19
center at atom 16
</pre>
:this will produce a file_1.com
:CHECK THIS FILE
::change the multiplicity and charge
::make constants the fixed atom and dummy atoms marking the axes

=pos_restartzmat.py=
<pre>
#!/opt/local/bin/python3
#
# pos_restartzmat.py
#
# python script to take cartesian coords from an electric field run and
# produce a file to continue the run, ie no re-orientation
# in a FIRST step you will need to extract the last set of coordinates from your optimisation job
# use extract_structure.py
# to run the script type python pos_restartzmat.py input_file_name (without extension)
# input file has extension .inp and format
# no of atoms
# x where we center at atom x
# atomic symbol and coordinates
#
import sys
import os
import numpy as np
dir=os.getcwd()
#
if len(sys.argv) == 1:
print('to run the script please type: python symb_restartzmat.py input_file_name $without extension$')
sys.exit()
else:
base=str(sys.argv[1])
file=base+'.inp'
out1=base+'_1.com'
s='directory is '
print('{0:}{1:}'.format(s,dir))
s='input file is '
print('{0:}{1:}'.format(s,file))
s='symbolic z-matrix output file is '
print('{0:}{1:}'.format(s,out1))
s='YOU MUST UPDATE THE FIELD AND CHECK CHARGE'
print('{0:}'.format(s))
s='YOU MUST MAKE THE FIXED ATOM xyz CONSTANTS'
print('{0:}'.format(s))
#close if
#
# set some defaults
atomtotal=0
atomcenter=0
nz1=0
nz2=0
nz3=0
col_atom=[]
col_x=[]
col_y=[]
col_z=[]
p=4.0

# open file and read lines one by one
f=open(file,"r")

#total number of atoms
line =f.readline()
#print('{0:}'.format(line))
atomtotal=int(line.rstrip())
atomtotal=atomtotal-3
s='total number of atoms '
print('{0:}{1:}'.format(s,atomtotal))

#center at atom
line =f.readline()
#print('{0:}'.format(line))
atomcenter=int(line.rstrip())
s='center at atom '
print('{0:}{1:}'.format(s,atomcenter))

#read in atoms and coordinates
mx=np.zeros(atomtotal,dtype=float)
my=np.zeros(atomtotal,dtype=float)
mz=np.zeros(atomtotal,dtype=float)
n=0
while n < atomtotal :
line =f.readline()
# print('{0:}'.format(line))
a1,b1,c1,d1=line.rstrip().split()
col_atom.append(a1)
col_x.append(float(b1))
col_y.append(float(c1))
col_z.append(float(d1))
n=n+1
#close while
#turn list into a numpty array
mx=np.array(col_x)
my=np.array(col_y)
mz=np.array(col_z)
#print(ny)

# write to the _symb.xyz file
c=open(out1,"w")
s="%nprocshared=32\n%mem=58GB\n"
c.write('{0:}'.format(s))
s='%chk='+base+'_1.chk\n'
c.write('{0:}'.format(s))
s="#b3lyp/6-311+g(d,p) int=ultrafine scf=conver=10 empiricaldispersion=gd3bj \n "
c.write('{0:}'.format(s))
s1="opt=(z-matrix,notrust,maxstep=60) field=x+50 "
s2="nosymm pop=(full,nbo7,dipole,chelpg) prop \n \n "
c.write('{0:}{1:}'.format(s1,s2))
s="Title Card Required \n\n"
c.write('{0:}'.format(s))
charge=-1
multiplicity=1
c.write('{0:} {1:} \n'.format(charge,multiplicity))
#
#write out z-matrix
n=0
while n < atomtotal:
m=n+1
c.write('{0:} 0 x{1:<4} y{2:<4} z{3:<4} \n'.format(col_atom[n],m,m,m))
n=n+1
#close while
m=n+1
c.write('{0:} 0 x{1:<4} y{2:<4} z{3:<4} \n'.format('Xx',m,m,m))
m=n+2
c.write('{0:} 0 x{1:<4} y{2:<4} z{3:<4} \n'.format('Xy',m,m,m))
m=n+3
c.write('{0:} 0 x{1:<4} y{2:<4} z{3:<4} \n'.format('Xz',m,m,m))
c.write('\n'.format())

#write out variables
n=0
while n < atomtotal:
m=n+1
c.write(' x{0:<3}={1:>9.6f} \n y{2:<3}={3:9.6f} \n z{4:<3}={5:9.6f} \n'.format(m,mx[n],m,my[n],m,mz[n]))
n=n + 1
#close while
c.write('\n'.format())
m=n+1
c.write(' x{0:<3}={1:>9.6f} \n y{2:<3}={3:9.6f} \n z{4:<3}={5:9.6f} \n'.format(m,p,m,0.0,m,0.0))
m=n+2
c.write(' x{0:<3}={1:>9.6f} \n y{2:<3}={3:9.6f} \n z{4:<3}={5:9.6f} \n'.format(m,0.0,m,p,m,0.0))
m=n+3
c.write(' x{0:<3}={1:>9.6f} \n y{2:<3}={3:9.6f} \n z{4:<3}={5:9.6f} \n'.format(m,0.0,m,0.0,m,p))
c.write('\n\n'.format())

# close all open files
f.close()
c.close()
#
</pre>

Mod:Hunt Research Group:restart symbolic zmat

2025-11-13T16:46:48Z

Wikiadmin: /* run the job */

Mod:Hunt Research Group:restart symbolic zmat

2025-11-13T16:45:41Z

Wikiadmin: /* run the job */

Mod:Hunt Research Group:restart symbolic zmat

2025-11-13T16:45:09Z

Wikiadmin: /* run the job */

Mod:Hunt Research Group:restart symbolic zmat

2025-11-13T16:44:48Z

Wikiadmin: /* run the job */

Mod:Hunt Research Group:restart symbolic zmat

2025-11-13T16:44:17Z

Wikiadmin: Created page with "=create an input file= *extract the final geometry from the optimisation log file first :: extract_structure.py filename (on your log file with without the .log extension) ::..."

HRG:HuntResearchGRoup

2025-11-13T16:39:50Z

Wikiadmin: /* to build new files from data or existing files */

==Hunt Research Group Wiki==
===Report and Paper Writing===
#procedures [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/report_procedures link]
#advice [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/report_writing link]
#report components [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/report_components link]
#files to provide when writing a paper [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/paper link]

===Data Base===
#File naming on the database [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/database-files link]
#Database xlsx instructions and template [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/database link]
#Database CREST and xlsx instructions and template [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/database-crest link]

===Methodology===
#Preferred Methodology [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/preferred_method link]
#Basis sets [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/different_basis_sets link]

===Key Papers===
#Best-Practice Protocols for choosing method and basis [https://doi.org/10.1002/anie.202205735 doi]
#Status and Challenges of Density Functional Theory [https://doi.org/10.1016/j.trechm.2020.02.005 doi]
#Meta study on DFT functionals [https://pubs.acs.org/doi/abs/10.1021/ct401111c doi]
#Molecular Geometry is relatively insensitive to basis set [https://doi.org/10.1021/acs.jctc.3c00388 doi]
#Scale factors for vibrational frequencies DFT [https://pubs.acs.org/doi/10.1021/acs.jpca.2c06908 doi] and MP2 [https://pubs.acs.org/doi/10.1021/jp048233q doi]
#M06 suite of DFT functionals [https://link.springer.com/article/10.1007/s00214-007-0310-x doi]
#SMD for ILs [https://pubs.acs.org/doi/abs/10.1021/jp304365v doi]
#Box size for MD simulations of ILs [https://dx.doi.org/10.1063/1.4748352 doi]

===HPC Resources===
#Getting started and introduction to the HPC: [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Getting_started_on_the_HPC link]
#Running jobs on the HPC Raapoi: [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Running_jobs_on_the_HPC link]
#Running jobs on the HPC NeSI: [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Running_jobs_on_NeSI link]
#How much memory (and disk) to use: [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/How_much_memory_to_use link]
#How to start an interactive session: [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/Start_interactive_session link]
#How to set-up access from your desktop to the hpc [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_remote link]
#How to use cloud storage resources [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group/cloud link]

===Using Windows PCs===
#use MobaXTerm [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/mobaxterm link]
#use Putty [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/putty link]
#very basic using a Terminal on a Windows PC [https://learn.microsoft.com/en-us/windows/terminal/ external link]
#install a Linux distribution [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/windows-linux link]
#How to fix Windows files under UNIX [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/Windowsfiles link]

===Tips and Tricks===
#Tired of entering your password all the time: set up a SSH keypair [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/SSHkeyfile link]
#How to make ssh more comfortable [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpSSH link]
#How to comfortably search through old BASH commands [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/searchbash link]
#A terminal emulator capable of splitting into multiple screens [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/iterm2 link]
#module command not working or giving error "bad argument" [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/module link]

===Gaussian General===
#We are starting a database of common errors encountered when running Gaussian jobs [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/gaussian_errors link]
# Here is an already existing database of common errors [https://docs.computecanada.ca/wiki/Gaussian_error_messages link]
#beginners starting from a chemdraw structure [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/from_chemdraw link]
#optimisation errors and problems [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/opt_problems link]
#partial optimisations and scans [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/z-matrix link]
#general procedure for locating transition state structures [[link]]
#problems with scf convergence [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/scf_convergence link]
#Population and charge analysis [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/population link]

===Gaussian Advanced===
#basic ONIOM (Mechanical Embedding) [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/basiconiom link]
#how to run at a higher temperature [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group:high_temp link]
#correcting the entropy due to low modes [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group:low_modes_entropy link]
#generating natural transition orbitals [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/nto link]
#computing excited state polarisabilities [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group:_ES_alpha link]
#dipoles in Gaussian [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group:dipoles link]
#molecules in an electric field [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group:molecules_in_an_electric_field link]
#computing deuterated and/or anharmonic spectra [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group:_Danharm link]
#for NMR calculations look here: [http://cheshirenmr.info/index.htm Chemical Shift Repository]
#old:systematic conformational scan for ion-pair dimers [https://sagacioushours.org.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ion_pair_scan link]
#old: optimisation of charged molecules in an electric field [https://sagacioushours.org.uk/wiki/index.php?title=Optimising_charged_molecules_in_electric_fields link]
#old: multidimensional Scans of Internal Coordinates [https://sagacioushours.org.uk/wiki/index.php?title=Multidimensional_Scans_of_Internal_Coordinates link]

===Solvation===
#Atomic radii [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/atomic_radii link]
#Using the SMD model [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/solvent link]
#Molecular volume calculations [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group/molecular_volume link]
#The cavity [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/solvent_cavity link]
#How to download and use GeomView to visualise solvation cavities [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group/geomview link]
#Surfaces (Solvent-Accessible and Connolly) in Jmol [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/jmolsurfaces link]
#Using SMD on ILs [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group:_Using_SMD_on_ILs link]
#Troublesome optimisations in SMD [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group:troublesome_smd link]

===QC Visualisation===
#Using AIMALL: density based visualisation
##download [http://aim.tkgristmill.com AIMALL]
##once downloaded and installed you need to send tricia your aimall-serialnumber.txt file, and she will arrange for a aimallpro.lic or license file for you
##basic instructions [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group:aim_basics link]
##AimAll volume / surface area calculations [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group:aim_volume link]
##AimAll with pseudo potentials [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group:aim_pseudopotentials link]
##AIMAll 19.10.12 on iMacs [https://sagacioushours.org.uk/wiki/index.php?title=Mod:AIMAllQuickFix link]
#FCHK and CUBE files and manipulation
##creating formatted checkpoint files [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group:usingchkfiles link]
##generating and manipulating cube files [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group:generate_and_manipulate_cube_files link]
##Format of cube files [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group/cube_format link]
#ESPs files and analysis
##Instructions for visualizing electrostatic potentials (Gaussview)[https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials link]
##Electrostatic Potentials II (Molden) [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials_2 link]
##Using A. Stone's distributed multipole analysis [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/GDMA link]
##Finding sigma hole (Vs,max and Vs,min values) using Multiwfn [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group:sigma_hole_multiwfn link]
#NCI Plots
##How to install NCIPlot on your mac [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/InstallNCIPlot link]
##Using NCIPlot [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/UseNCIPlot link]
#Using Multiwfn: density based visualisation
##Download Multiwfn [http://sobereva.com/multiwfn/download.html link]
##Installation of Multiwfn on Mac [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group:multiwfn_on_mac link]
##Using MP2 Densities in Multiwfn Surface Analysis [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group:multiwfn_mp2_density link]
##Generate BCPs [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group:multiwfn_bcps link]
#Jmol Visualisations
##Jmol basics [https://sagacioushours.org.uk/wiki/index.php?title=Mod:basic_jmol_instructions link]
##Visualising MOs using Jmol [https://sagacioushours.org.uk/wiki/index.php?title=Mod:basic_jmol_MOs link]
##Visualising vibrations using Jmol [https://sagacioushours.org.uk/wiki/index.php?title=Mod:basic_jmol_vibs link]
##Using Jmol to make a structure animation [https://sagacioushours.org.uk/wiki/index.php?title=Mod:struct_animate_jmol link]
##Jmol movie script [https://sagacioushours.org.uk/wiki/index.php?title=Mod:jmol_movie link]
##Using Jmol to overlap structures [https://sagacioushours.org.uk/wiki/index.php?title=Mod:struct_overlap_jmol link]
#VMD: a molecular dynamics visualisation package
##VMD can be installed from the [http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD VMD downloads page]
##Quick reminder [https://sagacioushours.org.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDReminder link]
##Colour in VMD [https://sagacioushours.org.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDColor link]
##Changing the graphical representation of your structures [https://sagacioushours.org.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/vmd link]
##VMD indexing [https://sagacioushours.org.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDindexing link]
##Using scripts in VMD [https://sagacioushours.org.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScripts link]
## Instructions for how to extract geometry and charges (ESP) into a .pdb file for visualising in VMD, especially if you want a blue-red colour variation rather than gaussviews red-greeen [https://sagacioushours.org.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ESP_charges_for_VMD link]
##Dealing with periodic boundaries and bonding (under construction) [https://sagacioushours.org.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScriptsPeriodic link]
##Dealing with bonding (under construction) [https://sagacioushours.org.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdBonding link]
##How to turn a Gaussian optimization into a VMD movie [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/VMDmovie link]
##Overlapping two structures [https://sagacioushours.org.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdVisual link]

===ORCA===
#This section is about using ORCA 6.1 on the HPC (Raapoi) [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/orca6_hpc link]
#Installing on a mac [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/orca6_macs link]
#Running ORCA [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/orca_run link]
#Using different basis sets and pseudopotentials for heavy elements in ORCA [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/orca6_PPs link]
#Plotting MOs with ORCA in GaussView format [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/orca6_MOs link]
#Visualize ORCA output files in GaussView [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/orca6_output_visuzlize link]
#Memory Specification in ORCA [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/orca6_Memory link]

===Other Programes===
#CREST [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group/crest link]
#ABCluster conformational search of atomic and molecular clusters [https://sagacioushours.org.uk/wiki/index.php?title=Mod:ABCluster#.inp_file_on_the_HPC link]
#MD programs and instructions [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/MD_info link]
#ADF Submission script [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/ADF_sricpt link]
#POLYRATE how to install [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/polyrate link]
#Psi4 and running SAPT calculations [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group/SAPT link]
#LDdecomposition (London Dispersion decomposition) [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group/LDD link]
#SpectroIBIS WINDOWS spectral data processing https://github.com/bbulcock/SpectroIBIS
#MultiWfn WINDOWS density/ESP analysis http://sobereva.com/multiwfn/

===Coding===
#'''installing Xcode and other programming environments'''
##to use many programs you will need a compiler, this is not installed by default on your mac
##How to install Xcode on your mac [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/InstallXcode link]
##using MacPorts as code for managing other codes on your mac [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/MacPorts link]
##HomeBrew and Fink are other options (HomeBrew is not advised for us)
##Runing windows codes using wine [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/Wine link]
##gfortran on your mac [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/Gfortran link]
##using python on your mac [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/python link]
#'''Ling's''' EMO Code [https://sagacioushours.org.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emo link]
#'''Jan's''' charge based analysis Code [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/Jan_charges link]
#'''Oxana's''' visualisation of ESPs Code [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Python_scripts_for_cube_files link]
#'''Richard M's''' Calculate pDoS/XP spectra code [https://sagacioushours.org.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Calc_XPS_Code link]
#'''Becky's''' script to extract frequency data from gaussian .log files and generate vibrational spectra [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group:frequency_spectrum_script link]

===Python scripts===
====Intro====
*'''note:''' scripts with "D" in front are those made to run on groups of files
::: they can be for when you have a large number of files from a crest run
::: they can be for use within a single directory, running on all files in that directory
::: made to be used with a set of specific gaussian log files, Tricia's ones are made to work on files with a structured naming sequence, for example struc_xx_B3LYP_D3BJ_6311pGdp_opt.log where xx is the individual number

====for set-up and running====
# '''sumbit.py''' script to submit G16 jobs: Code to auto-create a batch script [https://sagacioushours.org.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/create_batch_script link]
# '''Dsumbit.py''' script: Code to auto-create a batch script for ALL the com files in a partucluar directory and submit them to the que [https://sagacioushours.org.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Dsubmit link]
# '''suborca.py''' script to submit Orca jobs: Code to auto-create a batch script [https://sagacioushours.org.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/create_orca_batch_script link]
# '''Dsuborca.py''' script: Code to auto-create a batch script for a specified number of jobs with input files of the form base_xx.inp [https://sagacioushours.org.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Dsuborca link]
# '''get_energy.py''' script: Check a job while it is running, plot energy, find lowest force [https://sagacioushours.org.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/extract_energy link]
# '''tlog.py''' script: Check a G16 job while it is running by using tail, printing Max force, Max displacement, Energy and saving a version to your home directory [https://sagacioushours.org.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/tlog link]
# '''Dgetorca.py''' script: Check an orca job while it is running, or has finised [https://sagacioushours.org.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Dgetorca link]
# '''ocheck.py''' script: Check an orca job while it is running, or has finised [https://sagacioushours.org.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ocheck link]

====to extract structures====
# '''extract_structure.py''' script: Extract last Standard Orientation structure of gaussian log file [https://sagacioushours.org.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/extract_single_geom link]
# '''Dextract_structure.py''' script: Extract last Standard Orientation structure of multiple gaussian log files of the form struc_xx_B3LYP_D3BJ_6311pGdp_opt.log [https://sagacioushours.org.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Dextract_from_multiple_log_files link]
# '''extract_geom.py''' script: Extract Optimized Geometry Gaussian/ORCA log file into an .xyz or .com file [https://sagacioushours.org.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/extract_optimized_geom link]
# '''extract_steps.py''' script: Extract each optimised step from a scan into xyz coordinate file [https://sagacioushours.org.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/extract_scan_geom link]
# '''extract_crest_conf.py''' script: Extract given structure from a CREST conformer file and save to a *.xyz file (useful for using with Jmol) [https://sagacioushours.org.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/extract_crest_conf link]

==== to build new files from data or existing files====
# '''build_freq.py''' script: Build a frequency file from an optimisation file ready to submit, this will require editing for your particular job [https://sagacioushours.org.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/build_freq link]
# '''Dbuild_freq.py''' script: Extract last structure of gaussian optimisation and build a freq com file for multiple gaussian log files of the form struc_xx_B3LYP_D3BJ_6311pGdp_opt.log [https://sagacioushours.org.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Dbuild_freq_file link]
# '''symb_zmat.py''' script: Generate a symbolic z-matrix, requires you to use extract_structure.py and form a *.inp file with the xyz coords and a set of command words [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group:gen_symbolic_zmat link]
# '''pos_zmat.py''' script: Orientate the molecule along a specific axis, rotate by a defined angle and or fix a particular atom as the origin. Requires you to use extract_structure.py and form a *.inp file with the xyz coords and a set of command words, generates a symbolic z-matrix [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group:position_symbolic_zmat link]
# '''pos_restartzmat.py''' script: This script restarts a symbolic z-matrix job (used for electric fields). Requires you to use extract_structure.py and form a *.inp file with the xyz coords, generates a symbolic z-matrix file to continue an optimisation [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group:restart_symbolic_zmat link]

====to extract Thermochem data====
# '''getdata.py''' script: Extract thermodynamic data and low frequencies from a single log file into a formatted line to copy and paste into an excel files for the database [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group:model_freq_script link]
# '''Dgetdata.py''' script: Extract thermodynamic data and low frequencies from all the log files in a directory into a csv file for the database (Tricia) [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group:Dgetdata link]
# '''Dget_frequencies_data.py''' script: Extract thermodynamic data and low frequencies from all the log files in a directory to a csv file for the database (Muhammad) [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group:model_freq_script2 link]
# '''extract_vib.py''' script: for G16, extract vibrational data and make a plot [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group:extract_and_plot_vib link]
# '''orca_vib.py''' script: for orca, extract vibrational data and make a plot [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group:orca_vib link]

====to extract NMR data====
# '''Dboltzmann_NMR_of_conformers.py''' script: Extract NMR data from all conformed log files into an excel file (csv) for with individual shielding tensors, Boltzmann averaged tensors, Boltzmann factor etc. (Muhammad) [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group:nmr_of_conformers link]

====to extract charges and calculate dipole moment / charge arm====
# '''extract_charges.py''' script: Extract ESP and NBO charges [https://sagacioushours.org.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/extract_ESP_charges link]
# '''dipole_moment.py''' code to extract multiple charges and evaluate the dipole moment (Irelie) [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group/dipole_moment link]
# '''center-of-mass_calculation.py''' code to calculate center of mass (CoM) from an XYZ or log file (Muhammad) [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group/center_of_mass link]
# '''calculate_dipole_wrt_CoIR_CoP_g16.py''' code to calculate dipole moment w.r.t center of imidazolium ring from g16 log file (Muhammad) [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group/dipole_moment_CoIR link]
# '''calculate_dipole_wrt_atom_or_coordinate_g16.py''' code to calculate dipole moment w.r.t any atom or coordinate from g16 log file (Muhammad) [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group/dipole_moment_atom_coordinate link]

====Other quantities====
# '''extract_aim.py''' script: Extract volume data from AIMALL sumviz files [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group:extract_volume_aimall link]
# '''get_MOenergy.py''' script: Extract the MO orbital energies and convert to eV [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group/MO_energies link]
#'''plot_PES.py''' script: Plot a potential energy surface [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group/plot_potenital_energy_surface link]

====Historical codes====
# '''CArm.py''' script: Extract charges from *.fck and calculate the charge arm [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group/charge_arm link]
# '''freq.py''' historical python2 script" Extract thermodynamic data and low frequencies from log files [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group:simple_freq_script link]
# Codes to visualise data matrices (correlation matrices/heatmaps)[https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group/heatmap link]
# Python toolkit currently focussed towards gaussian analysis [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group/molLego link]
# Extract E2 Values (From NBO Calculations) [https://sagacioushours.org.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/NBO_Matlab_Code link]

===Admin Stuff===
#Not used to writing a wiki, make your test runs [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/testing on this page]
#How to set-up gaussian and gaussview on macs [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_setup link]
#Mac user admin basics [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_admin_users link]
#Moving large files and directories around [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/file_move link]
#How to launch on a Mac a Gaussview installed on a HPC [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/gv_hpc link]

===Old Imperial ===
#Old Imperial HPC information [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc link]
#Old Imperial use gaussview directly on the HPC [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/gview link]
#Old Imperial How to connect to HPC directory on desktop for file transfers [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_Directory_on_desktop link]
#Old Imperial How to run jobs interactively [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/run_interactive link]
#Old Imperial Computing resources available in the chemistry department [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/computing_resources link]
#Old Imperial New gf script (more convenient job submitting) [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group/new_gf_script link]
#Old Imperial How to make qsub more comfortable (gfunc) [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpQSUB link]
#Old Imperial How to use a slimmed down terminal on your IPhone [https://sagacioushours.org.uk/wiki/index.php?title=Mod:Hunt_Research_Group/termius link]

Mod:Hunt Research Group:molecules in an electric field

2025-10-23T00:24:35Z

Wikiadmin: /* scan a coordinate */

=Molecules in an electric field=
== introduction ==
getting started with the field keyword

which optimisation to use

accelerating optimisation

== using the field keyword ==
*we apply a field along an axial direction, x or y or z
<pre>field=x+250</pre>
:-for field=x+10 a field of 0.001au is applied
:-for more options goto the manual page here [https://gaussian.com/field/ link]

*units
:-conversion for an electric field: 1 au = 5.14220652 × 10^11 V/m =51.4 V/Å =514 V/nm
:-so 0.001au = 51.4/1000 V/Å = 0.0514 V/Å or 0.514V/nm
:-this is equivalent to 0.05V/Å
:-to apply 1V/nm we need approximately a field=x+20 (2*0.514V/nm=1.028V/nm)

== optimising in a field ==
*the field is applied along an axis direction
:-use the show axis option in gaussview to show this direction
:-by convention electric field arrows point from postive to negative
:-a positive x-axis field=+250 for example field will repel a negative ion (move it to -x)

*the molecule must not reorient when setting up the job
:-position the molecule explicitly where you want it within the coordinated system
:-you MUST use '''nosymm'''
:-things will go faster if you orient the molecular dipole with the field
:-in chemistry the dipole points positive to negative (in physics it can be the reverse!)
:-to get the correct dipole vector you must optimise first under the same conditions as will be applied with the field

*we have to be very careful in which cooridnates we optimise
:-this is because internal coordinates remove the center of mass motion which is relevant in an electric field
:-you MUST use '''opt=z-matrix'''
:-it is better to use '''symbolic cartesian coordinates'''
:-below is an example for acetate
:-the first zero tells gaussian that symbolic cartesian coordinates follow
:-if you run a charged molecule the molecule will move along the electric field
:-to avoid this '''fix one atom in the molecule''' to the center of the axial system
:-in the z-matrix format variables (to be optimised) are listed first and fixed constant are listed second
:-so the coordinates of the last atom below are held constant (at the origin)
<pre>
%chk=ch3co2.chk
# opt=(z-matrix,maxcycles=100) hf/3-21g nosymm field=x+250

Title Card Required

-1 1
6 0 x1 y1 z1
8 0 x2 y2 z2
8 0 x3 y3 z3
6 0 x4 y4 z4
1 0 x5 y5 z5
1 0 x6 y6 z6
1 0 x7 y7 z7

x2=-0.544205
y2=-1.144935
z2= 0.029999
x3=-0.568491
y3= 1.132502
z3= 0.024945
x4= 1.542020
y4= 0.011495
z4=-0.117920
x5= 1.805270
y5=-0.088033
z5=-1.168772
x6= 1.945393
y6= 0.945207
z6= 0.252204
x7= 1.965502
y7=-0.830194
z7= 0.416379

x1= 0.000000
y1= 0.000000
z1= 0.000000
</pre>
*refence state
:-make sure you run a reference state calculation without the field
:-this has the bonus of giving the dipole moment as well
:-currently we cannot orientate the dipole, but hopefully soon
:-first optimise the molecule (with the z-matrix as defined for the field calculation)
<pre>
# opt=(z-matrix,maxcycles=100) hf/3-21g nosymm
</pre>

== a code to orient the molecule ==
*copy the code pos_zmat into a file called pos_zmat.py in your bin directory
:'''pos_zmat.py''' [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/pos_zmat link]
*change the first line shebang to direct to YOUR python3
:mine is on my mac <code>#!/opt/local/bin/python3</code>
:on raapoi is <code>#!/usr/bin/env python3.8</code>
*extract the xyz coordinates for your molecule
:use "extract_structure.py"
:that is the xyz coordinates in the form <code>atom_symbol x y z</code>
:for example here are the coordinates of a water molecule
:note that we require atomic symbols not numbers
<pre>
O 1.995482 0.000000 -0.000000
H 2.637933 -0.000000 0.697270
H 2.637933 0.000000 -0.697270
</pre>
*create a file called '''water.inp'''
:below is the file for water
:info is given on each line
:1. number of atoms
:2. atom_1 atom_2 atom_3
:3. angle_1 angle_2 angle_3

:: atom_1 =atom to center the coordinates at (ie will be 0.0 0.0 0.0) in my case I want to center at atom 1
:: atom_2 =atom you want along the x-axis, in my case atom 2
:: atom_3 =atom to form the xy plane through atom_1, atom_2 and atom_3, the z-axis will be perpendicular to this plane
:: currently you can only give ONE angle the others must be set to 0.0
:: angle_1 rotatare in xy
:: angle_2 rotate in xz
:: angle_3 rotate in yx

:4. and on are your coordinates
:: note that you can insert a file using vi with the (comand mode)<code>:r filename</code> command

<pre>
3
1 2 3
10.0 0.0 0.0
O 1.995482 0.000000 -0.000000
H 2.637933 -0.000000 0.697270
H 2.637933 0.000000 -0.697270
</pre>

*run the code
:the water.inp file as an argument (without .inp)
:<code>pos_zmat.py water </code>
:you should see something like the following
<pre>
directory is /Volumes/Tricia_Home/work/jobs/musa
input file is water.inp
symbolic z-matrix output file is water_osymb.com
xyz coord output file is water_new.xyz
total number of atoms 3
center at atom 1
x-axis along bond to atom 2
atoms in the xy-plane 3
rotation of a-b around xy-pane (z-axis) by 10.0
centered
x-axis aligned
atoms aligned in xy plane
a-b vector rotated
write .xyz file
done!

</pre>

*output files
:you should see 2 files '''water_new.xyz''' and '''water_osymb.xyz'''
:water_new.xyz gives the new coordinate file in the standard format
<pre>
O 0.000000 0.000000 0.000000
H 0.915812 0.245391 0.000000
H -0.074822 -0.020048 -0.944949
Xx 4.000000 0.000000 0.000000
Xy 0.000000 4.000000 0.000000
Xz 0.000000 0.000000 4.000000
</pre>

:water_osymb.xyz gives the coordinates in the symbolic z-matrix format
:you will add these into your com file
:you can see that atom 1 is at the origin
:you can see that atom 2 has coordinates in the x and y direction very close to zero
:note that 3 dummy atoms are added on the position of the x,y and z axies to help with visualisation
<pre>
O 0 x1 y1 z1
H 0 x2 y2 z2
H 0 x3 y3 z3
Xx 0 x4 y4 z4
Xy 0 x5 y5 z5
Xz 0 x6 y6 z6

x1 = 0.000000
y1 = 0.000000
z1 = 0.000000
x2 = 0.915812
y2 = 0.245391
z2 = 0.000000
x3 =-0.074822
y3 =-0.020048
z3 =-0.944949
x4 = 4.000000
y4 = 0.000000
z4 = 0.000000
x5 = 0.000000
y5 = 4.000000
z5 = 0.000000
x6 = 0.000000
y6 = 0.000000
z6 = 4.000000

</pre>
*create a com file
:use the vi insert file option (comand mode)<code>:r geom_osymb.xyz</code>
:here is my new water_field.com file
:you MUST visualise this in gaussview to make sure everything is ok!
<pre>
%nprocshared=3
%mem=3GB
%chk=water_osymb.chk
#b3lyp/3-21G int=ultrafine scf=conver=10
opt=(maxcyc=50) nosymm field=x+250

Title Card Required

0 1
O 0 x1 y1 z1
H 0 x2 y2 z2
H 0 x3 y3 z3
Xx 0 x4 y4 z4
Xy 0 x5 y5 z5
Xz 0 x6 y6 z6

x1 = 0.000000
y1 = 0.000000
z1 = 0.000000
x2 = 0.933714
y2 = 0.164639
z2 = 0.000000
x3 =-0.240373
y3 = 0.917142
z3 =-0.000000
x4 = 4.000000
y4 = 0.000000
z4 = 0.000000
x5 = 0.000000
y5 = 4.000000
z5 = 0.000000
x6 = 0.000000
y6 = 0.000000
z6 = 4.000000
:
</pre>
:and here is my gaussview check
:with the x-axis to atom 2 angle of 10 degrees
[[File:Water_field_file.png|500px|caption]]

== scan a coordinate ==
*you need to build a z-matrix file that includes symbolic coordinates and internal coordinates together
*for z-matrix the first set of parameters are optimised and the second set are frozen
*shown by the example for water below
:atom1 is fixed in place with symbolic coords (note the 0 after the O label)
:O-H distance is allowed to vary (r1)
:the angle H-O-H is opened from 100º in 5 steps by 15º each time
:the scanned coordinate is "frozen" on each step so goes into the block of frozen variables
<pre>
%nprocshared=5
%mem=3GB
%chk=water_scan_osymb.chk
#b3lyp/3-21G nosymm field=x+50
opt=(z-matrix,maxcyc=5)

Title Card Required

0 1
O 0 x1 y1 z1
H 1 r1
H 1 r1 2 a1

r1 1.0

x1 = 0.000000
y1 = 0.000000
z1 = 0.000000
a1 100.0 S 2 15.0
</pre>
*a torsion angle rotation is more difficult
*unfortunately you cannot read the z-matrix from a checkpoint file so you need to start from a pre-optimised geometry and then set up the z-matrix rotation
*here is a demo job for alkyl rotation of emim
:the C2 is set at the origin (0,0,0) and the coords are frozen to keep the coordinate center fixed
:the ring atoms are also all frozen in cartesian coords
:then we need to define all the "moving" atoms with internal coordinates
:lastly I have the dummy atoms which are showing were the axes are
:notice the separation of active and frozen variables
:the scan coordinate is given LAST we are rotating 18 steps of 10 degrees
*obviously for your application you will want to improve the method/basis-set and maxcycles!
<pre>
%nprocshared=5
%mem=5GB
%chk=emim_outplane_scan2_osymb.chk
#b3lyp/3-21G nosymm field=x+50
opt=(z-matrix,maxcycles=25)

Title Card Required

1 1
6 0 x1 y1 z1
1 0 x2 y2 z2
6 0 x3 y3 z3
1 0 x4 y4 z4
6 0 x5 y5 z5
1 0 x6 y6 z6
7 0 x7 y7 z7
6 0 x8 y8 z8
1 0 x9 y9 z9
1 0 x10 y10 z10
1 0 x11 y11 z11
7 0 x12 y12 z12
6 12 rnc 5 acnc 3 dcncc
1 13 rch1 12 ahcn1 1 dhcn1
1 13 rch2 12 ahcn2 1 dhcn2
6 13 rcc 12 accn 1 dccnc
1 16 rch3 13 ahcc1 12 dhccn1
1 16 rch4 13 ahcc2 12 dhccn2
1 16 rch5 13 ahcc3 12 dhccn3
Xx 0 x20 y20 z20
Xy 0 x21 y21 z21
Xz 0 x22 y22 z22

rnc 1.481
acnc 126.0
dcncc 180.0
rch1 1.09
rch2 1.09
ahcn1 107.0
ahcn2 107.0
dhcn1 -135.0
dhcn2 -20.0
rcc 1.524
accn 112.0
rch3 1.09
rch4 1.09
rch5 1.09
ahcc1 112.0
ahcc2 112.0
ahcc3 112.0
dhccn1 -60.0
dhccn2 180.0
dhccn3 60.0

x2 = 1.076881
y2 = 0.000000
z2 = 0.000000
x3 =-2.100705
y3 = 0.680775
z3 = 0.000000
x4 =-2.914688
y4 = 1.384929
z4 =-0.004197
x5 =-2.099251
y5 =-0.680237
z5 =-0.004583
x6 =-2.913526
y6 =-1.383789
z6 =-0.010663
x7 =-0.779163
y7 = 1.086932
z7 = 0.003562
x8 =-0.313764
y8 = 2.480517
z8 =-0.001050
x9 = 0.773736
y9 = 2.489310
z9 = 0.017415
x10 =-0.666276
y10 = 2.977026
z10 =-0.904172
x11 =-0.696108
y11 = 2.991482
z11 = 0.881532
x12 =-0.778234
y12 =-1.085961
z12 =-0.008125
x1 = 0.000000
y1 = 0.000000
z1 = 0.000000
x20 = 4.000000
y20 = 0.000000
z20 = 0.000000
x21 = 0.000000
y21 = 4.000000
z21 = 0.000000
x22 = 0.000000
y22 = 0.000000
z22 = 4.000000
dccnc 100.0 S 18 10.0
</pre>

Mod:Hunt Research Group:molecules in an electric field

2025-10-23T00:19:42Z

Wikiadmin: /* scan a coordinate */

=Molecules in an electric field=
== introduction ==
getting started with the field keyword

which optimisation to use

accelerating optimisation

== using the field keyword ==
*we apply a field along an axial direction, x or y or z
<pre>field=x+250</pre>
:-for field=x+10 a field of 0.001au is applied
:-for more options goto the manual page here [https://gaussian.com/field/ link]

*units
:-conversion for an electric field: 1 au = 5.14220652 × 10^11 V/m =51.4 V/Å =514 V/nm
:-so 0.001au = 51.4/1000 V/Å = 0.0514 V/Å or 0.514V/nm
:-this is equivalent to 0.05V/Å
:-to apply 1V/nm we need approximately a field=x+20 (2*0.514V/nm=1.028V/nm)

== optimising in a field ==
*the field is applied along an axis direction
:-use the show axis option in gaussview to show this direction
:-by convention electric field arrows point from postive to negative
:-a positive x-axis field=+250 for example field will repel a negative ion (move it to -x)

*the molecule must not reorient when setting up the job
:-position the molecule explicitly where you want it within the coordinated system
:-you MUST use '''nosymm'''
:-things will go faster if you orient the molecular dipole with the field
:-in chemistry the dipole points positive to negative (in physics it can be the reverse!)
:-to get the correct dipole vector you must optimise first under the same conditions as will be applied with the field

*we have to be very careful in which cooridnates we optimise
:-this is because internal coordinates remove the center of mass motion which is relevant in an electric field
:-you MUST use '''opt=z-matrix'''
:-it is better to use '''symbolic cartesian coordinates'''
:-below is an example for acetate
:-the first zero tells gaussian that symbolic cartesian coordinates follow
:-if you run a charged molecule the molecule will move along the electric field
:-to avoid this '''fix one atom in the molecule''' to the center of the axial system
:-in the z-matrix format variables (to be optimised) are listed first and fixed constant are listed second
:-so the coordinates of the last atom below are held constant (at the origin)
<pre>
%chk=ch3co2.chk
# opt=(z-matrix,maxcycles=100) hf/3-21g nosymm field=x+250

Title Card Required

-1 1
6 0 x1 y1 z1
8 0 x2 y2 z2
8 0 x3 y3 z3
6 0 x4 y4 z4
1 0 x5 y5 z5
1 0 x6 y6 z6
1 0 x7 y7 z7

x2=-0.544205
y2=-1.144935
z2= 0.029999
x3=-0.568491
y3= 1.132502
z3= 0.024945
x4= 1.542020
y4= 0.011495
z4=-0.117920
x5= 1.805270
y5=-0.088033
z5=-1.168772
x6= 1.945393
y6= 0.945207
z6= 0.252204
x7= 1.965502
y7=-0.830194
z7= 0.416379

x1= 0.000000
y1= 0.000000
z1= 0.000000
</pre>
*refence state
:-make sure you run a reference state calculation without the field
:-this has the bonus of giving the dipole moment as well
:-currently we cannot orientate the dipole, but hopefully soon
:-first optimise the molecule (with the z-matrix as defined for the field calculation)
<pre>
# opt=(z-matrix,maxcycles=100) hf/3-21g nosymm
</pre>

== a code to orient the molecule ==
*copy the code pos_zmat into a file called pos_zmat.py in your bin directory
:'''pos_zmat.py''' [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/pos_zmat link]
*change the first line shebang to direct to YOUR python3
:mine is on my mac <code>#!/opt/local/bin/python3</code>
:on raapoi is <code>#!/usr/bin/env python3.8</code>
*extract the xyz coordinates for your molecule
:use "extract_structure.py"
:that is the xyz coordinates in the form <code>atom_symbol x y z</code>
:for example here are the coordinates of a water molecule
:note that we require atomic symbols not numbers
<pre>
O 1.995482 0.000000 -0.000000
H 2.637933 -0.000000 0.697270
H 2.637933 0.000000 -0.697270
</pre>
*create a file called '''water.inp'''
:below is the file for water
:info is given on each line
:1. number of atoms
:2. atom_1 atom_2 atom_3
:3. angle_1 angle_2 angle_3

:: atom_1 =atom to center the coordinates at (ie will be 0.0 0.0 0.0) in my case I want to center at atom 1
:: atom_2 =atom you want along the x-axis, in my case atom 2
:: atom_3 =atom to form the xy plane through atom_1, atom_2 and atom_3, the z-axis will be perpendicular to this plane
:: currently you can only give ONE angle the others must be set to 0.0
:: angle_1 rotatare in xy
:: angle_2 rotate in xz
:: angle_3 rotate in yx

:4. and on are your coordinates
:: note that you can insert a file using vi with the (comand mode)<code>:r filename</code> command

<pre>
3
1 2 3
10.0 0.0 0.0
O 1.995482 0.000000 -0.000000
H 2.637933 -0.000000 0.697270
H 2.637933 0.000000 -0.697270
</pre>

*run the code
:the water.inp file as an argument (without .inp)
:<code>pos_zmat.py water </code>
:you should see something like the following
<pre>
directory is /Volumes/Tricia_Home/work/jobs/musa
input file is water.inp
symbolic z-matrix output file is water_osymb.com
xyz coord output file is water_new.xyz
total number of atoms 3
center at atom 1
x-axis along bond to atom 2
atoms in the xy-plane 3
rotation of a-b around xy-pane (z-axis) by 10.0
centered
x-axis aligned
atoms aligned in xy plane
a-b vector rotated
write .xyz file
done!

</pre>

*output files
:you should see 2 files '''water_new.xyz''' and '''water_osymb.xyz'''
:water_new.xyz gives the new coordinate file in the standard format
<pre>
O 0.000000 0.000000 0.000000
H 0.915812 0.245391 0.000000
H -0.074822 -0.020048 -0.944949
Xx 4.000000 0.000000 0.000000
Xy 0.000000 4.000000 0.000000
Xz 0.000000 0.000000 4.000000
</pre>

:water_osymb.xyz gives the coordinates in the symbolic z-matrix format
:you will add these into your com file
:you can see that atom 1 is at the origin
:you can see that atom 2 has coordinates in the x and y direction very close to zero
:note that 3 dummy atoms are added on the position of the x,y and z axies to help with visualisation
<pre>
O 0 x1 y1 z1
H 0 x2 y2 z2
H 0 x3 y3 z3
Xx 0 x4 y4 z4
Xy 0 x5 y5 z5
Xz 0 x6 y6 z6

x1 = 0.000000
y1 = 0.000000
z1 = 0.000000
x2 = 0.915812
y2 = 0.245391
z2 = 0.000000
x3 =-0.074822
y3 =-0.020048
z3 =-0.944949
x4 = 4.000000
y4 = 0.000000
z4 = 0.000000
x5 = 0.000000
y5 = 4.000000
z5 = 0.000000
x6 = 0.000000
y6 = 0.000000
z6 = 4.000000

</pre>
*create a com file
:use the vi insert file option (comand mode)<code>:r geom_osymb.xyz</code>
:here is my new water_field.com file
:you MUST visualise this in gaussview to make sure everything is ok!
<pre>
%nprocshared=3
%mem=3GB
%chk=water_osymb.chk
#b3lyp/3-21G int=ultrafine scf=conver=10
opt=(maxcyc=50) nosymm field=x+250

Title Card Required

0 1
O 0 x1 y1 z1
H 0 x2 y2 z2
H 0 x3 y3 z3
Xx 0 x4 y4 z4
Xy 0 x5 y5 z5
Xz 0 x6 y6 z6

x1 = 0.000000
y1 = 0.000000
z1 = 0.000000
x2 = 0.933714
y2 = 0.164639
z2 = 0.000000
x3 =-0.240373
y3 = 0.917142
z3 =-0.000000
x4 = 4.000000
y4 = 0.000000
z4 = 0.000000
x5 = 0.000000
y5 = 4.000000
z5 = 0.000000
x6 = 0.000000
y6 = 0.000000
z6 = 4.000000
:
</pre>
:and here is my gaussview check
:with the x-axis to atom 2 angle of 10 degrees
[[File:Water_field_file.png|500px|caption]]

== scan a coordinate ==
*you need to build a z-matrix file that includes symbolic coordinates and internal coordinates together
*shown by the example for water below
:atom1 is fixed in place with symbolic coords (note the 0 after the O label)
:O-H distance is allowed to vary (r1)
:the angle H-O-H is openened from 100º in 5 steps by 15º each time
<pre>
%nprocshared=5
%mem=3GB
%chk=water_scan_osymb.chk
#b3lyp/3-21G nosymm field=x+50
opt=(z-matrix,maxcyc=5)

Title Card Required

0 1
O 0 x1 y1 z1
H 1 r1
H 1 r1 2 a1

r1 1.0

x1 = 0.000000
y1 = 0.000000
z1 = 0.000000
a1 100.0 S 2 15.0
</pre>
*a torsion angle rotation is more difficult
*unfortunately you cannot read the z-matrix from a checkpoint file so you need to start from a pre-optimised geometry and then set up the rotation
*here is a demo job for alkyl rotation of emim
<pre>
%nprocshared=5
%mem=5GB
%chk=emim_outplane_scan2_osymb.chk
#b3lyp/3-21G nosymm field=x+50
opt=(z-matrix,maxcycles=25)

Title Card Required

1 1
6 0 x1 y1 z1
1 0 x2 y2 z2
6 0 x3 y3 z3
1 0 x4 y4 z4
6 0 x5 y5 z5
1 0 x6 y6 z6
7 0 x7 y7 z7
6 0 x8 y8 z8
1 0 x9 y9 z9
1 0 x10 y10 z10
1 0 x11 y11 z11
7 0 x12 y12 z12
6 12 rnc 5 acnc 3 dcncc
1 13 rch1 12 ahcn1 1 dhcn1
1 13 rch2 12 ahcn2 1 dhcn2
6 13 rcc 12 accn 1 dccnc
1 16 rch3 13 ahcc1 12 dhccn1
1 16 rch4 13 ahcc2 12 dhccn2
1 16 rch5 13 ahcc3 12 dhccn3
Xx 0 x20 y20 z20
Xy 0 x21 y21 z21
Xz 0 x22 y22 z22

rnc 1.481
acnc 126.0
dcncc 180.0
rch1 1.09
rch2 1.09
ahcn1 107.0
ahcn2 107.0
dhcn1 -135.0
dhcn2 -20.0
rcc 1.524
accn 112.0
rch3 1.09
rch4 1.09
rch5 1.09
ahcc1 112.0
ahcc2 112.0
ahcc3 112.0
dhccn1 -60.0
dhccn2 180.0
dhccn3 60.0

x2 = 1.076881
y2 = 0.000000
z2 = 0.000000
x3 =-2.100705
y3 = 0.680775
z3 = 0.000000
x4 =-2.914688
y4 = 1.384929
z4 =-0.004197
x5 =-2.099251
y5 =-0.680237
z5 =-0.004583
x6 =-2.913526
y6 =-1.383789
z6 =-0.010663
x7 =-0.779163
y7 = 1.086932
z7 = 0.003562
x8 =-0.313764
y8 = 2.480517
z8 =-0.001050
x9 = 0.773736
y9 = 2.489310
z9 = 0.017415
x10 =-0.666276
y10 = 2.977026
z10 =-0.904172
x11 =-0.696108
y11 = 2.991482
z11 = 0.881532
x12 =-0.778234
y12 =-1.085961
z12 =-0.008125
x1 = 0.000000
y1 = 0.000000
z1 = 0.000000
x20 = 4.000000
y20 = 0.000000
z20 = 0.000000
x21 = 0.000000
y21 = 4.000000
z21 = 0.000000
x22 = 0.000000
y22 = 0.000000
z22 = 4.000000
dccnc 100.0 S 18 10.0
</pre>

Mod:Hunt Research Group:molecules in an electric field

2025-10-22T22:11:51Z

Wikiadmin: /* orientate to the dipole */

=Molecules in an electric field=
== introduction ==
getting started with the field keyword

which optimisation to use

accelerating optimisation

== using the field keyword ==
*we apply a field along an axial direction, x or y or z
<pre>field=x+250</pre>
:-for field=x+10 a field of 0.001au is applied
:-for more options goto the manual page here [https://gaussian.com/field/ link]

*units
:-conversion for an electric field: 1 au = 5.14220652 × 10^11 V/m =51.4 V/Å =514 V/nm
:-so 0.001au = 51.4/1000 V/Å = 0.0514 V/Å or 0.514V/nm
:-this is equivalent to 0.05V/Å
:-to apply 1V/nm we need approximately a field=x+20 (2*0.514V/nm=1.028V/nm)

== optimising in a field ==
*the field is applied along an axis direction
:-use the show axis option in gaussview to show this direction
:-by convention electric field arrows point from postive to negative
:-a positive x-axis field=+250 for example field will repel a negative ion (move it to -x)

*the molecule must not reorient when setting up the job
:-position the molecule explicitly where you want it within the coordinated system
:-you MUST use '''nosymm'''
:-things will go faster if you orient the molecular dipole with the field
:-in chemistry the dipole points positive to negative (in physics it can be the reverse!)
:-to get the correct dipole vector you must optimise first under the same conditions as will be applied with the field

*we have to be very careful in which cooridnates we optimise
:-this is because internal coordinates remove the center of mass motion which is relevant in an electric field
:-you MUST use '''opt=z-matrix'''
:-it is better to use '''symbolic cartesian coordinates'''
:-below is an example for acetate
:-the first zero tells gaussian that symbolic cartesian coordinates follow
:-if you run a charged molecule the molecule will move along the electric field
:-to avoid this '''fix one atom in the molecule''' to the center of the axial system
:-in the z-matrix format variables (to be optimised) are listed first and fixed constant are listed second
:-so the coordinates of the last atom below are held constant (at the origin)
<pre>
%chk=ch3co2.chk
# opt=(z-matrix,maxcycles=100) hf/3-21g nosymm field=x+250

Title Card Required

-1 1
6 0 x1 y1 z1
8 0 x2 y2 z2
8 0 x3 y3 z3
6 0 x4 y4 z4
1 0 x5 y5 z5
1 0 x6 y6 z6
1 0 x7 y7 z7

x2=-0.544205
y2=-1.144935
z2= 0.029999
x3=-0.568491
y3= 1.132502
z3= 0.024945
x4= 1.542020
y4= 0.011495
z4=-0.117920
x5= 1.805270
y5=-0.088033
z5=-1.168772
x6= 1.945393
y6= 0.945207
z6= 0.252204
x7= 1.965502
y7=-0.830194
z7= 0.416379

x1= 0.000000
y1= 0.000000
z1= 0.000000
</pre>
*refence state
:-make sure you run a reference state calculation without the field
:-this has the bonus of giving the dipole moment as well
:-currently we cannot orientate the dipole, but hopefully soon
:-first optimise the molecule (with the z-matrix as defined for the field calculation)
<pre>
# opt=(z-matrix,maxcycles=100) hf/3-21g nosymm
</pre>

== a code to orient the molecule ==
*copy the code pos_zmat into a file called pos_zmat.py in your bin directory
:'''pos_zmat.py''' [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/pos_zmat link]
*change the first line shebang to direct to YOUR python3
:mine is on my mac <code>#!/opt/local/bin/python3</code>
:on raapoi is <code>#!/usr/bin/env python3.8</code>
*extract the xyz coordinates for your molecule
:use "extract_structure.py"
:that is the xyz coordinates in the form <code>atom_symbol x y z</code>
:for example here are the coordinates of a water molecule
:note that we require atomic symbols not numbers
<pre>
O 1.995482 0.000000 -0.000000
H 2.637933 -0.000000 0.697270
H 2.637933 0.000000 -0.697270
</pre>
*create a file called '''water.inp'''
:below is the file for water
:info is given on each line
:1. number of atoms
:2. atom_1 atom_2 atom_3
:3. angle_1 angle_2 angle_3

:: atom_1 =atom to center the coordinates at (ie will be 0.0 0.0 0.0) in my case I want to center at atom 1
:: atom_2 =atom you want along the x-axis, in my case atom 2
:: atom_3 =atom to form the xy plane through atom_1, atom_2 and atom_3, the z-axis will be perpendicular to this plane
:: currently you can only give ONE angle the others must be set to 0.0
:: angle_1 rotatare in xy
:: angle_2 rotate in xz
:: angle_3 rotate in yx

:4. and on are your coordinates
:: note that you can insert a file using vi with the (comand mode)<code>:r filename</code> command

<pre>
3
1 2 3
10.0 0.0 0.0
O 1.995482 0.000000 -0.000000
H 2.637933 -0.000000 0.697270
H 2.637933 0.000000 -0.697270
</pre>

*run the code
:the water.inp file as an argument (without .inp)
:<code>pos_zmat.py water </code>
:you should see something like the following
<pre>
directory is /Volumes/Tricia_Home/work/jobs/musa
input file is water.inp
symbolic z-matrix output file is water_osymb.com
xyz coord output file is water_new.xyz
total number of atoms 3
center at atom 1
x-axis along bond to atom 2
atoms in the xy-plane 3
rotation of a-b around xy-pane (z-axis) by 10.0
centered
x-axis aligned
atoms aligned in xy plane
a-b vector rotated
write .xyz file
done!

</pre>

*output files
:you should see 2 files '''water_new.xyz''' and '''water_osymb.xyz'''
:water_new.xyz gives the new coordinate file in the standard format
<pre>
O 0.000000 0.000000 0.000000
H 0.915812 0.245391 0.000000
H -0.074822 -0.020048 -0.944949
Xx 4.000000 0.000000 0.000000
Xy 0.000000 4.000000 0.000000
Xz 0.000000 0.000000 4.000000
</pre>

:water_osymb.xyz gives the coordinates in the symbolic z-matrix format
:you will add these into your com file
:you can see that atom 1 is at the origin
:you can see that atom 2 has coordinates in the x and y direction very close to zero
:note that 3 dummy atoms are added on the position of the x,y and z axies to help with visualisation
<pre>
O 0 x1 y1 z1
H 0 x2 y2 z2
H 0 x3 y3 z3
Xx 0 x4 y4 z4
Xy 0 x5 y5 z5
Xz 0 x6 y6 z6

x1 = 0.000000
y1 = 0.000000
z1 = 0.000000
x2 = 0.915812
y2 = 0.245391
z2 = 0.000000
x3 =-0.074822
y3 =-0.020048
z3 =-0.944949
x4 = 4.000000
y4 = 0.000000
z4 = 0.000000
x5 = 0.000000
y5 = 4.000000
z5 = 0.000000
x6 = 0.000000
y6 = 0.000000
z6 = 4.000000

</pre>
*create a com file
:use the vi insert file option (comand mode)<code>:r geom_osymb.xyz</code>
:here is my new water_field.com file
:you MUST visualise this in gaussview to make sure everything is ok!
<pre>
%nprocshared=3
%mem=3GB
%chk=water_osymb.chk
#b3lyp/3-21G int=ultrafine scf=conver=10
opt=(maxcyc=50) nosymm field=x+250

Title Card Required

0 1
O 0 x1 y1 z1
H 0 x2 y2 z2
H 0 x3 y3 z3
Xx 0 x4 y4 z4
Xy 0 x5 y5 z5
Xz 0 x6 y6 z6

x1 = 0.000000
y1 = 0.000000
z1 = 0.000000
x2 = 0.933714
y2 = 0.164639
z2 = 0.000000
x3 =-0.240373
y3 = 0.917142
z3 =-0.000000
x4 = 4.000000
y4 = 0.000000
z4 = 0.000000
x5 = 0.000000
y5 = 4.000000
z5 = 0.000000
x6 = 0.000000
y6 = 0.000000
z6 = 4.000000
:
</pre>
:and here is my gaussview check
:with the x-axis to atom 2 angle of 10 degrees
[[File:Water_field_file.png|500px|caption]]

== scan a coordinate ==
*you need to build a z-matrix file that includes symbolic coordinates and internal coordinates together
*shown by the example for water below
:atom1 is fixed in place with symbolic coords (note the 0 after the O label)
:O-H distance is allowed to vary (r1)
:the angle H-O-H is openened from 100º in 5 steps by 15º each time
<pre>
%nprocshared=5
%mem=3GB
%chk=water_scan_osymb.chk
#b3lyp/3-21G nosymm field=x+50
opt=(z-matrix,maxcyc=5)

Title Card Required

0 1
O 0 x1 y1 z1
H 1 r1
H 1 r1 2 a1

r1 1.0

x1 = 0.000000
y1 = 0.000000
z1 = 0.000000
a1 100.0 S 2 15.0
</pre>

Mod:Hunt Research Group/z-matrix

2025-10-22T19:11:35Z

Wikiadmin: /* Links to G16 manual pages */

=Partial optimisations, scans and the z-matrix=
==Links to G16 manual pages==
*geom [link:https://gaussian.com/geom/]
*molecule specification [link:https://gaussian.com/molspec/]
*constructing z-matricies [link:https://gaussian.com/zmat/]
:look here for dummy atom description too
:cartesian coords are considered a special type of z-matrix
:symbolic cartesian coords have an extra "0" eg
<pre>
6 0 x1 y1 z1
</pre>
then define in the variables section
<pre>
x1 =0.000000
y1 =0.000000
z1 =0.000000
</pre>

==partial optimisations==
*involve freezing one coordinate while allowing all others to optimise
*very occasionally you freeze more than one coordinate, but the errors introduced become larger the more coordinates you freeze
* use OPT=(modredundant)
*in addition you add a section after the coordinates and connectivity
** identify the coordinate type B(bond), A(angle),T(torsion)
**give the atoms defining the coordinate and the value you want them to have
**give the atoms defining the coordinate and F to freeze the value
**if you want to activate the coordinate later change the F to A (activate)
*the following example is for two water molecules
**we define a bond between atoms 1 and 3 (O and H) to be 1 angsrom
**then we ask for this bond to be frozen
*in most cases there is a single important coordinate, but you can add more coordinates after the one given
<pre>%mem=1GB
%chk=2water.chk
# opt=(modredundant,maxcycles=12) b3lyp/6-31g geom=connectivity

Two water molecules

0 1
O -1.26602562 -0.36057693 0.00000000
H -0.30602562 -0.36057693 0.00000000
H -1.58648021 0.54435890 0.00000000
O -1.97115382 2.44391033 0.00000000
H -1.01115382 2.44391033 0.00000000
H -2.29160840 3.34884617 0.00000000

1 2 1.0 3 1.0
2
3
4 5 1.0 6 1.0
5
6

B 1 3 1.0
B 1 3 F
</pre>

==relaxed scan==
*involve specifying the value of one key coordinate and optimising all others
*the key coordinate is then varied in a systematic way
*use the OPT=(modredundant) keyword
*then in the section after the coordinates and connectivity add
**identify the coordinate type B(bond), A(angle),T(torsion)
**give the atoms defining the coordinate and the value you want them to have
**specify you want a scan with S and then the number of steps and the change in the variable on each step
*the following shows how you change the modredundant part of the input file
**here the O-H bond is specified and set to 1 angstrom
**then identify the coordinate and specify a scan (S) this time we will take 5 steps of 0.15
**this will carry out a partial optimisation for the r(O-H) coordinate set to the values =1.0,1.15,1.30,1.45 and 1.60
<pre>
B 1 3 1.0
B 1 3 S 5 0.15
</pre>

==simple scan==
*involve specifying the value of one key coordinate to alter on each step, all other coordinates are frozen
*this can be used to get a rough idea, it is not advisable to use this option
*use the SCAN keyword
*the molecular structure must be entered as a Z-matrix, more on the Z-matrix below

==complex partial optimisations==
*there are times when you want to freeze one coordinate and then scan another
*for example in H-bonds X---H---Y, you want to freeze the "bond" or distance between X and Y and then scan the H moving between them
*some of the options identified in the manual DO NOT WORK
*to freeze two atoms, use -1 in the cartesian coordinates (those not specified default to optimisation)
*add the redundant coordinate as usual
*the following freezes the oxygen atoms in place and then scans the O-H distance
<pre>%mem=1GB
%chk=test.chk
# opt=(modredundant) b3lyp/6-31g geom=connectivity

Title Card Required

0 1
O -1 -1.26602562 -0.36057693 0.00000000
H -0.30602562 -0.36057693 0.00000000
H -1.58648021 0.54435890 0.00000000
O -1 -1.97115382 2.44391033 0.00000000
H -1.01115382 2.44391033 0.00000000
H -2.29160840 3.34884617 0.00000000

1 2 1.0 3 1.0
2
3
4 5 1.0 6 1.0
5
6

B 1 3 1.0
B 1 3 S 5 0.15
</pre>
*the output will look something like this
<pre>
Initialization pass.
----------------------------
! Initial Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! X1 R(1,-1) -1.266 Frozen !
! Y1 R(1,-2) -0.3606 Frozen !
! Z1 R(1,-3) 0.0 Frozen !
! X4 R(4,-1) -1.9712 Frozen !
! Y4 R(4,-2) 2.4439 Frozen !
! Z4 R(4,-3) 0.0 Frozen !
! R1 R(1,2) 0.9653 estimate D2E/DX2 !
! R2 R(1,3) 1.0 Scan !
! R3 R(3,4) 1.8987 estimate D2E/DX2 !
! R4 R(3,5) 1.9826 estimate D2E/DX2 !
! R5 R(4,5) 0.9554 estimate D2E/DX2 !
! R6 R(4,6) 0.9807 estimate D2E/DX2
</pre>

==The Z-Matrix and optimising linear bonds==

The z-matrix is an additional method of describing atomic positions. This is very well described on the Gaussian webpage. [http://www.gaussian.com/g_tech/g_ur/c_zmat.htm | Gaussian Z-matricies]

Using Gaussview to build a z-matrix is generally a bad idea. While I was working with simple molecules it completely failed to build a z-matrix, instead building some weird cross over between cartesian coordinated and z-matricies that didn't make any sense. It is best to construct the z-matricies manually (if dealing with small molecules) using Gaussview to give bond lengths and angles.

Using a Z-Matrix to build a pentagon

[[File:Pentagon.jpg ]]

<pre>A
B 1 1.5
C 2 1.5 1 108
D 3 1.5 2 108 1 0.0 0
E 4 1.5 3 108 2 0.0 0
</pre>

The 0 at the end of lines 4&5 in the Z-matrix indicate that the final value is a dihedral angle. If this was to be a 1, the final value would be a second angle.

It doesn't matter where atom A is, as it is being used a reference point.
Atom B is connected to atom A (indicated by the 1) at a distance of 1.5.
Atom C is connected to atom B (indicated by the 2) at a distance of 1.5, with an A-B-C angle of 108.
Atom D is connected to atom C at a distance of 1.5, with a B-C-D angle of 108 and a dihedral angle of 0.0
Atom E is connected to atom D at a distance of 1.5, with a C-D-E angle of 108 and a dihedral angle of 0.0

The building of a pentagon is shown below.

[[File:Building-Pentagon.jpg ]]

It is possible to include variables that occur throughout a molecule, for example the C-H bond lengths in a long alkyl chain. This is done by using a term within the main body of the input, and the second line beneath the z-matrix putting the term and the value for the bond length/angle. As the N-H bonds lengths and angles will all be the same in the input structure the z-matrix has become.

<pre>A
B 1 B1
C 2 B1 1 A1
D 3 B1 2 A1 1 0.0 0
E 4 B1 3 A1 2 0.0 0

B1 1.5
A1 108

</pre>
The term B1 refers to the N-H bond distance, the A1 term refers to the H-N-H bond angle

It is also possible to include values which you wish to keep constant. This is done in a similar way to including variables. To include constants a empty line should be left after the variables, and then the constants are written, again using a term found in the z-matrix. To fix the bond length, the next z-matrix is needed.

<pre>A
B 1 B1
C 2 B1 1 A1
D 3 B1 2 A1 1 0.0 0
E 4 B1 3 A1 2 0.0 0

A1 108

B1 1.5
</pre>

If working with a larger molecule it is worth looking into combining z-matricies with cartesian coordinates, again this is explained well on the Gaussian webpage. Each atom can be described using either cartesian coordinates or z-matrix. If a atom is being described using a z-matrix the atoms used to define its position need to be included above the z-matrix line, using either a z-matirx or a cartesian coordinate system.

<pre>Y 0 -0.10608500 -0.05799800 0.01993400
Cl 0 -1.25351400 -1.98304000 1.34042900
Cl 0 1.62975500 1.12134800 1.60905800
Cl 0 1.11223600 -1.09533800 -1.98836000
Cl 0 -1.76438600 1.62418700 -0.79499400
Na 4 2.556 1 71.370 5 -1.410 0
</pre>

An example showing how an atom which is not bonded to the complex can be represented via a different method for describing atomic positions.

[[File:YCl4-Na2 opt com.jpg]]

'''Optimising Linear bond'''

To optimise linear bonds a dummy atom needs to be introduced. On the gaussian webpage linked earlier there is a section on how to introduce dummy atoms into calculations.

Dummy Atoms

Although being used here to help optimise linear bonds, the dummy atom is useful for other tasks, such as the optimisation of the NH3 molecule. Using a dummy atom allows for the angle between the lone pair and the H atoms to be more effectively described and retain the C3V structure.

<pre>N
X 1 1.
H 1 nh 2 hnx
H 1 nh 2 hnx 3 120.0
H 1 nh 2 hnx 3 -120.0

nh 1.0
hnx 70.0
</pre>

So here the nh bond length is set to 1.0 and the hnx bond angle is set to 70.

When introducing dummy atoms to linear bonds it is essential that the dummy atom is 'bonded' to the central atom, allowing the atoms either side to be set from the dummy atom. 'Bonded' is in quotes as the dummy atom should never have a formal bond attaching it to anything, think of it more as a point in space relative to the central atom of the linear bond.

Although optimising the CO2 molecule doesn't appear to need a dummy atom to be optimised, it has been included here to show one way of introducing it.

<pre>C
O 1 1.2
O 1 1.2 2 180.0
X 1 1.0 2 90.0 3 90.0 1
</pre>

The 1 at the end of the X input line represents a second angle needed for defining the linear angle. A dihedral can be used but its slightly more complex.

Mod:Hunt Research Group/z-matrix

2025-10-22T19:10:22Z

Wikiadmin: /* Links to G16 manual pages */

=Partial optimisations, scans and the z-matrix=
==Links to G16 manual pages==
geom [link:https://gaussian.com/geom/]
molecule specification [link:https://gaussian.com/molspec/]
constructing z-matricies [link:https://gaussian.com/zmat/]
:cartesian coords are considered a special type of z-matrix
:symbolic cartesian coords have an extra "0" eg
<pre>
6 0 x1 y1 z1
</pre>
then define in the variables section
<pre>
x1 =0.000000
y1 =0.000000
z1 =0.000000
</pre>

==partial optimisations==
*involve freezing one coordinate while allowing all others to optimise
*very occasionally you freeze more than one coordinate, but the errors introduced become larger the more coordinates you freeze
* use OPT=(modredundant)
*in addition you add a section after the coordinates and connectivity
** identify the coordinate type B(bond), A(angle),T(torsion)
**give the atoms defining the coordinate and the value you want them to have
**give the atoms defining the coordinate and F to freeze the value
**if you want to activate the coordinate later change the F to A (activate)
*the following example is for two water molecules
**we define a bond between atoms 1 and 3 (O and H) to be 1 angsrom
**then we ask for this bond to be frozen
*in most cases there is a single important coordinate, but you can add more coordinates after the one given
<pre>%mem=1GB
%chk=2water.chk
# opt=(modredundant,maxcycles=12) b3lyp/6-31g geom=connectivity

Two water molecules

0 1
O -1.26602562 -0.36057693 0.00000000
H -0.30602562 -0.36057693 0.00000000
H -1.58648021 0.54435890 0.00000000
O -1.97115382 2.44391033 0.00000000
H -1.01115382 2.44391033 0.00000000
H -2.29160840 3.34884617 0.00000000

1 2 1.0 3 1.0
2
3
4 5 1.0 6 1.0
5
6

B 1 3 1.0
B 1 3 F
</pre>

==relaxed scan==
*involve specifying the value of one key coordinate and optimising all others
*the key coordinate is then varied in a systematic way
*use the OPT=(modredundant) keyword
*then in the section after the coordinates and connectivity add
**identify the coordinate type B(bond), A(angle),T(torsion)
**give the atoms defining the coordinate and the value you want them to have
**specify you want a scan with S and then the number of steps and the change in the variable on each step
*the following shows how you change the modredundant part of the input file
**here the O-H bond is specified and set to 1 angstrom
**then identify the coordinate and specify a scan (S) this time we will take 5 steps of 0.15
**this will carry out a partial optimisation for the r(O-H) coordinate set to the values =1.0,1.15,1.30,1.45 and 1.60
<pre>
B 1 3 1.0
B 1 3 S 5 0.15
</pre>

==simple scan==
*involve specifying the value of one key coordinate to alter on each step, all other coordinates are frozen
*this can be used to get a rough idea, it is not advisable to use this option
*use the SCAN keyword
*the molecular structure must be entered as a Z-matrix, more on the Z-matrix below

==complex partial optimisations==
*there are times when you want to freeze one coordinate and then scan another
*for example in H-bonds X---H---Y, you want to freeze the "bond" or distance between X and Y and then scan the H moving between them
*some of the options identified in the manual DO NOT WORK
*to freeze two atoms, use -1 in the cartesian coordinates (those not specified default to optimisation)
*add the redundant coordinate as usual
*the following freezes the oxygen atoms in place and then scans the O-H distance
<pre>%mem=1GB
%chk=test.chk
# opt=(modredundant) b3lyp/6-31g geom=connectivity

Title Card Required

0 1
O -1 -1.26602562 -0.36057693 0.00000000
H -0.30602562 -0.36057693 0.00000000
H -1.58648021 0.54435890 0.00000000
O -1 -1.97115382 2.44391033 0.00000000
H -1.01115382 2.44391033 0.00000000
H -2.29160840 3.34884617 0.00000000

1 2 1.0 3 1.0
2
3
4 5 1.0 6 1.0
5
6

B 1 3 1.0
B 1 3 S 5 0.15
</pre>
*the output will look something like this
<pre>
Initialization pass.
----------------------------
! Initial Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! X1 R(1,-1) -1.266 Frozen !
! Y1 R(1,-2) -0.3606 Frozen !
! Z1 R(1,-3) 0.0 Frozen !
! X4 R(4,-1) -1.9712 Frozen !
! Y4 R(4,-2) 2.4439 Frozen !
! Z4 R(4,-3) 0.0 Frozen !
! R1 R(1,2) 0.9653 estimate D2E/DX2 !
! R2 R(1,3) 1.0 Scan !
! R3 R(3,4) 1.8987 estimate D2E/DX2 !
! R4 R(3,5) 1.9826 estimate D2E/DX2 !
! R5 R(4,5) 0.9554 estimate D2E/DX2 !
! R6 R(4,6) 0.9807 estimate D2E/DX2
</pre>

==The Z-Matrix and optimising linear bonds==

The z-matrix is an additional method of describing atomic positions. This is very well described on the Gaussian webpage. [http://www.gaussian.com/g_tech/g_ur/c_zmat.htm | Gaussian Z-matricies]

Using Gaussview to build a z-matrix is generally a bad idea. While I was working with simple molecules it completely failed to build a z-matrix, instead building some weird cross over between cartesian coordinated and z-matricies that didn't make any sense. It is best to construct the z-matricies manually (if dealing with small molecules) using Gaussview to give bond lengths and angles.

Using a Z-Matrix to build a pentagon

[[File:Pentagon.jpg ]]

<pre>A
B 1 1.5
C 2 1.5 1 108
D 3 1.5 2 108 1 0.0 0
E 4 1.5 3 108 2 0.0 0
</pre>

The 0 at the end of lines 4&5 in the Z-matrix indicate that the final value is a dihedral angle. If this was to be a 1, the final value would be a second angle.

It doesn't matter where atom A is, as it is being used a reference point.
Atom B is connected to atom A (indicated by the 1) at a distance of 1.5.
Atom C is connected to atom B (indicated by the 2) at a distance of 1.5, with an A-B-C angle of 108.
Atom D is connected to atom C at a distance of 1.5, with a B-C-D angle of 108 and a dihedral angle of 0.0
Atom E is connected to atom D at a distance of 1.5, with a C-D-E angle of 108 and a dihedral angle of 0.0

The building of a pentagon is shown below.

[[File:Building-Pentagon.jpg ]]

It is possible to include variables that occur throughout a molecule, for example the C-H bond lengths in a long alkyl chain. This is done by using a term within the main body of the input, and the second line beneath the z-matrix putting the term and the value for the bond length/angle. As the N-H bonds lengths and angles will all be the same in the input structure the z-matrix has become.

<pre>A
B 1 B1
C 2 B1 1 A1
D 3 B1 2 A1 1 0.0 0
E 4 B1 3 A1 2 0.0 0

B1 1.5
A1 108

</pre>
The term B1 refers to the N-H bond distance, the A1 term refers to the H-N-H bond angle

It is also possible to include values which you wish to keep constant. This is done in a similar way to including variables. To include constants a empty line should be left after the variables, and then the constants are written, again using a term found in the z-matrix. To fix the bond length, the next z-matrix is needed.

<pre>A
B 1 B1
C 2 B1 1 A1
D 3 B1 2 A1 1 0.0 0
E 4 B1 3 A1 2 0.0 0

A1 108

B1 1.5
</pre>

If working with a larger molecule it is worth looking into combining z-matricies with cartesian coordinates, again this is explained well on the Gaussian webpage. Each atom can be described using either cartesian coordinates or z-matrix. If a atom is being described using a z-matrix the atoms used to define its position need to be included above the z-matrix line, using either a z-matirx or a cartesian coordinate system.

<pre>Y 0 -0.10608500 -0.05799800 0.01993400
Cl 0 -1.25351400 -1.98304000 1.34042900
Cl 0 1.62975500 1.12134800 1.60905800
Cl 0 1.11223600 -1.09533800 -1.98836000
Cl 0 -1.76438600 1.62418700 -0.79499400
Na 4 2.556 1 71.370 5 -1.410 0
</pre>

An example showing how an atom which is not bonded to the complex can be represented via a different method for describing atomic positions.

[[File:YCl4-Na2 opt com.jpg]]

'''Optimising Linear bond'''

To optimise linear bonds a dummy atom needs to be introduced. On the gaussian webpage linked earlier there is a section on how to introduce dummy atoms into calculations.

Dummy Atoms

Although being used here to help optimise linear bonds, the dummy atom is useful for other tasks, such as the optimisation of the NH3 molecule. Using a dummy atom allows for the angle between the lone pair and the H atoms to be more effectively described and retain the C3V structure.

<pre>N
X 1 1.
H 1 nh 2 hnx
H 1 nh 2 hnx 3 120.0
H 1 nh 2 hnx 3 -120.0

nh 1.0
hnx 70.0
</pre>

So here the nh bond length is set to 1.0 and the hnx bond angle is set to 70.

When introducing dummy atoms to linear bonds it is essential that the dummy atom is 'bonded' to the central atom, allowing the atoms either side to be set from the dummy atom. 'Bonded' is in quotes as the dummy atom should never have a formal bond attaching it to anything, think of it more as a point in space relative to the central atom of the linear bond.

Although optimising the CO2 molecule doesn't appear to need a dummy atom to be optimised, it has been included here to show one way of introducing it.

<pre>C
O 1 1.2
O 1 1.2 2 180.0
X 1 1.0 2 90.0 3 90.0 1
</pre>

The 1 at the end of the X input line represents a second angle needed for defining the linear angle. A dihedral can be used but its slightly more complex.

Mod:Hunt Research Group/z-matrix

2025-10-22T19:06:35Z

Wikiadmin: /* Partial optimisations, scans and the z-matrix */

=Partial optimisations, scans and the z-matrix=
==Links to G16 manual pages==
molecule specification [link:https://gaussian.com/molspec/]
==partial optimisations==
*involve freezing one coordinate while allowing all others to optimise
*very occasionally you freeze more than one coordinate, but the errors introduced become larger the more coordinates you freeze
* use OPT=(modredundant)
*in addition you add a section after the coordinates and connectivity
** identify the coordinate type B(bond), A(angle),T(torsion)
**give the atoms defining the coordinate and the value you want them to have
**give the atoms defining the coordinate and F to freeze the value
**if you want to activate the coordinate later change the F to A (activate)
*the following example is for two water molecules
**we define a bond between atoms 1 and 3 (O and H) to be 1 angsrom
**then we ask for this bond to be frozen
*in most cases there is a single important coordinate, but you can add more coordinates after the one given
<pre>%mem=1GB
%chk=2water.chk
# opt=(modredundant,maxcycles=12) b3lyp/6-31g geom=connectivity

Two water molecules

0 1
O -1.26602562 -0.36057693 0.00000000
H -0.30602562 -0.36057693 0.00000000
H -1.58648021 0.54435890 0.00000000
O -1.97115382 2.44391033 0.00000000
H -1.01115382 2.44391033 0.00000000
H -2.29160840 3.34884617 0.00000000

1 2 1.0 3 1.0
2
3
4 5 1.0 6 1.0
5
6

B 1 3 1.0
B 1 3 F
</pre>

==relaxed scan==
*involve specifying the value of one key coordinate and optimising all others
*the key coordinate is then varied in a systematic way
*use the OPT=(modredundant) keyword
*then in the section after the coordinates and connectivity add
**identify the coordinate type B(bond), A(angle),T(torsion)
**give the atoms defining the coordinate and the value you want them to have
**specify you want a scan with S and then the number of steps and the change in the variable on each step
*the following shows how you change the modredundant part of the input file
**here the O-H bond is specified and set to 1 angstrom
**then identify the coordinate and specify a scan (S) this time we will take 5 steps of 0.15
**this will carry out a partial optimisation for the r(O-H) coordinate set to the values =1.0,1.15,1.30,1.45 and 1.60
<pre>
B 1 3 1.0
B 1 3 S 5 0.15
</pre>

==simple scan==
*involve specifying the value of one key coordinate to alter on each step, all other coordinates are frozen
*this can be used to get a rough idea, it is not advisable to use this option
*use the SCAN keyword
*the molecular structure must be entered as a Z-matrix, more on the Z-matrix below

==complex partial optimisations==
*there are times when you want to freeze one coordinate and then scan another
*for example in H-bonds X---H---Y, you want to freeze the "bond" or distance between X and Y and then scan the H moving between them
*some of the options identified in the manual DO NOT WORK
*to freeze two atoms, use -1 in the cartesian coordinates (those not specified default to optimisation)
*add the redundant coordinate as usual
*the following freezes the oxygen atoms in place and then scans the O-H distance
<pre>%mem=1GB
%chk=test.chk
# opt=(modredundant) b3lyp/6-31g geom=connectivity

Title Card Required

0 1
O -1 -1.26602562 -0.36057693 0.00000000
H -0.30602562 -0.36057693 0.00000000
H -1.58648021 0.54435890 0.00000000
O -1 -1.97115382 2.44391033 0.00000000
H -1.01115382 2.44391033 0.00000000
H -2.29160840 3.34884617 0.00000000

1 2 1.0 3 1.0
2
3
4 5 1.0 6 1.0
5
6

B 1 3 1.0
B 1 3 S 5 0.15
</pre>
*the output will look something like this
<pre>
Initialization pass.
----------------------------
! Initial Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! X1 R(1,-1) -1.266 Frozen !
! Y1 R(1,-2) -0.3606 Frozen !
! Z1 R(1,-3) 0.0 Frozen !
! X4 R(4,-1) -1.9712 Frozen !
! Y4 R(4,-2) 2.4439 Frozen !
! Z4 R(4,-3) 0.0 Frozen !
! R1 R(1,2) 0.9653 estimate D2E/DX2 !
! R2 R(1,3) 1.0 Scan !
! R3 R(3,4) 1.8987 estimate D2E/DX2 !
! R4 R(3,5) 1.9826 estimate D2E/DX2 !
! R5 R(4,5) 0.9554 estimate D2E/DX2 !
! R6 R(4,6) 0.9807 estimate D2E/DX2
</pre>

==The Z-Matrix and optimising linear bonds==

The z-matrix is an additional method of describing atomic positions. This is very well described on the Gaussian webpage. [http://www.gaussian.com/g_tech/g_ur/c_zmat.htm | Gaussian Z-matricies]

Using Gaussview to build a z-matrix is generally a bad idea. While I was working with simple molecules it completely failed to build a z-matrix, instead building some weird cross over between cartesian coordinated and z-matricies that didn't make any sense. It is best to construct the z-matricies manually (if dealing with small molecules) using Gaussview to give bond lengths and angles.

Using a Z-Matrix to build a pentagon

[[File:Pentagon.jpg ]]

<pre>A
B 1 1.5
C 2 1.5 1 108
D 3 1.5 2 108 1 0.0 0
E 4 1.5 3 108 2 0.0 0
</pre>

The 0 at the end of lines 4&5 in the Z-matrix indicate that the final value is a dihedral angle. If this was to be a 1, the final value would be a second angle.

It doesn't matter where atom A is, as it is being used a reference point.
Atom B is connected to atom A (indicated by the 1) at a distance of 1.5.
Atom C is connected to atom B (indicated by the 2) at a distance of 1.5, with an A-B-C angle of 108.
Atom D is connected to atom C at a distance of 1.5, with a B-C-D angle of 108 and a dihedral angle of 0.0
Atom E is connected to atom D at a distance of 1.5, with a C-D-E angle of 108 and a dihedral angle of 0.0

The building of a pentagon is shown below.

[[File:Building-Pentagon.jpg ]]

It is possible to include variables that occur throughout a molecule, for example the C-H bond lengths in a long alkyl chain. This is done by using a term within the main body of the input, and the second line beneath the z-matrix putting the term and the value for the bond length/angle. As the N-H bonds lengths and angles will all be the same in the input structure the z-matrix has become.

<pre>A
B 1 B1
C 2 B1 1 A1
D 3 B1 2 A1 1 0.0 0
E 4 B1 3 A1 2 0.0 0

B1 1.5
A1 108

</pre>
The term B1 refers to the N-H bond distance, the A1 term refers to the H-N-H bond angle

It is also possible to include values which you wish to keep constant. This is done in a similar way to including variables. To include constants a empty line should be left after the variables, and then the constants are written, again using a term found in the z-matrix. To fix the bond length, the next z-matrix is needed.

<pre>A
B 1 B1
C 2 B1 1 A1
D 3 B1 2 A1 1 0.0 0
E 4 B1 3 A1 2 0.0 0

A1 108

B1 1.5
</pre>

If working with a larger molecule it is worth looking into combining z-matricies with cartesian coordinates, again this is explained well on the Gaussian webpage. Each atom can be described using either cartesian coordinates or z-matrix. If a atom is being described using a z-matrix the atoms used to define its position need to be included above the z-matrix line, using either a z-matirx or a cartesian coordinate system.

<pre>Y 0 -0.10608500 -0.05799800 0.01993400
Cl 0 -1.25351400 -1.98304000 1.34042900
Cl 0 1.62975500 1.12134800 1.60905800
Cl 0 1.11223600 -1.09533800 -1.98836000
Cl 0 -1.76438600 1.62418700 -0.79499400
Na 4 2.556 1 71.370 5 -1.410 0
</pre>

An example showing how an atom which is not bonded to the complex can be represented via a different method for describing atomic positions.

[[File:YCl4-Na2 opt com.jpg]]

'''Optimising Linear bond'''

To optimise linear bonds a dummy atom needs to be introduced. On the gaussian webpage linked earlier there is a section on how to introduce dummy atoms into calculations.

Dummy Atoms

Although being used here to help optimise linear bonds, the dummy atom is useful for other tasks, such as the optimisation of the NH3 molecule. Using a dummy atom allows for the angle between the lone pair and the H atoms to be more effectively described and retain the C3V structure.

<pre>N
X 1 1.
H 1 nh 2 hnx
H 1 nh 2 hnx 3 120.0
H 1 nh 2 hnx 3 -120.0

nh 1.0
hnx 70.0
</pre>

So here the nh bond length is set to 1.0 and the hnx bond angle is set to 70.

When introducing dummy atoms to linear bonds it is essential that the dummy atom is 'bonded' to the central atom, allowing the atoms either side to be set from the dummy atom. 'Bonded' is in quotes as the dummy atom should never have a formal bond attaching it to anything, think of it more as a point in space relative to the central atom of the linear bond.

Although optimising the CO2 molecule doesn't appear to need a dummy atom to be optimised, it has been included here to show one way of introducing it.

<pre>C
O 1 1.2
O 1 1.2 2 180.0
X 1 1.0 2 90.0 3 90.0 1
</pre>

The 1 at the end of the X input line represents a second angle needed for defining the linear angle. A dihedral can be used but its slightly more complex.

File:Water field file.png

2025-10-22T18:13:49Z

Wikiadmin: Wikiadmin uploaded a new version of File:Water field file.png

Mod:Hunt Research Group:molecules in an electric field

2025-10-22T18:11:05Z

Wikiadmin: /* a code to orient the molecule */

=Molecules in an electric field=
== introduction ==
getting started with the field keyword

which optimisation to use

accelerating optimisation

== using the field keyword ==
*we apply a field along an axial direction, x or y or z
<pre>field=x+250</pre>
:-for field=x+10 a field of 0.001au is applied
:-for more options goto the manual page here [https://gaussian.com/field/ link]

*units
:-conversion for an electric field: 1 au = 5.14220652 × 10^11 V/m =51.4 V/Å =514 V/nm
:-so 0.001au = 51.4/1000 V/Å = 0.0514 V/Å or 0.514V/nm
:-this is equivalent to 0.05V/Å
:-to apply 1V/nm we need approximately a field=x+20 (2*0.514V/nm=1.028V/nm)

== optimising in a field ==
*the field is applied along an axis direction
:-use the show axis option in gaussview to show this direction
:-by convention electric field arrows point from postive to negative
:-a positive x-axis field=+250 for example field will repel a negative ion (move it to -x)

*the molecule must not reorient when setting up the job
:-position the molecule explicitly where you want it within the coordinated system
:-you MUST use '''nosymm'''
:-things will go faster if you orient the molecular dipole with the field
:-in chemistry the dipole points positive to negative (in physics it can be the reverse!)
:-to get the correct dipole vector you must optimise first under the same conditions as will be applied with the field

*we have to be very careful in which cooridnates we optimise
:-this is because internal coordinates remove the center of mass motion which is relevant in an electric field
:-you MUST use '''opt=z-matrix'''
:-it is better to use '''symbolic cartesian coordinates'''
:-below is an example for acetate
:-the first zero tells gaussian that symbolic cartesian coordinates follow
:-if you run a charged molecule the molecule will move along the electric field
:-to avoid this '''fix one atom in the molecule''' to the center of the axial system
:-in the z-matrix format variables (to be optimised) are listed first and fixed constant are listed second
:-so the coordinates of the last atom below are held constant (at the origin)
<pre>
%chk=ch3co2.chk
# opt=(z-matrix,maxcycles=100) hf/3-21g nosymm field=x+250

Title Card Required

-1 1
6 0 x1 y1 z1
8 0 x2 y2 z2
8 0 x3 y3 z3
6 0 x4 y4 z4
1 0 x5 y5 z5
1 0 x6 y6 z6
1 0 x7 y7 z7

x2=-0.544205
y2=-1.144935
z2= 0.029999
x3=-0.568491
y3= 1.132502
z3= 0.024945
x4= 1.542020
y4= 0.011495
z4=-0.117920
x5= 1.805270
y5=-0.088033
z5=-1.168772
x6= 1.945393
y6= 0.945207
z6= 0.252204
x7= 1.965502
y7=-0.830194
z7= 0.416379

x1= 0.000000
y1= 0.000000
z1= 0.000000
</pre>
*refence state
:-make sure you run a reference state calculation without the field
:-this has the bonus of giving the dipole moment as well
:-currently we cannot orientate the dipole, but hopefully soon
:-first optimise the molecule (with the z-matrix as defined for the field calculation)
<pre>
# opt=(z-matrix,maxcycles=100) hf/3-21g nosymm
</pre>

== a code to orient the molecule ==
*copy the code pos_zmat into a file called pos_zmat.py in your bin directory
:'''pos_zmat.py''' [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/pos_zmat link]
*change the first line shebang to direct to YOUR python3
:mine is on my mac <code>#!/opt/local/bin/python3</code>
:on raapoi is <code>#!/usr/bin/env python3.8</code>
*extract the xyz coordinates for your molecule
:use "extract_structure.py"
:that is the xyz coordinates in the form <code>atom_symbol x y z</code>
:for example here are the coordinates of a water molecule
:note that we require atomic symbols not numbers
<pre>
O 1.995482 0.000000 -0.000000
H 2.637933 -0.000000 0.697270
H 2.637933 0.000000 -0.697270
</pre>
*create a file called '''water.inp'''
:below is the file for water
:info is given on each line
:1. number of atoms
:2. atom_1 atom_2 atom_3
:3. angle_1 angle_2 angle_3

:: atom_1 =atom to center the coordinates at (ie will be 0.0 0.0 0.0) in my case I want to center at atom 1
:: atom_2 =atom you want along the x-axis, in my case atom 2
:: atom_3 =atom to form the xy plane through atom_1, atom_2 and atom_3, the z-axis will be perpendicular to this plane
:: currently you can only give ONE angle the others must be set to 0.0
:: angle_1 rotatare in xy
:: angle_2 rotate in xz
:: angle_3 rotate in yx

:4. and on are your coordinates
:: note that you can insert a file using vi with the (comand mode)<code>:r filename</code> command

<pre>
3
1 2 3
10.0 0.0 0.0
O 1.995482 0.000000 -0.000000
H 2.637933 -0.000000 0.697270
H 2.637933 0.000000 -0.697270
</pre>

*run the code
:the water.inp file as an argument (without .inp)
:<code>pos_zmat.py water </code>
:you should see something like the following
<pre>
directory is /Volumes/Tricia_Home/work/jobs/musa
input file is water.inp
symbolic z-matrix output file is water_osymb.com
xyz coord output file is water_new.xyz
total number of atoms 3
center at atom 1
x-axis along bond to atom 2
atoms in the xy-plane 3
rotation of a-b around xy-pane (z-axis) by 10.0
centered
x-axis aligned
atoms aligned in xy plane
a-b vector rotated
write .xyz file
done!

</pre>

*output files
:you should see 2 files '''water_new.xyz''' and '''water_osymb.xyz'''
:water_new.xyz gives the new coordinate file in the standard format
<pre>
O 0.000000 0.000000 0.000000
H 0.915812 0.245391 0.000000
H -0.074822 -0.020048 -0.944949
Xx 4.000000 0.000000 0.000000
Xy 0.000000 4.000000 0.000000
Xz 0.000000 0.000000 4.000000
</pre>

:water_osymb.xyz gives the coordinates in the symbolic z-matrix format
:you will add these into your com file
:you can see that atom 1 is at the origin
:you can see that atom 2 has coordinates in the x and y direction very close to zero
:note that 3 dummy atoms are added on the position of the x,y and z axies to help with visualisation
<pre>
O 0 x1 y1 z1
H 0 x2 y2 z2
H 0 x3 y3 z3
Xx 0 x4 y4 z4
Xy 0 x5 y5 z5
Xz 0 x6 y6 z6

x1 = 0.000000
y1 = 0.000000
z1 = 0.000000
x2 = 0.915812
y2 = 0.245391
z2 = 0.000000
x3 =-0.074822
y3 =-0.020048
z3 =-0.944949
x4 = 4.000000
y4 = 0.000000
z4 = 0.000000
x5 = 0.000000
y5 = 4.000000
z5 = 0.000000
x6 = 0.000000
y6 = 0.000000
z6 = 4.000000

</pre>
*create a com file
:use the vi insert file option (comand mode)<code>:r geom_osymb.xyz</code>
:here is my new water_field.com file
:you MUST visualise this in gaussview to make sure everything is ok!
<pre>
%nprocshared=3
%mem=3GB
%chk=water_osymb.chk
#b3lyp/3-21G int=ultrafine scf=conver=10
opt=(maxcyc=50) nosymm field=x+250

Title Card Required

0 1
O 0 x1 y1 z1
H 0 x2 y2 z2
H 0 x3 y3 z3
Xx 0 x4 y4 z4
Xy 0 x5 y5 z5
Xz 0 x6 y6 z6

x1 = 0.000000
y1 = 0.000000
z1 = 0.000000
x2 = 0.933714
y2 = 0.164639
z2 = 0.000000
x3 =-0.240373
y3 = 0.917142
z3 =-0.000000
x4 = 4.000000
y4 = 0.000000
z4 = 0.000000
x5 = 0.000000
y5 = 4.000000
z5 = 0.000000
x6 = 0.000000
y6 = 0.000000
z6 = 4.000000
:
</pre>
:and here is my gaussview check
:with the x-axis to atom 2 angle of 10 degrees
[[File:Water_field_file.png|500px|caption]]

== orientate to the dipole ==
*you can orient the molecule so the dipole aligns with the electric field
:-''python script to be added!''

Mod:Hunt Research Group:molecules in an electric field

2025-10-22T18:05:57Z

Wikiadmin: /* a code to orient the molecule */

=Molecules in an electric field=
== introduction ==
getting started with the field keyword

which optimisation to use

accelerating optimisation

== using the field keyword ==
*we apply a field along an axial direction, x or y or z
<pre>field=x+250</pre>
:-for field=x+10 a field of 0.001au is applied
:-for more options goto the manual page here [https://gaussian.com/field/ link]

*units
:-conversion for an electric field: 1 au = 5.14220652 × 10^11 V/m =51.4 V/Å =514 V/nm
:-so 0.001au = 51.4/1000 V/Å = 0.0514 V/Å or 0.514V/nm
:-this is equivalent to 0.05V/Å
:-to apply 1V/nm we need approximately a field=x+20 (2*0.514V/nm=1.028V/nm)

== optimising in a field ==
*the field is applied along an axis direction
:-use the show axis option in gaussview to show this direction
:-by convention electric field arrows point from postive to negative
:-a positive x-axis field=+250 for example field will repel a negative ion (move it to -x)

*the molecule must not reorient when setting up the job
:-position the molecule explicitly where you want it within the coordinated system
:-you MUST use '''nosymm'''
:-things will go faster if you orient the molecular dipole with the field
:-in chemistry the dipole points positive to negative (in physics it can be the reverse!)
:-to get the correct dipole vector you must optimise first under the same conditions as will be applied with the field

*we have to be very careful in which cooridnates we optimise
:-this is because internal coordinates remove the center of mass motion which is relevant in an electric field
:-you MUST use '''opt=z-matrix'''
:-it is better to use '''symbolic cartesian coordinates'''
:-below is an example for acetate
:-the first zero tells gaussian that symbolic cartesian coordinates follow
:-if you run a charged molecule the molecule will move along the electric field
:-to avoid this '''fix one atom in the molecule''' to the center of the axial system
:-in the z-matrix format variables (to be optimised) are listed first and fixed constant are listed second
:-so the coordinates of the last atom below are held constant (at the origin)
<pre>
%chk=ch3co2.chk
# opt=(z-matrix,maxcycles=100) hf/3-21g nosymm field=x+250

Title Card Required

-1 1
6 0 x1 y1 z1
8 0 x2 y2 z2
8 0 x3 y3 z3
6 0 x4 y4 z4
1 0 x5 y5 z5
1 0 x6 y6 z6
1 0 x7 y7 z7

x2=-0.544205
y2=-1.144935
z2= 0.029999
x3=-0.568491
y3= 1.132502
z3= 0.024945
x4= 1.542020
y4= 0.011495
z4=-0.117920
x5= 1.805270
y5=-0.088033
z5=-1.168772
x6= 1.945393
y6= 0.945207
z6= 0.252204
x7= 1.965502
y7=-0.830194
z7= 0.416379

x1= 0.000000
y1= 0.000000
z1= 0.000000
</pre>
*refence state
:-make sure you run a reference state calculation without the field
:-this has the bonus of giving the dipole moment as well
:-currently we cannot orientate the dipole, but hopefully soon
:-first optimise the molecule (with the z-matrix as defined for the field calculation)
<pre>
# opt=(z-matrix,maxcycles=100) hf/3-21g nosymm
</pre>

== a code to orient the molecule ==
*copy the code pos_zmat into a file called pos_zmat.py in your bin directory
:'''pos_zmat.py''' [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/pos_zmat link]
*change the first line shebang to direct to YOUR python3
:mine is on my mac <code>#!/opt/local/bin/python3</code>
:on raapoi is <code>#!/usr/bin/env python3.8</code>
*extract the xyz coordinates for your molecule
:use "extract_structure.py"
:that is the xyz coordinates in the form <code>atom_symbol x y z</code>
:for example here are the coordinates of a water molecule
:note that we require atomic symbols not numbers
<pre>
O 1.995482 0.000000 -0.000000
H 2.637933 -0.000000 0.697270
H 2.637933 0.000000 -0.697270
</pre>
*create a file called '''water.inp'''
:below is the file for water
:info is given on each line
:1. number of atoms
:2. atom_1 atom_2 atom_3
:3. angle_1 angle_2 angle_3

:: atom_1 =atom to center the coordinates at (ie will be 0.0 0.0 0.0) in my case I want to center at atom 1
:: atom_2 =atom you want along the x-axis, in my case atom 2
:: atom_3 =atom to form the xy plane through atom_1, atom_2 and atom_3, the z-axis will be perpendicular to this plane
:: currently you can only give ONE angle the others must be set to 0.0
:: angle_1 rotatare in xy
:: angle_2 rotate in xz
:: angle_3 rotate in yx

:4. and on are your coordinates
:: note that you can insert a file using vi with the (comand mode)<code>:r filename</code> command

<pre>
3
1 2 3
10.0 0.0 0.0
O 1.995482 0.000000 -0.000000
H 2.637933 -0.000000 0.697270
H 2.637933 0.000000 -0.697270
</pre>

*run the code
:the water.inp file as an argument (without .inp)
:<code>pos_zmat.py water </code>
:you should see something like the following
<pre>
directory is /Volumes/Tricia_Home/work/jobs/musa
input file is water.inp
symbolic z-matrix output file is water_osymb.com
xyz coord output file is water_new.xyz
total number of atoms 3
center at atom 1
x-axis along bond to atom 2
atoms in the xy-plane 3
rotation of a-b around xy-pane (z-axis) by 10.0
centered
x-axis aligned
atoms aligned in xy plane
a-b vector rotated
write .xyz file
done!

</pre>

*output files
:you should see 2 files '''water_new.xyz''' and '''water_osymb.xyz'''
:water_new.xyz gives the new coordinate file in the standard format
<pre>
O 0.000000 0.000000 0.000000
H 0.915812 0.245391 0.000000
H -0.074822 -0.020048 -0.944949
Xx 4.000000 0.000000 0.000000
Xy 0.000000 4.000000 0.000000
Xz 0.000000 0.000000 4.000000
</pre>

:water_osymb.xyz gives the coordinates in the symbolic z-matrix format
:you will add these into your com file
:you can see that atom 1 is at the origin
:you can see that atom 2 has coordinates in the x and y direction very close to zero
:note that 3 dummy atoms are added on the position of the x,y and z axies to help with visualisation
<pre>
O 0 x1 y1 z1
H 0 x2 y2 z2
H 0 x3 y3 z3
Xx 0 x4 y4 z4
Xy 0 x5 y5 z5
Xz 0 x6 y6 z6

x1 = 0.000000
y1 = 0.000000
z1 = 0.000000
x2 = 0.915812
y2 = 0.245391
z2 = 0.000000
x3 =-0.074822
y3 =-0.020048
z3 =-0.944949
x4 = 4.000000
y4 = 0.000000
z4 = 0.000000
x5 = 0.000000
y5 = 4.000000
z5 = 0.000000
x6 = 0.000000
y6 = 0.000000
z6 = 4.000000

</pre>
*create a com file
:use the vi insert file option (comand mode)<code>:r geom_osymb.xyz</code>
:here is my new water_field.com file
:you MUST visualise this in gaussview to make sure everything is ok!
<pre>
%chk=water_field.chk
# opt=(z-matrix,maxcycles=100) hf/3-21g nosymm field=x+250

Title Card Required

0 1
O 0 x1 y1 z1
H 0 x2 y2 z2
H 0 x3 y3 z3
Xx 0 x4 y4 z4
Xy 0 x5 y5 z5
Xz 0 x6 y6 z6

x1 = 0.000000
y1 = 0.000000
z1 = 0.000000
x2 = 0.915812
y2 = 0.245391
z2 = 0.000000
x3 =-0.074822
y3 =-0.020048
z3 =-0.944949
x4 = 4.000000
y4 = 0.000000
z4 = 0.000000
x5 = 0.000000
y5 = 4.000000
z5 = 0.000000
x6 = 0.000000
y6 = 0.000000
z6 = 4.000000

</pre>
:and here is my gaussview check
:with the x-axis to atom 2 angle of 15 degrees
[[File:Water_field_file.png|500px|caption]]

== orientate to the dipole ==
*you can orient the molecule so the dipole aligns with the electric field
:-''python script to be added!''

Mod:Hunt Research Group:molecules in an electric field

2025-10-22T18:03:28Z

Wikiadmin: /* a code to orient the molecule */

=Molecules in an electric field=
== introduction ==
getting started with the field keyword

which optimisation to use

accelerating optimisation

== using the field keyword ==
*we apply a field along an axial direction, x or y or z
<pre>field=x+250</pre>
:-for field=x+10 a field of 0.001au is applied
:-for more options goto the manual page here [https://gaussian.com/field/ link]

*units
:-conversion for an electric field: 1 au = 5.14220652 × 10^11 V/m =51.4 V/Å =514 V/nm
:-so 0.001au = 51.4/1000 V/Å = 0.0514 V/Å or 0.514V/nm
:-this is equivalent to 0.05V/Å
:-to apply 1V/nm we need approximately a field=x+20 (2*0.514V/nm=1.028V/nm)

== optimising in a field ==
*the field is applied along an axis direction
:-use the show axis option in gaussview to show this direction
:-by convention electric field arrows point from postive to negative
:-a positive x-axis field=+250 for example field will repel a negative ion (move it to -x)

*the molecule must not reorient when setting up the job
:-position the molecule explicitly where you want it within the coordinated system
:-you MUST use '''nosymm'''
:-things will go faster if you orient the molecular dipole with the field
:-in chemistry the dipole points positive to negative (in physics it can be the reverse!)
:-to get the correct dipole vector you must optimise first under the same conditions as will be applied with the field

*we have to be very careful in which cooridnates we optimise
:-this is because internal coordinates remove the center of mass motion which is relevant in an electric field
:-you MUST use '''opt=z-matrix'''
:-it is better to use '''symbolic cartesian coordinates'''
:-below is an example for acetate
:-the first zero tells gaussian that symbolic cartesian coordinates follow
:-if you run a charged molecule the molecule will move along the electric field
:-to avoid this '''fix one atom in the molecule''' to the center of the axial system
:-in the z-matrix format variables (to be optimised) are listed first and fixed constant are listed second
:-so the coordinates of the last atom below are held constant (at the origin)
<pre>
%chk=ch3co2.chk
# opt=(z-matrix,maxcycles=100) hf/3-21g nosymm field=x+250

Title Card Required

-1 1
6 0 x1 y1 z1
8 0 x2 y2 z2
8 0 x3 y3 z3
6 0 x4 y4 z4
1 0 x5 y5 z5
1 0 x6 y6 z6
1 0 x7 y7 z7

x2=-0.544205
y2=-1.144935
z2= 0.029999
x3=-0.568491
y3= 1.132502
z3= 0.024945
x4= 1.542020
y4= 0.011495
z4=-0.117920
x5= 1.805270
y5=-0.088033
z5=-1.168772
x6= 1.945393
y6= 0.945207
z6= 0.252204
x7= 1.965502
y7=-0.830194
z7= 0.416379

x1= 0.000000
y1= 0.000000
z1= 0.000000
</pre>
*refence state
:-make sure you run a reference state calculation without the field
:-this has the bonus of giving the dipole moment as well
:-currently we cannot orientate the dipole, but hopefully soon
:-first optimise the molecule (with the z-matrix as defined for the field calculation)
<pre>
# opt=(z-matrix,maxcycles=100) hf/3-21g nosymm
</pre>

== a code to orient the molecule ==
*copy the code pos_zmat into a file called pos_zmat.py in your bin directory
:'''pos_zmat.py''' [https://sagacioushours.org.uk/wiki/index.php/Mod:Hunt_Research_Group/pos_zmat link]
*change the first line shebang to direct to YOUR python3
:mine is on my mac <code>#!/opt/local/bin/python3</code>
:on raapoi is <code>#!/usr/bin/env python3.8</code>
*extract the xyz coordinates for your molecule
:use "extract_structure.py"
:that is the xyz coordinates in the form <code>atom_symbol x y z</code>
:for example here are the coordinates of a water molecule
:note that we require atomic symbols not numbers
<pre>
O 1.995482 0.000000 -0.000000
H 2.637933 -0.000000 0.697270
H 2.637933 0.000000 -0.697270
</pre>
*create a file called '''geom.inp'''
:below is the file for water
:info is given on each line
:1. number of atoms
:2. atom_1 atom_2 atom_3
:3. angle_1 angle_2 angle_3

:: atom_1 =atom to center the coordinates at (ie will be 0.0 0.0 0.0) in my case I want to center at atom 1
:: atom_2 =atom you want along the x-axis, in my case atom 2
:: atom_3 =atom to form the xy plane through atom_1, atom_2 and atom_3, the z-axis will be perpendicular to this plane
:: currently you can only give ONE angle the others must be set to 0.0
:: angle_1 rotatare in xy
:: angle_2 rotate in xz
:: angle_3 rotate in yx

:4. and on are your coordinates
:: note that you can insert a file using vi with the (comand mode)<code>:r filename</code> command

<pre>
3
1 2 3
10.0 0.0 0.0
O 1.995482 0.000000 -0.000000
H 2.637933 -0.000000 0.697270
H 2.637933 0.000000 -0.697270
</pre>

*run the code
:the geom.inp file as an argument (without .inp)
:<code>pos_zmat.py geom </code>
:you should see something like the following
<pre>
directory is /Users/tricia/Files/work/jobs/field
input file is geom.inp
symbolic z-matrix output file is geom_osymb.xyz
xyz coord output file is geom_new.xyz
total number of atoms 3
center at atom 1
x-axis along bond to atom 2
NOT WORKING YET rotation around xy-pane (x-axis) OR around xz-plane (y-axis) OR around yz-plane (x-axis}15.0 0.0
NOT WORKING YET z-axis perpendicular to the plane of atoms 1, 2, 3
center at O1 1.995482, 0.000000,-0.000000
align along atom vector O1 H2
atom H2 2.637933,-0.000000, 0.697270
</pre>

*output files
:you should see 2 files '''geom_new.xyz''' and '''geom_osymb.xyz'''
:geom_new.xyz gives the new coordinate file in the standard format
<pre>
O 0.000000 0.000000 0.000000
H 0.915812 0.245391 0.000000
H -0.074822 -0.020048 -0.944949
Xx 4.000000 0.000000 0.000000
Xy 0.000000 4.000000 0.000000
Xz 0.000000 0.000000 4.000000
</pre>

:geom_osymb.xyz gives the coordinates in the symbolic z-matrix format
:you will add these into your com file
:you can see that atom 1 is at the origin
:you can see that atom 2 has coordinates in the x and y direction very close to zero
:note that 3 dummy atoms are added on the position of the x,y and z axies to help with visualisation
<pre>
O 0 x1 y1 z1
H 0 x2 y2 z2
H 0 x3 y3 z3
Xx 0 x4 y4 z4
Xy 0 x5 y5 z5
Xz 0 x6 y6 z6

x1 = 0.000000
y1 = 0.000000
z1 = 0.000000
x2 = 0.915812
y2 = 0.245391
z2 = 0.000000
x3 =-0.074822
y3 =-0.020048
z3 =-0.944949
x4 = 4.000000
y4 = 0.000000
z4 = 0.000000
x5 = 0.000000
y5 = 4.000000
z5 = 0.000000
x6 = 0.000000
y6 = 0.000000
z6 = 4.000000

</pre>
*create a com file
:use the vi insert file option (comand mode)<code>:r geom_osymb.xyz</code>
:here is my new water_field.com file
:you MUST visualise this in gaussview to make sure everything is ok!
<pre>
%chk=water_field.chk
# opt=(z-matrix,maxcycles=100) hf/3-21g nosymm field=x+250

Title Card Required

0 1
O 0 x1 y1 z1
H 0 x2 y2 z2
H 0 x3 y3 z3
Xx 0 x4 y4 z4
Xy 0 x5 y5 z5
Xz 0 x6 y6 z6

x1 = 0.000000
y1 = 0.000000
z1 = 0.000000
x2 = 0.915812
y2 = 0.245391
z2 = 0.000000
x3 =-0.074822
y3 =-0.020048
z3 =-0.944949
x4 = 4.000000
y4 = 0.000000
z4 = 0.000000
x5 = 0.000000
y5 = 4.000000
z5 = 0.000000
x6 = 0.000000
y6 = 0.000000
z6 = 4.000000

</pre>
:and here is my gaussview check
:with the x-axis to atom 2 angle of 15 degrees
[[File:Water_field_file.png|500px|caption]]

== orientate to the dipole ==
*you can orient the molecule so the dipole aligns with the electric field
:-''python script to be added!''

Mod:Hunt Research Group/pos zmat

2025-10-22T17:57:24Z

Wikiadmin:

<pre>
#!/opt/local/bin/python3
#
# pos_zmat.py
#
# python script to take cartesian coords and orient a molecule and convert to a symbolic z-matrix format.
# the *.xyz file can be draged into jmol
# the symbolic matrix file is saved in *.com format
#
# to run the script you need an input file *.inp
# if you have a log file run extract_structure.py filename (without log extension) first to get the xyz coordinates
# then copy this file to filename.inp and add the following at the top
# no of atoms
# a b c
# xx yy zz
# where
# a atom to center at
# b x-axis will align along bond a-b
# c the atoms a-b-c will form the xy plane
# this means the z-axis is perpendicular to the plane of these 3 atoms
# xx yy zz the angle to rotate the a-b bond (vector) in the xy, xz, or yz planes
# currently only active for one axis at a time!
# then follows a section for atomic symbol/atomic no and coordinates
#
# to run the script type python pos_zmat.py input_file_name (without extension)
#
# this will produce the files
# filename_new.xyz (for jmol)
# filename_osymb.com (for G16)
#
import sys
import os
import math
import numpy as np
dir=os.getcwd()
from numpy import (array, dot, arccos, clip)
from numpy.linalg import norm
#
if len(sys.argv) >= 3:
print('to run the script please type: python symb_zmat.py input_file_name (without extension)')
sys.exit()
else:
base=str(sys.argv[1])
file=base+'.inp'
out1=base+'_osymb.com'
out2=base+'_new.xyz'
s='directory is '
print('{0:}{1:}'.format(s,dir))
s='input file is '
print('{0:}{1:}'.format(s,file))
s='symbolic z-matrix output file is '
print('{0:}{1:}'.format(s,out1))
s='xyz coord output file is '
print('{0:}{1:}'.format(s,out2))
#close if
#
# set some defaults
atomtotal=0
atomcenter=0
atomxaxis=0
atomyaxis=0
xa=0.0
xb=0.0
xc=0.0
rotanglex=0.0
rotangley=0.0
rotanglez=0.0
dipole=0.0
nz1=0
nz2=0
nz3=0
a=[]
col_atom=[]
col_x=[]
col_y=[]
col_z=[]
newcol_x=[]
newcol_y=[]
newcol_z=[]
v1=np.zeros(3,dtype=float)
v2=np.zeros(3,dtype=float)
v3=np.zeros(3,dtype=float)

# open file and read lines one by one
f=open(file,"r")

#total number of atoms
line =f.readline()
#print('{0:}'.format(line))
atomtotal=int(line.rstrip())
s='total number of atoms '
print('{0:}{1:}'.format(s,atomtotal))

#read in data center atom, xaxis atom, xy plane atom
line =f.readline()
#print('{0:}'.format(line))
a=line.rstrip().split()
atomcenter=int(a[0])
atomxaxis=int(a[1])
atomyaxis=int(a[2])
s='center at atom '
print('{0:}{1:}'.format(s,atomcenter))
s='x-axis along bond to atom '
print('{0:}{1:}'.format(s,atomxaxis))
s='atoms in the xy-plane '
print('{0:}{1:}'.format(s,atomyaxis))

#read in the rotation angles (degrees)
line =f.readline()
b1,c1,d1=line.rstrip().split()
rotplanexy=float(b1)
rotplanexz=float(c1)
rotplaneyz=float(d1)
if rotplanexy != 0:
s='rotation of a-b around xy-pane (z-axis) by '
print('{0:}{1:}'.format(s,rotplanexy))
elif rotplanexz != 0:
s='rotation a-b around xz-pane (y-axis) by '
print('{0:}{1:}'.format(s,rotplanexz))
elif rotplaneyz != 0:
s='rotation a-b around yz-pane (x-axis) by '
print('{0:}{1:}'.format(s,rotplaneyz))
else:
print('no rotations')
#endif

#read in atoms and coordinates
mx=np.zeros(atomtotal,dtype=float)
my=np.zeros(atomtotal,dtype=float)
mz=np.zeros(atomtotal,dtype=float)
mx1=np.zeros(atomtotal,dtype=float)
my1=np.zeros(atomtotal,dtype=float)
mz1=np.zeros(atomtotal,dtype=float)
mxf=np.zeros(atomtotal,dtype=float)
myf=np.zeros(atomtotal,dtype=float)
mzf=np.zeros(atomtotal,dtype=float)
#print(ny)
n=0
while n < atomtotal :
line =f.readline()
# print('{0:}'.format(line))
a1,b1,c1,d1=line.rstrip().split()
col_atom.append(a1)
col_x.append(float(b1))
col_y.append(float(c1))
col_z.append(float(d1))
n=n+1
#close while
#turn list into a numpty array
mx=np.array(col_x)
my=np.array(col_y)
mz=np.array(col_z)
#print(ny)

#center at atomcenter
c=atomcenter-1
#print('center at {0:} {1:9.6f},{2:9.6f},{3:9.6f}'.format(atomcenter,col_x[c],col_y[c],col_z[c]))
mx = mx - mx[c]
my = my - my[c]
mz = mz - mz[c]
print('centered')

#align along x-y atom vector
a=atomcenter-1
b=atomxaxis-1
#print('align along atom vector {0:} {1:}'.format(atomcenter,atomxaxis))
#print('old atom coords {0:} {1:9.4f},{2:9.4f},{3:9.4f}'.format(atomxaxis,col_x[b],col_y[b],col_z[b]))
#print('new atom coords {0:} {1:9.4f},{2:9.4f},{3:9.4f}'.format(atomxaxis,mx[b],my[b],mz[b]))
v0=np.zeros(2,dtype=float)
vxy=np.zeros(2,dtype=float)
vxz=np.zeros(2,dtype=float)
print('x-axis aligned')

#first rotate xy plane
#ie rotate around z-axis
#note that atan2 give the correct quadrant
theta=math.atan2(my[b],mx[b])
t2_deg=math.degrees(theta)
#print('theta ',round(theta,2), 'radians')
#print('theta ',round(t2_deg,2), 'degrees')
#rotate backwards!
t2_rad=-theta
mx1=mx*np.cos(t2_rad)-my*np.sin(t2_rad)
my1=mx*np.sin(t2_rad)+my*np.cos(t2_rad)
mz1=mz
#print('after xy rotation {0:9.4f}, {1:9.4f}, {2:9.4f}'.format(mx1[b],my1[b],mz1[b]))

#then rotate in xz plane
#ie rotate "down"around y-axis
theta=math.atan2(mz1[b],mx1[b])
t2_deg=math.degrees(theta)
#print('theta ',round(theta,2), 'radians')
#print('theta ',round(t2_deg,2), 'degrees')
#rotate backwards!
t2_rad=-theta
mx=mx1*np.cos(t2_rad)-mz1*np.sin(t2_rad)
my=my1
mz=mx1*np.sin(t2_rad)+mz1*np.cos(t2_rad)
#print('after xz rotation {0:9.4f}, {1:9.4f}, {2:9.4f}'.format(mx[b],my[b],mz[b]))

#then rotate in yz plane
#ie rotate "down"around x-axis
#to bring atom c into the xy plane
b=atomyaxis-1
theta=math.atan2(mz[b],my[b])
t2_deg=math.degrees(theta)
#print('theta ',round(theta,2), 'radians')
#print('theta ',round(t2_deg,2), 'degrees')
#rotate backwards!
t2_rad=-theta
mx1=mx
my1=my*np.cos(t2_rad)-mz*np.sin(t2_rad)
mz1=my*np.sin(t2_rad)+mz*np.cos(t2_rad)
#print('after yz rotation {0:9.4f}, {1:9.4f}, {2:9.4f}'.format(mx1[b],my1[b],mz1[b]))
print('atoms aligned in xy plane')

#reset so mx,my,mz contain current values too
mx=mx1
my=my1
mz=mz1

#if rotangle is not zero rotate the bond in xy,xz or yz planes
t=0
if rotplanexy != 0.0 :
a=np.deg2rad(rotplanexy)
mx1=mx*np.cos(a)-my*np.sin(a)
my1=mx*np.sin(a)+my*np.cos(a)
mz1=mz
t=1
# endif

if t==0 and rotplanexz != 0.0 :
print('rotate in xz plane')
a=np.deg2rad(rotplanexz)
mx1=mx*np.cos(a)-mz*np.sin(a)
my1=my
mz1=mx*np.sin(a)+mz*np.cos(a)
t=1
#endif

if t==0 and rotplaneyz != 0.0 :
a=np.deg2rad(rotplaneyz)
mx1=mx
my1=my*np.cos(a)-mz*np.sin(a)
mz1=my*np.sin(a)+mz*np.cos(a)
t=1
#endif
print('a-b vector rotated')

mfx=mx1
mfy=my1
mfz=mz1

#now write to the _new.xyz file
c=open(out2,"w")
c.write('{0:<3} \n'.format(atomtotal+3))
c.write('{0:<5} \n'.format('title'))
n=0
while n < atomtotal:
c.write('{0:<3} {1:9.6f} {2:9.6f} {3:9.6f} \n'.format(col_atom[n],mfx[n],mfy[n],mfz[n]))
n=n+1
#close while
#postions dummy atoms on axis
print('write .xyz file')
p=4.0
c.write('{0:<3} {1:9.6f} {2:9.6f} {3:9.6f} \n'.format('Xx',p,0.0,0.0))
c.write('{0:<3} {1:9.6f} {2:9.6f} {3:9.6f} \n'.format('Xy',0.0,p,0.0))
c.write('{0:<3} {1:9.6f} {2:9.6f} {3:9.6f} \n'.format('Xz',0.0,0.0,p))
#
#now write to the _symb.com file
c=open(out1,"w")
s="%nprocshared=16\n%mem=30GB\n"
c.write('{0:}'.format(s))
s='%chk='+base+'_osymb.chk\n'
c.write('{0:}'.format(s))
s="#b3lyp/6-311+g(d,p) int=ultrafine scf=conver=10 empiricaldispersion=gd3bj \n "
c.write('{0:}'.format(s))
s="opt=(maxcyc=50) nosymm field=x+50 \n \n "
c.write('{0:}'.format(s))
s="Title Card Required\n\n"
c.write('{0:}'.format(s))
charge=0
multiplicity=1
c.write('{0:} {1:} \n'.format(charge,multiplicity))
#
#write out z-matrix
n=0
while n < atomtotal:
m=n+1
c.write('{0:} 0 x{1:<4} y{2:<4} z{3:<4} \n'.format(col_atom[n],m,m,m))
n=n+1
#close while
m=n+1
c.write('{0:} 0 x{1:<4} y{2:<4} z{3:<4} \n'.format('Xx',m,m,m))
m=n+2
c.write('{0:} 0 x{1:<4} y{2:<4} z{3:<4} \n'.format('Xy',m,m,m))
m=n+3
c.write('{0:} 0 x{1:<4} y{2:<4} z{3:<4} \n'.format('Xz',m,m,m))
c.write('\n'.format())

#write out variables
n=0
while n < atomtotal:
m=n+1
c.write(' x{0:<3}={1:>9.6f} \n y{2:<3}={3:9.6f} \n z{4:<3}={5:9.6f} \n'.format(m,mfx[n],m,mfy[n],m,mfz[n]))
n=n + 1
#close while
m=n+1
c.write(' x{0:<3}={1:>9.6f} \n y{2:<3}={3:9.6f} \n z{4:<3}={5:9.6f} \n'.format(m,p,m,0.0,m,0.0))
m=n+2
c.write(' x{0:<3}={1:>9.6f} \n y{2:<3}={3:9.6f} \n z{4:<3}={5:9.6f} \n'.format(m,0.0,m,p,m,0.0))
m=n+3
c.write(' x{0:<3}={1:>9.6f} \n y{2:<3}={3:9.6f} \n z{4:<3}={5:9.6f} \n'.format(m,0.0,m,0.0,m,p))
c.write('\n\n'.format())

# close all open files
f.close()
c.close()
print('done!')
exit(0)
#
</pre>