== How to... comfortably search trough your shell history ==

If you use the bash, you are probably aware of the possibility to search through your old commands by pressing the 'up' or 'down' button. A little less well known is the possibility to press 'Ctrl + R' and then start typing the beginning of a command. Then pressing 'Ctrl+R' repeatedly lets you cycle through all commands starting with the letters you entered. To make this a bit more clear: If you press 'Ctrl+R' and then enter ''vi '', pressing 'Ctrl+R' again and again will cycle through all files you opened with VI. To actually execute the command you have to press enter. Be aware that this will show any command from your history starting with what you entered, so ''qs'' would produce every 'qsub' as well as 'qstat'.

This can be further simplified by opening (or creating) the file ''~/.inputrc'' and adding the following two lines to it (You might want to check, that the two keys are not already mapped to something else. Just search for the first few letters to the colon):

<pre> "\e[5~": history-search-backward
"\e[6~": history-search-forward
</pre>

Now log out and back in. If you are logged in from a PC, just start typing a command, like ''qs'' and try pressing page-up or page-down. It should do exactly what 'Strg+R' does, but without messing up your command prompt. You can also move the cursor back and forth in your command and start searching something else. So if you had the files 'file_a.com', 'file_b' and 'file_c' and they had all been opened with 'VI' at some point, along with a million other files, I would have to type ''vi'' and the cycle to the first instance of 'file*'. I would then move the cursor to the right up to the '_' and if I now pressed page-up or -down I would just be going through all the commands starting with ''vi file_'', so only my files 'a', 'b' and 'c'. It may sound pointless in this example, but once you actually start using it, you wouldn't want anything else...

If you happen to be using a MAC, you can NOT simply press page-up or page-down. You have to press 'Shift+[[Image:Menusym-pageup.gif]]' or 'Shift+[[Image:Menusym-pagedown.gif]]'.

File:Menusym-pageup.gif

2009-07-14T17:05:29Z

Hn306:

File:Menusym-pagedown.gif

2009-07-14T17:05:18Z

Hn306:

2009-07-10T16:07:35Z

Hn306:

Mod:Hunt Research Group

2009-07-10T16:07:26Z

Hn306:

[[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd | Car-Parrinello Molecular Dynamics (notes by Ling)]]

[[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/vmd | VMD (notes by Ling)]]

[[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc | HPC servers and run scripts (notes by Ling)]]

[[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_connections | HPC Connections (notes by Hieu)]]

[[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dlpoly_install | DLPOLY Installation on iMac (notes by Ling)]]

[[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/voids | Voids in ILs (notes by Ling)]]

[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Windowsfiles How to... fix Windows files under UNIX]

[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpSSH How to... make the SSH client more comfortable]
[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/SSHkeyfile How to... set up a SSH keypair]

Mod:Hunt Research Group/SSHkeyfile

2009-07-10T16:06:43Z

2009-07-10T14:51:23Z

Hn306: New page: In case you ever copied a plain ASCII textfile from a windows machine to the Cluster (especially happens, if it ends on *.com) you might have noticed, that G03 will not accept it, though i...

In case you ever copied a plain ASCII textfile from a windows machine to the Cluster (especially happens, if it ends on *.com) you might have noticed, that G03 will not accept it, though it may look fine with VI.

This is most likely due to the fact that the linefeed is coded in as it would be for Windows, which is different to a linefeed in UNIX ([http://en.wikipedia.org/wiki/Linebreak#Representations Look it up in the Wikipedia]).

To fix this, most unix machines provide a command called 'dos2unix'. Simply run ''dos2unix [filename]'' and your file will be converted.

In case you wonder: Most sFTP/SCP programs will take care of this problem for you. But to do this, they need to know that they are dealing with a text file, not a binary. This is usually done based on the file extension. So if you had renamed your file to *.txt, copied it to the HPC and then named it back, it would already have been converted... If you suspect the conversion to be a problem, open your file in VI. The status line at the bottom of the screen should read [DOS] (among other things...).

Rep:Mod:longjohnsilver359

2008-12-01T17:19:29Z

Hn306:

‘'''DAY 1'''

'''BH3'''

H-B ''bond length'' = 1.19435 Å

HBH ''angle'' = 120.0°

''What is the file type?''
Plain textfile

''What is the calculation type?''
Geometry optimization? Search for Minimum on hypersurface. I'm not sure about the answer expected

''What is the calculation method?''
DFT/b3lyp

''What is the basis set?''
3-21g

''What is the final energy in atomic units (au)?''
-26.4622643765

''What is the dipole moment?''
0

''What is the point group of your molecule?''
D3H

''How long did your calculation take?''
25s CPU time

'''BCl3'''

Cl-B ''bond length'' = 1.86592 Å

ClBCl ''angle'' = 120.0°

''What is the file type?''
Plain textfile

''What is the calculation type?''
Geometry optimization? Search for Minimum on hypersurface. I'm not sure about the answer expected

''What is the calculation method?''
DFT/b3lyp

''What is the basis set?''
lanl2mb

''What is the final energy in atomic units (au)?''
-69.4392811

''What is the dipole moment?''
0

''What is the point group of your molecule?''
D3H

''How long did your calculation take?''
13s CPU time

'''Small molecule'''

Analysis of a small molecule in similar fashion

'''Animating the vibrations'''

{| class="wikitable"
|+ Summary of vibrations
! no. !! form of the vibration !! frequency !! intensity !! symmetry
|-
| 1 || x || 1145.72 || 92.6991 || A“2
|-
| 2 || x || 1204.66 || 12.3789 || E'
|-
| 3 || x || 1204.66 || 12.3814 || E'
|-
| 4 || x || 2592.79 || 0 || A'1
|-
| 5 || x || 2731.31 || 103.837 || E'
|-
| 6 || x || 2731.31 || 103.83 || E'
|}

[[Image:Hjn_Bh3freq.JPG]]

Number of vibrations:
* Has to contain x,y or z
* degenerated vib. appear as one

'''MO'''

MO diagram (to be nicked from a student)

* MOs in good agreement.
* Different order of MOs

very valuable for qualitative understanding.

'''DAY 2'''

''geometry''

Ecis-Etrans=-7,69 kJ/mol

{| class="wikitable"
|+ Key parameters of ''cis'' and ''trans'' geometry
! parameter !! ''cis'' !! ''trans''
|-
| r(MoP) || 2.652 || 2.572
|-
| r(MoC)trans || 2.032 || 2.029
|-
| r(MoC)cis || 1.983
|-
| r(CO)trans || 1.188 || 1.190
|-
| r(CO)cis || 1.191
|-
| a(MoPMe) || 114.1 || 117.2
|}

[http://dx.doi.org/10.1016/S0020-1693(96)05133-X DOI]

a more bulky ligand might change the relativ energy in favour of the ''trans'' geometrie

''Vibrational Spectra''

trans CO: 1838,6;1838,8;1882,3;1954,1

'''DAY 3'''
'''Symmetry'''

[[Image:Hjn_Nh3c1dft.JPG]]
[[Image:Hjn_Nh3c3vdft.JPG]]
[[Image:Hjn_Nh3d3hdft.JPG]]

''has the symmetry made any difference to the final structure obtained?''

almost constant bond length. c1/c3v = 100,6pm d3h = 100,5pm. angle c1/c3v = 115,9/116,2

''has the symmetry made any difference to the time it took to optimise the geometry?''

higher symmetry results in faster calculations for simillar starting geometries. (Though to be 100% precise, none of the three examples can really be compared on this timescale)

''what implication does symmetry have for the time it takes to do a calculation?''

???

''can a molecule "break symmetry" during an optimisation?''

No, it can't.

''what implications does this have if you enter a high symmetry structure to optimise?''

You will not be able to find a lower lying minimum of lower symmetry.

''which is the lowest energy geometry?''

C3v

''what is the energy in kJ/mol of the other two isomers above the energy of the lowest energy structure? Hint: take ΔE=E(high energy)-E(low energy), the energy units are reported in atomic units so you will need to convert the energy difference to kJ/mol.
is the energy differences between these structures significant? Explain why.''

ΔE=0,91 kJ/mol; activation energy of inversion (-> transition state)

'''MP2'''

''how long do these calculations take compared to your lower level ones?''

they take between 0 and 20 seconds longer.

''determine the barrier height to inversion by finding the relative energy at this level of calculation ΔE=E(D3h)-E(C3v) in kJ/mol''

20,48 kJ/mol

''has ΔE changed much between the B3LYP/6-31G and MP2/6-311+G(d,p) sets of calculations?''

it is by a factor or 22,6 or 19,58kJ/mol larger.

''how do your results compare to the experimentally determined barrier which is 24.3 kJ/mol?''

they are in reasonably good agreement, and it might be possible to improve them by using a third and better method.

'''IR'''

[[Image:Hjn_Nh3c3vfreq.JPG]]
[[Image:Hjn_Nh3d3hfreq.JPG]]

''how many positive frequencies are there for the C3v and the D3h structures?''

C3v=458,5;2*1681,0;3575,7;2*3776,6
D3h=(-351,8;)2*1636,8;3657,9;2*3877,6
Signal at 3657 has intensity 0

''draw the vibrational modes for both structures (visualise them with gaussview) and match them up, ie which vibrational modes have the same character of motion for the C3v and D3h structures''

same order.

''compare the calculated frequencies for the C3v structure to those obtained experimentally (you will have to look them up). The C3v structure is the ground state structure, ground state structures always have all positive frequencies.''

''The D3h structure is a transition state structure, transition states always have only one negative frequency, what is the value of negative frequency?
which vibration in the C3v and D3h structures "follows" the inversion reaction path?''

follows the A''2/A1

value: -351,8

Rep:Mod:longjohnsilver359

2008-11-30T14:07:08Z

Hn306:

‘'''DAY 1'''

'''BH3'''

H-B ''bond length'' = 1.19435 Å

HBH ''angle'' = 120.0°

''What is the file type?''
Plain textfile

''What is the calculation type?''
Geometry optimization? Search for Minimum on hypersurface. I'm not sure about the answer expected

''What is the calculation method?''
DFT/b3lyp

''What is the basis set?''
3-21g

''What is the final energy in atomic units (au)?''
-26.4622643765

''What is the dipole moment?''
0

''What is the point group of your molecule?''
D3H

''How long did your calculation take?''
25s CPU time

'''BCl3'''

Cl-B ''bond length'' = 1.86592 Å

ClBCl ''angle'' = 120.0°

''What is the file type?''
Plain textfile

''What is the calculation type?''
Geometry optimization? Search for Minimum on hypersurface. I'm not sure about the answer expected

''What is the calculation method?''
DFT/b3lyp

''What is the basis set?''
lanl2mb

''What is the final energy in atomic units (au)?''
-69.4392811

''What is the dipole moment?''
0

''What is the point group of your molecule?''
D3H

''How long did your calculation take?''
13s CPU time

'''Small molecule'''

Analysis of a small molecule in similar fashion

'''Animating the vibrations'''

{| class="wikitable"
|+ Summary of vibrations
! no. !! form of the vibration !! frequency !! intensity !! symmetry
|-
| 1 || x || 1145.72 || 92.6991 || A“2
|-
| 2 || x || 1204.66 || 12.3789 || E'
|-
| 3 || x || 1204.66 || 12.3814 || E'
|-
| 4 || x || 2592.79 || 0 || A'1
|-
| 5 || x || 2731.31 || 103.837 || E'
|-
| 6 || x || 2731.31 || 103.83 || E'
|}

[[Image:Hjn_Bh3freq.JPG]]

Number of vibrations:
* Has to contain x,y or z
* degenerated vib. appear as one

'''MO'''

MO diagram (to be nicked from a student)

* non degenerate MOs in good agreement.
* Different order of MOs
* e MOs linear recombination of simple theorie

very valuable for qualitative understanding.

'''DAY 2'''

''geometry''

Ecis-Etrans=-7,69 kJ/mol

{| class="wikitable"
|+ Key parameters of ''cis'' and ''trans'' geometry
! parameter !! ''cis'' !! ''trans''
|-
| r(MoP) || 2.652 || 2.572
|-
| r(MoC)trans || 2.032 || 2.029
|-
| r(MoC)cis || 1.983
|-
| r(CO)trans || 1.188 || 1.190
|-
| r(CO)cis || 1.191
|-
| a(MoPMe) || 114.1 || 117.2
|}

[http://dx.doi.org/10.1016/S0020-1693(96)05133-X DOI]

a more bulky ligand might change the relativ energy in favour of the ''trans'' geometrie

''Vibrational Spectra''

trans CO: 1838,6;1838,8;1882,3;1954,1

'''DAY 3'''
'''Symmetry'''

[[Image:Hjn_Nh3c1dft.JPG]]
[[Image:Hjn_Nh3c3vdft.JPG]]
[[Image:Hjn_Nh3d3hdft.JPG]]

''has the symmetry made any difference to the final structure obtained?''

almost constant bond length. c1/c3v = 100,6pm d3h = 100,5pm. angle c1/c3v = 115,9/116,2

''has the symmetry made any difference to the time it took to optimise the geometry?''

higher symmetry results in faster calculations for simillar starting geometries. (Though to be 100% precise, none of the three examples can really be compared on this timescale)

''what implication does symmetry have for the time it takes to do a calculation?''

???

''can a molecule "break symmetry" during an optimisation?''

No, it can't.

''what implications does this have if you enter a high symmetry structure to optimise?''

You will not be able to find a lower lying minimum of lower symmetry.

''which is the lowest energy geometry?''

C3v

''what is the energy in kJ/mol of the other two isomers above the energy of the lowest energy structure? Hint: take ΔE=E(high energy)-E(low energy), the energy units are reported in atomic units so you will need to convert the energy difference to kJ/mol.
is the energy differences between these structures significant? Explain why.''

ΔE=0,91 kJ/mol; activation energy of inversion (-> transition state)

'''MP2'''

''how long do these calculations take compared to your lower level ones?''

they take between 0 and 20 seconds longer.

''determine the barrier height to inversion by finding the relative energy at this level of calculation ΔE=E(D3h)-E(C3v) in kJ/mol''

20,48 kJ/mol

''has ΔE changed much between the B3LYP/6-31G and MP2/6-311+G(d,p) sets of calculations?''

it is by a factor or 22,6 or 19,58kJ/mol larger.

''how do your results compare to the experimentally determined barrier which is 24.3 kJ/mol?''

they are in reasonably good agreement, and it might be possible to improve them by using a third and better method.

'''IR'''

[[Image:Hjn_Nh3c3vfreq.JPG]]
[[Image:Hjn_Nh3d3hfreq.JPG]]

''how many positive frequencies are there for the C3v and the D3h structures?''

C3v=458,5;2*1681,0;3575,7;2*3776,6
D3h=(-351,8;)2*1636,8;3657,9;2*3877,6
Signal at 3657 has intensity 0

''draw the vibrational modes for both structures (visualise them with gaussview) and match them up, ie which vibrational modes have the same character of motion for the C3v and D3h structures''

same order.

''compare the calculated frequencies for the C3v structure to those obtained experimentally (you will have to look them up). The C3v structure is the ground state structure, ground state structures always have all positive frequencies.''

''The D3h structure is a transition state structure, transition states always have only one negative frequency, what is the value of negative frequency?
which vibration in the C3v and D3h structures "follows" the inversion reaction path?''

follows the A''2/A1

value: -351,8

2008-11-26T17:32:33Z

Hn306: