ChemWiki - User contributions [en]

Mod:Hunt Research Group/calendar

2015-06-16T07:34:42Z

Bw1911:

Back to the main [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group wiki-page]
== Calendar ==

{| class="wikitable"
|-
! 1
! 2
! 3
! 4
|-
| Tricia (Not Done)
| Bryan Ward (Done)
| Claire Ashworth (Not Done)
| Precious Ugbomah (Not Done)
|-
| Vincent Chen (Not Done)
| Gabriel Lau (Not Done)
| Rebecca Rowe (Not Done)
| Ken Watson (Not Done)
|-
| Laila Bana (Not Done)
| Oliver Benton (Not Done)
| Christopher Sewell (Not Done)
| Chen Chen (Not Done)
|-
| Aiswarya Prabha (Not Done)
|Ziyun Zhang (Not Done)
|Richard Fogarty (Not Done)
|
|-
|-)
|}

<table border="1" cellpadding="5" width="1190">
<tr bgcolor="#66CCFF">
<th width="170px">Mon</th>
<th width="170px">Tues</th>
<th width="170px">Wed</th>
<th width="170px">Thur</th>
<th width="170px">Fri</th>
<th width="170px">Sat</th>
<th width="170px">Sun</th>
</tr>

<tr valign="top">
<td bgcolor="#4357CFF">'''1st June''' </td>
<td>2nd </td>
<td>3rd </td>
<td>4th </td>
<td>5th </td>
<td bgcolor="#33CC99">6th </td>
<td bgcolor="#33CC99">7th </td>
</tr>
<tr valign="top">
<td>8th </td>
<td>9th </td>
<td>10th </td>
<td>11th </td>
<td>12th </td>
<td bgcolor="#33CC99">13th </td>
<td bgcolor="#33CC99">14th </td>
</tr>
<tr valign="top">
<td>15th </td>
<td>16th </td>
<td>17th </td>
<td>18th </td>
<td>19th Bryan Away </td>
<td bgcolor="#33CC99">20th Bryan Away </td>
<td bgcolor="#33CC99">21st Bryan Away </td>
</tr>
<tr valign="top">
<td>22nd Bryan Away </td>
<td>23rd Bryan Away </td>
<td>24th Bryan Away </td>
<td>25th Bryan Away </td>
<td>26th Bryan Away </td>
<td bgcolor="#33CC99">27th Bryan Away </td>
<td bgcolor="#33CC99">28th Bryan Away </td>
</tr>
<tr valign="top">
<td >29th Bryan Away </td>
<td>30th </td>
<td bgcolor="#4357CFF">'''1st July''' </td>
<td>2nd </td>
<td>3rd </td>
<td bgcolor="#33CC99">4th </td>
<td bgcolor="#33CC99">5th </td>
</tr>
<tr valign="top">
<td >6th </td>
<td>7th </td>
<td>8th </td>
<td>9th </td>
<td>10th </td>
<td bgcolor="#33CC99">11th </td>
<td bgcolor="#33CC99">12th </td>
</tr>
<tr valign="top">
<td>13th </td>
<td>14th </td>
<td>15th </td>
<td>16th </td>
<td>17th </td>
<td bgcolor="#33CC99">18th </td>
<td bgcolor="#33CC99">19th </td>
</tr>
<tr valign="top">
<td>20th </td>
<td>21st </td>
<td>22nd </td>
<td>23rd </td>
<td>24th </td>
<td bgcolor="#33CC99">25th </td>
<td bgcolor="#33CC99">26th </td>
</tr>
<tr valign="top">
<td>27th </td>
<td>28th </td>
<td>29th </td>
<td>30th </td>
<td>31st </td>
<td bgcolor="#4357CFF">'''1st August''' </td>
<td bgcolor="#33CC99">2nd </td>
</tr>
<tr valign="top">
<td>3rd </td>
<td>4th </td>
<td>5th </td>
<td>6th </td>
<td>7th </td>
<td bgcolor="#33CC99">8th </td>
<td bgcolor="#33CC99">9th </td>
</tr>
<tr valign="top">
<td>10th </td>
<td>11th </td>
<td>12th </td>
<td>13th </td>
<td>14th </td>
<td bgcolor="#33CC99">15th </td>
<td bgcolor="#33CC99">16th </td>
</tr>
<tr valign="top">
<td>17th </td>
<td>18th </td>
<td>19th </td>
<td>20th </td>
<td>21st </td>
<td bgcolor="#33CC99">22nd </td>
<td bgcolor="#33CC99">23rd </td>
</tr>
<tr valign="top">
<td>24th </td>
<td>25th </td>
<td>26th </td>
<td>27th </td>
<td>28th </td>
<td bgcolor="#33CC99">29th </td>
<td bgcolor="#33CC99">30th </td>
</tr>
<tr valign="top">
<td>31st </td>
<td bgcolor="#4357CFF">'''1st September''' </td>
<td>2nd </td>
<td>3rd </td>
<td>4th </td>
<td bgcolor="#33CC99">5th </td>
<td bgcolor="#33CC99">6th </td>
</tr>
<tr valign="top">
<td>7th </td>
<td>8th </td>
<td>9th </td>
<td>10th </td>
<td>11th </td>
<td bgcolor="#33CC99">12th </td>
<td bgcolor="#33CC99">13th </td>
</tr>
<tr valign="top">
<td>14th </td>
<td>15th </td>
<td>16th </td>
<td>17th </td>
<td>18th </td>
<td bgcolor="#33CC99">19th </td>
<td bgcolor="#33CC99">20th </td>
</tr>
<tr valign="top">
<td>21st </td>
<td>22nd </td>
<td>23rd </td>
<td>24th </td>
<td>25th </td>
<td bgcolor="#33CC99">26th </td>
<td bgcolor="#33CC99">27th </td>
</tr>
<tr valign="top">
<td>28th </td>
<td>29th </td>
<td>30th </td>
<td bgcolor="#4357CFF">'''1st October''' </td>
<td>2nd </td>
<td bgcolor="#33CC99">3rd </td>
<td bgcolor="#33CC99">4th </td>
</tr>
</table>

Mod:Hunt Research Group/calendar

2015-06-16T07:33:19Z

Bw1911: /* Calendar */

Back to the main [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group wiki-page]
== Calendar ==

{| class="wikitable"
|-
! 1
! 2
! 3
! 4
|-
| Tricia (Not Done)
| Bryan Ward (Not Done)
| Claire Ashworth (Not Done)
| Precious Ugbomah (Not Done)
|-
| Vincent Chen (Not Done)
| Gabriel Lau (Not Done)
| Rebecca Rowe (Not Done)
| Ken Watson (Not Done)
|-
| Laila Bana (Not Done)
| Oliver Benton (Not Done)
| Christopher Sewell (Not Done)
| Chen Chen (Not Done)
|-
| Aiswarya Prabha (Not Done)
|Ziyun Zhang (Not Done)
|Richard Fogarty (Not Done)
|
|-
|-)
|}

<table border="1" cellpadding="5" width="1190">
<tr bgcolor="#66CCFF">
<th width="170px">Mon</th>
<th width="170px">Tues</th>
<th width="170px">Wed</th>
<th width="170px">Thur</th>
<th width="170px">Fri</th>
<th width="170px">Sat</th>
<th width="170px">Sun</th>
</tr>

<tr valign="top">
<td bgcolor="#4357CFF">'''1st June''' </td>
<td>2nd </td>
<td>3rd </td>
<td>4th </td>
<td>5th </td>
<td bgcolor="#33CC99">6th </td>
<td bgcolor="#33CC99">7th </td>
</tr>
<tr valign="top">
<td>8th </td>
<td>9th </td>
<td>10th </td>
<td>11th </td>
<td>12th </td>
<td bgcolor="#33CC99">13th </td>
<td bgcolor="#33CC99">14th </td>
</tr>
<tr valign="top">
<td>15th </td>
<td>16th </td>
<td>17th </td>
<td>18th </td>
<td>19th Bryan Away </td>
<td bgcolor="#33CC99">20th Bryan Away </td>
<td bgcolor="#33CC99">21st Bryan Away </td>
</tr>
<tr valign="top">
<td>22nd Bryan Away </td>
<td>23rd Bryan Away </td>
<td>24th Bryan Away </td>
<td>25th Bryan Away </td>
<td>26th Bryan Away </td>
<td bgcolor="#33CC99">27th Bryan Away </td>
<td bgcolor="#33CC99">28th Bryan Away </td>
</tr>
<tr valign="top">
<td >29th Bryan Away </td>
<td>30th </td>
<td bgcolor="#4357CFF">'''1st July''' </td>
<td>2nd </td>
<td>3rd </td>
<td bgcolor="#33CC99">4th </td>
<td bgcolor="#33CC99">5th </td>
</tr>
<tr valign="top">
<td >6th </td>
<td>7th </td>
<td>8th </td>
<td>9th </td>
<td>10th </td>
<td bgcolor="#33CC99">11th </td>
<td bgcolor="#33CC99">12th </td>
</tr>
<tr valign="top">
<td>13th </td>
<td>14th </td>
<td>15th </td>
<td>16th </td>
<td>17th </td>
<td bgcolor="#33CC99">18th </td>
<td bgcolor="#33CC99">19th </td>
</tr>
<tr valign="top">
<td>20th </td>
<td>21st </td>
<td>22nd </td>
<td>23rd </td>
<td>24th </td>
<td bgcolor="#33CC99">25th </td>
<td bgcolor="#33CC99">26th </td>
</tr>
<tr valign="top">
<td>27th </td>
<td>28th </td>
<td>29th </td>
<td>30th </td>
<td>31st </td>
<td bgcolor="#4357CFF">'''1st August''' </td>
<td bgcolor="#33CC99">2nd </td>
</tr>
<tr valign="top">
<td>3rd </td>
<td>4th </td>
<td>5th </td>
<td>6th </td>
<td>7th </td>
<td bgcolor="#33CC99">8th </td>
<td bgcolor="#33CC99">9th </td>
</tr>
<tr valign="top">
<td>10th </td>
<td>11th </td>
<td>12th </td>
<td>13th </td>
<td>14th </td>
<td bgcolor="#33CC99">15th </td>
<td bgcolor="#33CC99">16th </td>
</tr>
<tr valign="top">
<td>17th </td>
<td>18th </td>
<td>19th </td>
<td>20th </td>
<td>21st </td>
<td bgcolor="#33CC99">22nd </td>
<td bgcolor="#33CC99">23rd </td>
</tr>
<tr valign="top">
<td>24th </td>
<td>25th </td>
<td>26th </td>
<td>27th </td>
<td>28th </td>
<td bgcolor="#33CC99">29th </td>
<td bgcolor="#33CC99">30th </td>
</tr>
<tr valign="top">
<td>31st </td>
<td bgcolor="#4357CFF">'''1st September''' </td>
<td>2nd </td>
<td>3rd </td>
<td>4th </td>
<td bgcolor="#33CC99">5th </td>
<td bgcolor="#33CC99">6th </td>
</tr>
<tr valign="top">
<td>7th </td>
<td>8th </td>
<td>9th </td>
<td>10th </td>
<td>11th </td>
<td bgcolor="#33CC99">12th </td>
<td bgcolor="#33CC99">13th </td>
</tr>
<tr valign="top">
<td>14th </td>
<td>15th </td>
<td>16th </td>
<td>17th </td>
<td>18th </td>
<td bgcolor="#33CC99">19th </td>
<td bgcolor="#33CC99">20th </td>
</tr>
<tr valign="top">
<td>21st </td>
<td>22nd </td>
<td>23rd </td>
<td>24th </td>
<td>25th </td>
<td bgcolor="#33CC99">26th </td>
<td bgcolor="#33CC99">27th </td>
</tr>
<tr valign="top">
<td>28th </td>
<td>29th </td>
<td>30th </td>
<td bgcolor="#4357CFF">'''1st October''' </td>
<td>2nd </td>
<td bgcolor="#33CC99">3rd </td>
<td bgcolor="#33CC99">4th </td>
</tr>
</table>

Mod:Hunt Research Group/calendar

2015-04-23T11:37:54Z

Bw1911:

Back to the main [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group wiki-page]
== Calendar ==

{| class="wikitable"
|-
! 1
! 2
! 3
! 4
|-
| Tricia (Done)
| Bryan Ward (Done)
| Claire Ashworth (Done)
| Precious Ugbomah (Done)
|-
| Vincent Chen (Done)
| Gabriel Lau (Not Done)
| Rebecca Rowe (Done)
| Ken Watson (Done)
|-
| Laila Bana (Done)
| Oliver Benton (Done)
| Christopher Sewell (Done)
| Chen Chen (Not Done)
|-
| Aiswarya Prabha (Done)
|Ziyun Zhang (Done)
|Richard Fogarty (Done)
|
|-
|-)
|}

<table border="1" cellpadding="5" width="1190">
<tr bgcolor="#66CCFF">
<th width="170px">Mon</th>
<th width="170px">Tues</th>
<th width="170px">Wed</th>
<th width="170px">Thur</th>
<th width="170px">Fri</th>
<th width="170px" bgcolor="#CCCCCC">Sat</th>
<th width="170px" bgcolor="#CCCCCC">Sun</th>
</tr>

<tr valign="top">
<td>16th </td>
<td>17th </td>
<td>18th </td>
<td>19th </td>
<td>20th </td>
<td bgcolor="#CCCCCC">21st </td>
<td bgcolor="#CCCCCC">22nd </td>
</tr>
<tr valign="top">
<td>23rd Richard F Away </td>
<td>24th Richard F Away </td>
<td>25th Richard F Away </td>
<td>26th </td>
<td bgcolor="#FFFF00">27th '''END OF TERM'''</td>
<td bgcolor="#CCCCCC">28th </td>
<td bgcolor="#CCCCCC">29th </td>
</tr>
<tr valign="top">
<td>30th </td>
<td>31st </td>
<td bgcolor="#4357CFF">'''1st April''' </td>
<td bgcolor="#33CC99">2nd '''College closed'''</td>
<td bgcolor="#33CC99">3rd Good Friday '''College closed'''</td>
<td bgcolor="#33CC99">4th '''College closed'''</td>
<td bgcolor="#33CC99">5th '''College closed'''</td>
</tr>
<tr valign="top">
<td bgcolor="#33CC99">6th Easter Monday '''College closed'''</td>
<td bgcolor="#33CC99">7th '''College closed''' </td>
<td>8th Precious Away Bryan Away Richard Away Oli Away Becky Away Chris Away</td>
<td>9th Chris Away Becky Away</td>
<td>10th Ken Away Tricia Away Claire Away Chris Away Vincent Away</td>
<td bgcolor="#CCCCCC">11th </td>
<td bgcolor="#CCCCCC">12th </td>
</tr>
<tr valign="top">
<td >13th Ken Away Chris Away</td>
<td>14th </td>
<td>15th </td>
<td>16th </td>
<td>17th </td>
<td bgcolor="#CCCCCC">18th </td>
<td bgcolor="#CCCCCC">19th </td>
</tr>
<tr valign="top">
<td >20th </td>
<td>21st </td>
<td>22nd </td>
<td>23rd </td>
<td>24th </td>
<td bgcolor="#CCCCCC">25th </td>
<td bgcolor="#CCCCCC">26th </td>
</tr>
<tr valign="top">
<td bgcolor="#FFFF00" >27th '''NEW TERM'''</td>
<td>28th </td>
<td>29th </td>
<td>30th </td>
<td bgcolor="#4357CFF">'''1st May''' Bryan Away </td>
<td bgcolor="#CCCCCC">2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
</tr>
<tr valign="top">
<td bgcolor="#33CC99">4th Bank Holiday '''College closed'''</td>
<td>5th </td>
<td>6th </td>
<td>7th </td>
<td>8th </td>
<td bgcolor="#CCCCCC">9th </td>
<td bgcolor="#CCCCCC">10th </td>
</tr>
<tr valign="top">
<td>11th </td>
<td>12th </td>
<td>13th </td>
<td>14th </td>
<td>15th </td>
<td bgcolor="#CCCCCC">16th </td>
<td bgcolor="#CCCCCC">17th </td>
</tr>
<tr valign="top">
<td>18th </td>
<td>19th </td>
<td>20th </td>
<td>21st </td>
<td>22nd </td>
<td bgcolor="#CCCCCC">23rd </td>
<td bgcolor="#CCCCCC">24th </td>
</tr>
<tr valign="top">
<td bgcolor="#33CC99">25th Bank Holiday '''College closed'''</td>
<td>26th </td>
<td>27th </td>
<td>28th </td>
<td>29th </td>
<td bgcolor="#CCCCCC">30th </td>
<td bgcolor="#CCCCCC">31st </td>
</tr>
</table>

Mod:Hunt Research Group/calendar

2015-03-31T15:40:11Z

Bw1911:

Back to the main [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group wiki-page]
== Calendar ==

{| class="wikitable"
|-
! 1
! 2
! 3
! 4
|-
| Tricia (Done)
| Bryan Ward (Done)
| Claire Ashworth (Done)
| Precious Ugbomah (Done)
|-
| Vincent Chen (Not Done)
| Gabriel Lau (Not Done)
| Rebecca Rowe (Not Done)
| Ken Watson (Not Done)
|-
| Laila Bana (Not Done)
| Oliver Benton (Done)
| Christopher Sewell (Not Done)
| Chen Chen (Not Done)
|-
| Aiswarya Prabha (Done)
|Ziyun Zhang (Done)
|
|
|-
|-)
|}

<table border="1" cellpadding="5" width="1190">
<tr bgcolor="#66CCFF">
<th width="170px">Mon</th>
<th width="170px">Tues</th>
<th width="170px">Wed</th>
<th width="170px">Thur</th>
<th width="170px">Fri</th>
<th width="170px" bgcolor="#CCCCCC">Sat</th>
<th width="170px" bgcolor="#CCCCCC">Sun</th>
</tr>

<tr valign="top">
<td>16th </td>
<td>17th </td>
<td>18th </td>
<td>19th </td>
<td>20th </td>
<td bgcolor="#CCCCCC">21st </td>
<td bgcolor="#CCCCCC">22nd </td>
</tr>
<tr valign="top">
<td>23rd Richard F Away </td>
<td>24th Richard F Away </td>
<td>25th Richard F Away </td>
<td>26th </td>
<td bgcolor="#FFFF00">27th '''END OF TERM'''</td>
<td bgcolor="#CCCCCC">28th </td>
<td bgcolor="#CCCCCC">29th </td>
</tr>
<tr valign="top">
<td>30th </td>
<td>31st </td>
<td bgcolor="#4357CFF">'''1st April''' </td>
<td bgcolor="#33CC99">2nd '''College closed'''</td>
<td bgcolor="#33CC99">3rd Good Friday '''College closed'''</td>
<td bgcolor="#33CC99">4th '''College closed'''</td>
<td bgcolor="#33CC99">5th '''College closed'''</td>
</tr>
<tr valign="top">
<td bgcolor="#33CC99">6th Easter Monday '''College closed'''</td>
<td bgcolor="#33CC99">7th '''College closed''' </td>
<td>8th Precious Away Bryan Away</td>
<td>9th 
<td>10th Ken Away Tricia Away Claire Away</td>
<td bgcolor="#CCCCCC">11th </td>
<td bgcolor="#CCCCCC">12th </td>
</tr>
<tr valign="top">
<td >13th Ken Away</td>
<td>14th </td>
<td>15th </td>
<td>16th </td>
<td>17th </td>
<td bgcolor="#CCCCCC">18th </td>
<td bgcolor="#CCCCCC">19th </td>
</tr>
<tr valign="top">
<td >20th </td>
<td>21st </td>
<td>22nd </td>
<td>23rd </td>
<td>24th </td>
<td bgcolor="#CCCCCC">25th </td>
<td bgcolor="#CCCCCC">26th </td>
</tr>
<tr valign="top">
<td bgcolor="#FFFF00" >27th '''NEW TERM'''</td>
<td>28th </td>
<td>29th </td>
<td>30th </td>
<td bgcolor="#4357CFF">'''1st May''' </td>
<td bgcolor="#CCCCCC">2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
</tr>
<tr valign="top">
<td bgcolor="#33CC99">4th Bank Holiday '''College closed'''</td>
<td>5th </td>
<td>6th </td>
<td>7th </td>
<td>8th </td>
<td bgcolor="#CCCCCC">9th </td>
<td bgcolor="#CCCCCC">10th </td>
</tr>
<tr valign="top">
<td>11th </td>
<td>12th </td>
<td>13th </td>
<td>14th </td>
<td>15th </td>
<td bgcolor="#CCCCCC">16th </td>
<td bgcolor="#CCCCCC">17th </td>
</tr>
<tr valign="top">
<td>18th </td>
<td>19th </td>
<td>20th </td>
<td>21st </td>
<td>22nd </td>
<td bgcolor="#CCCCCC">23rd </td>
<td bgcolor="#CCCCCC">24th </td>
</tr>
<tr valign="top">
<td bgcolor="#33CC99">25th Bank Holiday '''College closed'''</td>
<td>26th </td>
<td>27th </td>
<td>28th </td>
<td>29th </td>
<td bgcolor="#CCCCCC">30th </td>
<td bgcolor="#CCCCCC">31st </td>
</tr>
</table>

Mod:Hunt Research Group/calendar

2015-03-31T12:19:00Z

Bw1911:

Back to the main [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group wiki-page]
== Calendar ==

{| class="wikitable"
|-
! 1
! 2
! 3
! 4
|-
| Tricia (Done)
| Bryan Ward (Done)
| Claire Ashworth (Done)
| Precious Ugbomah (Done)
|-
| Vincent Chen (Not Done)
| Gabriel Lau (Not Done)
| Rebecca Rowe (Not Done)
| Ken Watson (Not Done)
|-
| Laila Bana (Not Done)
| Oliver Benton (Done)
| Christopher Sewell (Not Done)
| Chen Chen (Not Done)
|-
| Aiswarya Prabha (Done)
|Ziyun Zhang (Not Done)
|
|
|-
|-)
|}

<table border="1" cellpadding="5" width="1190">
<tr bgcolor="#66CCFF">
<th width="170px">Mon</th>
<th width="170px">Tues</th>
<th width="170px">Wed</th>
<th width="170px">Thur</th>
<th width="170px">Fri</th>
<th width="170px" bgcolor="#CCCCCC">Sat</th>
<th width="170px" bgcolor="#CCCCCC">Sun</th>
</tr>

<tr valign="top">
<td>16th </td>
<td>17th </td>
<td>18th </td>
<td>19th </td>
<td>20th </td>
<td bgcolor="#CCCCCC">21st </td>
<td bgcolor="#CCCCCC">22nd </td>
</tr>
<tr valign="top">
<td>23rd Richard F Away </td>
<td>24th Richard F Away </td>
<td>25th Richard F Away </td>
<td>26th </td>
<td bgcolor="#FFFF00">27th '''END OF TERM'''</td>
<td bgcolor="#CCCCCC">28th </td>
<td bgcolor="#CCCCCC">29th </td>
</tr>
<tr valign="top">
<td>30th </td>
<td>31st </td>
<td bgcolor="#4357CFF">'''1st April''' </td>
<td bgcolor="#33CC99">2nd '''College closed'''</td>
<td bgcolor="#33CC99">3rd Good Friday '''College closed'''</td>
<td bgcolor="#33CC99">4th '''College closed'''</td>
<td bgcolor="#33CC99">5th '''College closed'''</td>
</tr>
<tr valign="top">
<td bgcolor="#33CC99">6th Easter Monday '''College closed'''</td>
<td bgcolor="#33CC99">7th '''College closed''' </td>
<td>8th Precious Away Bryan Away</td>
<td>9th 
<td>10th Ken Away Tricia Away Claire Away</td>
<td bgcolor="#CCCCCC">11th </td>
<td bgcolor="#CCCCCC">12th </td>
</tr>
<tr valign="top">
<td >13th Ken Away</td>
<td>14th </td>
<td>15th </td>
<td>16th </td>
<td>17th </td>
<td bgcolor="#CCCCCC">18th </td>
<td bgcolor="#CCCCCC">19th </td>
</tr>
<tr valign="top">
<td >20th </td>
<td>21st </td>
<td>22nd </td>
<td>23rd </td>
<td>24th </td>
<td bgcolor="#CCCCCC">25th </td>
<td bgcolor="#CCCCCC">26th </td>
</tr>
<tr valign="top">
<td bgcolor="#FFFF00" >27th '''NEW TERM'''</td>
<td>28th </td>
<td>29th </td>
<td>30th </td>
<td bgcolor="#4357CFF">'''1st May''' </td>
<td bgcolor="#CCCCCC">2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
</tr>
<tr valign="top">
<td bgcolor="#33CC99">4th Bank Holiday '''College closed'''</td>
<td>5th </td>
<td>6th </td>
<td>7th </td>
<td>8th </td>
<td bgcolor="#CCCCCC">9th </td>
<td bgcolor="#CCCCCC">10th </td>
</tr>
<tr valign="top">
<td>11th </td>
<td>12th </td>
<td>13th </td>
<td>14th </td>
<td>15th </td>
<td bgcolor="#CCCCCC">16th </td>
<td bgcolor="#CCCCCC">17th </td>
</tr>
<tr valign="top">
<td>18th </td>
<td>19th </td>
<td>20th </td>
<td>21st </td>
<td>22nd </td>
<td bgcolor="#CCCCCC">23rd </td>
<td bgcolor="#CCCCCC">24th </td>
</tr>
<tr valign="top">
<td bgcolor="#33CC99">25th Bank Holiday '''College closed'''</td>
<td>26th </td>
<td>27th </td>
<td>28th </td>
<td>29th </td>
<td bgcolor="#CCCCCC">30th </td>
<td bgcolor="#CCCCCC">31st </td>
</tr>
</table>

Mod:Hunt Research Group/calendar

2014-12-12T16:13:18Z

Bw1911: /* Calendar */

Back to the main [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group wiki-page]
== Calendar ==

{| class="wikitable"
|-
! 1
! 2
! 3
! 4
|-
| Tricia (Not Done)
| Matthew Clough (Not Done)
| Bryan Ward (Done)
| Claire Ashworth (Done)
|-
| Precious Ugbomah (Not Done)
| Richard Matthews (Not Done)
| Vincent Chen (Not Done)
| Gabriel Lau (Not Done)
|-
| Rebecca Rowe (Not Done)
| Patricia Ho (Done)
| Ken Watson (Done)
| Laila Bana (Not Done)
|-
| Oliver Benton (Not Done)
|Christopher Sewell (Not Done)
|Chen Chen (Not Done)
|Aiswarya Prabha (Not Done)
|-
|-)
|}

<table border="1" cellpadding="5" width="1190">
<tr bgcolor="#66CCFF">
<th width="170px">Mon</th>
<th width="170px">Tues</th>
<th width="170px">Wed</th>
<th width="170px">Thur</th>
<th width="170px">Fri</th>
<th width="170px" bgcolor="#CCCCCC">Sat</th>
<th width="170px" bgcolor="#CCCCCC">Sun</th>
</tr>
<tr valign="top">
<td>29th Tricia APCIL </td>
<td>30th Tricia APCIL </td>
<td bgcolor="#4357CFF">'''1st October''' Tricia APCIL </td>
<td>2nd Tricia flying </td>
<td>3rd Tricia flying </td>
<td bgcolor="#CCCCCC">4th </td>
<td bgcolor="#CCCCCC">5th </td>
</tr>
<tr valign="top">
<td bgcolor="#FFFF00">6th '''NEW TERM''' </td>
<td>7th </td>
<td>8th </td>
<td>9th </td>
<td>10th </td>
<td bgcolor="#CCCCCC">11th </td>
<td bgcolor="#CCCCCC">12th </td>
</tr>
<tr valign="top">
<td>13th </td>
<td>14th </td>
<td>15th </td>
<td>16th </td>
<td>17th </td>
<td bgcolor="#CCCCCC">18th </td>
<td bgcolor="#CCCCCC">19th </td>
</tr>
<tr valign="top">
<td>20th </td>
<td>21st </td>
<td>22nd </td>
<td>23rd </td>
<td>24th </td>
<td bgcolor="#CCCCCC">25th </td>
<td bgcolor="#CCCCCC">26th '''Clocks go back!'''</td>
</tr>
<tr valign="top">
<td>27th </td>
<td>28th </td>
<td>29th </td>
<td>30th </td>
<td>31st </td>
<td bgcolor="#4357CFF">'''1st November''' </td>
<td bgcolor="#CCCCCC">2nd </td>
</tr>
<tr valign="top">
<td>3rd </td>
<td>4th Richard F Away </td>
<td>5th </td>
<td>6th </td>
<td>7th </td>
<td bgcolor="#CCCCCC">8th </td>
<td bgcolor="#CCCCCC">9th </td>
</tr>
<tr valign="top">
<td>10th </td>
<td>11th </td>
<td>12th </td>
<td>13th </td>
<td>14th </td>
<td bgcolor="#CCCCCC">15th </td>
<td bgcolor="#CCCCCC">16th </td>
</tr>
<tr valign="top">
<td>17th </td>
<td>18th </td>
<td>19th </td>
<td>20th </td>
<td>21st </td>
<td bgcolor="#CCCCCC">22nd </td>
<td bgcolor="#CCCCCC">23rd </td>
</tr>
<tr valign="top">
<td>24th </td>
<td>25th '''Christmas Meal''' </td>
<td>26th </td>
<td>27th </td>
<td>28th </td>
<td bgcolor="#CCCCCC">29th </td>
<td bgcolor="#CCCCCC">30th </td>
</tr>
<tr valign="top">
<td bgcolor="#4357CFF">'''1st December''' </td>
<td>2nd </td>
<td>3rd </td>
<td>4th </td>
<td>5th </td>
<td bgcolor="#CCCCCC">6th </td>
<td bgcolor="#CCCCCC">7th </td>
</tr>
<tr valign="top">
<td>8th Richard F Away </td>
<td>9th Richard F Away </td>
<td>10th Richard F Away </td>
<td>11th Richard F Away </td>
<td>12th </td>
<td bgcolor="#CCCCCC">13th </td>
<td bgcolor="#CCCCCC">14th </td>
</tr>
<tr valign="top">
<td>15th </td>
<td>16th </td>
<td>17th Richard F Away </td>
<td>18th Richard F Away </td>
<td bgcolor="#FFFF00">19th '''END OF TERM''' Bryan Away </td>
<td bgcolor="#CCCCCC">20th Bryan Away </td>
<td bgcolor="#CCCCCC">21st Bryan Away </td>
</tr>
<tr valign="top">
<td>22nd Ken Away Bryan Away </td>
<td>23rd Ken Away Claire Away Bryan Away </td>
<td bgcolor="#33CC99">24th '''College closed'''</td>
<td bgcolor="#33CC99">25th '''College closed'''</td>
<td bgcolor="#33CC99">26th '''College closed'''</td>
<td bgcolor="#CCCCCC">27th Bryan Away </td>
<td bgcolor="#CCCCCC">28th Bryan Away </td>
</tr>
<tr valign="top">
<td bgcolor="#33CC99">29th '''College closed'''</td>
<td bgcolor="#33CC99">30th '''College closed'''</td>
<td bgcolor="#33CC99">31st '''College closed'''</td>
<td bgcolor="#4357CFF">'''1st January 2015''' '''College closed'''</td>
<td bgcolor="#33CC99">2nd '''College closed'''</td>
<td bgcolor="#CCCCCC">3rd </td>
<td bgcolor="#CCCCCC">4th </td>
<tr valign="top">
<td>5th </td>
<td>6th </td>
<td>7th </td>
<td>8th </td>
<td>9th </td>
<td bgcolor="#CCCCCC">10th </td>
<td bgcolor="#CCCCCC">11th </td>
</tr>
<tr valign="top">
<td bgcolor="#FFFF00">12th '''NEW TERM'''</td>
<td>13th </td>
<td>14th </td>
<td>15th </td>
<td>16th </td>
<td bgcolor="#CCCCCC">17th </td>
<td bgcolor="#CCCCCC">18th </td>
</tr>
<tr valign="top">
<td>19th </td>
<td>20th </td>
<td>21st </td>
<td>22nd </td>
<td>23rd </td>
<td bgcolor="#CCCCCC">24th </td>
<td bgcolor="#CCCCCC">25th </td>
</tr>
<tr valign="top">
<td>26th </td>
<td>27th </td>
<td>28th </td>
<td>29th </td>
<td>30th </td>
<td bgcolor="#CCCCCC">31st </td>
<td bgcolor="#4357CFF">'''1st February 2015''' </td>
</tr>
</table>

Mod:Hunt Research Group/calendar

2014-12-12T16:12:47Z

Bw1911:

Back to the main [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group wiki-page]
== Calendar ==

{| class="wikitable"
|-
! 1
! 2
! 3
! 4
|-
| Tricia (Not Done)
| Matthew Clough (Not Done)
| Bryan Ward (Not Done)
| Claire Ashworth (Done)
|-
| Precious Ugbomah (Not Done)
| Richard Matthews (Not Done)
| Vincent Chen (Not Done)
| Gabriel Lau (Not Done)
|-
| Rebecca Rowe (Not Done)
| Patricia Ho (Done)
| Ken Watson (Done)
| Laila Bana (Not Done)
|-
| Oliver Benton (Not Done)
|Christopher Sewell (Not Done)
|Chen Chen (Not Done)
|Aiswarya Prabha (Not Done)
|-
|-)
|}

<table border="1" cellpadding="5" width="1190">
<tr bgcolor="#66CCFF">
<th width="170px">Mon</th>
<th width="170px">Tues</th>
<th width="170px">Wed</th>
<th width="170px">Thur</th>
<th width="170px">Fri</th>
<th width="170px" bgcolor="#CCCCCC">Sat</th>
<th width="170px" bgcolor="#CCCCCC">Sun</th>
</tr>
<tr valign="top">
<td>29th Tricia APCIL </td>
<td>30th Tricia APCIL </td>
<td bgcolor="#4357CFF">'''1st October''' Tricia APCIL </td>
<td>2nd Tricia flying </td>
<td>3rd Tricia flying </td>
<td bgcolor="#CCCCCC">4th </td>
<td bgcolor="#CCCCCC">5th </td>
</tr>
<tr valign="top">
<td bgcolor="#FFFF00">6th '''NEW TERM''' </td>
<td>7th </td>
<td>8th </td>
<td>9th </td>
<td>10th </td>
<td bgcolor="#CCCCCC">11th </td>
<td bgcolor="#CCCCCC">12th </td>
</tr>
<tr valign="top">
<td>13th </td>
<td>14th </td>
<td>15th </td>
<td>16th </td>
<td>17th </td>
<td bgcolor="#CCCCCC">18th </td>
<td bgcolor="#CCCCCC">19th </td>
</tr>
<tr valign="top">
<td>20th </td>
<td>21st </td>
<td>22nd </td>
<td>23rd </td>
<td>24th </td>
<td bgcolor="#CCCCCC">25th </td>
<td bgcolor="#CCCCCC">26th '''Clocks go back!'''</td>
</tr>
<tr valign="top">
<td>27th </td>
<td>28th </td>
<td>29th </td>
<td>30th </td>
<td>31st </td>
<td bgcolor="#4357CFF">'''1st November''' </td>
<td bgcolor="#CCCCCC">2nd </td>
</tr>
<tr valign="top">
<td>3rd </td>
<td>4th Richard F Away </td>
<td>5th </td>
<td>6th </td>
<td>7th </td>
<td bgcolor="#CCCCCC">8th </td>
<td bgcolor="#CCCCCC">9th </td>
</tr>
<tr valign="top">
<td>10th </td>
<td>11th </td>
<td>12th </td>
<td>13th </td>
<td>14th </td>
<td bgcolor="#CCCCCC">15th </td>
<td bgcolor="#CCCCCC">16th </td>
</tr>
<tr valign="top">
<td>17th </td>
<td>18th </td>
<td>19th </td>
<td>20th </td>
<td>21st </td>
<td bgcolor="#CCCCCC">22nd </td>
<td bgcolor="#CCCCCC">23rd </td>
</tr>
<tr valign="top">
<td>24th </td>
<td>25th '''Christmas Meal''' </td>
<td>26th </td>
<td>27th </td>
<td>28th </td>
<td bgcolor="#CCCCCC">29th </td>
<td bgcolor="#CCCCCC">30th </td>
</tr>
<tr valign="top">
<td bgcolor="#4357CFF">'''1st December''' </td>
<td>2nd </td>
<td>3rd </td>
<td>4th </td>
<td>5th </td>
<td bgcolor="#CCCCCC">6th </td>
<td bgcolor="#CCCCCC">7th </td>
</tr>
<tr valign="top">
<td>8th Richard F Away </td>
<td>9th Richard F Away </td>
<td>10th Richard F Away </td>
<td>11th Richard F Away </td>
<td>12th </td>
<td bgcolor="#CCCCCC">13th </td>
<td bgcolor="#CCCCCC">14th </td>
</tr>
<tr valign="top">
<td>15th </td>
<td>16th </td>
<td>17th Richard F Away </td>
<td>18th Richard F Away </td>
<td bgcolor="#FFFF00">19th '''END OF TERM''' Bryan Away </td>
<td bgcolor="#CCCCCC">20th Bryan Away </td>
<td bgcolor="#CCCCCC">21st Bryan Away </td>
</tr>
<tr valign="top">
<td>22nd Ken Away Bryan Away </td>
<td>23rd Ken Away Claire Away Bryan Away </td>
<td bgcolor="#33CC99">24th '''College closed'''</td>
<td bgcolor="#33CC99">25th '''College closed'''</td>
<td bgcolor="#33CC99">26th '''College closed'''</td>
<td bgcolor="#CCCCCC">27th Bryan Away </td>
<td bgcolor="#CCCCCC">28th Bryan Away </td>
</tr>
<tr valign="top">
<td bgcolor="#33CC99">29th '''College closed'''</td>
<td bgcolor="#33CC99">30th '''College closed'''</td>
<td bgcolor="#33CC99">31st '''College closed'''</td>
<td bgcolor="#4357CFF">'''1st January 2015''' '''College closed'''</td>
<td bgcolor="#33CC99">2nd '''College closed'''</td>
<td bgcolor="#CCCCCC">3rd </td>
<td bgcolor="#CCCCCC">4th </td>
<tr valign="top">
<td>5th </td>
<td>6th </td>
<td>7th </td>
<td>8th </td>
<td>9th </td>
<td bgcolor="#CCCCCC">10th </td>
<td bgcolor="#CCCCCC">11th </td>
</tr>
<tr valign="top">
<td bgcolor="#FFFF00">12th '''NEW TERM'''</td>
<td>13th </td>
<td>14th </td>
<td>15th </td>
<td>16th </td>
<td bgcolor="#CCCCCC">17th </td>
<td bgcolor="#CCCCCC">18th </td>
</tr>
<tr valign="top">
<td>19th </td>
<td>20th </td>
<td>21st </td>
<td>22nd </td>
<td>23rd </td>
<td bgcolor="#CCCCCC">24th </td>
<td bgcolor="#CCCCCC">25th </td>
</tr>
<tr valign="top">
<td>26th </td>
<td>27th </td>
<td>28th </td>
<td>29th </td>
<td>30th </td>
<td bgcolor="#CCCCCC">31st </td>
<td bgcolor="#4357CFF">'''1st February 2015''' </td>
</tr>
</table>

Talk:Mod:Hunt Research Group/VmdVisual

2014-10-24T08:21:33Z

Bw1911: /* More Advance Visualisation */

=More Advance Visualisation=

==how to overlay two structures for comparison==

===Introduction===

In this example we will compare the same complex optimized using different DFT functionals. The complex in question is a calcium ß-diketiminate complex with a bound alkyl phosphine substrate.

===Loading molecule files===

VMD can use many file types however the file type required in this instance is .xyz

In the VMD Main window, navigate to:

<pre>File => New Molecule</pre>

This will prompt the Molecule File Browser to load.

[[File:Molecule_file_browser.png]]

To load the first file click "Browse" and navigate to the location of your first file. It is handy if the first file loaded is your reference structure.

You will see the in the Load files for: box, in the Molecule File Browser, now reads 0:filename and a wireframe image has appeared in the OpenGL Display.

Every additional file must be loaded as a New molecule. To do this, press the arrow in the "Load files for" box. Select "New molecule" and repeat the procedure above for your remaining files.

===Overlaying Structures===

You will now notice in the OpenGL Display that the overlaid images are in disarray.

[[File:OpenGL_with_misaligned_structs.png]]

In order to superimpose the images on top of one another use the following procedure.

In the VMD Main window navigate to:

<pre>Graphics => Representations</pre>

The following window will pop up

[[File:Graphical_representations_window.png]]

We can use the Graphical Representations window to temporarily remove two of the overlaid images to leave our reference image. To do this in the Selected Molecule box select one of the files you wish to temporarily remove then in the Style Color Selection box double click the Lines Name all entry.

If done correctly the colour of the font in Lines Name all should turn red. You should also notice the structure corresponding to the file is no longer displayed in the OpenGL Display.

Repeat this procedure for the remaining files until you are left with the reference geometry in the OpenGL Display.

In order to superimpose the structures correctly you need a point of reference in the structure which all the additional representations will be aligned to.

Your reference point in the reference structure needs to be a region whihc is least likely to change from one representation to another. In this worked example, the 3 atoms in the backbone of the complex will act as the reference point.

[[File:OpenGL_with_atom_labels.png]]

Next we need the atom numbers corresponding to the reference point in the structure. To do this first ensure you are working in the OpenGL Display window.

Press "1" on the keyboard. You will know if this has happened correctly as the mouse arrow should change to a crosshair. Using the crosshair, click the atoms which you wish to act as your reference point in the structure. As you select the atoms, green text will appear beside the atom (as shown in the image above.

Now in the VMD Main window, navigate to:

<pre>Graphics => Labels</pre>

The following labels window will appear on screen

[[File:Labels_window.png]]

This window will display information on the atoms selected.

The information we require is found in the index box. As you select each label you will notice the index number changes. These numbers correspond to the atom numbering within your xyz file. Take a note of the index numbers.

In the VMD Main window navigate to:

<pre>Extensions => Analysis => RMSD Calculator</pre>

The following window will appear:

[[File:RMSD_tool_window_std.png]]

Using the index information type the following information into the box which is currently filled with residue # to #

<pre>index first index no. or index second index no. or index third index no. or index fourth index no.</pre>

and so forth. This entry will depend on how many numbers you decide to use as a reference.

In the worked example, the entry is as follows:

<pre>index 7 or index 9 or index 10</pre>

Once you have added this text press enter.

Now untick the backbone only box, and select Selected (this will deselect Top). Finally in ID molecule click on your reference file.

Once you are finished the window should resemble something like this:

[[File:RMSD_tool_modified.png]]

Now press Align.... it will appear as if nothing has happened

Return to your Graphical Representations window and unhide the representations you hid earlier. (Select the file you hid in Selected Molecule box and double click Lines Name all whereby the font should turn from red to black.

<strike>Hopefully</strike> In the OpenGL display window you should observe the structures align to your chosen reference atoms as displayed in the table below under 'After'.

{|border="1" cellpadding="5" cellspacing="0" align="center"
|+
!Before
! After
|-
|[[File:OpenGL_with_misaligned_structs.png]]
|[[File:OpenGL_with_aligned_structs.png]]
|}

If you still have green text next to your reference atoms, return to the Labels window, select the label and press delete.

The wire representation of your overlaid structures can be difficult to decipher. You can make things easier to visualise by following the instructions on [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/vmd this] page.

===Troubleshooting===

*The aligning of the structures can be a little temperamental. You may need to press the align button more than once.
*The quality of alignment is dependent on the number of atoms you use as your reference. (Use a minimum of three??)
*No amount of "Align" button pressing will overlay structures correctly when the numbering of your atoms in the files are different from one another. The atom numbering must be consistent in all files.

==how to visualise a selection of atoms within radial distance of a selected molecule/atom==

*make a selection within a certain radius
::under GRAPHICAL_REP:SELECTIONS type "within x.xx of element Y) and name "Z"
::ADDREP
::this will select the atoms of name Z within x.xx angstrom of element Y
::you can then colour these atoms differently (and or make their VDW spheres larger/smaller)
::for example use COLOURID

*The clipping can not be what you want
::play around with the following in the TK console
::display nearclip set 10.000000
::display nearclip set 0.000000

Mod:Hunt Research Group

2014-10-24T08:18:13Z

Bw1911: /* Visualisation */

==Hunt Group Wiki==

Back to the main [http://www.ch.ic.ac.uk/hunt web-page]
===HPC Resources===
#Computing resources available in the chemistry department [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/computing_resources link]
#HPC servers and run scripts [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc link]
#Setting up a connection to HPC if you have a PC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_connections link]
#How to fix Windows files under UNIX [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Windowsfiles link]
#How to make ssh more comfortable [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpSSH link]
#How to make qsub more comfortable (gfunc) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpQSUB link]
#How to set up a SSH keypair [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/SSHkeyfile link]
#How to use gaussview directly on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gview link]
#How to comfortably search through old BASH commands [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/searchbash link]
#How to connect to HPC directory on desktop for file transfers [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_Directory_on_desktop link]
#How to set up cx2 [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cx2 link]

===Visualisation===
*'''ESPs'''
#Instructions for visualizing electrostatic potentials (Gaussview)[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials link]
#Electrostatic Potentials II (Molden) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials_2 link]
*'''VMD: a molecular dynamics visualisation package'''
#Download VMD [//wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/download_vmd link]
#Quick reminder [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDReminder link]
#Tricks and tips [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDTips link]
#Changing the graphical representation of your structures [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/vmd link]
#Basic visualisation of a trajectory [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VisualisingyourSimulation link]
#How to turn a Gaussian optimization into a VMD movie [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/VMDmovie link]
#Using scripts in VMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScripts link]
#Dealing with periodic boundaries and bonding (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScriptsPeriodic link]
#Dealing with bonding (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdBonding link]
#Atom selection and more advanced GUI based visualisation (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdVisual link]
*'''JMol'''
#Visualising MOs using Jmol [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:basic_jmol_instructions link]
#Surfaces (Solvent-Accessible and Connolly) in Jmol [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/jmolsurfaces link]
*'''EMO Code'''
#How to use Ling's emo plot code[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emoplot link]
#How to plot EMOs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emo link]

===Gaussian General===
#A database of common errors encountered when running Gaussian jobs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gaussian_errors link]
# [http://www.ch.ic.ac.uk/hunt/g03_man/index.htm G03 Manual]
#How to run NBO5.9 on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/NBO5.9 link]
#How to include dispersion [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dispersion link]
#Basic ONIOM (Mechanical Embedding) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/basiconiom link]
#M0n and DFT-D [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/DFTD link]
#IL ONIOM clusters [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/oniomclusers link]
#Molecular volume calculations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/molecular_volume link]
#problems with scf convergence [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/scf_convergence link]

===Setup and Running Ab-Initio MD Simulations===
#CPMD: Car-Parrinello Molecular Dynamics [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd link]
#How to run CPMD to study aqueous solutions [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd_water link]
#How to run CP2K [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cp2k_how link]
#[bmim]Cl using CPMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/bmimCl_cpmd link]
#[bmim]Cl using CP2K [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/bmimCl_cp2k link]
#mman using CPMD and Gaussian [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/mman link]
#[emim]SCN using CP2K[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emimscn link]
#CP2K Donts [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cp2k link]

===Setup and Running Classical MD Simulations===
#DLPOLY a MD simulation package, Installation on an IMac (old needs to be updated) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dlpoly_install link]
#DL_POLY FAQs [http://www.stfc.ac.uk/cse/DL_POLY/ccp1gui/38621.aspx] from DL_POLY webpage.
#Packmol for generating starting configurations [http://www.ime.unicamp.br/~martinez/packmol/] from Packmol webpage.
#Getting started: generating a solvated structure and "relaxing" it [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Starting_MD link]
#local [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/packmol_to_dlpoly_scripts packmol to dlpoly] conversion scripts
#Getting the Force Field [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Wheretostart link]
#Choosing an Ensemble [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Ensembles link]
#Equilibration and production simulations [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/EquilibrationandProduction link]
#Energy Drift [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/EnergyDrift link]
#Voids in ILs[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/voids link]
#How to equilibrate an MD run[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/equilibration link]
#Equilibration of [bmim][BF4] and [bmim][NO3][https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/BmimBF4_equilibration link]
#Summary of discussions with Ruth[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Aug09QtoRuth link]

===Running QM/MM Simulations in ChemShell===
#ChemShell official website which contains the manual and a tutorial [http://www.stfc.ac.uk/CSE/randd/ccg/36254.aspx link]
#Introduction to ChemShell - Copper in water [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Introduction link]
#Defining the system: Cu2+ and its first 2 solvation shells [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_System_Aqeuous_Cu(II) link]
#Defining the force field parameters [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Force_Field_Parameters_Aqueous_Cu(II) link]
#Single point QM/MM energy calculation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_SP_Aqeuous_Cu(II) link]
#QM/MM Optimisation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_OPT_Aqeuous_Cu(II) link]
#QM/MM Molecular Dynamics [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_MD_Aqeuous_Cu(II) link]

===Research Notes===
#Cl- in water [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/wannier_centre link]
#The use of Legendre time correlation functions to study reorientational dynamics in liquids[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/legendre link]
#Functional for ILs using CPMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/IL_cpmd_functional link]
#Solving the angular part of the Schrödinger equation for a hydrogen atom [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/angular_schrodinger link] (notes by Vincent)
#Systematic conformational scan for ion-pair dimers [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ion_pair_scan link]

===Installing and using other packages===
#How to install POLYRATE [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/polyrate link]
#How to install Geomview [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/geomview link]
#XMGRACE, gfortran, c compilers for Lion [http://hpc.sourceforge.net/]

===Admin Stuff===
#Not used to writing a wiki, make your test runs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/testing on this page]
#How to set-up new macs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_setup link]
#How to set-up remote desktop [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_remote link]
#[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/calendar Calendar]
#Demonstrating in the 3rd year computational chemistry lab [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/compchemlab Timetable]
#How to switch the printer HP CP3525dn duplex on and off [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/printing link]

Talk:Mod:Hunt Research Group/vmd

2014-10-24T08:16:29Z

Bw1911: /* Resizing the OpenGL Display Window */

==Changing the graphical representation of your structures==

===Introduction===

When working in the Graphical representations box you should be aware that any changes made (as described below) will affect the file which is shown in the Selected molecule box. In order to be consistent any changes you make will need to be repeated for any other files you have loaded. This is particularly relevant when [//wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdVisual overlaying structures].

===Structure model===

The wireframe representation can be difficult to work with. A better representation is Licorice.

To change to this representation, navigate to the Drawing method drop down menu in the Graphical Representations window and select Licorice.

In the OpenGL Display you will notice the representation for the particular file you are working with change.

You can change the width of the bonds as follows:

{|border="1" cellpadding="5" cellspacing="0" align="center"
|+ Settings for Licorice representation in VMD
!Before
! After
|-
|[[File:Licorice_std.png]]
VMD default settings
|[[File:Licorice_modified.png]]
Our default settings
|}

Please note there are many other model representations you can use.

===Model colour===

You can change the colour of your model under the Coloring method drop down menu and select "Color ID". A new drop down box will appear adjacent to Color ID (as shown below) which will allow you to choose various colours.

[[File:Color_modified.png]]

Alternatively by selecting "Element" under Coloring method the atoms will be coloured with the familiar CPK Coloring, inspired by CPK plastic molecular model kits by Corey, Pauling and Koltun.

CPK coloring conventionally depicts:

hydrogen as white,

carbon as black or grey,

nitrogen as blue,

oxygen as red,

phosphorus as orange, and

sulfur as yellow.

Other colors that are not always standard include:

green for magnesium and / or chlorine,

orange for iron, and

pink for unknown elements or those with atomic numbers over 57.

This can be used in conjunction with Drawing Method (CPK) to truly emulate our plastic model kits.

==Manipulating OpenGL Display==

===Changing the background colour===

In the VMD Main window navigate to:

<pre>Graphics => Colors</pre>

The following window will pop up:

[[File:OpenGL_display_colors.png]]

Under Categories => select Display, under Names => select Background and under Colors select your desired background colour.

===Resizing the OpenGL Display Window===

To resize the window, click the bottom right corner and drag to desired size.

As you can see, in the example below we can amend the representation of multiple files in order to make visualisation easier. If you want to learn HOW to overlay structures then click [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdVisual here].

[[File:Worked_example_final.png]]

Good times!!

==How to read the coordinates of selected atom==

Mouse => Query => then click the atom and read the information (atom name, index, coordinates) of the atom in terminal window.

Talk:Mod:Hunt Research Group/vmd

2014-10-24T08:12:30Z

Bw1911: /* how to change the graphical representation of your structures */

==Changing the graphical representation of your structures==

===Introduction===

When working in the Graphical representations box you should be aware that any changes made (as described below) will affect the file which is shown in the Selected molecule box. In order to be consistent any changes you make will need to be repeated for any other files you have loaded. This is particularly relevant when [//wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdVisual overlaying structures].

===Structure model===

The wireframe representation can be difficult to work with. A better representation is Licorice.

To change to this representation, navigate to the Drawing method drop down menu in the Graphical Representations window and select Licorice.

In the OpenGL Display you will notice the representation for the particular file you are working with change.

You can change the width of the bonds as follows:

{|border="1" cellpadding="5" cellspacing="0" align="center"
|+ Settings for Licorice representation in VMD
!Before
! After
|-
|[[File:Licorice_std.png]]
VMD default settings
|[[File:Licorice_modified.png]]
Our default settings
|}

Please note there are many other model representations you can use.

===Model colour===

You can change the colour of your model under the Coloring method drop down menu and select "Color ID". A new drop down box will appear adjacent to Color ID (as shown below) which will allow you to choose various colours.

[[File:Color_modified.png]]

Alternatively by selecting "Element" under Coloring method the atoms will be coloured with the familiar CPK Coloring, inspired by CPK plastic molecular model kits by Corey, Pauling and Koltun.

CPK coloring conventionally depicts:

hydrogen as white,

carbon as black or grey,

nitrogen as blue,

oxygen as red,

phosphorus as orange, and

sulfur as yellow.

Other colors that are not always standard include:

green for magnesium and / or chlorine,

orange for iron, and

pink for unknown elements or those with atomic numbers over 57.

This can be used in conjunction with Drawing Method (CPK) to truly emulate our plastic model kits.

==Manipulating OpenGL Display==

===Changing the background colour===

In the VMD Main window navigate to:

<pre>Graphics => Colors</pre>

The following window will pop up:

[[File:OpenGL_display_colors.png]]

Under Categories => select Display, under Names => select Background and under Colors select your desired background colour.

===Resizing the OpenGL Display Window===

To resize the window, click the bottom right corner and drag to desired size.

The worked example now looks like this:

[[File:Worked_example_final.png]]

Good times!!

==How to read the coordinates of selected atom==

Mouse => Query => then click the atom and read the information (atom name, index, coordinates) of the atom in terminal window.

Mod:Hunt Research Group

2014-10-24T08:07:43Z

Bw1911: /* Visualisation */

==Hunt Group Wiki==

Back to the main [http://www.ch.ic.ac.uk/hunt web-page]
===HPC Resources===
#Computing resources available in the chemistry department [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/computing_resources link]
#HPC servers and run scripts [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc link]
#Setting up a connection to HPC if you have a PC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_connections link]
#How to fix Windows files under UNIX [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Windowsfiles link]
#How to make ssh more comfortable [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpSSH link]
#How to make qsub more comfortable (gfunc) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpQSUB link]
#How to set up a SSH keypair [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/SSHkeyfile link]
#How to use gaussview directly on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gview link]
#How to comfortably search through old BASH commands [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/searchbash link]
#How to connect to HPC directory on desktop for file transfers [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_Directory_on_desktop link]
#How to set up cx2 [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cx2 link]

===Visualisation===
*'''ESPs'''
#Instructions for visualizing electrostatic potentials (Gaussview)[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials link]
#Electrostatic Potentials II (Molden) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials_2 link]
*'''VMD: a molecular dynamics visualisation package'''
#Download VMD [//wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/download_vmd link]
#Quick reminder [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDReminder link]
#Tricks and tips [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDTips link]
#Beginners guide to VMD [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/vmd link]
#Basic visualisation of a trajectory [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VisualisingyourSimulation link]
#How to turn a Gaussian optimization into a VMD movie [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/VMDmovie link]
#Using scripts in VMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScripts link]
#Dealing with periodic boundaries and bonding (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScriptsPeriodic link]
#Dealing with bonding (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdBonding link]
#Atom selection and more advanced GUI based visualisation (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdVisual link]
*'''JMol'''
#Visualising MOs using Jmol [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:basic_jmol_instructions link]
#Surfaces (Solvent-Accessible and Connolly) in Jmol [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/jmolsurfaces link]
*'''EMO Code'''
#How to use Ling's emo plot code[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emoplot link]
#How to plot EMOs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emo link]

===Gaussian General===
#A database of common errors encountered when running Gaussian jobs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gaussian_errors link]
# [http://www.ch.ic.ac.uk/hunt/g03_man/index.htm G03 Manual]
#How to run NBO5.9 on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/NBO5.9 link]
#How to include dispersion [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dispersion link]
#Basic ONIOM (Mechanical Embedding) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/basiconiom link]
#M0n and DFT-D [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/DFTD link]
#IL ONIOM clusters [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/oniomclusers link]
#Molecular volume calculations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/molecular_volume link]
#problems with scf convergence [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/scf_convergence link]

===Setup and Running Ab-Initio MD Simulations===
#CPMD: Car-Parrinello Molecular Dynamics [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd link]
#How to run CPMD to study aqueous solutions [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd_water link]
#How to run CP2K [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cp2k_how link]
#[bmim]Cl using CPMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/bmimCl_cpmd link]
#[bmim]Cl using CP2K [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/bmimCl_cp2k link]
#mman using CPMD and Gaussian [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/mman link]
#[emim]SCN using CP2K[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emimscn link]
#CP2K Donts [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cp2k link]

===Setup and Running Classical MD Simulations===
#DLPOLY a MD simulation package, Installation on an IMac (old needs to be updated) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dlpoly_install link]
#DL_POLY FAQs [http://www.stfc.ac.uk/cse/DL_POLY/ccp1gui/38621.aspx] from DL_POLY webpage.
#Packmol for generating starting configurations [http://www.ime.unicamp.br/~martinez/packmol/] from Packmol webpage.
#Getting started: generating a solvated structure and "relaxing" it [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Starting_MD link]
#local [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/packmol_to_dlpoly_scripts packmol to dlpoly] conversion scripts
#Getting the Force Field [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Wheretostart link]
#Choosing an Ensemble [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Ensembles link]
#Equilibration and production simulations [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/EquilibrationandProduction link]
#Energy Drift [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/EnergyDrift link]
#Voids in ILs[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/voids link]
#How to equilibrate an MD run[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/equilibration link]
#Equilibration of [bmim][BF4] and [bmim][NO3][https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/BmimBF4_equilibration link]
#Summary of discussions with Ruth[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Aug09QtoRuth link]

===Running QM/MM Simulations in ChemShell===
#ChemShell official website which contains the manual and a tutorial [http://www.stfc.ac.uk/CSE/randd/ccg/36254.aspx link]
#Introduction to ChemShell - Copper in water [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Introduction link]
#Defining the system: Cu2+ and its first 2 solvation shells [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_System_Aqeuous_Cu(II) link]
#Defining the force field parameters [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Force_Field_Parameters_Aqueous_Cu(II) link]
#Single point QM/MM energy calculation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_SP_Aqeuous_Cu(II) link]
#QM/MM Optimisation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_OPT_Aqeuous_Cu(II) link]
#QM/MM Molecular Dynamics [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_MD_Aqeuous_Cu(II) link]

===Research Notes===
#Cl- in water [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/wannier_centre link]
#The use of Legendre time correlation functions to study reorientational dynamics in liquids[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/legendre link]
#Functional for ILs using CPMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/IL_cpmd_functional link]
#Solving the angular part of the Schrödinger equation for a hydrogen atom [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/angular_schrodinger link] (notes by Vincent)
#Systematic conformational scan for ion-pair dimers [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ion_pair_scan link]

===Installing and using other packages===
#How to install POLYRATE [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/polyrate link]
#How to install Geomview [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/geomview link]
#XMGRACE, gfortran, c compilers for Lion [http://hpc.sourceforge.net/]

===Admin Stuff===
#Not used to writing a wiki, make your test runs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/testing on this page]
#How to set-up new macs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_setup link]
#How to set-up remote desktop [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_remote link]
#[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/calendar Calendar]
#Demonstrating in the 3rd year computational chemistry lab [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/compchemlab Timetable]
#How to switch the printer HP CP3525dn duplex on and off [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/printing link]

Mod:Hunt Research Group

2014-10-24T08:07:18Z

Bw1911: /* Visualisation */

==Hunt Group Wiki==

Back to the main [http://www.ch.ic.ac.uk/hunt web-page]
===HPC Resources===
#Computing resources available in the chemistry department [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/computing_resources link]
#HPC servers and run scripts [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc link]
#Setting up a connection to HPC if you have a PC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_connections link]
#How to fix Windows files under UNIX [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Windowsfiles link]
#How to make ssh more comfortable [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpSSH link]
#How to make qsub more comfortable (gfunc) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpQSUB link]
#How to set up a SSH keypair [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/SSHkeyfile link]
#How to use gaussview directly on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gview link]
#How to comfortably search through old BASH commands [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/searchbash link]
#How to connect to HPC directory on desktop for file transfers [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_Directory_on_desktop link]
#How to set up cx2 [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cx2 link]

===Visualisation===
*'''ESPs'''
#Instructions for visualizing electrostatic potentials (Gaussview)[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials link]
#Electrostatic Potentials II (Molden) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials_2 link]
*'''VMD: a molecular dynamics visualisation package'''
#Download VMD[//wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/download_vmd link]
#Quick reminder [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDReminder link]
#Tricks and tips [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDTips link]
#Beginners guide to VMD [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/vmd link]
#Basic visualisation of a trajectory [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VisualisingyourSimulation link]
#How to turn a Gaussian optimization into a VMD movie [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/VMDmovie link]
#Using scripts in VMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScripts link]
#Dealing with periodic boundaries and bonding (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScriptsPeriodic link]
#Dealing with bonding (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdBonding link]
#Atom selection and more advanced GUI based visualisation (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdVisual link]
*'''JMol'''
#Visualising MOs using Jmol [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:basic_jmol_instructions link]
#Surfaces (Solvent-Accessible and Connolly) in Jmol [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/jmolsurfaces link]
*'''EMO Code'''
#How to use Ling's emo plot code[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emoplot link]
#How to plot EMOs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emo link]

===Gaussian General===
#A database of common errors encountered when running Gaussian jobs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gaussian_errors link]
# [http://www.ch.ic.ac.uk/hunt/g03_man/index.htm G03 Manual]
#How to run NBO5.9 on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/NBO5.9 link]
#How to include dispersion [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dispersion link]
#Basic ONIOM (Mechanical Embedding) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/basiconiom link]
#M0n and DFT-D [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/DFTD link]
#IL ONIOM clusters [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/oniomclusers link]
#Molecular volume calculations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/molecular_volume link]
#problems with scf convergence [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/scf_convergence link]

===Setup and Running Ab-Initio MD Simulations===
#CPMD: Car-Parrinello Molecular Dynamics [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd link]
#How to run CPMD to study aqueous solutions [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd_water link]
#How to run CP2K [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cp2k_how link]
#[bmim]Cl using CPMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/bmimCl_cpmd link]
#[bmim]Cl using CP2K [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/bmimCl_cp2k link]
#mman using CPMD and Gaussian [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/mman link]
#[emim]SCN using CP2K[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emimscn link]
#CP2K Donts [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cp2k link]

===Setup and Running Classical MD Simulations===
#DLPOLY a MD simulation package, Installation on an IMac (old needs to be updated) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dlpoly_install link]
#DL_POLY FAQs [http://www.stfc.ac.uk/cse/DL_POLY/ccp1gui/38621.aspx] from DL_POLY webpage.
#Packmol for generating starting configurations [http://www.ime.unicamp.br/~martinez/packmol/] from Packmol webpage.
#Getting started: generating a solvated structure and "relaxing" it [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Starting_MD link]
#local [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/packmol_to_dlpoly_scripts packmol to dlpoly] conversion scripts
#Getting the Force Field [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Wheretostart link]
#Choosing an Ensemble [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Ensembles link]
#Equilibration and production simulations [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/EquilibrationandProduction link]
#Energy Drift [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/EnergyDrift link]
#Voids in ILs[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/voids link]
#How to equilibrate an MD run[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/equilibration link]
#Equilibration of [bmim][BF4] and [bmim][NO3][https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/BmimBF4_equilibration link]
#Summary of discussions with Ruth[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Aug09QtoRuth link]

===Running QM/MM Simulations in ChemShell===
#ChemShell official website which contains the manual and a tutorial [http://www.stfc.ac.uk/CSE/randd/ccg/36254.aspx link]
#Introduction to ChemShell - Copper in water [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Introduction link]
#Defining the system: Cu2+ and its first 2 solvation shells [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_System_Aqeuous_Cu(II) link]
#Defining the force field parameters [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Force_Field_Parameters_Aqueous_Cu(II) link]
#Single point QM/MM energy calculation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_SP_Aqeuous_Cu(II) link]
#QM/MM Optimisation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_OPT_Aqeuous_Cu(II) link]
#QM/MM Molecular Dynamics [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_MD_Aqeuous_Cu(II) link]

===Research Notes===
#Cl- in water [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/wannier_centre link]
#The use of Legendre time correlation functions to study reorientational dynamics in liquids[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/legendre link]
#Functional for ILs using CPMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/IL_cpmd_functional link]
#Solving the angular part of the Schrödinger equation for a hydrogen atom [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/angular_schrodinger link] (notes by Vincent)
#Systematic conformational scan for ion-pair dimers [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ion_pair_scan link]

===Installing and using other packages===
#How to install POLYRATE [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/polyrate link]
#How to install Geomview [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/geomview link]
#XMGRACE, gfortran, c compilers for Lion [http://hpc.sourceforge.net/]

===Admin Stuff===
#Not used to writing a wiki, make your test runs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/testing on this page]
#How to set-up new macs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_setup link]
#How to set-up remote desktop [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_remote link]
#[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/calendar Calendar]
#Demonstrating in the 3rd year computational chemistry lab [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/compchemlab Timetable]
#How to switch the printer HP CP3525dn duplex on and off [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/printing link]

Talk:Mod:Hunt Research Group/download vmd

2014-10-24T08:06:45Z

Bw1911: Created page with "=Downloading VMD= VMD can be installed from the [http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD VMD downloads page]"

=Downloading VMD=
VMD can be installed from the [http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD VMD downloads page]

Talk:Mod:Hunt Research Group/vmd

2014-10-24T08:03:12Z

Bw1911:

==how to change the graphical representation of your structures==

===Introduction===

When working in the Graphical representations box you should be aware that any changes made (as described below) will affect the file which is shown in the Selected molecule box. In order to be consistent any changes you make will need to be repeated for any other files you have loaded. This is particularly relevant when [//wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdVisual overlaying structures].

===Structure model===

The wireframe representation can be difficult to work with. A better representation is Licorice.

To change to this representation, navigate to the Drawing method drop down menu in the Graphical Representations window and select Licorice.

In the OpenGL Display you will notice the representation for the particular file you are working with change.

You can change the width of the bonds as follows:

{|border="1" cellpadding="5" cellspacing="0" align="center"
|+ Settings for Licorice representation in VMD
!Before
! After
|-
|[[File:Licorice_std.png]]
VMD default settings
|[[File:Licorice_modified.png]]
Our default settings
|}

Please note there are many other model representations you can use.

===Model colour===

You can change the colour of your model under the Coloring method drop down menu and select "Color ID". A new drop down box will appear adjacent to Color ID (as shown below) which will allow you to choose various colours.

[[File:Color_modified.png]]

Alternatively by selecting "Element" under Coloring method the atoms will be coloured with the familiar CPK Coloring, inspired by CPK plastic molecular model kits by Corey, Pauling and Koltun.

CPK coloring conventionally depicts:

hydrogen as white,

carbon as black or grey,

nitrogen as blue,

oxygen as red,

phosphorus as orange, and

sulfur as yellow.

Other colors that are not always standard include:

green for magnesium and / or chlorine,

orange for iron, and

pink for unknown elements or those with atomic numbers over 57.

This can be used in conjunction with Drawing Method (CPK) to truly emulate our plastic model kits.

==Manipulating OpenGL Display==

===Changing the background colour===

In the VMD Main window navigate to:

<pre>Graphics => Colors</pre>

The following window will pop up:

[[File:OpenGL_display_colors.png]]

Under Categories => select Display, under Names => select Background and under Colors select your desired background colour.

===Resizing the OpenGL Display Window===

To resize the window, click the bottom right corner and drag to desired size.

The worked example now looks like this:

[[File:Worked_example_final.png]]

Good times!!

==How to read the coordinates of selected atom==

Mouse => Query => then click the atom and read the information (atom name, index, coordinates) of the atom in terminal window.

Mod:Hunt Research Group

2014-10-24T07:59:41Z

Bw1911: /* Visualisation */

==Hunt Group Wiki==

Back to the main [http://www.ch.ic.ac.uk/hunt web-page]
===HPC Resources===
#Computing resources available in the chemistry department [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/computing_resources link]
#HPC servers and run scripts [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc link]
#Setting up a connection to HPC if you have a PC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_connections link]
#How to fix Windows files under UNIX [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Windowsfiles link]
#How to make ssh more comfortable [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpSSH link]
#How to make qsub more comfortable (gfunc) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpQSUB link]
#How to set up a SSH keypair [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/SSHkeyfile link]
#How to use gaussview directly on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gview link]
#How to comfortably search through old BASH commands [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/searchbash link]
#How to connect to HPC directory on desktop for file transfers [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_Directory_on_desktop link]
#How to set up cx2 [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cx2 link]

===Visualisation===
*'''ESPs'''
#Instructions for visualizing electrostatic potentials (Gaussview)[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials link]
#Electrostatic Potentials II (Molden) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials_2 link]
*'''VMD: a molecular dynamics visualisation package'''
#Download VMD
#Quick reminder [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDReminder link]
#Tricks and tips [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDTips link]
#Beginners guide to VMD [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/vmd link]
#Basic visualisation of a trajectory [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VisualisingyourSimulation link]
#How to turn a Gaussian optimization into a VMD movie [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/VMDmovie link]
#Using scripts in VMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScripts link]
#Dealing with periodic boundaries and bonding (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScriptsPeriodic link]
#Dealing with bonding (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdBonding link]
#Atom selection and more advanced GUI based visualisation (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdVisual link]
*'''JMol'''
#Visualising MOs using Jmol [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:basic_jmol_instructions link]
#Surfaces (Solvent-Accessible and Connolly) in Jmol [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/jmolsurfaces link]
*'''EMO Code'''
#How to use Ling's emo plot code[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emoplot link]
#How to plot EMOs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emo link]

===Gaussian General===
#A database of common errors encountered when running Gaussian jobs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gaussian_errors link]
# [http://www.ch.ic.ac.uk/hunt/g03_man/index.htm G03 Manual]
#How to run NBO5.9 on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/NBO5.9 link]
#How to include dispersion [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dispersion link]
#Basic ONIOM (Mechanical Embedding) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/basiconiom link]
#M0n and DFT-D [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/DFTD link]
#IL ONIOM clusters [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/oniomclusers link]
#Molecular volume calculations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/molecular_volume link]
#problems with scf convergence [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/scf_convergence link]

===Setup and Running Ab-Initio MD Simulations===
#CPMD: Car-Parrinello Molecular Dynamics [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd link]
#How to run CPMD to study aqueous solutions [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd_water link]
#How to run CP2K [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cp2k_how link]
#[bmim]Cl using CPMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/bmimCl_cpmd link]
#[bmim]Cl using CP2K [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/bmimCl_cp2k link]
#mman using CPMD and Gaussian [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/mman link]
#[emim]SCN using CP2K[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emimscn link]
#CP2K Donts [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cp2k link]

===Setup and Running Classical MD Simulations===
#DLPOLY a MD simulation package, Installation on an IMac (old needs to be updated) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dlpoly_install link]
#DL_POLY FAQs [http://www.stfc.ac.uk/cse/DL_POLY/ccp1gui/38621.aspx] from DL_POLY webpage.
#Packmol for generating starting configurations [http://www.ime.unicamp.br/~martinez/packmol/] from Packmol webpage.
#Getting started: generating a solvated structure and "relaxing" it [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Starting_MD link]
#local [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/packmol_to_dlpoly_scripts packmol to dlpoly] conversion scripts
#Getting the Force Field [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Wheretostart link]
#Choosing an Ensemble [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Ensembles link]
#Equilibration and production simulations [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/EquilibrationandProduction link]
#Energy Drift [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/EnergyDrift link]
#Voids in ILs[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/voids link]
#How to equilibrate an MD run[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/equilibration link]
#Equilibration of [bmim][BF4] and [bmim][NO3][https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/BmimBF4_equilibration link]
#Summary of discussions with Ruth[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Aug09QtoRuth link]

===Running QM/MM Simulations in ChemShell===
#ChemShell official website which contains the manual and a tutorial [http://www.stfc.ac.uk/CSE/randd/ccg/36254.aspx link]
#Introduction to ChemShell - Copper in water [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Introduction link]
#Defining the system: Cu2+ and its first 2 solvation shells [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_System_Aqeuous_Cu(II) link]
#Defining the force field parameters [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Force_Field_Parameters_Aqueous_Cu(II) link]
#Single point QM/MM energy calculation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_SP_Aqeuous_Cu(II) link]
#QM/MM Optimisation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_OPT_Aqeuous_Cu(II) link]
#QM/MM Molecular Dynamics [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_MD_Aqeuous_Cu(II) link]

===Research Notes===
#Cl- in water [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/wannier_centre link]
#The use of Legendre time correlation functions to study reorientational dynamics in liquids[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/legendre link]
#Functional for ILs using CPMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/IL_cpmd_functional link]
#Solving the angular part of the Schrödinger equation for a hydrogen atom [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/angular_schrodinger link] (notes by Vincent)
#Systematic conformational scan for ion-pair dimers [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ion_pair_scan link]

===Installing and using other packages===
#How to install POLYRATE [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/polyrate link]
#How to install Geomview [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/geomview link]
#XMGRACE, gfortran, c compilers for Lion [http://hpc.sourceforge.net/]

===Admin Stuff===
#Not used to writing a wiki, make your test runs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/testing on this page]
#How to set-up new macs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_setup link]
#How to set-up remote desktop [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_remote link]
#[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/calendar Calendar]
#Demonstrating in the 3rd year computational chemistry lab [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/compchemlab Timetable]
#How to switch the printer HP CP3525dn duplex on and off [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/printing link]

Mod:Hunt Research Group

2014-10-24T07:58:33Z

Bw1911: /* Visualisation */

==Hunt Group Wiki==

Back to the main [http://www.ch.ic.ac.uk/hunt web-page]
===HPC Resources===
#Computing resources available in the chemistry department [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/computing_resources link]
#HPC servers and run scripts [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc link]
#Setting up a connection to HPC if you have a PC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_connections link]
#How to fix Windows files under UNIX [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Windowsfiles link]
#How to make ssh more comfortable [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpSSH link]
#How to make qsub more comfortable (gfunc) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpQSUB link]
#How to set up a SSH keypair [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/SSHkeyfile link]
#How to use gaussview directly on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gview link]
#How to comfortably search through old BASH commands [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/searchbash link]
#How to connect to HPC directory on desktop for file transfers [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_Directory_on_desktop link]
#How to set up cx2 [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cx2 link]

===Visualisation===
*'''ESPs'''
#Instructions for visualizing electrostatic potentials (Gaussview)[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials link]
#Electrostatic Potentials II (Molden) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials_2 link]
*'''VMD: a molecular dynamics visualisation package'''
#Quick remdiner [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDReminder link]
#Tricks and tips [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDTips link]
#Beginners guide to VMD [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/vmd link]
#Basic visualisation of a trajectory [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VisualisingyourSimulation link]
#How to turn a Gaussian optimization into a VMD movie [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/VMDmovie link]
#Using scripts in VMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScripts link]
#Dealing with periodic boundaries and bonding (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScriptsPeriodic link]
#Dealing with bonding (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdBonding link]
#Atom selection and more advanced GUI based visualisation (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdVisual link]
*'''JMol'''
#Visualising MOs using Jmol [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:basic_jmol_instructions link]
#Surfaces (Solvent-Accessible and Connolly) in Jmol [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/jmolsurfaces link]
*'''EMO Code'''
#How to use Ling's emo plot code[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emoplot link]
#How to plot EMOs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emo link]

===Gaussian General===
#A database of common errors encountered when running Gaussian jobs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gaussian_errors link]
# [http://www.ch.ic.ac.uk/hunt/g03_man/index.htm G03 Manual]
#How to run NBO5.9 on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/NBO5.9 link]
#How to include dispersion [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dispersion link]
#Basic ONIOM (Mechanical Embedding) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/basiconiom link]
#M0n and DFT-D [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/DFTD link]
#IL ONIOM clusters [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/oniomclusers link]
#Molecular volume calculations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/molecular_volume link]
#problems with scf convergence [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/scf_convergence link]

===Setup and Running Ab-Initio MD Simulations===
#CPMD: Car-Parrinello Molecular Dynamics [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd link]
#How to run CPMD to study aqueous solutions [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd_water link]
#How to run CP2K [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cp2k_how link]
#[bmim]Cl using CPMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/bmimCl_cpmd link]
#[bmim]Cl using CP2K [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/bmimCl_cp2k link]
#mman using CPMD and Gaussian [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/mman link]
#[emim]SCN using CP2K[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emimscn link]
#CP2K Donts [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cp2k link]

===Setup and Running Classical MD Simulations===
#DLPOLY a MD simulation package, Installation on an IMac (old needs to be updated) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dlpoly_install link]
#DL_POLY FAQs [http://www.stfc.ac.uk/cse/DL_POLY/ccp1gui/38621.aspx] from DL_POLY webpage.
#Packmol for generating starting configurations [http://www.ime.unicamp.br/~martinez/packmol/] from Packmol webpage.
#Getting started: generating a solvated structure and "relaxing" it [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Starting_MD link]
#local [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/packmol_to_dlpoly_scripts packmol to dlpoly] conversion scripts
#Getting the Force Field [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Wheretostart link]
#Choosing an Ensemble [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Ensembles link]
#Equilibration and production simulations [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/EquilibrationandProduction link]
#Energy Drift [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/EnergyDrift link]
#Voids in ILs[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/voids link]
#How to equilibrate an MD run[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/equilibration link]
#Equilibration of [bmim][BF4] and [bmim][NO3][https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/BmimBF4_equilibration link]
#Summary of discussions with Ruth[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Aug09QtoRuth link]

===Running QM/MM Simulations in ChemShell===
#ChemShell official website which contains the manual and a tutorial [http://www.stfc.ac.uk/CSE/randd/ccg/36254.aspx link]
#Introduction to ChemShell - Copper in water [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Introduction link]
#Defining the system: Cu2+ and its first 2 solvation shells [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_System_Aqeuous_Cu(II) link]
#Defining the force field parameters [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Force_Field_Parameters_Aqueous_Cu(II) link]
#Single point QM/MM energy calculation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_SP_Aqeuous_Cu(II) link]
#QM/MM Optimisation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_OPT_Aqeuous_Cu(II) link]
#QM/MM Molecular Dynamics [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_MD_Aqeuous_Cu(II) link]

===Research Notes===
#Cl- in water [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/wannier_centre link]
#The use of Legendre time correlation functions to study reorientational dynamics in liquids[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/legendre link]
#Functional for ILs using CPMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/IL_cpmd_functional link]
#Solving the angular part of the Schrödinger equation for a hydrogen atom [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/angular_schrodinger link] (notes by Vincent)
#Systematic conformational scan for ion-pair dimers [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ion_pair_scan link]

===Installing and using other packages===
#How to install POLYRATE [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/polyrate link]
#How to install Geomview [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/geomview link]
#XMGRACE, gfortran, c compilers for Lion [http://hpc.sourceforge.net/]

===Admin Stuff===
#Not used to writing a wiki, make your test runs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/testing on this page]
#How to set-up new macs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_setup link]
#How to set-up remote desktop [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_remote link]
#[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/calendar Calendar]
#Demonstrating in the 3rd year computational chemistry lab [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/compchemlab Timetable]
#How to switch the printer HP CP3525dn duplex on and off [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/printing link]

Talk:Mod:Hunt Research Group/vmd

2014-10-24T07:51:45Z

Bw1911: /* Introduction */

=Beginners Guide to VMD=

VMD can be installed from the [http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD VMD downloads page]
==Changing the graphical representation of your structures==

===Introduction===

When working in the Graphical representations box you should be aware that any changes made (as described below) will affect the file which is shown in the Selected molecule box. In order to be consistent any changes you make will need to be repeated for any other files you have loaded. This is particularly relevant when [//wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdVisual overlaying structures].

===Structure model===

The wireframe representation can be difficult to work with. A better representation is Licorice.

To change to this representation, navigate to the Drawing method drop down menu in the Graphical Representations window and select Licorice.

In the OpenGL Display you will notice the representation for the particular file you are working with change.

You can change the width of the bonds as follows:

{|border="1" cellpadding="5" cellspacing="0" align="center"
|+ Settings for Licorice representation in VMD
!Before
! After
|-
|[[File:Licorice_std.png]]
VMD default settings
|[[File:Licorice_modified.png]]
Our default settings
|}

Please note there are many other model representations you can use.

===Model colour===

You can change the colour of your model under the Coloring method drop down menu and select "Color ID". A new drop down box will appear adjacent to Color ID (as shown below) which will allow you to choose various colours.

[[File:Color_modified.png]]

Alternatively by selecting "Element" under Coloring method the atoms will be coloured with the familiar CPK Coloring, inspired by CPK plastic molecular model kits by Corey, Pauling and Koltun.

CPK coloring conventionally depicts:

hydrogen as white,

carbon as black or grey,

nitrogen as blue,

oxygen as red,

phosphorus as orange, and

sulfur as yellow.

Other colors that are not always standard include:

green for magnesium and / or chlorine,

orange for iron, and

pink for unknown elements or those with atomic numbers over 57.

This can be used in conjunction with Drawing Method (CPK) to truly emulate our plastic model kits.

==Manipulating OpenGL Display==

===Changing the background colour===

In the VMD Main window navigate to:

<pre>Graphics => Colors</pre>

The following window will pop up:

[[File:OpenGL_display_colors.png]]

Under Categories => select Display, under Names => select Background and under Colors select your desired background colour.

===Resizing the OpenGL Display Window===

To resize the window, click the bottom right corner and drag to desired size.

The worked example now looks like this:

[[File:Worked_example_final.png]]

Good times!!

==How to read the coordinates of selected atom==

Mouse => Query => then click the atom and read the information (atom name, index, coordinates) of the atom in terminal window.

Talk:Mod:Hunt Research Group/vmd

2014-10-24T07:51:23Z

Bw1911: /* Changing the graphical representation of your structures */

=Beginners Guide to VMD=

VMD can be installed from the [http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD VMD downloads page]
==Changing the graphical representation of your structures==

===Introduction===

When working in the Graphical representations box you should be aware that any changes made (as described below) will affect the file which is shown in the Selected molecule box. In order to be consistent any changes you make will need to be repeated for any other files you have loaded. This is particularly relevant when [//wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdVisual link overlaying structures].

===Structure model===

The wireframe representation can be difficult to work with. A better representation is Licorice.

To change to this representation, navigate to the Drawing method drop down menu in the Graphical Representations window and select Licorice.

In the OpenGL Display you will notice the representation for the particular file you are working with change.

You can change the width of the bonds as follows:

{|border="1" cellpadding="5" cellspacing="0" align="center"
|+ Settings for Licorice representation in VMD
!Before
! After
|-
|[[File:Licorice_std.png]]
VMD default settings
|[[File:Licorice_modified.png]]
Our default settings
|}

Please note there are many other model representations you can use.

===Model colour===

You can change the colour of your model under the Coloring method drop down menu and select "Color ID". A new drop down box will appear adjacent to Color ID (as shown below) which will allow you to choose various colours.

[[File:Color_modified.png]]

Alternatively by selecting "Element" under Coloring method the atoms will be coloured with the familiar CPK Coloring, inspired by CPK plastic molecular model kits by Corey, Pauling and Koltun.

CPK coloring conventionally depicts:

hydrogen as white,

carbon as black or grey,

nitrogen as blue,

oxygen as red,

phosphorus as orange, and

sulfur as yellow.

Other colors that are not always standard include:

green for magnesium and / or chlorine,

orange for iron, and

pink for unknown elements or those with atomic numbers over 57.

This can be used in conjunction with Drawing Method (CPK) to truly emulate our plastic model kits.

==Manipulating OpenGL Display==

===Changing the background colour===

In the VMD Main window navigate to:

<pre>Graphics => Colors</pre>

The following window will pop up:

[[File:OpenGL_display_colors.png]]

Under Categories => select Display, under Names => select Background and under Colors select your desired background colour.

===Resizing the OpenGL Display Window===

To resize the window, click the bottom right corner and drag to desired size.

The worked example now looks like this:

[[File:Worked_example_final.png]]

Good times!!

==How to read the coordinates of selected atom==

Mouse => Query => then click the atom and read the information (atom name, index, coordinates) of the atom in terminal window.

Talk:Mod:Hunt Research Group/VmdVisual

2014-10-24T07:38:23Z

Bw1911: /* how to overlay two structures for comparison */

=More Advance Visualisation=

==how to overlay two structures for comparison==

===Introduction===

In this example we will compare the same complex optimized using different DFT functionals. The complex in question is a calcium ß-diketiminate complex with a bound alkyl phosphine substrate.

===Loading molecule files===

VMD can use many file types however the file type required in this instance is .xyz

In the VMD Main window, navigate to:

<pre>File => New Molecule</pre>

This will prompt the Molecule File Browser to load.

[[File:Molecule_file_browser.png]]

To load the first file click "Browse" and navigate to the location of your first file. It is handy if the first file loaded is your reference structure.

You will see the in the Load files for: box, in the Molecule File Browser, now reads 0:filename and a wireframe image has appeared in the OpenGL Display.

Every additional file must be loaded as a New molecule. To do this, press the arrow in the "Load files for" box. Select "New molecule" and repeat the procedure above for your remaining files.

===Overlaying Structures===

You will now notice in the OpenGL Display that the overlaid images are in disarray.

[[File:OpenGL_with_misaligned_structs.png]]

In order to superimpose the images on top of one another use the following procedure.

In the VMD Main window navigate to:

<pre>Graphics => Representations</pre>

The following window will pop up

[[File:Graphical_representations_window.png]]

We can use the Graphical Representations window to temporarily remove two of the overlaid images to leave our reference image. To do this in the Selected Molecule box select one of the files you wish to temporarily remove then in the Style Color Selection box double click the Lines Name all entry.

If done correctly the colour of the font in Lines Name all should turn red. You should also notice the structure corresponding to the file is no longer displayed in the OpenGL Display.

Repeat this procedure for the remaining files until you are left with the reference geometry in the OpenGL Display.

In order to superimpose the structures correctly you need a point of reference in the structure which all the additional representations will be aligned to.

Your reference point in the reference structure needs to be a region whihc is least likely to change from one representation to another. In this worked example, the 3 atoms in the backbone of the complex will act as the reference point.

[[File:OpenGL_with_atom_labels.png]]

Next we need the atom numbers corresponding to the reference point in the structure. To do this first ensure you are working in the OpenGL Display window.

Press "1" on the keyboard. You will know if this has happened correctly as the mouse arrow should change to a crosshair. Using the crosshair, click the atoms which you wish to act as your reference point in the structure. As you select the atoms, green text will appear beside the atom (as shown in the image above.

Now in the VMD Main window, navigate to:

<pre>Graphics => Labels</pre>

The following labels window will appear on screen

[[File:Labels_window.png]]

This window will display information on the atoms selected.

The information we require is found in the index box. As you select each label you will notice the index number changes. These numbers correspond to the atom numbering within your xyz file. Take a note of the index numbers.

In the VMD Main window navigate to:

<pre>Extensions => Analysis => RMSD Calculator</pre>

The following window will appear:

[[File:RMSD_tool_window_std.png]]

Using the index information type the following information into the box which is currently filled with residue # to #

<pre>index first index no. or index second index no. or index third index no. or index fourth index no.</pre>

and so forth. This entry will depend on how many numbers you decide to use as a reference.

In the worked example, the entry is as follows:

<pre>index 7 or index 9 or index 10</pre>

Once you have added this text press enter.

Now untick the backbone only box, and select Selected (this will deselect Top). Finally in ID molecule click on your reference file.

Once you are finished the window should resemble something like this:

[[File:RMSD_tool_modified.png]]

Now press Align.... it will appear as if nothing has happened

Return to your Graphical Representations window and unhide the representations you hid earlier. (Select the file you hid in Selected Molecule box and double click Lines Name all whereby the font should turn from red to black.

<strike>Hopefully</strike> In the OpenGL display window you should observe the structures align to your chosen reference atoms as displayed in the table below under 'After'.

{|border="1" cellpadding="5" cellspacing="0" align="center"
|+
!Before
! After
|-
|[[File:OpenGL_with_misaligned_structs.png]]
|[[File:OpenGL_with_aligned_structs.png]]
|}

If you still have green text next to your reference atoms, return to the Labels window, select the label and press delete.

===Troubleshooting===

*The aligning of the structures can be a little temperamental. You may need to press the align button more than once.
*The quality of alignment is dependent on the number of atoms you use as your reference. (Use a minimum of three??)
*No amount of "Align" button pressing will overlay structures correctly when the numbering of your atoms in the files are different from one another. The atom numbering must be consistent in all files.

==how to visualise a selection of atoms within radial distance of a selected molecule/atom==

*make a selection within a certain radius
::under GRAPHICAL_REP:SELECTIONS type "within x.xx of element Y) and name "Z"
::ADDREP
::this will select the atoms of name Z within x.xx angstrom of element Y
::you can then colour these atoms differently (and or make their VDW spheres larger/smaller)
::for example use COLOURID

*The clipping can not be what you want
::play around with the following in the TK console
::display nearclip set 10.000000
::display nearclip set 0.000000

Talk:Mod:Hunt Research Group/vmd

2014-10-24T07:37:04Z

Bw1911:

=Beginners Guide to VMD=

VMD can be installed from the [http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD VMD downloads page]
==Changing the graphical representation of your structures==

When working in the Graphical representations box you should be aware that any changes made (as described below) will affect the file which is shown in the Selected molecule box. In order to be consistent any changes you make will need to be repeated for any other files you have loaded.

===Structure model===

The wireframe representation can be difficult to work with. A better representation is Licorice.

To change to this representation, navigate to the Drawing method drop down menu in the Graphical Representations window and select Licorice.

In the OpenGL Display you will notice the representation for the particular file you are working with change.

You can change the width of the bonds as follows:

{|border="1" cellpadding="5" cellspacing="0" align="center"
|+ Settings for Licorice representation in VMD
!Before
! After
|-
|[[File:Licorice_std.png]]
VMD default settings
|[[File:Licorice_modified.png]]
Our default settings
|}

Please note there are many other model representations you can use.

===Model colour===

You can change the colour of your model under the Coloring method drop down menu and select "Color ID". A new drop down box will appear adjacent to Color ID (as shown below) which will allow you to choose various colours.

[[File:Color_modified.png]]

Alternatively by selecting "Element" under Coloring method the atoms will be coloured with the familiar CPK Coloring, inspired by CPK plastic molecular model kits by Corey, Pauling and Koltun.

CPK coloring conventionally depicts:

hydrogen as white,

carbon as black or grey,

nitrogen as blue,

oxygen as red,

phosphorus as orange, and

sulfur as yellow.

Other colors that are not always standard include:

green for magnesium and / or chlorine,

orange for iron, and

pink for unknown elements or those with atomic numbers over 57.

This can be used in conjunction with Drawing Method (CPK) to truly emulate our plastic model kits.

==Manipulating OpenGL Display==

===Changing the background colour===

In the VMD Main window navigate to:

<pre>Graphics => Colors</pre>

The following window will pop up:

[[File:OpenGL_display_colors.png]]

Under Categories => select Display, under Names => select Background and under Colors select your desired background colour.

===Resizing the OpenGL Display Window===

To resize the window, click the bottom right corner and drag to desired size.

The worked example now looks like this:

[[File:Worked_example_final.png]]

Good times!!

==How to read the coordinates of selected atom==

Mouse => Query => then click the atom and read the information (atom name, index, coordinates) of the atom in terminal window.

Mod:Hunt Research Group/calendar

2014-06-24T20:43:13Z

Bw1911:

== Calendar ==

*Tricia (Not Done)
*Abdihakim Hassan (Not Done)
*Bryan Ward (Not Done)
*Claire Ashworth (Not Done)
*Matthew Clough (Not Done)
*Precious Ugbomah (Not Done)
*Richard Matthews (Not Done)
*Vincent Chen (Not Done)
*Gabriel Lau (Not Done)
*Rebecca Rowe (Not Done)
*Patricia Ho (Done)
*Giacomo Damilano (Not Done)
*Richard Fogarty (Not Done)

<table border="1" cellpadding="5" width="1190">
<tr bgcolor="#66CCFF">
<th width="170px">Mon</th>
<th width="170px">Tues</th>
<th width="170px">Wed</th>
<th width="170px">Thur</th>
<th width="170px">Fri</th>
<th width="170px" bgcolor="#CCCCCC">Sat</th>
<th width="170px" bgcolor="#CCCCCC">Sun</th>
<tr valign="top">
<td bgcolor="#339933">26th '''College closed''' '''Bank holiday'''</td>
<td >27th </td>
<td>28th </td>
<td>29th </td>
<td>30th (Giacomo Away)</td>
<td bgcolor="#CCCCCC">31st </td>
<td bgcolor="#4357CFF">1st June (Giacomo Away) </td>
</tr>
<tr valign="top">
<td>2nd (Giacomo Away)</td>
<td>3rd '''(Richard F - paper)''' (Giacomo Away)</td>
<td>4th CECAM workshop Claire away (Giacomo Away) (Patricia away)</td>
<td>5th CECAM workshop Claire away (Patricia away) (Giacomo Away) (Richard F away)</td>
<td>6th CECAM workshop Claire away (Patricia away)</td>
<td bgcolor="#CCCCCC">7th </td>
<td bgcolor="#CCCCCC">8th </td>
</tr>
<tr valign="top">
<td>9th </td>
<td>10th '''(Matt - paper)'''</td>
<td>11th </td>
<td>12th </td>
<td>13th </td>
<td bgcolor="#CCCCCC">14th </td>
<td bgcolor="#CCCCCC">15th </td>
</tr>
<tr valign="top">
<td>16th LIBLICE conference-Gabriel </td>
<td>17th '''(Hakim-presentation practice)''' LIBLICE conference-Gabriel </td>
<td>18th LIBLICE conference-Gabriel </td>
<td>19th LIBLICE conference-Gabriel </td>
<td>20th LIBLICE conference-Gabriel </td>
<td bgcolor="#CCCCCC">21st </td>
<td bgcolor="#CCCCCC">22nd </td>
</tr>
<tr valign="top">
<td>23rd </td>
<td>24th </td>
<td>25th </td>
<td>26th '''(Talk practice)'''</td>
<td bgcolor="#FFA500">27th '''End of term'''</td>
<td bgcolor="#CCCCCC">28th </td>
<td bgcolor="#CCCCCC">29th </td>
</tr>
<tr valign="top">
<td>30th (Richard F away)</td>
<td bgcolor="#4357CFF" >1st July {{fontcolor|#FFD700|'''PhD Symposium (Chem.)'''}} (Richard F away)</td>
<td>2nd (Richard F away)</td>
<td>3rd </td>
<td>4th </td>
<td bgcolor="#CCCCCC">5th </td>
<td bgcolor="#CCCCCC">6th EUCHEM-Richard & Claire</td>
</tr>
<tr valign="top">
<td>7th Bryan Away EUCHEM-Richard&Claire</td>
<td>8th Bryan Away EUCHEM-Richard & Claire</td>
<td>9th Bryan Away EUCHEM-Richard & Claire</td>
<td>10th Bryan Away EUCHEM-Richard & Claire</td>
<td>11th Bryan Away EUCHEM-Richard & Claire</td>
<td bgcolor="#CCCCCC">12th </td>
<td bgcolor="#CCCCCC">13th </td>
</tr>
<tr valign="top">
<td>14th Bryan Away Richard away Claire away</td>
<td>15th Bryan Away Richard away Claire away</td>
<td>16th Bryan Away Richard away Claire away</td>
<td>17th Bryan Away Richard away Claire away</td>
<td>18th Bryan Away Richard away Claire away</td>
<td bgcolor="#CCCCCC">19th </td>
<td bgcolor="#CCCCCC">20th </td>
</tr>
<tr valign="top">
<td>21st Liquid Matter-Gabriel</td>
<td>22nd Liquid Matter-Gabriel</td>
<td>23rd Gaussian workshop - Claire & Bryan Liquid Matter-Gabriel</td>
<td>24th Gaussian workshop - Claire & Bryan Liquid Matter-Gabriel </td>
<td>25th Liquid Matter-Gabriel </td>
<td bgcolor="#CCCCCC">26th </td>
<td bgcolor="#CCCCCC">27th </td>
</tr>
<tr valign="top">
<td>28th </td>
<td>29th </td>
<td>30th </td>
<td>31st Bryan Away </td>
<td bgcolor="#4357CFF">1st August Bryan Away </td>
<td bgcolor="#CCCCCC">2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
</tr>
<tr valign="top">
<td>4th Bryan on hiatus </td>
<td>5th Bryan on hiatus </td>
<td>6th Bryan on hiatus </td>
<td>7th Bryan on hiatus </td>
<td>8th Bryan on hiatus </td>
<td bgcolor="#CCCCCC">9th </td>
<td bgcolor="#CCCCCC">10th </td>
</tr>
<tr valign="top">
<td>11th Bryan on hiatus </td>
<td>12th Bryan on hiatus </td>
<td>13th Bryan on hiatus </td>
<td>14th Bryan on hiatus </td>
<td>15th Bryan on hiatus </td>
<td bgcolor="#CCCCCC">16th </td>
<td bgcolor="#CCCCCC">17th </td>
</tr>
<tr valign="top">
<td>18th Bryan on hiatus </td>
<td>19th Bryan on hiatus </td>
<td>20th Bryan on hiatus </td>
<td>21st Bryan on hiatus </td>
<td>22nd Bryan on hiatus </td>
<td bgcolor="#CCCCCC">23rd </td>
<td bgcolor="#CCCCCC">24th </td>
</tr>
<tr valign="top">
<td bgcolor="#339933">25th '''College closed''' '''Bank holiday'''</td>
<td>26th Bryan on hiatus </td>
<td>27th Bryan on hiatus </td>
<td>28th Bryan on hiatus </td>
<td>39th Bryan on hiatus </td>
<td bgcolor="#CCCCCC">30th </td>
<td bgcolor="#CCCCCC">31st </td>
</tr>
<tr valign="top">
<td bgcolor="#4357CFF">1st September Bryan on hiatus </td>
<td>2nd Bryan on hiatus </td>
<td>3rd Bryan on hiatus </td>
<td>4th Bryan on hiatus </td>
<td>5th Bryan on hiatus </td>
<td bgcolor="#CCCCCC">6th </td>
<td bgcolor="#CCCCCC">7th </td>
</tr>
<tr valign="top">
<td>8th </td>
<td>9th </td>
<td>10th </td>
<td>11th </td>
<td>12th </td>
<td bgcolor="#CCCCCC">13th </td>
<td bgcolor="#CCCCCC">14th </td>
</tr>
<tr valign="top">
<td>15th </td>
<td>16th </td>
<td>17th </td>
<td>18th </td>
<td>19th </td>
<td bgcolor="#CCCCCC">20th </td>
<td bgcolor="#CCCCCC">21st </td>
</tr>
<tr valign="top">
<td>22nd </td>
<td>23rd </td>
<td>24th </td>
<td>25th </td>
<td>26th </td>
<td bgcolor="#CCCCCC">27th </td>
<td bgcolor="#CCCCCC">28th </td>
</tr>
<tr valign="top">
<td>29th </td>
<td>30th </td>
<td bgcolor="#4357CFF">1st October </td>
<td> </td>
<td> </td>
<td bgcolor="#CCCCCC"> </td>
<td bgcolor="#CCCCCC"> </td>
</tr>
</table>

Mod:Hunt Research Group/calendar

2014-06-24T14:33:07Z

Bw1911:

== Calendar ==

*Tricia (Not Done)
*Abdihakim Hassan (Not Done)
*Bryan Ward (Not Done)
*Claire Ashworth (Not Done)
*Matthew Clough (Not Done)
*Precious Ugbomah (Not Done)
*Richard Matthews (Not Done)
*Vincent Chen (Not Done)
*Gabriel Lau (Not Done)
*Rebecca Rowe (Not Done)
*Patricia Ho (Done)
*Giacomo Damilano (Not Done)
*Richard Fogarty (Not Done)

<table border="1" cellpadding="5" width="1190">
<tr bgcolor="#66CCFF">
<th width="170px">Mon</th>
<th width="170px">Tues</th>
<th width="170px">Wed</th>
<th width="170px">Thur</th>
<th width="170px">Fri</th>
<th width="170px" bgcolor="#CCCCCC">Sat</th>
<th width="170px" bgcolor="#CCCCCC">Sun</th>
<tr valign="top">
<td bgcolor="#339933">26th '''College closed''' '''Bank holiday'''</td>
<td >27th </td>
<td>28th </td>
<td>29th </td>
<td>30th (Giacomo Away)</td>
<td bgcolor="#CCCCCC">31st </td>
<td bgcolor="#4357CFF">1st June (Giacomo Away) </td>
</tr>
<tr valign="top">
<td>2nd (Giacomo Away)</td>
<td>3rd '''(Richard F - paper)''' (Giacomo Away)</td>
<td>4th CECAM workshop Claire away (Giacomo Away) (Patricia away)</td>
<td>5th CECAM workshop Claire away (Patricia away) (Giacomo Away) (Richard F away)</td>
<td>6th CECAM workshop Claire away (Patricia away)</td>
<td bgcolor="#CCCCCC">7th </td>
<td bgcolor="#CCCCCC">8th </td>
</tr>
<tr valign="top">
<td>9th </td>
<td>10th '''(Matt - paper)'''</td>
<td>11th </td>
<td>12th </td>
<td>13th </td>
<td bgcolor="#CCCCCC">14th </td>
<td bgcolor="#CCCCCC">15th </td>
</tr>
<tr valign="top">
<td>16th LIBLICE conference-Gabriel </td>
<td>17th '''(Hakim-presentation practice)''' LIBLICE conference-Gabriel </td>
<td>18th LIBLICE conference-Gabriel </td>
<td>19th LIBLICE conference-Gabriel </td>
<td>20th LIBLICE conference-Gabriel </td>
<td bgcolor="#CCCCCC">21st </td>
<td bgcolor="#CCCCCC">22nd </td>
</tr>
<tr valign="top">
<td>23rd </td>
<td>24th </td>
<td>25th </td>
<td>26th '''(Talk practice)'''</td>
<td bgcolor="#FFA500">27th '''End of term'''</td>
<td bgcolor="#CCCCCC">28th </td>
<td bgcolor="#CCCCCC">29th </td>
</tr>
<tr valign="top">
<td>30th (Richard F away)</td>
<td bgcolor="#4357CFF" >1st July {{fontcolor|#FFD700|'''PhD Symposium (Chem.)'''}} (Richard F away)</td>
<td>2nd (Richard F away)</td>
<td>3rd </td>
<td>4th </td>
<td bgcolor="#CCCCCC">5th </td>
<td bgcolor="#CCCCCC">6th EUCHEM-Richard & Claire</td>
</tr>
<tr valign="top">
<td>7th Bryan Away EUCHEM-Richard&Claire</td>
<td>8th Bryan Away EUCHEM-Richard & Claire</td>
<td>9th Bryan Away EUCHEM-Richard & Claire</td>
<td>10th Bryan Away EUCHEM-Richard & Claire</td>
<td>11th Bryan Away EUCHEM-Richard & Claire</td>
<td bgcolor="#CCCCCC">12th </td>
<td bgcolor="#CCCCCC">13th </td>
</tr>
<tr valign="top">
<td>14th Bryan Away Richard away Claire away</td>
<td>15th Bryan Away Richard away Claire away</td>
<td>16th Bryan Away Richard away Claire away</td>
<td>17th Bryan Away Richard away Claire away</td>
<td>18th Bryan Away Richard away Claire away</td>
<td bgcolor="#CCCCCC">19th </td>
<td bgcolor="#CCCCCC">20th </td>
</tr>
<tr valign="top">
<td>21st Liquid Matter-Gabriel</td>
<td>22nd Liquid Matter-Gabriel</td>
<td>23rd Gaussian workshop - Claire & Bryan Liquid Matter-Gabriel</td>
<td>24th Gaussian workshop - Claire & Bryan Liquid Matter-Gabriel </td>
<td>25th Liquid Matter-Gabriel </td>
<td bgcolor="#CCCCCC">26th </td>
<td bgcolor="#CCCCCC">27th </td>
</tr>
<tr valign="top">
<td>28th </td>
<td>29th </td>
<td>30th </td>
<td>31st </td>
<td bgcolor="#4357CFF">1st August </td>
<td bgcolor="#CCCCCC">2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
</tr>
<tr valign="top">
<td>4th Bryan on hiatus </td>
<td>5th Bryan on hiatus </td>
<td>6th Bryan on hiatus </td>
<td>7th Bryan on hiatus </td>
<td>8th Bryan on hiatus </td>
<td bgcolor="#CCCCCC">9th </td>
<td bgcolor="#CCCCCC">10th </td>
</tr>
<tr valign="top">
<td>11th Bryan on hiatus </td>
<td>12th Bryan on hiatus </td>
<td>13th Bryan on hiatus </td>
<td>14th Bryan on hiatus </td>
<td>15th Bryan on hiatus </td>
<td bgcolor="#CCCCCC">16th </td>
<td bgcolor="#CCCCCC">17th </td>
</tr>
<tr valign="top">
<td>18th Bryan on hiatus </td>
<td>19th Bryan on hiatus </td>
<td>20th Bryan on hiatus </td>
<td>21st Bryan on hiatus </td>
<td>22nd Bryan on hiatus </td>
<td bgcolor="#CCCCCC">23rd </td>
<td bgcolor="#CCCCCC">24th </td>
</tr>
<tr valign="top">
<td bgcolor="#339933">25th '''College closed''' '''Bank holiday'''</td>
<td>26th Bryan on hiatus </td>
<td>27th Bryan on hiatus </td>
<td>28th Bryan on hiatus </td>
<td>39th Bryan on hiatus </td>
<td bgcolor="#CCCCCC">30th </td>
<td bgcolor="#CCCCCC">31st </td>
</tr>
<tr valign="top">
<td bgcolor="#4357CFF">1st September Bryan on hiatus </td>
<td>2nd Bryan on hiatus </td>
<td>3rd Bryan on hiatus </td>
<td>4th Bryan on hiatus </td>
<td>5th Bryan on hiatus </td>
<td bgcolor="#CCCCCC">6th </td>
<td bgcolor="#CCCCCC">7th </td>
</tr>
<tr valign="top">
<td>8th </td>
<td>9th </td>
<td>10th </td>
<td>11th </td>
<td>12th </td>
<td bgcolor="#CCCCCC">13th </td>
<td bgcolor="#CCCCCC">14th </td>
</tr>
<tr valign="top">
<td>15th </td>
<td>16th </td>
<td>17th </td>
<td>18th </td>
<td>19th </td>
<td bgcolor="#CCCCCC">20th </td>
<td bgcolor="#CCCCCC">21st </td>
</tr>
<tr valign="top">
<td>22nd </td>
<td>23rd </td>
<td>24th </td>
<td>25th </td>
<td>26th </td>
<td bgcolor="#CCCCCC">27th </td>
<td bgcolor="#CCCCCC">28th </td>
</tr>
<tr valign="top">
<td>29th </td>
<td>30th </td>
<td bgcolor="#4357CFF">1st October </td>
<td> </td>
<td> </td>
<td bgcolor="#CCCCCC"> </td>
<td bgcolor="#CCCCCC"> </td>
</tr>
</table>

Mod:Hunt Research Group/calendar

2014-06-24T14:32:15Z

Bw1911:

== Calendar ==

*Tricia (Not Done)
*Abdihakim Hassan (Not Done)
*Bryan Ward (Not Done)
*Claire Ashworth (Not Done)
*Matthew Clough (Not Done)
*Precious Ugbomah (Not Done)
*Richard Matthews (Not Done)
*Vincent Chen (Not Done)
*Gabriel Lau (Not Done)
*Rebecca Rowe (Not Done)
*Patricia Ho (Done)
*Giacomo Damilano (Not Done)
*Richard Fogarty (Not Done)

<table border="1" cellpadding="5" width="1190">
<tr bgcolor="#66CCFF">
<th width="170px">Mon</th>
<th width="170px">Tues</th>
<th width="170px">Wed</th>
<th width="170px">Thur</th>
<th width="170px">Fri</th>
<th width="170px" bgcolor="#CCCCCC">Sat</th>
<th width="170px" bgcolor="#CCCCCC">Sun</th>
<tr valign="top">
<td bgcolor="#339933">26th '''College closed''' '''Bank holiday'''</td>
<td >27th </td>
<td>28th </td>
<td>29th </td>
<td>30th (Giacomo Away)</td>
<td bgcolor="#CCCCCC">31st </td>
<td bgcolor="#4357CFF">1st June (Giacomo Away) </td>
</tr>
<tr valign="top">
<td>2nd (Giacomo Away)</td>
<td>3rd '''(Richard F - paper)''' (Giacomo Away)</td>
<td>4th CECAM workshop Claire away (Giacomo Away) (Patricia away)</td>
<td>5th CECAM workshop Claire away (Patricia away) (Giacomo Away) (Richard F away)</td>
<td>6th CECAM workshop Claire away (Patricia away)</td>
<td bgcolor="#CCCCCC">7th </td>
<td bgcolor="#CCCCCC">8th </td>
</tr>
<tr valign="top">
<td>9th </td>
<td>10th '''(Matt - paper)'''</td>
<td>11th </td>
<td>12th </td>
<td>13th </td>
<td bgcolor="#CCCCCC">14th </td>
<td bgcolor="#CCCCCC">15th </td>
</tr>
<tr valign="top">
<td>16th LIBLICE conference-Gabriel </td>
<td>17th '''(Hakim-presentation practice)''' LIBLICE conference-Gabriel </td>
<td>18th LIBLICE conference-Gabriel </td>
<td>19th LIBLICE conference-Gabriel </td>
<td>20th LIBLICE conference-Gabriel </td>
<td bgcolor="#CCCCCC">21st </td>
<td bgcolor="#CCCCCC">22nd </td>
</tr>
<tr valign="top">
<td>23rd </td>
<td>24th </td>
<td>25th </td>
<td>26th '''(Talk practice)'''</td>
<td bgcolor="#FFA500">27th '''End of term'''</td>
<td bgcolor="#CCCCCC">28th </td>
<td bgcolor="#CCCCCC">29th </td>
</tr>
<tr valign="top">
<td>30th (Richard F away)</td>
<td bgcolor="#4357CFF" >1st July {{fontcolor|#FFD700|'''PhD Symposium (Chem.)'''}} (Richard F away)</td>
<td>2nd (Richard F away)</td>
<td>3rd </td>
<td>4th </td>
<td bgcolor="#CCCCCC">5th </td>
<td bgcolor="#CCCCCC">6th EUCHEM-Richard & Claire</td>
</tr>
<tr valign="top">
<td>7th Bryan Away EUCHEM-Richard&Claire</td>
<td>8th Bryan Away EUCHEM-Richard & Claire</td>
<td>9th Bryan Away EUCHEM-Richard & Claire</td>
<td>10th Bryan Away EUCHEM-Richard & Claire</td>
<td>11th Bryan Away EUCHEM-Richard & Claire</td>
<td bgcolor="#CCCCCC">12th </td>
<td bgcolor="#CCCCCC">13th </td>
</tr>
<tr valign="top">
<td>14th Bryan Away Richard away Claire away</td>
<td>15th Bryan Away Richard away Claire away</td>
<td>16th Bryan Away Richard away Claire away</td>
<td>17th Bryan Away Richard away Claire away</td>
<td>18th Bryan Away Richard away Claire away</td>
<td bgcolor="#CCCCCC">19th </td>
<td bgcolor="#CCCCCC">20th </td>
</tr>
<tr valign="top">
<td>21st Liquid Matter-Gabriel</td>
<td>22nd Liquid Matter-Gabriel</td>
<td>23rd Gaussian workshop - Claire & Bryan Liquid Matter-Gabriel</td>
<td>24th Gaussian workshop - Claire & Bryan Liquid Matter-Gabriel </td>
<td>25th Liquid Matter-Gabriel </td>
<td bgcolor="#CCCCCC">26th </td>
<td bgcolor="#CCCCCC">27th </td>
</tr>
<tr valign="top">
<td>28th </td>
<td>29th </td>
<td>30th </td>
<td>31st </td>
<td bgcolor="#4357CFF">1st August </td>
<td bgcolor="#CCCCCC">2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
</tr>
<tr valign="top">
<td>4th Bryan on hiatus </td>
<td>5th Bryan on hiatus </td>
<td>6th Bryan on hiatus </td>
<td>7th Bryan on hiatus </td>
<td>8th Bryan on hiatus </td>
<td bgcolor="#CCCCCC">9th </td>
<td bgcolor="#CCCCCC">10th </td>
</tr>
<tr valign="top">
<td>11th Bryan on hiatus </td>
<td>12th Bryan on hiatus </td>
<td>13th Bryan on hiatus </td>
<td>14th Bryan on hiatus </td>
<td>15th Bryan on hiatus </td>
<td bgcolor="#CCCCCC">16th </td>
<td bgcolor="#CCCCCC">17th </td>
</tr>
<tr valign="top">
<td>18th Bryan on hiatus </td>
<td>19th Bryan on hiatus </td>
<td>20th Bryan on hiatus </td>
<td>21st Bryan on hiatus </td>
<td>22nd Bryan on hiatus </td>
<td bgcolor="#CCCCCC">23rd </td>
<td bgcolor="#CCCCCC">24th </td>
</tr>
<tr valign="top">
<td bgcolor="#339933">25th '''College closed''' '''Bank holiday'''</td>
<td>26th Bryan on hiatus </td>
<td>27th Bryan on hiatus </td>
<td>28th Bryan on hiatus </td>
<td>39th Bryan on hiatus </td>
<td bgcolor="#CCCCCC">30th </td>
<td bgcolor="#CCCCCC">31st </td>
</tr>
<tr valign="top">
<td bgcolor="#4357CFF">1st September </td>
<td>2nd Bryan on hiatus </td>
<td>3rd Bryan on hiatus </td>
<td>4th Bryan on hiatus </td>
<td>5th Bryan on hiatus </td>
<td bgcolor="#CCCCCC">6th </td>
<td bgcolor="#CCCCCC">7th </td>
</tr>
<tr valign="top">
<td>8th </td>
<td>9th </td>
<td>10th </td>
<td>11th </td>
<td>12th </td>
<td bgcolor="#CCCCCC">13th </td>
<td bgcolor="#CCCCCC">14th </td>
</tr>
<tr valign="top">
<td>15th </td>
<td>16th </td>
<td>17th </td>
<td>18th </td>
<td>19th </td>
<td bgcolor="#CCCCCC">20th </td>
<td bgcolor="#CCCCCC">21st </td>
</tr>
<tr valign="top">
<td>22nd </td>
<td>23rd </td>
<td>24th </td>
<td>25th </td>
<td>26th </td>
<td bgcolor="#CCCCCC">27th </td>
<td bgcolor="#CCCCCC">28th </td>
</tr>
<tr valign="top">
<td>29th </td>
<td>30th </td>
<td bgcolor="#4357CFF">1st October </td>
<td> </td>
<td> </td>
<td bgcolor="#CCCCCC"> </td>
<td bgcolor="#CCCCCC"> </td>
</tr>
</table>

Mod:Hunt Research Group/calendar

2014-06-24T14:31:56Z

Bw1911:

== Calendar ==

*Tricia (Not Done)
*Abdihakim Hassan (Not Done)
*Bryan Ward (Not Done)
*Claire Ashworth (Not Done)
*Matthew Clough (Not Done)
*Precious Ugbomah (Not Done)
*Richard Matthews (Not Done)
*Vincent Chen (Not Done)
*Gabriel Lau (Not Done)
*Rebecca Rowe (Not Done)
*Patricia Ho (Done)
*Giacomo Damilano (Not Done)
*Richard Fogarty (Not Done)

<table border="1" cellpadding="5" width="1190">
<tr bgcolor="#66CCFF">
<th width="170px">Mon</th>
<th width="170px">Tues</th>
<th width="170px">Wed</th>
<th width="170px">Thur</th>
<th width="170px">Fri</th>
<th width="170px" bgcolor="#CCCCCC">Sat</th>
<th width="170px" bgcolor="#CCCCCC">Sun</th>
<tr valign="top">
<td bgcolor="#339933">26th '''College closed''' '''Bank holiday'''</td>
<td >27th </td>
<td>28th </td>
<td>29th </td>
<td>30th (Giacomo Away)</td>
<td bgcolor="#CCCCCC">31st </td>
<td bgcolor="#4357CFF">1st June (Giacomo Away) </td>
</tr>
<tr valign="top">
<td>2nd (Giacomo Away)</td>
<td>3rd '''(Richard F - paper)''' (Giacomo Away)</td>
<td>4th CECAM workshop Claire away (Giacomo Away) (Patricia away)</td>
<td>5th CECAM workshop Claire away (Patricia away) (Giacomo Away) (Richard F away)</td>
<td>6th CECAM workshop Claire away (Patricia away)</td>
<td bgcolor="#CCCCCC">7th </td>
<td bgcolor="#CCCCCC">8th </td>
</tr>
<tr valign="top">
<td>9th </td>
<td>10th '''(Matt - paper)'''</td>
<td>11th </td>
<td>12th </td>
<td>13th </td>
<td bgcolor="#CCCCCC">14th </td>
<td bgcolor="#CCCCCC">15th </td>
</tr>
<tr valign="top">
<td>16th LIBLICE conference-Gabriel </td>
<td>17th '''(Hakim-presentation practice)''' LIBLICE conference-Gabriel </td>
<td>18th LIBLICE conference-Gabriel </td>
<td>19th LIBLICE conference-Gabriel </td>
<td>20th LIBLICE conference-Gabriel </td>
<td bgcolor="#CCCCCC">21st </td>
<td bgcolor="#CCCCCC">22nd </td>
</tr>
<tr valign="top">
<td>23rd </td>
<td>24th </td>
<td>25th </td>
<td>26th '''(Talk practice)'''</td>
<td bgcolor="#FFA500">27th '''End of term'''</td>
<td bgcolor="#CCCCCC">28th </td>
<td bgcolor="#CCCCCC">29th </td>
</tr>
<tr valign="top">
<td>30th (Richard F away)</td>
<td bgcolor="#4357CFF" >1st July {{fontcolor|#FFD700|'''PhD Symposium (Chem.)'''}} (Richard F away)</td>
<td>2nd (Richard F away)</td>
<td>3rd </td>
<td>4th </td>
<td bgcolor="#CCCCCC">5th </td>
<td bgcolor="#CCCCCC">6th EUCHEM-Richard & Claire</td>
</tr>
<tr valign="top">
<td>7th Bryan Away EUCHEM-Richard&Claire</td>
<td>8th Bryan Away EUCHEM-Richard & Claire</td>
<td>9th Bryan Away EUCHEM-Richard & Claire</td>
<td>10th Bryan Away EUCHEM-Richard & Claire</td>
<td>11th Bryan Away EUCHEM-Richard & Claire</td>
<td bgcolor="#CCCCCC">12th </td>
<td bgcolor="#CCCCCC">13th </td>
</tr>
<tr valign="top">
<td>14th Bryan Away Richard away Claire away</td>
<td>15th Bryan Away Richard away Claire away</td>
<td>16th Bryan Away Richard away Claire away</td>
<td>17th Bryan Away Richard away Claire away</td>
<td>18th Bryan Away Richard away Claire away</td>
<td bgcolor="#CCCCCC">19th </td>
<td bgcolor="#CCCCCC">20th </td>
</tr>
<tr valign="top">
<td>21st Liquid Matter-Gabriel</td>
<td>22nd Liquid Matter-Gabriel</td>
<td>23rd Gaussian workshop - Claire & Bryan Liquid Matter-Gabriel</td>
<td>24th Gaussian workshop - Claire & Bryan Liquid Matter-Gabriel </td>
<td>25th Liquid Matter-Gabriel </td>
<td bgcolor="#CCCCCC">26th </td>
<td bgcolor="#CCCCCC">27th </td>
</tr>
<tr valign="top">
<td>28th </td>
<td>29th </td>
<td>30th </td>
<td>31st </td>
<td bgcolor="#4357CFF">1st August </td>
<td bgcolor="#CCCCCC">2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
</tr>
<tr valign="top">
<td>4th Bryan on hiatus </td>
<td>5th Bryan on hiatus </td>
<td>6th Bryan on hiatus </td>
<td>7th Bryan on hiatus </td>
<td>8th Bryan on hiatus </td>
<td bgcolor="#CCCCCC">9th </td>
<td bgcolor="#CCCCCC">10th </td>
</tr>
<tr valign="top">
<td>11th Bryan on hiatus </td>
<td>12th Bryan on hiatus </td>
<td>13th Bryan on hiatus </td>
<td>14th Bryan on hiatus </td>
<td>15th </td>
<td bgcolor="#CCCCCC">16th </td>
<td bgcolor="#CCCCCC">17th </td>
</tr>
<tr valign="top">
<td>18th Bryan on hiatus </td>
<td>19th Bryan on hiatus </td>
<td>20th Bryan on hiatus </td>
<td>21st Bryan on hiatus </td>
<td>22nd Bryan on hiatus </td>
<td bgcolor="#CCCCCC">23rd </td>
<td bgcolor="#CCCCCC">24th </td>
</tr>
<tr valign="top">
<td bgcolor="#339933">25th '''College closed''' '''Bank holiday'''</td>
<td>26th Bryan on hiatus </td>
<td>27th Bryan on hiatus </td>
<td>28th Bryan on hiatus </td>
<td>39th Bryan on hiatus </td>
<td bgcolor="#CCCCCC">30th </td>
<td bgcolor="#CCCCCC">31st </td>
</tr>
<tr valign="top">
<td bgcolor="#4357CFF">1st September </td>
<td>2nd Bryan on hiatus </td>
<td>3rd Bryan on hiatus </td>
<td>4th Bryan on hiatus </td>
<td>5th Bryan on hiatus </td>
<td bgcolor="#CCCCCC">6th </td>
<td bgcolor="#CCCCCC">7th </td>
</tr>
<tr valign="top">
<td>8th </td>
<td>9th </td>
<td>10th </td>
<td>11th </td>
<td>12th </td>
<td bgcolor="#CCCCCC">13th </td>
<td bgcolor="#CCCCCC">14th </td>
</tr>
<tr valign="top">
<td>15th </td>
<td>16th </td>
<td>17th </td>
<td>18th </td>
<td>19th </td>
<td bgcolor="#CCCCCC">20th </td>
<td bgcolor="#CCCCCC">21st </td>
</tr>
<tr valign="top">
<td>22nd </td>
<td>23rd </td>
<td>24th </td>
<td>25th </td>
<td>26th </td>
<td bgcolor="#CCCCCC">27th </td>
<td bgcolor="#CCCCCC">28th </td>
</tr>
<tr valign="top">
<td>29th </td>
<td>30th </td>
<td bgcolor="#4357CFF">1st October </td>
<td> </td>
<td> </td>
<td bgcolor="#CCCCCC"> </td>
<td bgcolor="#CCCCCC"> </td>
</tr>
</table>

Mod:Hunt Research Group/calendar

2014-05-29T11:17:08Z

Bw1911:

== Calendar ==

*Tricia (Not Done)
*Abdihakim Hassan (Not Done)
*Bryan Ward (Not Done)
*Claire Ashworth (Not Done)
*Matthew Clough (Not Done)
*Precious Ugbomah (Not Done)
*Richard Matthews (Not Done)
*Vincent Chen (Not Done)
*Gabriel Lau (Not Done)
*Rebecca Rowe (Not Done)
*Patricia Ho (Done)
*Giacomo Damilano (Not Done)
*Richard Fogarty (Not Done)

<table border="1" cellpadding="5" width="1190">
<tr bgcolor="#66CCFF">
<th width="170px">Mon</th>
<th width="170px">Tues</th>
<th width="170px">Wed</th>
<th width="170px">Thur</th>
<th width="170px">Fri</th>
<th width="170px" bgcolor="#CCCCCC">Sat</th>
<th width="170px" bgcolor="#CCCCCC">Sun</th>
<tr valign="top">
<td bgcolor="#339933">21st '''College Closed'''</td>
<td bgcolor="#339933" >22nd '''College Closed'''</td>
<td>23rd Tricia away Richard away Precious away Giacomo away Gabriel away </td>
<td>24th Richard away Giacomo away Gabriel away Precious away </td>
<td>25th Richard away Giacomo away Precious away Gabriel away </td>
<td bgcolor="#FFA500">26th '''Start of term''' Giacomo away </td>
<td bgcolor="#CCCCCC">27th Giacomo away </td>
</tr>
<tr valign="top">
<td>28th Giacomo away </td>
<td >29th '''(Vincent & Gabriel)'''</td>
<td>30th </td>
<td bgcolor="#4357CFF">1st May </td>
<td>2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
<td bgcolor="#CCCCCC">4th </td>
</tr>
<tr valign="top">
<td bgcolor="#339933">5th '''College Closed''' '''Bank holiday'''</td>
<td >6th '''(Kevin)'''</td>
<td>7th </td>
<td>8th </td>
<td>9th </td>
<td bgcolor="#CCCCCC">10th </td>
<td bgcolor="#CCCCCC">11th </td>
</tr>
<tr valign="top">
<td >12th </td>
<td >13th </td>
<td>14th </td>
<td>15th </td>
<td>16th </td>
<td bgcolor="#CCCCCC">17th </td>
<td bgcolor="#CCCCCC">18th </td>
</tr>
<tr valign="top">
<td >19th Careers course - Vincent, Gabriel</td>
<td >20th Careers course - Vincent, Gabriel</td>
<td>21st Careers course - Vincent, Gabriel</td>
<td>22nd </td>
<td>23rd </td>
<td bgcolor="#CCCCCC">24th </td>
<td bgcolor="#CCCCCC">25th </td>
</tr>
<tr valign="top">
<td bgcolor="#339933">26th '''College closed''' '''Bank holiday'''</td>
<td >27th </td>
<td>28th </td>
<td>29th </td>
<td>30th (Giacomo Away)</td>
<td bgcolor="#CCCCCC">31st </td>
<td bgcolor="#4357CFF">1st June (Giacomo Away) </td>
</tr>
<tr valign="top">
<td>2nd (Giacomo Away)</td>
<td>3rd '''(Richard F - paper)''' (Giacomo Away)</td>
<td>4th CECAM workshop Claire away (Giacomo Away) (Patricia away)</td>
<td>5th CECAM workshop Claire away (Patricia away) (Giacomo Away)</td>
<td>6th CECAM workshop Claire away (Patricia away)</td>
<td bgcolor="#CCCCCC">7th </td>
<td bgcolor="#CCCCCC">8th </td>
</tr>
<tr valign="top">
<td>9th </td>
<td>10th '''(Matt - paper)'''</td>
<td>11th </td>
<td>12th </td>
<td>13th </td>
<td bgcolor="#CCCCCC">14th </td>
<td bgcolor="#CCCCCC">15th </td>
</tr>
<tr valign="top">
<td>16th </td>
<td>17th '''(Hakim-presentation practice)'''</td>
<td>18th </td>
<td>19th '''(Talk practice)'''</td>
<td>20th </td>
<td bgcolor="#CCCCCC">21st </td>
<td bgcolor="#CCCCCC">22nd </td>
</tr>
<tr valign="top">
<td>23rd </td>
<td>24th </td>
<td>25th '''(Talk practice)'''</td>
<td>26th </td>
<td bgcolor="#FFA500">27th '''End of term'''</td>
<td bgcolor="#CCCCCC">28th </td>
<td bgcolor="#CCCCCC">29th </td>
</tr>
<tr valign="top">
<td>30th </td>
<td bgcolor="#4357CFF" >1st July {{fontcolor|#FFD700|'''PhD Symposium (Chem.)'''}}</td>
<td>2nd </td>
<td>3rd </td>
<td>4th </td>
<td bgcolor="#CCCCCC">5th </td>
<td bgcolor="#CCCCCC">6th EUCHEM-Richard & Claire</td>
</tr>
<tr valign="top">
<td>7th Bryan Away EUCHEM-Richard&Claire</td>
<td>8th Bryan Away EUCHEM-Richard & Claire</td>
<td>9th Bryan Away EUCHEM-Richard & Claire</td>
<td>10th Bryan Away EUCHEM-Richard & Claire</td>
<td>11th Bryan Away EUCHEM-Richard & Claire</td>
<td bgcolor="#CCCCCC">12th </td>
<td bgcolor="#CCCCCC">13th </td>
</tr>
<tr valign="top">
<td>14th Bryan Away Richard away Claire away</td>
<td>15th Bryan Away Richard away Claire away</td>
<td>16th Bryan Away Richard away Claire away</td>
<td>17th Bryan Away Richard away Claire away</td>
<td>18th Bryan Away Richard away Claire away</td>
<td bgcolor="#CCCCCC">19th </td>
<td bgcolor="#CCCCCC">20th </td>
</tr>
<tr valign="top">
<td>21st </td>
<td>22nd </td>
<td>23rd Gaussian workshop - Claire & Bryan</td>
<td>24th Gaussian workshop - Claire & Bryan</td>
<td>25th </td>
<td bgcolor="#CCCCCC">26th </td>
<td bgcolor="#CCCCCC">27th </td>
</tr>
<tr valign="top">
<td>28th </td>
<td>29th </td>
<td>30th </td>
<td>31st </td>
<td bgcolor="#4357CFF">1st August </td>
<td bgcolor="#CCCCCC">2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
</tr>
<tr valign="top">
<td>4th </td>
<td>5th </td>
<td>6th </td>
<td>7th </td>
<td>8th </td>
<td bgcolor="#CCCCCC">9th </td>
<td bgcolor="#CCCCCC">10th </td>
</tr>
<tr valign="top">
<td>11th </td>
<td>12th </td>
<td>13th </td>
<td>14th </td>
<td>15th </td>
<td bgcolor="#CCCCCC">16th </td>
<td bgcolor="#CCCCCC">17th </td>
</tr>
<tr valign="top">
<td>18th </td>
<td>19th </td>
<td>20th </td>
<td>21st </td>
<td>22nd </td>
<td bgcolor="#CCCCCC">23rd </td>
<td bgcolor="#CCCCCC">24th </td>
</tr>
<tr valign="top">
<td bgcolor="#339933">25th '''College closed''' '''Bank holiday'''</td>
<td>26th </td>
<td>27th </td>
<td>28th </td>
<td>39th </td>
<td bgcolor="#CCCCCC">30th </td>
<td bgcolor="#CCCCCC">31st </td>
</tr>
<tr valign="top">
<td bgcolor="#4357CFF">1st September </td>
<td>2nd </td>
<td>3rd </td>
<td>4th </td>
<td>5th </td>
<td bgcolor="#CCCCCC">6th </td>
<td bgcolor="#CCCCCC">7th </td>
</tr>
<tr valign="top">
<td>8th </td>
<td>9th </td>
<td>10th </td>
<td>11th </td>
<td>12th </td>
<td bgcolor="#CCCCCC">13th </td>
<td bgcolor="#CCCCCC">14th </td>
</tr>
<tr valign="top">
<td>15th </td>
<td>16th </td>
<td>17th </td>
<td>18th </td>
<td>19th </td>
<td bgcolor="#CCCCCC">20th </td>
<td bgcolor="#CCCCCC">21st </td>
</tr>
<tr valign="top">
<td>22nd </td>
<td>23rd </td>
<td>24th </td>
<td>25th </td>
<td>26th </td>
<td bgcolor="#CCCCCC">27th </td>
<td bgcolor="#CCCCCC">28th </td>
</tr>
<tr valign="top">
<td>29th </td>
<td>30th </td>
<td bgcolor="#4357CFF">1st October </td>
<td> </td>
<td> </td>
<td bgcolor="#CCCCCC"> </td>
<td bgcolor="#CCCCCC"> </td>
</tr>
</table>

Mod:Hunt Research Group/calendar

2014-04-07T09:33:33Z

Bw1911: /* Calendar */

== Calendar ==

*Tricia (Done)
*Abdihakim Hassan (Done)
*Bryan Ward (Done)
*Claire Ashworth (Done)
*Matthew Clough (Done)
*Precious Ugbomah (Done)
*Richard Matthews (Done)
*Vincent Chen (Not Done)
*Gabriel Lau (Not Done)
*Rebecca Rowe (Done)
*Patricia Ho (Not Done)
*Giacomo Damilano (Done)

<table border="1" cellpadding="5" width="1190">
<tr bgcolor="#66CCFF">
<th width="170px">Mon</th>
<th width="170px">Tues</th>
<th width="170px">Wed</th>
<th width="170px">Thur</th>
<th width="170px">Fri</th>
<th width="170px" bgcolor="#CCCCCC">Sat</th>
<th width="170px" bgcolor="#CCCCCC">Sun</th>
<tr valign="top">
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td bgcolor="#4357CFF">1st March </td>
<td bgcolor="#CCCCCC">2nd </td>
</tr>
<tr valign="top">
<td>3rd Richard away </td>
<td>4th '''(Vincent)''' Richard away </td>
<td>5th Richard away Vincent away </td>
<td>6th Richard away </td>
<td>7th Richard away </td>
<td bgcolor="#CCCCCC">8th </td>
<td bgcolor="#CCCCCC">9th </td>
</tr>
<tr valign="top">
<td>10th Richard away </td>
<td>11th '''(Becky)''' Richard away </td>
<td>12th Richard away </td>
<td>13th Richard away </td>
<td>14th Richard away </td>
<td bgcolor="#CCCCCC">15th </td>
<td bgcolor="#CCCCCC">16th </td>
</tr>
<tr valign="top">
<td>17th </td>
<td>18th '''(Giacomo)''' Richard postdoc workshop</td>
<td>19th </td>
<td>20th </td>
<td>21st Claire away</td>
<td bgcolor="#CCCCCC">22nd </td>
<td bgcolor="#CCCCCC">23rd </td>
</tr>
<tr valign="top">
<td>24th </td>
<td>25th '''(Patricia)'''</td>
<td>26th </td>
<td>27th </td>
<td bgcolor="#FFA500">28th '''End of term'''</td>
<td bgcolor="#CCCCCC">29th </td>
<td bgcolor="#CCCCCC">30th </td>
</tr>
<tr valign="top">
<td>31st Becky away rowing </td>
<td bgcolor="#4357CFF">1st April '''(Precious)''' DL_Poly workshop - Claire, Richard</td>
<td>2nd DL_Poly workshop - Claire, Richard Becky away rowing </td>
<td>3rd Becky away rowing </td>
<td>4th Becky away rowing </td>
<td bgcolor="#CCCCCC">5th Becky away rowing </td>
<td bgcolor="#CCCCCC">6th Becky away rowing </td>
</tr>
<tr valign="top">
<td>7th Becky away rowing </td>
<td >8th '''(Matthew)''' Becky away rowing </td>
<td>9th Matthew Away Becky away rowing </td>
<td>10th Matthew Away </td>
<td>11th Matthew Away </td>
<td bgcolor="#CCCCCC">12th </td>
<td bgcolor="#CCCCCC">13th </td>
</tr>
<tr valign="top">
<td>14th Bryan Away </td>
<td >15th Bryan Away '''(Group activity)'''</td>
<td>16th Tricia away Giacomo away </td>
<td bgcolor="#339933">17th '''College Closed'''</td>
<td bgcolor="#339933">18th '''College Closed'''</td>
<td bgcolor="#CCCCCC">19th '''College Closed'''</td>
<td bgcolor="#CCCCCC">20th '''College Closed'''</td>
</tr>
<tr valign="top">
<td bgcolor="#339933">21st '''College Closed'''</td>
<td bgcolor="#339933" >22nd '''College Closed'''</td>
<td>23rd Tricia away Richard away Precious away Giacomo away </td>
<td>24th Richard away Giacomo away </td>
<td>25th Richard away Giacomo away </td>
<td bgcolor="#FFA500">26th '''Start of term''' Giacomo away </td>
<td bgcolor="#CCCCCC">27th Giacomo away </td>
</tr>
<tr valign="top">
<td>28th Giacomo away </td>
<td >29th </td>
<td>30th </td>
<td bgcolor="#4357CFF">1st May </td>
<td>2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
<td bgcolor="#CCCCCC">4th </td>
</tr>
<tr valign="top">
<td bgcolor="#339933">5th '''College Closed''' '''Bank holiday'''</td>
<td >6th '''(Tricia-DFT functionals)'''</td>
<td>7th </td>
<td>8th </td>
<td>9th </td>
<td bgcolor="#CCCCCC">10th </td>
<td bgcolor="#CCCCCC">11th </td>
</tr>
<tr valign="top">
<td >12th </td>
<td >13th </td>
<td>14th </td>
<td>15th </td>
<td>16th </td>
<td bgcolor="#CCCCCC">17th </td>
<td bgcolor="#CCCCCC">18th </td>
</tr>
<tr valign="top">
<td >19th </td>
<td >20th </td>
<td>21st </td>
<td>22nd </td>
<td>23rd </td>
<td bgcolor="#CCCCCC">24th </td>
<td bgcolor="#CCCCCC">25th </td>
</tr>
<tr valign="top">
<td bgcolor="#339933">26th '''College closed''' '''Bank holiday'''</td>
<td >27th </td>
<td>28th </td>
<td>29th </td>
<td>30th </td>
<td bgcolor="#CCCCCC">31st </td>
<td bgcolor="#4357CFF">1st June </td>
</tr>
<tr valign="top">
<td>2nd </td>
<td>3rd </td>
<td>4th CECAM workshop</td>
<td>5th CECAM workshop Claire away</td>
<td>6th CECAM workshop Claire away</td>
<td bgcolor="#CCCCCC">7th </td>
<td bgcolor="#CCCCCC">8th </td>
</tr>
<tr valign="top">
<td>9th </td>
<td>10th </td>
<td>11th </td>
<td>12th </td>
<td>13th </td>
<td bgcolor="#CCCCCC">14th </td>
<td bgcolor="#CCCCCC">15th </td>
</tr>
<tr valign="top">
<td>16th </td>
<td>17th </td>
<td>18th </td>
<td>19th </td>
<td>20th </td>
<td bgcolor="#CCCCCC">21st </td>
<td bgcolor="#CCCCCC">22nd </td>
</tr>
<tr valign="top">
<td>23rd </td>
<td>24th </td>
<td>25th </td>
<td>26th </td>
<td bgcolor="#FFA500">27th '''End of term'''</td>
<td bgcolor="#CCCCCC">28th </td>
<td bgcolor="#CCCCCC">29th </td>
</tr>
<tr valign="top">
<td>30th </td>
<td bgcolor="#4357CFF" >1st July {{fontcolor|#FFD700|'''PhD Symposium (Chem.)'''}}</td>
<td>2nd </td>
<td>3rd </td>
<td>4th </td>
<td bgcolor="#CCCCCC">5th </td>
<td bgcolor="#CCCCCC">6th EUCHEM</td>
</tr>
<tr valign="top">
<td>7th EUCHEM</td>
<td>8th EUCHEM</td>
<td>9th EUCHEM</td>
<td>10th EUCHEM</td>
<td>11th EUCHEM</td>
<td bgcolor="#CCCCCC">12th </td>
<td bgcolor="#CCCCCC">13th </td>
</tr>
<tr valign="top">
<td>14th Richard away</td>
<td>15th Richard away</td>
<td>16th Richard away</td>
<td>17th Richard away</td>
<td>18th Richard away</td>
<td bgcolor="#CCCCCC">19th </td>
<td bgcolor="#CCCCCC">20th </td>
</tr>
<tr valign="top">
<td>21st </td>
<td>22nd </td>
<td>23rd Gaussian workshop - Claire</td>
<td>24th Gaussian workshop - Claire</td>
<td>25th </td>
<td bgcolor="#CCCCCC">26th </td>
<td bgcolor="#CCCCCC">27th </td>
</tr>

<tr valign="top">
<td>28th </td>
<td>29th </td>
<td>30th </td>
<td>31st </td>
<td bgcolor="#4357CFF">1st August </td>
<td bgcolor="#CCCCCC">2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
</tr>
</table>

Mod:Hunt Research Group/calendar

2014-04-07T09:32:59Z

Bw1911:

== Calendar ==

*Tricia (Done)
*Abdihakim Hassan (Done)
*Bryan Ward (Not Done)
*Claire Ashworth (Done)
*Matthew Clough (Done)
*Precious Ugbomah (Done)
*Richard Matthews (Done)
*Vincent Chen (Not Done)
*Gabriel Lau (Not Done)
*Rebecca Rowe (Done)
*Patricia Ho (Not Done)
*Giacomo Damilano (Done)

<table border="1" cellpadding="5" width="1190">
<tr bgcolor="#66CCFF">
<th width="170px">Mon</th>
<th width="170px">Tues</th>
<th width="170px">Wed</th>
<th width="170px">Thur</th>
<th width="170px">Fri</th>
<th width="170px" bgcolor="#CCCCCC">Sat</th>
<th width="170px" bgcolor="#CCCCCC">Sun</th>
<tr valign="top">
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td bgcolor="#4357CFF">1st March </td>
<td bgcolor="#CCCCCC">2nd </td>
</tr>
<tr valign="top">
<td>3rd Richard away </td>
<td>4th '''(Vincent)''' Richard away </td>
<td>5th Richard away Vincent away </td>
<td>6th Richard away </td>
<td>7th Richard away </td>
<td bgcolor="#CCCCCC">8th </td>
<td bgcolor="#CCCCCC">9th </td>
</tr>
<tr valign="top">
<td>10th Richard away </td>
<td>11th '''(Becky)''' Richard away </td>
<td>12th Richard away </td>
<td>13th Richard away </td>
<td>14th Richard away </td>
<td bgcolor="#CCCCCC">15th </td>
<td bgcolor="#CCCCCC">16th </td>
</tr>
<tr valign="top">
<td>17th </td>
<td>18th '''(Giacomo)''' Richard postdoc workshop</td>
<td>19th </td>
<td>20th </td>
<td>21st Claire away</td>
<td bgcolor="#CCCCCC">22nd </td>
<td bgcolor="#CCCCCC">23rd </td>
</tr>
<tr valign="top">
<td>24th </td>
<td>25th '''(Patricia)'''</td>
<td>26th </td>
<td>27th </td>
<td bgcolor="#FFA500">28th '''End of term'''</td>
<td bgcolor="#CCCCCC">29th </td>
<td bgcolor="#CCCCCC">30th </td>
</tr>
<tr valign="top">
<td>31st Becky away rowing </td>
<td bgcolor="#4357CFF">1st April '''(Precious)''' DL_Poly workshop - Claire, Richard</td>
<td>2nd DL_Poly workshop - Claire, Richard Becky away rowing </td>
<td>3rd Becky away rowing </td>
<td>4th Becky away rowing </td>
<td bgcolor="#CCCCCC">5th Becky away rowing </td>
<td bgcolor="#CCCCCC">6th Becky away rowing </td>
</tr>
<tr valign="top">
<td>7th Becky away rowing </td>
<td >8th '''(Matthew)''' Becky away rowing </td>
<td>9th Matthew Away Becky away rowing </td>
<td>10th Matthew Away </td>
<td>11th Matthew Away </td>
<td bgcolor="#CCCCCC">12th </td>
<td bgcolor="#CCCCCC">13th </td>
</tr>
<tr valign="top">
<td>14th Bryan Away </td>
<td >15th Bryan Away '''(Group activity)'''</td>
<td>16th Tricia away Giacomo away </td>
<td bgcolor="#339933">17th '''College Closed'''</td>
<td bgcolor="#339933">18th '''College Closed'''</td>
<td bgcolor="#CCCCCC">19th '''College Closed'''</td>
<td bgcolor="#CCCCCC">20th '''College Closed'''</td>
</tr>
<tr valign="top">
<td bgcolor="#339933">21st '''College Closed'''</td>
<td bgcolor="#339933" >22nd '''College Closed'''</td>
<td>23rd Tricia away Richard away Precious away Giacomo away </td>
<td>24th Richard away Giacomo away </td>
<td>25th Richard away Giacomo away </td>
<td bgcolor="#FFA500">26th '''Start of term''' Giacomo away </td>
<td bgcolor="#CCCCCC">27th Giacomo away </td>
</tr>
<tr valign="top">
<td>28th Giacomo away </td>
<td >29th </td>
<td>30th </td>
<td bgcolor="#4357CFF">1st May </td>
<td>2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
<td bgcolor="#CCCCCC">4th </td>
</tr>
<tr valign="top">
<td bgcolor="#339933">5th '''College Closed''' '''Bank holiday'''</td>
<td >6th '''(Tricia-DFT functionals)'''</td>
<td>7th </td>
<td>8th </td>
<td>9th </td>
<td bgcolor="#CCCCCC">10th </td>
<td bgcolor="#CCCCCC">11th </td>
</tr>
<tr valign="top">
<td >12th </td>
<td >13th </td>
<td>14th </td>
<td>15th </td>
<td>16th </td>
<td bgcolor="#CCCCCC">17th </td>
<td bgcolor="#CCCCCC">18th </td>
</tr>
<tr valign="top">
<td >19th </td>
<td >20th </td>
<td>21st </td>
<td>22nd </td>
<td>23rd </td>
<td bgcolor="#CCCCCC">24th </td>
<td bgcolor="#CCCCCC">25th </td>
</tr>
<tr valign="top">
<td bgcolor="#339933">26th '''College closed''' '''Bank holiday'''</td>
<td >27th </td>
<td>28th </td>
<td>29th </td>
<td>30th </td>
<td bgcolor="#CCCCCC">31st </td>
<td bgcolor="#4357CFF">1st June </td>
</tr>
<tr valign="top">
<td>2nd </td>
<td>3rd </td>
<td>4th CECAM workshop</td>
<td>5th CECAM workshop Claire away</td>
<td>6th CECAM workshop Claire away</td>
<td bgcolor="#CCCCCC">7th </td>
<td bgcolor="#CCCCCC">8th </td>
</tr>
<tr valign="top">
<td>9th </td>
<td>10th </td>
<td>11th </td>
<td>12th </td>
<td>13th </td>
<td bgcolor="#CCCCCC">14th </td>
<td bgcolor="#CCCCCC">15th </td>
</tr>
<tr valign="top">
<td>16th </td>
<td>17th </td>
<td>18th </td>
<td>19th </td>
<td>20th </td>
<td bgcolor="#CCCCCC">21st </td>
<td bgcolor="#CCCCCC">22nd </td>
</tr>
<tr valign="top">
<td>23rd </td>
<td>24th </td>
<td>25th </td>
<td>26th </td>
<td bgcolor="#FFA500">27th '''End of term'''</td>
<td bgcolor="#CCCCCC">28th </td>
<td bgcolor="#CCCCCC">29th </td>
</tr>
<tr valign="top">
<td>30th </td>
<td bgcolor="#4357CFF" >1st July {{fontcolor|#FFD700|'''PhD Symposium (Chem.)'''}}</td>
<td>2nd </td>
<td>3rd </td>
<td>4th </td>
<td bgcolor="#CCCCCC">5th </td>
<td bgcolor="#CCCCCC">6th EUCHEM</td>
</tr>
<tr valign="top">
<td>7th EUCHEM</td>
<td>8th EUCHEM</td>
<td>9th EUCHEM</td>
<td>10th EUCHEM</td>
<td>11th EUCHEM</td>
<td bgcolor="#CCCCCC">12th </td>
<td bgcolor="#CCCCCC">13th </td>
</tr>
<tr valign="top">
<td>14th Richard away</td>
<td>15th Richard away</td>
<td>16th Richard away</td>
<td>17th Richard away</td>
<td>18th Richard away</td>
<td bgcolor="#CCCCCC">19th </td>
<td bgcolor="#CCCCCC">20th </td>
</tr>
<tr valign="top">
<td>21st </td>
<td>22nd </td>
<td>23rd Gaussian workshop - Claire</td>
<td>24th Gaussian workshop - Claire</td>
<td>25th </td>
<td bgcolor="#CCCCCC">26th </td>
<td bgcolor="#CCCCCC">27th </td>
</tr>

<tr valign="top">
<td>28th </td>
<td>29th </td>
<td>30th </td>
<td>31st </td>
<td bgcolor="#4357CFF">1st August </td>
<td bgcolor="#CCCCCC">2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
</tr>
</table>

Mod:Hunt Research Group/calendar

2013-11-20T13:42:11Z

Bw1911: /* Calendar */

== Calendar ==

*Tricia (Not Done)
*Abdihakim Hassan (Not Done)
*Bryan Ward (Done)
*Claire Ashworth (Done)
*Matthew Clough (Not Done)
*Precious Ugbomah (Not Done)
*Richard Matthews (Done)
*Vincent Chen (Not Done)
*Gabriel Lau (Not Done)
*Rebecca Rowe (Not Done)
*Patricia Ho (Not Done)
*Giacomo Damilano (Not Done)

<table border="1" cellpadding="5" width="1190">
<tr bgcolor="#66CCFF">
<th width="170px">Mon</th>
<th width="170px">Tues</th>
<th width="170px">Wed</th>
<th width="170px">Thur</th>
<th width="170px">Fri</th>
<th width="170px" bgcolor="#CCCCCC">Sat</th>
<th width="170px" bgcolor="#CCCCCC">Sun</th>

<tr valign="top">
<td>28th </td>
<td>29th '''(Matthew)'''</td>
<td>30th </td>
<td>31st </td>
<td bgcolor="#4357CFF">1st November </td>
<td bgcolor="#CCCCCC">2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
</tr>
<tr valign="top">
<td>4th </td>
<td>5th '''(Vincent)'''</td>
<td>6th </td>
<td>7th </td>
<td>8th</td>
<td bgcolor="#CCCCCC">9th </td>
<td bgcolor="#CCCCCC">10th </td>
</tr>
<tr valign="top">
<td>11th </td>
<td>12th '''(Gabriel)'''</td>
<td>13th </td>
<td>14th </td>
<td>15th</td>
<td bgcolor="#CCCCCC">16th </td>
<td bgcolor="#CCCCCC">17th </td>
</tr>
<tr valign="top">
<td>18th </td>
<td>19th '''(Hakim)'''</td>
<td>20th </td>
<td>21st </td>
<td>22nd</td>
<td bgcolor="#CCCCCC">23rd </td>
<td bgcolor="#CCCCCC">24th </td>
</tr>
<tr valign="top">
<td>25th </td>
<td>26th '''(Group Outing)'''</td>
<td>27th </td>
<td>28th </td>
<td>29th</td>
<td bgcolor="#CCCCCC">30th </td>
<td bgcolor="#4357CFF">1st December </td>
</tr>
<tr valign="top">
<td>2nd </td>
<td>3rd '''(Richard)''' Bryan Away</td>
<td>4th Bryan Away</td>
<td>5th Bryan Away</td>
<td>6th Bryan Away</td>
<td bgcolor="#CCCCCC">7th Bryan Away</td>
<td bgcolor="#CCCCCC">8th Bryan Away</td>
</tr>
<tr valign="top">
<td>9th Bryan Away</td>
<td>10th '''(Becky)''' Bryan Away</td>
<td>11th </td>
<td>12th </td>
<td bgcolor="#FFA500">13th '''End of term'''</td>
<td bgcolor="#CCCCCC">14th </td>
<td bgcolor="#CCCCCC">15th </td>
</tr>
<tr valign="top">
<td>16th </td>
<td>17th '''(CV Workshop)'''</td>
<td>18th </td>
<td>19th </td>
<td>20th </td>
<td bgcolor="#CCCCCC">21st </td>
<td bgcolor="#CCCCCC">22nd </td>
</tr>
<tr valign="top">
<td bgcolor="#228B22">23rd '''College closed'''</td>
<td bgcolor="#228B22">24th '''College closed'''</td>
<td bgcolor="#228B22">25th '''College closed'''</td>
<td bgcolor="#228B22">26th '''College closed'''</td>
<td bgcolor="#228B22">27th '''College closed'''</td>
<td bgcolor="#228B22">28th '''College closed'''</td>
<td bgcolor="#228B22">29th '''College closed'''</td>
</tr>
<tr valign="top">
<td bgcolor="#228B22">30th '''College closed'''</td>
<td bgcolor="#228B22">31st '''College closed'''</td>
<td bgcolor="#4357CFF">1st January '''College closed'''</td>
<td>2nd Richard away Claire away </td>
<td>3rd Richard away Gabriel & Vincent - Science Communication Course Bryan Away</td>
<td bgcolor="#CCCCCC">4th Gabriel & Vincent - Science Communication Course Bryan Away</td>
<td bgcolor="#CCCCCC">5th Gabriel & Vincent - Science Communication Course Bryan Away</td>
</tr>
<tr valign="top">
<td>6th Bryan Away</td>
<td>7th Bryan Away</td>
<td>8th Bryan Away</td>
<td>9th Bryan Away</td>
<td>10th Bryan Away</td>
<td bgcolor="#FFA500">11th '''Start of term'''</td>
<td bgcolor="#CCCCCC">12th </td>
</tr>
<tr valign="top">
<td>13th </td>
<td>14th </td>
<td>15th </td>
<td>16th </td>
<td>17th </td>
<td bgcolor="#CCCCCC">18th </td>
<td bgcolor="#CCCCCC">18th </td>
</tr>
<tr valign="top">
<td>20th </td>
<td>21st </td>
<td>22nd </td>
<td>23rd </td>
<td>24th </td>
<td bgcolor="#CCCCCC">25th </td>
<td bgcolor="#CCCCCC">26th </td>
</tr>
</table>

Mod:Hunt Research Group/calendar

2013-11-20T13:41:33Z

Bw1911: /* Calendar */

== Calendar ==

*Tricia (Not Done)
*Abdihakim Hassan (Not Done)
*Bryan Ward (Not Done)
*Claire Ashworth (Done)
*Matthew Clough (Not Done)
*Precious Ugbomah (Not Done)
*Richard Matthews (Done)
*Vincent Chen (Not Done)
*Gabriel Lau (Not Done)
*Rebecca Rowe (Not Done)
*Patricia Ho (Not Done)
*Giacomo Damilano (Not Done)

<table border="1" cellpadding="5" width="1190">
<tr bgcolor="#66CCFF">
<th width="170px">Mon</th>
<th width="170px">Tues</th>
<th width="170px">Wed</th>
<th width="170px">Thur</th>
<th width="170px">Fri</th>
<th width="170px" bgcolor="#CCCCCC">Sat</th>
<th width="170px" bgcolor="#CCCCCC">Sun</th>

<tr valign="top">
<td>28th </td>
<td>29th '''(Matthew)'''</td>
<td>30th </td>
<td>31st </td>
<td bgcolor="#4357CFF">1st November </td>
<td bgcolor="#CCCCCC">2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
</tr>
<tr valign="top">
<td>4th </td>
<td>5th '''(Vincent)'''</td>
<td>6th </td>
<td>7th </td>
<td>8th</td>
<td bgcolor="#CCCCCC">9th </td>
<td bgcolor="#CCCCCC">10th </td>
</tr>
<tr valign="top">
<td>11th </td>
<td>12th '''(Gabriel)'''</td>
<td>13th </td>
<td>14th </td>
<td>15th</td>
<td bgcolor="#CCCCCC">16th </td>
<td bgcolor="#CCCCCC">17th </td>
</tr>
<tr valign="top">
<td>18th </td>
<td>19th '''(Hakim)'''</td>
<td>20th </td>
<td>21st </td>
<td>22nd</td>
<td bgcolor="#CCCCCC">23rd </td>
<td bgcolor="#CCCCCC">24th </td>
</tr>
<tr valign="top">
<td>25th </td>
<td>26th '''(Group Outing)'''</td>
<td>27th </td>
<td>28th </td>
<td>29th</td>
<td bgcolor="#CCCCCC">30th </td>
<td bgcolor="#4357CFF">1st December </td>
</tr>
<tr valign="top">
<td>2nd </td>
<td>3rd '''(Richard)''' Bryan Away</td>
<td>4th Bryan Away</td>
<td>5th Bryan Away</td>
<td>6th Bryan Away</td>
<td bgcolor="#CCCCCC">7th </td>
<td bgcolor="#CCCCCC">8th </td>
</tr>
<tr valign="top">
<td>9th Bryan Away</td>
<td>10th '''(Becky)''' Bryan Away</td>
<td>11th </td>
<td>12th </td>
<td bgcolor="#FFA500">13th '''End of term'''</td>
<td bgcolor="#CCCCCC">14th </td>
<td bgcolor="#CCCCCC">15th </td>
</tr>
<tr valign="top">
<td>16th </td>
<td>17th '''(CV Workshop)'''</td>
<td>18th </td>
<td>19th </td>
<td>20th </td>
<td bgcolor="#CCCCCC">21st </td>
<td bgcolor="#CCCCCC">22nd </td>
</tr>
<tr valign="top">
<td bgcolor="#228B22">23rd '''College closed'''</td>
<td bgcolor="#228B22">24th '''College closed'''</td>
<td bgcolor="#228B22">25th '''College closed'''</td>
<td bgcolor="#228B22">26th '''College closed'''</td>
<td bgcolor="#228B22">27th '''College closed'''</td>
<td bgcolor="#228B22">28th '''College closed'''</td>
<td bgcolor="#228B22">29th '''College closed'''</td>
</tr>
<tr valign="top">
<td bgcolor="#228B22">30th '''College closed'''</td>
<td bgcolor="#228B22">31st '''College closed'''</td>
<td bgcolor="#4357CFF">1st January '''College closed'''</td>
<td>2nd Richard away Claire away </td>
<td>3rd Richard away Gabriel & Vincent - Science Communication Course Bryan Away</td>
<td bgcolor="#CCCCCC">4th Gabriel & Vincent - Science Communication Course Bryan Away</td>
<td bgcolor="#CCCCCC">5th Gabriel & Vincent - Science Communication Course Bryan Away</td>
</tr>
<tr valign="top">
<td>6th Bryan Away</td>
<td>7th Bryan Away</td>
<td>8th Bryan Away</td>
<td>9th Bryan Away</td>
<td>10th Bryan Away</td>
<td bgcolor="#FFA500">11th '''Start of term'''</td>
<td bgcolor="#CCCCCC">12th </td>
</tr>
<tr valign="top">
<td>13th </td>
<td>14th </td>
<td>15th </td>
<td>16th </td>
<td>17th </td>
<td bgcolor="#CCCCCC">18th </td>
<td bgcolor="#CCCCCC">18th </td>
</tr>
<tr valign="top">
<td>20th </td>
<td>21st </td>
<td>22nd </td>
<td>23rd </td>
<td>24th </td>
<td bgcolor="#CCCCCC">25th </td>
<td bgcolor="#CCCCCC">26th </td>
</tr>
</table>

Mod:Hunt Research Group/calendar

2013-07-18T11:59:03Z

Bw1911: /* Calendar */

== Calendar ==

*Tricia (Done)
*Abdihakim Hassan (Not Done)
*Bryan Ward (Not Done)
*Claire Ashworth (Not Done)
*Matthew Clough (Done)
*Precious Ugbomah (Done)
*Richard Matthews (Done)
*Vincent Chen (Not Done)
*Gabriel Lau (Not Done)
*Sarah Smith (Not Done)

{| class="wikitable" border="1" style="text-align:center"
|+ Theory Group Meetings: 2-3.30pm every other Thursday
!Meeting !! Topic || Name || Date
|-
| <s>1</s> || <s>Differentiation and Integration</s> || Matthew || <s>20th June</s>
|-
| <s>2</s> || <s>Differential Equations</s> || Claire || <s>27th</s> <s>June</s>
|-
| 3|| Matrix Mechanics ||Gabriel|| 25th July
|-
| 4 || Linear Algebra || Richard || 8th August
|-
| 5 || Perturbation Theory ||Precious & Bryan || 22nd August
|-
| 6 ||Fourier and Laplace Transformations || Vincent || 5th September
|}

<table border="1" cellpadding="5" width="1190">
<tr bgcolor="#66CCFF">
<th width="170px">Mon</th>
<th width="170px">Tues</th>
<th width="170px">Wed</th>
<th width="170px">Thur</th>
<th width="170px">Fri</th>
<th width="170px" bgcolor="#CCCCCC">Sat</th>
<th width="170px" bgcolor="#CCCCCC">Sun</th>
</tr>
<tr valign="top">
<td bgcolor="#4357CFF">1st July </td>
<td>2nd '''PhD Symposium '''</td>
<td>3rd </td>
<td>4th </td>
<td>5th Bryan Away ChemShell Workshop 10am-4pm</td>
<td bgcolor="#CCCCCC">6th </td>
<td bgcolor="#CCCCCC">7th </td>
</tr>
<tr valign="top">
<td>8th Richard Away Sarah Away Precious Away Bryan Away </td>
<td>9th '''(Vincent)''' Richard Away Sarah Away Matthew Away MSDG Precious Away </td>
<td>10th Richard Away Sarah Away Matthew Away MSDG Precious Away </td>
<td>11th Richard Away Sarah Away Matthew Away MSDG Precious Away </td>
<td>12th Richard Away Sarah Away Precious Away </td>
<td bgcolor="#CCCCCC">13th </td>
<td bgcolor="#CCCCCC">14th </td>
</tr>
<tr valign="top">
<td>15th Precious Away </td>
<td>16th '''(Gabriel)''' Precious Away </td>
<td>17th Precious Away </td>
<td>18th Matthew Away Precious Away </td>
<td>19th Matthew Away Precious away </td>
<td bgcolor="#CCCCCC">20th </td>
<td bgcolor="#CCCCCC">21st </td>
</tr>
<tr valign="top">
<td>22nd </td>
<td>23rd '''(Sarah)'''</td>
<td>24th </td>
<td>25th '''Theory Meeting''' </td>
<td>26th Matthew Away Bryan Away </td>
<td bgcolor="#CCCCCC">27th </td>
<td bgcolor="#CCCCCC">28th </td>
</tr>
<tr valign="top">
<td>29th Matthew Away </td>
<td>30th '''(Tricia)'''</td>
<td>31st </td>
<td bgcolor="#4357CFF">1st August </td>
<td>2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
<td bgcolor="#CCCCCC">4th Matthew/Claire-GSC-6</td>
</tr>
<tr valign="top">
<td>5th Tricia away Vincent Away Matthew/Claire-GSC-6</td>
<td>6th Tricia away Vincent Away Matthew/Claire-GSC-6 </td>
<td>7th Tricia away Vincent Away Bryan Away Matthew/Claire-GSC-6</td>
<td>8th '''Theory Meeting''' Tricia away Vincent Away Bryan Away</td>
<td>9th Tricia away Vincent Away Bryan Away</td>
<td bgcolor="#CCCCCC">10th </td>
<td bgcolor="#CCCCCC">11th </td>
</tr>
<tr valign="top">
<td>12th Tricia away Vincent Away Matthew Away Bryan Away</td>
<td>13th Tricia away Vincent Away Matthew Away Bryan Away</td>
<td>14th Tricia away Vincent Away Matthew Away Bryan Away</td>
<td>15th Tricia away Vincent Away Matthew Away Bryan Away</td>
<td>16th Tricia away Vincent Away Matthew Away Bryan Away</td>
<td bgcolor="#CCCCCC">17th </td>
<td bgcolor="#CCCCCC">18th </td>
</tr>
<tr valign="top">
<td>19th Vincent Away Bryan Away</td>
<td>20th Vincent Away</td>
<td>21st Vincent Away</td>
<td>22nd '''Theory Meeting''' Vincent Away</td>
<td>23rd Vincent Away</td>
<td bgcolor="#CCCCCC">24th </td>
<td bgcolor="#CCCCCC">25th </td>
</tr>
<tr valign="top">
<td bgcolor="#2E8B57">26th College Closed '''Bank Holiday'''</td>
<td>27th </td>
<td>28th </td>
<td>29th </td>
<td>30th </td>
<td bgcolor="#CCCCCC">31st </td>
<td bgcolor="#4357CFF">1st September </td>
</tr>
<tr valign="top">
<td>2nd Tricia -CPMD 2013</td>
<td>3rd Tricia -CPMD 2013</td>
<td>4th Tricia -CPMD 2013</td>
<td>5th '''Theory Meeting''' Tricia -CPMD 2013</td>
<td>6th Tricia -CPMD 2013</td>
<td bgcolor="#CCCCCC">7th </td>
<td bgcolor="#CCCCCC">8th </td>
</tr>
<tr valign="top">
<td>9th Tricia away </td>
<td>10th Tricia away </td>
<td>11th Tricia away </td>
<td>12th Tricia away Claire-Rio Workshop </td>
<td>13th Tricia away Claire-Rio Workshop </td>
<td bgcolor="#CCCCCC">14th </td>
<td bgcolor="#CCCCCC">15th </td>
</tr>
<tr valign="top">
<td>16th </td>
<td>17th </td>
<td>18th </td>
<td>19th '''Theory Meeting''' </td>
<td>20th </td>
<td bgcolor="#CCCCCC">21st </td>
<td bgcolor="#CCCCCC">22nd </td>
</tr>
<tr valign="top">
<td>23rd </td>
<td>24th </td>
<td>25th </td>
<td>26th </td>
<td>27th </td>
<td bgcolor="#FFA500">28th '''Start of Term'''</td>
<td bgcolor="#CCCCCC">29th </td>
</tr>
<tr valign="top">
<td>30th </td>
<td bgcolor="#4357CFF">1st October </td>
<td>2nd </td>
<td>3rd '''Theory Meeting''' </td>
<td>4th </td>
<td bgcolor="#CCCCCC">5th </td>
<td bgcolor="#CCCCCC">6th </td>
</tr>
</table>

Mod:Hunt Research Group/calendar

2013-07-10T16:22:39Z

Bw1911: /* Calendar */

== Calendar ==

*Tricia (Done)
*Abdihakim Hassan (Not Done)
*Bryan Ward (Not Done)
*Claire Ashworth (Not Done)
*Matthew Clough (Done)
*Precious Ugbomah (Done)
*Richard Matthews (Done)
*Vincent Chen (Not Done)
*Gabriel Lau (Not Done)
*Sarah Smith (Not Done)

{| class="wikitable" border="1" style="text-align:center"
|+ Theory Group Meetings: 2-3.30pm every other Thursday
!Meeting !! Topic || Name || Date
|-
| <s>1</s> || <s>Differentiation and Integration</s> || Matthew || <s>20th June</s>
|-
| <s>2</s> || <s>Differential Equations</s> || Claire || <s>27th</s> <s>June</s>
|-
| 3|| Matrix Mechanics ||Gabriel|| 25th July
|-
| 4 || Linear Algebra || Richard || 8th August
|-
| 5 || Perturbation Theory ||Precious & Bryan || 22nd August
|-
| 6 ||Fourier and Laplace Transformations || Vincent || 5th September
|}

<table border="1" cellpadding="5" width="1190">
<tr bgcolor="#66CCFF">
<th width="170px">Mon</th>
<th width="170px">Tues</th>
<th width="170px">Wed</th>
<th width="170px">Thur</th>
<th width="170px">Fri</th>
<th width="170px" bgcolor="#CCCCCC">Sat</th>
<th width="170px" bgcolor="#CCCCCC">Sun</th>
</tr>
<tr valign="top">
<td bgcolor="#4357CFF">1st July </td>
<td>2nd '''PhD Symposium '''</td>
<td>3rd </td>
<td>4th </td>
<td>5th Bryan Away ChemShell Workshop 10am-4pm</td>
<td bgcolor="#CCCCCC">6th </td>
<td bgcolor="#CCCCCC">7th </td>
</tr>
<tr valign="top">
<td>8th Richard Away Sarah Away Precious Away Bryan Away </td>
<td>9th '''(Vincent)''' Richard Away Sarah Away Matthew Away MSDG Precious Away </td>
<td>10th Richard Away Sarah Away Matthew Away MSDG Precious Away </td>
<td>11th Richard Away Sarah Away Matthew Away MSDG Precious Away </td>
<td>12th Richard Away Sarah Away Precious Away </td>
<td bgcolor="#CCCCCC">13th </td>
<td bgcolor="#CCCCCC">14th </td>
</tr>
<tr valign="top">
<td>15th Precious Away </td>
<td>16th '''(Gabriel)''' Precious Away </td>
<td>17th Precious Away </td>
<td>18th Matthew Away Precious Away </td>
<td>19th Matthew Away Precious away </td>
<td bgcolor="#CCCCCC">20th </td>
<td bgcolor="#CCCCCC">21st </td>
</tr>
<tr valign="top">
<td>22nd </td>
<td>23rd '''(Sarah)'''</td>
<td>24th </td>
<td>25th '''Theory Meeting''' </td>
<td>26th Matthew Away </td>
<td bgcolor="#CCCCCC">27th </td>
<td bgcolor="#CCCCCC">28th </td>
</tr>
<tr valign="top">
<td>29th Matthew Away </td>
<td>30th '''(Tricia)'''</td>
<td>31st </td>
<td bgcolor="#4357CFF">1st August </td>
<td>2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
<td bgcolor="#CCCCCC">4th Matthew/Claire-GSC-6</td>
</tr>
<tr valign="top">
<td>5th Tricia away Vincent Away Matthew/Claire-GSC-6</td>
<td>6th Tricia away Vincent Away Matthew/Claire-GSC-6 </td>
<td>7th Tricia away Vincent Away Bryan Away Matthew/Claire-GSC-6</td>
<td>8th '''Theory Meeting''' Tricia away Vincent Away Bryan Away</td>
<td>9th Tricia away Vincent Away Bryan Away</td>
<td bgcolor="#CCCCCC">10th </td>
<td bgcolor="#CCCCCC">11th </td>
</tr>
<tr valign="top">
<td>12th Tricia away Vincent Away Matthew Away Bryan Away</td>
<td>13th Tricia away Vincent Away Matthew Away Bryan Away</td>
<td>14th Tricia away Vincent Away Matthew Away Bryan Away</td>
<td>15th Tricia away Vincent Away Matthew Away Bryan Away</td>
<td>16th Tricia away Vincent Away Matthew Away Bryan Away</td>
<td bgcolor="#CCCCCC">17th </td>
<td bgcolor="#CCCCCC">18th </td>
</tr>
<tr valign="top">
<td>19th Vincent Away Bryan Away</td>
<td>20th Vincent Away</td>
<td>21st Vincent Away</td>
<td>22nd '''Theory Meeting''' Vincent Away</td>
<td>23rd Vincent Away</td>
<td bgcolor="#CCCCCC">24th </td>
<td bgcolor="#CCCCCC">25th </td>
</tr>
<tr valign="top">
<td bgcolor="#2E8B57">26th College Closed '''Bank Holiday'''</td>
<td>27th </td>
<td>28th </td>
<td>29th </td>
<td>30th </td>
<td bgcolor="#CCCCCC">31st </td>
<td bgcolor="#4357CFF">1st September </td>
</tr>
<tr valign="top">
<td>2nd Tricia -CPMD 2013</td>
<td>3rd Tricia -CPMD 2013</td>
<td>4th Tricia -CPMD 2013</td>
<td>5th '''Theory Meeting''' Tricia -CPMD 2013</td>
<td>6th Tricia -CPMD 2013</td>
<td bgcolor="#CCCCCC">7th </td>
<td bgcolor="#CCCCCC">8th </td>
</tr>
<tr valign="top">
<td>9th </td>
<td>10th </td>
<td>11th </td>
<td>12th </td>
<td>13th </td>
<td bgcolor="#CCCCCC">14th </td>
<td bgcolor="#CCCCCC">15th </td>
</tr>
<tr valign="top">
<td>16th </td>
<td>17th </td>
<td>18th </td>
<td>19th '''Theory Meeting''' </td>
<td>20th </td>
<td bgcolor="#CCCCCC">21st </td>
<td bgcolor="#CCCCCC">22nd </td>
</tr>
<tr valign="top">
<td>23rd </td>
<td>24th </td>
<td>25th </td>
<td>26th </td>
<td>27th </td>
<td bgcolor="#FFA500">28th '''Start of Term'''</td>
<td bgcolor="#CCCCCC">29th </td>
</tr>
<tr valign="top">
<td>30th </td>
<td bgcolor="#4357CFF">1st October </td>
<td>2nd </td>
<td>3rd '''Theory Meeting''' </td>
<td>4th </td>
<td bgcolor="#CCCCCC">5th </td>
<td bgcolor="#CCCCCC">6th </td>
</tr>
</table>

Mod:Hunt Research Group/calendar

2013-06-28T15:16:57Z

Bw1911: /* Calendar */

== Calendar ==

*Tricia (Done)
*Abdihakim Hassan (Not Done)
*Bryan Ward (Not Done)
*Claire Ashworth (Not Done)
*Matthew Clough (Not Done)
*Precious Ugbomah (Done)
*Richard Matthews (Not Done)
*Vincent Chen (Not Done)
*Gabriel Lau (Not Done)
*Sarah Smith (Not Done)

{| class="wikitable" border="1" style="text-align:center"
|+ Theory Group Meetings: 2-3.30pm every other Thursday
!Meeting !! Topic || Name || Date
|-
| <s>1</s> || <s>Differentiation and Integration</s> || Matthew || <s>20th June</s>
|-
| <s>2</s> || <s>Differential Equations</s> || Claire || <s>27th</s> <s>June</s>
|-
| 3|| Matrix Mechanics ||Gabriel|| 11th July
|-
| 4 || Linear Algebra || Richard || 25th July
|-
| 5 || Perturbation Theory ||Precious & Bryan || 8th August
|-
| 6 ||Fourier and Laplace Transformations || Vincent || TBD
|}

 
<table border="1" cellpadding="5" width="1190">
<tr bgcolor="#66CCFF">
<th width="170px">Mon</th>
<th width="170px">Tues</th>
<th width="170px">Wed</th>
<th width="170px">Thur</th>
<th width="170px">Fri</th>
<th width="170px" bgcolor="#CCCCCC">Sat</th>
<th width="170px" bgcolor="#CCCCCC">Sun</th>
</tr>
<tr valign="top">
<td>29th </td>
<td>30th </td>
<td bgcolor="#4357CFF">1st May </td>
<td>2nd Matthew away </td>
<td>3rd Matthew away </td>
<td bgcolor="#CCCCCC">4th </td>
<td bgcolor="#CCCCCC">5th </td>
</tr>
<tr valign="top">
<td bgcolor="#2E8B57">6th College Closed '''Bank Holiday'''</td>
<td>7th </td>
<td>8th </td>
<td>9th </td>
<td>10th </td>
<td bgcolor="#CCCCCC">11th </td>
<td bgcolor="#CCCCCC">12th </td>
</tr>
<tr valign="top">
<td>13th </td>
<td>14th </td>
<td>15th </td>
<td>16th </td>
<td>17th </td>
<td bgcolor="#CCCCCC">18th </td>
<td bgcolor="#CCCCCC">19th </td>
</tr>
<tr valign="top">
<td>20th </td>
<td>21st ''(Richard)''</td>
<td>22nd </td>
<td>23rd </td>
<td>24th </td>
<td bgcolor="#CCCCCC">25th </td>
<td bgcolor="#CCCCCC">26th </td>
</tr>
<tr valign="top">
<td bgcolor="#2E8B57">27th College Closed '''Bank Holiday'''</td>
<td>28th ''(Hakim)''</td>
<td>29th </td>
<td>30th </td>
<td>31st 2nd Yr PhD Students: '''deadline'''-submission of draft poster (A4 copy) and full title to Blackboard</td>
<td bgcolor="#4357CFF">1st June </td>
<td bgcolor="#CCCCCC">2nd </td>
</tr>
<tr valign="top">
<td>3rd </td>
<td>4th ''(Bryan)''</td>
<td>5th </td>
<td>6th </td>
<td>7th </td>
<td bgcolor="#CCCCCC">8th </td>
<td bgcolor="#CCCCCC">9th </td>
</tr>
<tr valign="top">
<td>10th </td>
<td>11th ''(Claire)''</td>
<td>12th </td>
<td>13th </td>
<td>14th </td>
<td bgcolor="#CCCCCC">15th </td>
<td bgcolor="#CCCCCC">16th </td>
</tr>
<tr valign="top">
<td>17th </td>
<td>18th ''(Precious)''</td>
<td>19th Tricia away</td>
<td>20th '''Theory Meeting''' Tricia away</td>
<td>21st Tricia away Claire work from home</td>
<td bgcolor="#CCCCCC">22nd </td>
<td bgcolor="#CCCCCC">23rd </td>
</tr>
<tr valign="top">
<td>24th Tricia away</td>
<td>25th ''(Matthew)''</td>
<td>26th 2nd Yr PhD Students: '''deadline'''-submission of final poster (A4 copy) to Blackboard</td>
<td>27th '''Theory Meeting''' </td>
<td>28th </td>
<td bgcolor="#CCCCCC">29th </td>
<td bgcolor="#CCCCCC">30th </td>
</tr>
<tr valign="top">
<td bgcolor="#4357CFF">1st July </td>
<td>2nd '''PhD Symposium '''</td>
<td>3rd </td>
<td>4th </td>
<td>5th Bryan Away ChemShell Workshop 10am-4pm</td>
<td bgcolor="#CCCCCC">6th </td>
<td bgcolor="#CCCCCC">7th </td>
</tr>
<tr valign="top">
<td>8th Sarah Away Precious Away Bryan Away </td>
<td>9th ''(Vincent)'' Sarah Away Precious Away </td>
<td>10th Sarah Away Precious Away </td>
<td>11th '''Theory Meeting''' Sarah Away Precious Away </td>
<td>12th Sarah Away Precious Away </td>
<td bgcolor="#CCCCCC">13th </td>
<td bgcolor="#CCCCCC">14th </td>
</tr>
<tr valign="top">
<td>15th Precious Away </td>
<td>16th ''(Sarah)'' Precious Away </td>
<td>17th Precious Away </td>
<td>18th Precious Away </td>
<td>19th </td>
<td bgcolor="#CCCCCC">20th </td>
<td bgcolor="#CCCCCC">21st </td>
</tr>
<tr valign="top">
<td>22nd </td>
<td>23rd ''(Gabriel)''</td>
<td>24th </td>
<td>25th '''Theory Meeting''' </td>
<td>26th </td>
<td bgcolor="#CCCCCC">27th </td>
<td bgcolor="#CCCCCC">28th </td>
</tr>
<tr valign="top">
<td>29th </td>
<td>30th ''(Tricia)''</td>
<td>31st </td>
<td bgcolor="#4357CFF">1st August </td>
<td>2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
<td bgcolor="#CCCCCC">4th Matthew/Claire-GSC-6</td>
</tr>
<tr valign="top">
<td>5th Tricia away Vincent Away Matthew/Claire-GSC-6</td>
<td>6th Tricia away (Richard) Vincent Away Matthew/Claire-GSC-6 </td>
<td>7th Tricia away Vincent Away Matthew/Claire-GSC-6</td>
<td>8th '''Theory Meeting'''Tricia away Vincent Away</td>
<td>9th Tricia away Vincent Away</td>
<td bgcolor="#CCCCCC">10th </td>
<td bgcolor="#CCCCCC">11th </td>
</tr>
<tr valign="top">
<td>12th Tricia away Vincent Away </td>
<td>13th Tricia away Vincent Away</td>
<td>14th Tricia away Vincent Away</td>
<td>15th Tricia away Vincent Away</td>
<td>16th Tricia away Vincent Away</td>
<td bgcolor="#CCCCCC">17th </td>
<td bgcolor="#CCCCCC">18th </td>
</tr>
<tr valign="top">
<td>19th Vincent Away </td>
<td>20th Vincent Away</td>
<td>21st Vincent Away</td>
<td>22nd '''Theory Meeting''' Vincent Away</td>
<td>23rd Vincent Away</td>
<td bgcolor="#CCCCCC">24th </td>
<td bgcolor="#CCCCCC">25th </td>
</tr>
<tr valign="top">
<td bgcolor="#2E8B57">26th College Closed '''Bank Holiday'''</td>
<td>27th </td>
<td>28th </td>
<td>29th </td>
<td>30th </td>
<td bgcolor="#CCCCCC">31st </td>
<td bgcolor="#4357CFF">1st September </td>
</tr>
</table>

Mod:Hunt Research Group/calendar

2013-03-25T13:43:14Z

Bw1911: /* Calendar */

== Calendar ==

*Tricia (Done)
*Abdihakim Hassan (Not Done)
*Bryan Ward (Done)
*Claire Ashworth (Done)
*Matthew Clough (Not Done)
*Dimitrios Katsikadakos (Not Done)
*Ling Ge (Not Done)
*Precious Ugbomah (Done)
*Richard Matthews (Not Done)
*Vincent Chen (Done)
*Gabriel Lau (Not Done)
*Sarah Smith (Not Done)

{| class="wikitable" border="1" style="text-align:center"
|+ Group Meetings: Tuesday 3pm
! Week !! Meeting
|-
| 1 || Theory
|-
| 2 || Ionic Liquids: Structure and Reactivity
|-
| 3|| Rio Tinto (Chemistry)
|-
| 4 || Catalysis and Water
|-
| (5) || CAKE TIME! (i.e. social)
|}

 
<table border="1" cellpadding="5">
<tr bgcolor="#66CCFF">
<th width="115px">Mon</th>
<th width="115px">Tues</th>
<th width="115px">Wed</th>
<th width="115px">Thur</th>
<th width="115px">Fri</th>
<th width="115px" bgcolor="#CCCCCC">Sat</th>
<th width="115px" bgcolor="#CCCCCC">Sun</th>
</tr>
<tr valign="top">
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td bgcolor="#4357CFF">1st February Claire Away</td>
<td bgcolor="#CCCCCC">2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
</tr>
<tr valign="top">
<td>4th </td>
<td>5th ''(Theory)'' </td>
<td>6th </td>
<td>7th </td>
<td>8th </td>
<td bgcolor="#CCCCCC">9th </td>
<td bgcolor="#CCCCCC">10th </td>
</tr>
<tr valign="top">
<td>11th </td>
<td>12th ''(ILs)'' </td>
<td>13th </td>
<td>14th Matthew Away </td>
<td>15th </td>
<td bgcolor="#CCCCCC">16th </td>
<td bgcolor="#CCCCCC">17th </td>
</tr>
<tr valign="top">
<td>18th </td>
<td>19th ''(Rio)''</td>
<td>20th Claire working from home</td>
<td>21st </td>
<td>22nd </td>
<td bgcolor="#CCCCCC">23rd </td>
<td bgcolor="#CCCCCC">24th </td>
</tr>
<tr valign="top">
<td>25th </td>
<td>26th ''(Cat.+H2O)'' </td>
<td>27th </td>
<td>28th </td>
<td bgcolor="#4357CFF">1st March </td>
<td bgcolor="#CCCCCC">2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
</tr>
<tr valign="top">
<td >4th </td>
<td>5th ''(Theory)'' </td>
<td>6th </td>
<td>7th </td>
<td>8th </td>
<td bgcolor="#CCCCCC">9th </td>
<td bgcolor="#CCCCCC">10th </td>
</tr>
<tr valign="top">
<td>11th </td>
<td>12th ''(ILs)'' </td>
<td>13th </td>
<td>14th </td>
<td>15th </td>
<td bgcolor="#CCCCCC">16th </td>
<td bgcolor="#CCCCCC">17th </td>
</tr>
<tr valign="top">
<td>18th </td>
<td>19th ''(Rio)'' </td>
<td>20th </td>
<td>21st </td>
<td bgcolor="#FFCCFF">22nd End of Spring Term</td>
<td bgcolor="#CCCCCC">23rd </td>
<td bgcolor="#CCCCCC">24th </td>
</tr>
<tr valign="top">
<td> 25th</td>
<td>26th ''(Cat.+H2O)'' Precious away </td>
<td>27th Precious, Tricia away </td>
<td bgcolor="#2E8B57">28th College Closed Precious away on a course, Tricia in but not available</td>
<td bgcolor="#2E8B57">29th College Closed '''Good Friday''' Holiday</td>
<td bgcolor="#2E8B57">30th College Closed Holiday</td>
<td bgcolor="#2E8B57">31st College Closed '''Easter Sunday''' Holiday</td>
</tr>
<tr valign="top">
<td bgcolor="#4357CFF">1st April College Closed '''Easter Monday''' Precious away Claire away </td>
<td bgcolor="#2E8B57">2nd College Closed Bryan, Precious, Claire away Tricia work from home</td>
<td>3rd Precious, Tricia working from home Claire away</td>
<td>4th Claire, Tricia work from home</td>
<td>5th Claire working at home Tricia will be in!</td>
<td bgcolor="#CCCCCC">6th </td>
<td bgcolor="#CCCCCC">7th </td>
</tr>

<tr valign="top">
<td>8th </td>
<td>9th ''(ILs)''</td>
<td>10th </td>
<td>11th </td>
<td>12th 6 month progress report '''deadline''' (Blackboard) </td>
<td bgcolor="#CCCCCC">13th </td>
<td bgcolor="#CCCCCC">14th </td>
</tr>
<tr valign="top">
<td>15th Vincent away </td>
<td>16th ''(Rio)'' Vincent away</td>
<td>17th Vincent away</td>
<td>18th Vincent away</td>
<td>19th Vincent away</td>
<td bgcolor="#CCCCCC">20th </td>
<td bgcolor="#CCCCCC">21st </td>
</tr>
<tr valign="top">
<td>22nd Vincent away</td>
<td>23rd ''(Cat.+H2O)'' Vincent away</td>
<td>24th Vincent away</td>
<td>25th Vincent away </td>
<td>26th Vincent away</td>
<td bgcolor="#FFCCFF">27th Start of Summer Term</td>
<td bgcolor="#CCCCCC">28th </td>
</tr>
<tr valign="top">
<td>29th </td>
<td>30th ''(CAKE)''</td>
<td bgcolor="#4357CFF">1st May </td>
<td>2nd </td>
<td>3rd </td>
<td bgcolor="#CCCCCC">4th </td>
<td bgcolor="#CCCCCC">5th </td>
</tr>
<tr valign="top">
<td bgcolor="#2E8B57">6th College Closed '''Bank Holiday'''</td>
<td>7th ''(Theory)''</td>
<td>8th </td>
<td>9th </td>
<td>10th </td>
<td bgcolor="#CCCCCC">11th </td>
<td bgcolor="#CCCCCC">12th </td>
</tr>
<tr valign="top">
<td>13th </td>
<td>14th ''(ILs)''</td>
<td>15th </td>
<td>16th </td>
<td>17th </td>
<td bgcolor="#CCCCCC">18th </td>
<td bgcolor="#CCCCCC">19th </td>
</tr>
<tr valign="top">
<td>20th </td>
<td>21st ''(Rio)''</td>
<td>22nd </td>
<td>23rd </td>
<td>24th </td>
<td bgcolor="#CCCCCC">25th </td>
<td bgcolor="#CCCCCC">26th </td>
</tr>
<tr valign="top">
<td bgcolor="#2E8B57">27th College Closed '''Bank Holiday'''</td>
<td>28th ''(Cat.+H2O)''</td>
<td>29th </td>
<td>30th </td>
<td>31st 2nd Yr PhD Students: '''deadline''' for submission of draft poster to Blackboard</td>
<td bgcolor="#4357CFF">1st June </td>
<td bgcolor="#CCCCCC">2nd </td>
</tr>

</table>

Mod:Hunt Research Group/calendar

2013-03-25T13:42:48Z

Bw1911: /* Calendar */

== Calendar ==

*Tricia (Done)
*Abdihakim Hassan (Not Done)
*Bryan Ward (Not Done)
*Claire Ashworth (Done)
*Matthew Clough (Not Done)
*Dimitrios Katsikadakos (Not Done)
*Ling Ge (Not Done)
*Precious Ugbomah (Done)
*Richard Matthews (Not Done)
*Vincent Chen (Done)
*Gabriel Lau (Not Done)
*Sarah Smith (Not Done)

{| class="wikitable" border="1" style="text-align:center"
|+ Group Meetings: Tuesday 3pm
! Week !! Meeting
|-
| 1 || Theory
|-
| 2 || Ionic Liquids: Structure and Reactivity
|-
| 3|| Rio Tinto (Chemistry)
|-
| 4 || Catalysis and Water
|-
| (5) || CAKE TIME! (i.e. social)
|}

 
<table border="1" cellpadding="5">
<tr bgcolor="#66CCFF">
<th width="115px">Mon</th>
<th width="115px">Tues</th>
<th width="115px">Wed</th>
<th width="115px">Thur</th>
<th width="115px">Fri</th>
<th width="115px" bgcolor="#CCCCCC">Sat</th>
<th width="115px" bgcolor="#CCCCCC">Sun</th>
</tr>
<tr valign="top">
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td bgcolor="#4357CFF">1st February Claire Away</td>
<td bgcolor="#CCCCCC">2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
</tr>
<tr valign="top">
<td>4th </td>
<td>5th ''(Theory)'' </td>
<td>6th </td>
<td>7th </td>
<td>8th </td>
<td bgcolor="#CCCCCC">9th </td>
<td bgcolor="#CCCCCC">10th </td>
</tr>
<tr valign="top">
<td>11th </td>
<td>12th ''(ILs)'' </td>
<td>13th </td>
<td>14th Matthew Away </td>
<td>15th </td>
<td bgcolor="#CCCCCC">16th </td>
<td bgcolor="#CCCCCC">17th </td>
</tr>
<tr valign="top">
<td>18th </td>
<td>19th ''(Rio)''</td>
<td>20th Claire working from home</td>
<td>21st </td>
<td>22nd </td>
<td bgcolor="#CCCCCC">23rd </td>
<td bgcolor="#CCCCCC">24th </td>
</tr>
<tr valign="top">
<td>25th </td>
<td>26th ''(Cat.+H2O)'' </td>
<td>27th </td>
<td>28th </td>
<td bgcolor="#4357CFF">1st March </td>
<td bgcolor="#CCCCCC">2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
</tr>
<tr valign="top">
<td >4th </td>
<td>5th ''(Theory)'' </td>
<td>6th </td>
<td>7th </td>
<td>8th </td>
<td bgcolor="#CCCCCC">9th </td>
<td bgcolor="#CCCCCC">10th </td>
</tr>
<tr valign="top">
<td>11th </td>
<td>12th ''(ILs)'' </td>
<td>13th </td>
<td>14th </td>
<td>15th </td>
<td bgcolor="#CCCCCC">16th </td>
<td bgcolor="#CCCCCC">17th </td>
</tr>
<tr valign="top">
<td>18th </td>
<td>19th ''(Rio)'' </td>
<td>20th </td>
<td>21st </td>
<td bgcolor="#FFCCFF">22nd End of Spring Term</td>
<td bgcolor="#CCCCCC">23rd </td>
<td bgcolor="#CCCCCC">24th </td>
</tr>
<tr valign="top">
<td> 25th</td>
<td>26th ''(Cat.+H2O)'' Precious away </td>
<td>27th Precious, Tricia away </td>
<td bgcolor="#2E8B57">28th College Closed Precious away on a course, Tricia in but not available</td>
<td bgcolor="#2E8B57">29th College Closed '''Good Friday''' Holiday</td>
<td bgcolor="#2E8B57">30th College Closed Holiday</td>
<td bgcolor="#2E8B57">31st College Closed '''Easter Sunday''' Holiday</td>
</tr>
<tr valign="top">
<td bgcolor="#4357CFF">1st April College Closed '''Easter Monday''' Precious away Claire away </td>
<td bgcolor="#2E8B57">2nd College Closed Bryan, Precious, Claire away Tricia work from home</td>
<td>3rd Precious, Tricia working from home Claire away</td>
<td>4th Claire, Tricia work from home</td>
<td>5th Claire working at home Tricia will be in!</td>
<td bgcolor="#CCCCCC">6th </td>
<td bgcolor="#CCCCCC">7th </td>
</tr>

<tr valign="top">
<td>8th </td>
<td>9th ''(ILs)''</td>
<td>10th </td>
<td>11th </td>
<td>12th 6 month progress report '''deadline''' (Blackboard) </td>
<td bgcolor="#CCCCCC">13th </td>
<td bgcolor="#CCCCCC">14th </td>
</tr>
<tr valign="top">
<td>15th Vincent away </td>
<td>16th ''(Rio)'' Vincent away</td>
<td>17th Vincent away</td>
<td>18th Vincent away</td>
<td>19th Vincent away</td>
<td bgcolor="#CCCCCC">20th </td>
<td bgcolor="#CCCCCC">21st </td>
</tr>
<tr valign="top">
<td>22nd Vincent away</td>
<td>23rd ''(Cat.+H2O)'' Vincent away</td>
<td>24th Vincent away</td>
<td>25th Vincent away </td>
<td>26th Vincent away</td>
<td bgcolor="#FFCCFF">27th Start of Summer Term</td>
<td bgcolor="#CCCCCC">28th </td>
</tr>
<tr valign="top">
<td>29th </td>
<td>30th ''(CAKE)''</td>
<td bgcolor="#4357CFF">1st May </td>
<td>2nd </td>
<td>3rd </td>
<td bgcolor="#CCCCCC">4th </td>
<td bgcolor="#CCCCCC">5th </td>
</tr>
<tr valign="top">
<td bgcolor="#2E8B57">6th College Closed '''Bank Holiday'''</td>
<td>7th ''(Theory)''</td>
<td>8th </td>
<td>9th </td>
<td>10th </td>
<td bgcolor="#CCCCCC">11th </td>
<td bgcolor="#CCCCCC">12th </td>
</tr>
<tr valign="top">
<td>13th </td>
<td>14th ''(ILs)''</td>
<td>15th </td>
<td>16th </td>
<td>17th </td>
<td bgcolor="#CCCCCC">18th </td>
<td bgcolor="#CCCCCC">19th </td>
</tr>
<tr valign="top">
<td>20th </td>
<td>21st ''(Rio)''</td>
<td>22nd </td>
<td>23rd </td>
<td>24th </td>
<td bgcolor="#CCCCCC">25th </td>
<td bgcolor="#CCCCCC">26th </td>
</tr>
<tr valign="top">
<td bgcolor="#2E8B57">27th College Closed '''Bank Holiday'''</td>
<td>28th ''(Cat.+H2O)''</td>
<td>29th </td>
<td>30th </td>
<td>31st 2nd Yr PhD Students: '''deadline''' for submission of draft poster to Blackboard</td>
<td bgcolor="#4357CFF">1st June </td>
<td bgcolor="#CCCCCC">2nd </td>
</tr>

</table>

Y2s-spring-azulene

2013-03-12T15:35:11Z

Bw1911: /* Facilities and support */

=Second Year Synthesis Labs, Spring Term=

=Computational Exercise, Experiment 3S: Preparation of Azulene=

The purpose of this computational exercise is to gain experience with the Gaussian system for molecular modelling and to show the relevance of modelling in a practical context within Chemistry.

You will have done some modelling exercises this year with Ghemical and ChemBio3D, however these programs have some limitations on what is possible. Gaussian is a much more powerful tool for molecular calculations, however it is correspondingly more complex to use. Through this exercise for experiment 3S you will gain a level of familiarity with Gaussian which will be of benefit to you throughout your career in practical Chemistry. This exercise '''should not take more than 3 hours''', and each calculation should not take more than 5 minutes to run on the cluster computers. It is intended that this exercise can be done while your final reflux of the azulene preparation is in progress. '''ENSURE YOUR REACTION IS SAFE BEFORE LEAVING THE LAB'''

Gaussian is only available on cluster computers within the Chemistry department; the departmental site license does not cover installations on personal computers.

==Facilities and support==

The 2nd floor computer cluster has been booked on Thursday afternoons from 1pm to 4pm for this exercise. Second year students carrying out Experiment 3S have priority over other users at this time.

The demonstrator providing support for this exercise is '''Lee Thompson''' ('''email:'''

l.thompson09 @imperial.ac.uk). He will be 'on call' between 2 and 4pm on Thursday afternoons; if you are having difficulties or simply want to ask further questions, email Lee and he will come to the cluster to provide assistance.

==Introduction to the Gaussian Workflow==

Gaussian is a UNIX based system (though has been adapted to run on Microsoft Windows), and before a calculation can be run an ''input file'' must be created. This input file lays out the molecule, , the theory used to model the electrons and nuclei, the parameters under which the calculation will be run, whether to consider a solvent environment etc. The real power in Gaussian comes from its ability to ''nest'' calculations; that is to take the output of one calculation and carry it forward into another calculation, or combine the output of multiple calculations into a further calculation. This is useful for considerations of complex molecules or multiple molecules.

This process can be automated, however in this exercise you should set up each calculation to ensure you understand what is happening at each stage.

===Preparation of the input file===
The first step is to build the molecule of interest. This involves defining the position of all atoms in the molecule and the manner in which they are connected to each other, using either cartesian or ''z-matrix'' coordinates - understandably this is not easy for us to enter by hand even for a simple molecule such as methane! To help generate the input file we use the program "GaussView". This will act as the front end for Gaussian and will completely build the input file and submit it to Gaussian for us.

{|
! scope="col" width="500" |
! scope="col" width="300" |
|-
|Launch Gaussview
* Upon launching GaussView you should see a window layout as shown here (Figure 1). The main window contains the fragment display - this is the fragment which will be placed when you click in the Molecule Build window.
|[[File:Gv-screen2.png|thumb|upright=1.25|Figure 1]]
|-
|The GaussView toolbars
* The toolbars are exploded here to give you an idea what to expect (Figure 2). If in doubt, hover your mouse pointer over a toolbar item to see what it does. Build your molecule using the builder tools; to add an atom, select the atom required and click the end of the bond to which you wish to add it.
|[[File:Gv-screen1.png|thumb|upright=1.25|Figure 2]]
|-
|Modifying a bond
* To modify a bond, choose the bond tool you wish to use, then select the atoms between which the bond tool applies; to change the properties of a bond (single, double, aromatic etc), select the two atoms at either end of the bond (Figure 3). For a bond angle, select three atoms (to control the bond angle between them), and for a dihedral angle, select four atoms.
|[[File:Gv-screen3-2bond.png|thumb|upright=1.25|Figure 3]]
|}

Once you have built your molecule, you need to set up your calculation. The first step in this process is to optimise the structure of your molecule to the ground state minimum energy structure. If we calculate the molecules energy and plot this as a function of nuclear coordinates so that we obtain a ''Potential Energy Surface'', this corresponds to a well in the surface (e.g. the minimum in the Morse Potential). It is of most interest as in an ensemble of molecules at room temperature and pressure, most of them lie in this region of the PES and the spectroscopic properties observed reflect this.

====Setting up the calculation====
In the toolbar, select "Calculate -> Gaussian Calculation Setup" (or select the 'calculate' button from the toolbar). This will present you with the window shown in Figure 4.[[Image:Gv-screen4-calc1.png|thumb|250px|Figure 4: Setting up the Gaussian calculation]]

This gives all the parameters available for your calculation. This can look quite daunting at first glance, but a summary of the various tabs is shown below.

#Job Type:
#* Here you specify the calculation being run. Options available are:
#*# Energy: optimizes the electronic energy at a given set of nuclear coordinates
#*# Optimization: optimises the nuclear as well as electronic energy of a molecule
#*# Frequency
#*# Opt+Freq
#*# IRC
#*# Scan
#*# Stability
#*# NMR
# Method
#* This sets the theory and basis set for the job you are running (The basis set is a way to express the wavefunction in terms of simple mathematical functions called ''Gaussians'')
# Title
#* You can enter a title for your job here so you remember what it was
# Link [not needed in this exercise]
#* Here you can start to link jobs together
# General [not needed in this exercise]
#* This contains some general options for your calculations
# Guess
#* This defines the initial guess for the wavefunction, i.e. the distribution of electrons. As the calculation of the wavefunction is iterative (i.e. there is no analytical solution for all but the simplest of systems so we have to keep changing our guess until the energy stops changing, called convergence) the closer the guess is to the final solution the faster our calculation is. For the first calculation you will use the "Default" setting, however after this you will want to use the output of previous calculations. To do this, select "Read Checkpoint File" (note the checkpoint file MUST have the same filename as your input file, e.g., calc1.chk if your input file name is calc1.com)
# NBO [not needed in this exercise]
#* Helps the chemist visualize important features of the wavefunction by changing it to look more like orbitals found in atoms or diatoms.
# PBC [not needed in this exercise]
# Solvation
#* Here you can specify the effect of having a solvation shell around the molecule. This can affect spectra so is worth experimenting with.
# Add. Input [not used in this exercise]
#* You can specify additional input parameters, or use the results of other calculations in your new calculation.

====Optimizing the structure====

Set "Job Type" to "Optimize". In the "Method" tab, perform a "Ground State" "Semi-Empirical" calculation with "Default Spin", using the [http://en.wikipedia.org/wiki/Austin_Model_1 AM1 forcefield]. Give your job a "Title" and ensure your "Guess" is set to 'default'. If you wish, specify a "Solvation" environment (it is worth specifying the solvent in which you are going to record a spectrum to ensure a sound basis for comparison). Once done, select "Submit". You will be prompted to save an input file; give your file an appropriate name, and submit the job to Gaussian. This is a basic calculation and will perform the first step in optimizing the structure.

'''Gaussian output''':
Two output files will result; a checkpoint file (calc1.chk) and a log file (calc1.log). Both can be displayed in GaussView, but each display different parameters about the molecule.

A more accurate model can be obtained by doing further optimizations using progressively more accurate basis sets and feeding the results of one calculation into the next. Set up a further optimization (job type: Optimize) to perform a "ground state" [http://en.wikipedia.org/wiki/Density_functional_theory "DFT"] calculation with "default spin" using the [http://en.wikipedia.org/wiki/Hybrid_functional "B3LYP"] function. This function needs a [http://en.wikipedia.org/wiki/Basis_set_%28chemistry%29 basis set]; try first a calculation with the STO-3G basis set, then a further calculation with the 6-31Gd basis set. To use the previous checkpoint file (generated from the AM1 calculation above), select the "Guess" to "Read Checkpoint File". You must then save the Gaussian input file to the same filename as before for this to work. ('''This will overwrite your file''' - make sure you back up your original files first!)

'''BACKUP''' - It is good practice to backup your previous calculations, saving a copy of them to a different folder, or under a different filename. For example; if your working input filename is "calc1.com", you will obtain the output checkpoint of "calc1.chk". After doing one calculation, save a copy of this to a 'backup' directory and rename it to the conditions under which the calculation was performed; e.g., "calc1-input-AM1-optimize.chk", "calc1-input-AM1-optimize.com" etc.

Upon submitting the job to Gaussian, save your input file as "calc1.com" again, to match up with the checkpoint file from earlier calculations.

The reason for using several methods to optimize the structure is that at each stage we are using progressively more complex basis sets; by optimizing geometries with simpler basis sets first, we limit the number of trials required by the more complex calculations. Were we to use the most complex basis set to start with, a calculation would take much longer than the combined time of the preliminary stages.

After having optimized your structure with these operations, you can now determine some spectral characteristics of your molecule. For electronic spectra (UV/vis) we need to calculate orbital energies. Gaussian can predict an MO diagram for the molecule and a UV spectrum together with the MO transitions.

====Predicting UV/Vis spectra====

Having optimized the structure, we will use the checkpoint output from your final optimization to predict electronic spectra of your molecule.

Set "Job Type" to "Energy". The "Method" this time is a [http://en.wikipedia.org/wiki/Self_consistent_field "TD-SCF"] using "DFT" with a "B3LYP" function. Try using a STO-3G basis set. Remember to "Read Checkpoint File", and check the "Solvation" - this must be the same solvation shell on which the supporting calculations were based. Submit the file to Gaussian.

This may take up to 10 minutes to calculate depending on computer equipment.

Once run, load the log file into GaussView; this will then display your optimized molecule. You can now select Results -> UV/Vis spectrum to display a predicted UV/Vis spectrum. To identify the electronic transitions responsible for each peak, you will need to view the stream output file (Results -> View Stream Output File). This will look quite daunting, but scan through it; you will find a portion dedicated to "Excited states". This will tell you which MOs (molecular orbitals) electrons have been excited from/to for each peak in your UV/vis.

In order to make sense of this however, you will need to view the MO diagram. Click "Edit -> MOs", this will open a window with the MO diagram, within which you can display a graphic of each MO (select MO, click "Visualize", then "Update". You may need to reload the .chk file within the New MOs tab). You can then infer information about the change in electron density from the shapes of the MOs upon excitation of an electron, even predicting a qualitative change in dipoles. Images may be saved by right-clicking the graphics windows.

==Azulene exercise==

As part of the experiment, you will record a UV/vis spectrum of azulene. Use Gaussian to model azulene and to assign a transition for the three main peaks in the UV/vis spectrum. How would you expect the UV/Vis spectrum to change if one hydrogen atom around the bicyclic structure is substituted for a chlorine? Your analysis of the UV spectrum and correct identification of the main transitions will be assessed on Friday afternoon.

Compare the predicted UV/vis spectrum of Azulene with your experimentally recorded spectrum; if there are any differences, can you account for them?

It is worth bearing in mind that the output from your calculations (i.e., the excitation energy) will not exactly match with your experimental measurements (and may differ quite wildly, depending on your calculation input parameters) - '''why might this be'''?

'''Look on Blackboard for the "Criteria for Marking" to find out what to present to the marker.'''

Mod:timetable

2013-01-17T15:57:47Z

Bw1911: /* Timetable for computational experiments */

See also: [[Mod:timetable|Timetable]], [[mod:laptop|Laptop use]], [[mod:programs|Programs]], [[mod:organic|Module 1]], [[Mod:inorganic|Module 2]], [[Mod:physical|Module 3]],[[Mod:writeup|Writing up]]

= Timetable for computational experiments =

The 2012-2013 list of groups are available {{pdf|Lab allocations 2013.pdf|here:}}. If for whatever reason you have swapped a course, please let us know so that we do not allocate zero marks for you. For each group, the course runs for four weeks, during which time you have to attempt '''TWO''' modules and submit '''TWO''' Wiki reports of your experiments. The first of these is due on the Friday at 17.00 at the end of the first two weeks, and the second on the Friday at 17.00 at the end of four weeks.

Dr Hunt, Dr Bearpark and Professor Rzepa will be available for personal discussion as follows and at other times by email or by arrangement with them. However, it is best if you direct your questions to a demonstrator first, as they are on hand and can solve most problems straight away.
*Module 1 [mailto:rzepa@imperial.ac.uk Henry Rzepa (169)] Monday afternoons, Weeks 1-4 of the course, and Friday afternoons, weeks 2 and 4. Paul Dingwall will be available as a demonstrator 12-1 and 3-4 Tuesdays.
*Module 2 [mailto:p.hunt@imperial.ac.uk Patricia Hunt (167)] or [mailto:richard.matthews@imperial.ac.uk Richard Matthews] Tuesday afternoons 2-3, Weeks 1-4 of the course, and Friday 12-1, weeks 2 and 4. Bryan Ward will be available as a demonstrator 12-1 and 3-4 on Thursdays
*Module 3 [mailto:m.bearpark@imperial.ac.uk Michael Bearpark (160a)]. Thursday afternoons, Weeks 1-4 of the course, and as needed throughout the course. Lee Thompson will be available as a demonstrator 12-1 and 3-4 on Mondays.

== Specific times ==

*Week 1 (Monday): Laptop sign-out (12.00-12.30) from Room 237A.
*Day 1 (Monday): Check-up (have you got started) in level 2 computer room, Henry Rzepa.
*Laptop return is four weeks later (Monday) again in Room 242, 11-12 during the study week following the course. '''THIS SESSION hand in will be Tuesday 11 Dec 11-12'''.

Although the schedule shows activity for only Mon, Tue, Thur and Fri of any week, you are of course free to use your laptop 24/7 and to work at times which best suit you. We strongly recommend you attend the first day's introductory sessions, these will tell set you up for the rest of the lab. The timetable above is a guideline. You should spend approximately 8 working lab-days per module, using your judgement on how you can make most effective use of your time (thus you might decide to interleave two modules concurrently). Previous groups have shown that '''time management''' is a skill that has to be cultivated, and you will get a chance to do so with this course! It is up to you to manage your time, not to do too much and not to do too little. Ask a staff member if you are at all unsure.

== Report submission ==

Submit the URL for your Wiki report from [https://vle.imperial.ac.uk/webct/logon/5047144695021 this address] by the appropriate deadline. These deadlines are on the Friday of the end of the second week of the course for the first module you attempt, and again on the Friday of the 4th week of the course, at 17.00 for the second module you attempt. You can do the modules in any order you wish provided you hand two reports in over the four week period at the times indicated.

If we do not receive the URL of your report (submitted via the Blackboard system, and '''NOT''' emailed to the individual members of the course team), we will attempt to contact you by email within one working day (Mon-Fri) of the deadline to check it has not gone missing. You should expect to get a grade on blackboard within 10 working days. If you have heard nothing and have not received a grade in blackboard, please contact the relevant member of staff for each module (Henry Rzepa for mod 1), Tricia Hunt (Mod 2) or Mike Bearpark (module 3).

'''The coursework hand-in times are fixed, there will be a penalty applied for every 24hrs after 5pm of the submit date.''' Any sections completed by the hand-in date will be assessed for full marks, additional material added after this will incur a penalty. If you are having problems, are ill or have extenuating circumstances please see [mailto:p.hunt@ic.ac.uk Dr Hunt] as early as possible, extensions may be granted and will be determined on a case-by-case basis.

----
See also: [[Mod:timetable|Timetable]], [[mod:laptop|Laptop use]], [[mod:programs|Programs]], [[mod:organic|Module 1]], [[Mod:inorganic|Module 2]], [[Mod:physical|Module 3]], [[Mod:writeup|Writing up]]

Mod:timetable

2013-01-14T14:26:57Z

Bw1911:

See also: [[Mod:timetable|Timetable]], [[mod:laptop|Laptop use]], [[mod:programs|Programs]], [[mod:organic|Module 1]], [[Mod:inorganic|Module 2]], [[Mod:physical|Module 3]],[[Mod:writeup|Writing up]]

= Timetable for computational experiments =

The 2012-2013 list of groups are available {{pdf|Lab allocations 2013.pdf|here:}}. If for whatever reason you have swapped a course, please let us know so that we do not allocate zero marks for you. For each group, the course runs for four weeks, during which time you have to attempt '''TWO''' modules and submit '''TWO''' Wiki reports of your experiments. The first of these is due on the Friday at 17.00 at the end of the first two weeks, and the second on the Friday at 17.00 at the end of four weeks.

Dr Hunt, Dr Bearpark and Professor Rzepa will be available for personal discussion as follows and at other times by email or by arrangement with them. However, it is best if you direct your questions to a demonstrator first, as they are on hand and can solve most problems straight away.
*Module 1 [mailto:rzepa@imperial.ac.uk Henry Rzepa (169)] Monday afternoons, Weeks 1-4 of the course, and Friday afternoons, weeks 2 and 4. Paul Dingwall will be available as a demonstrator 12-1 and 3-4 Tuesdays.
*Module 2 [mailto:p.hunt@imperial.ac.uk Patricia Hunt (167)] or [mailto:richard.matthews@imperial.ac.uk Richard Matthews] Tuesday afternoons 2-3, Weeks 1-4 of the course, and Friday 12-1, weeks 2 and 4. Bryan Ward will be available as a demonstrator 12-1 and 4-5 on Thursdays
*Module 3 [mailto:m.bearpark@imperial.ac.uk Michael Bearpark (160a)]. Thursday afternoons, Weeks 1-4 of the course, and as needed throughout the course. Lee Thompson will be available as a demonstrator 12-1 and 3-4 on Mondays.

== Specific times ==

*Week 1 (Monday): Laptop sign-out (12.00-12.30) from Room 237A.
*Day 1 (Monday): Check-up (have you got started) in level 2 computer room, Henry Rzepa.
*Laptop return is four weeks later (Monday) again in Room 242, 11-12 during the study week following the course. '''THIS SESSION hand in will be Tuesday 11 Dec 11-12'''.

Although the schedule shows activity for only Mon, Tue, Thur and Fri of any week, you are of course free to use your laptop 24/7 and to work at times which best suit you. We strongly recommend you attend the first day's introductory sessions, these will tell set you up for the rest of the lab. The timetable above is a guideline. You should spend approximately 8 working lab-days per module, using your judgement on how you can make most effective use of your time (thus you might decide to interleave two modules concurrently). Previous groups have shown that '''time management''' is a skill that has to be cultivated, and you will get a chance to do so with this course! It is up to you to manage your time, not to do too much and not to do too little. Ask a staff member if you are at all unsure.

== Report submission ==

Submit the URL for your Wiki report from [https://vle.imperial.ac.uk/webct/logon/5047144695021 this address] by the appropriate deadline. These deadlines are on the Friday of the end of the second week of the course for the first module you attempt, and again on the Friday of the 4th week of the course, at 17.00 for the second module you attempt. You can do the modules in any order you wish provided you hand two reports in over the four week period at the times indicated.

If we do not receive the URL of your report (submitted via the Blackboard system, and '''NOT''' emailed to the individual members of the course team), we will attempt to contact you by email within one working day (Mon-Fri) of the deadline to check it has not gone missing. You should expect to get a grade on blackboard within 10 working days. If you have heard nothing and have not received a grade in blackboard, please contact the relevant member of staff for each module (Henry Rzepa for mod 1), Tricia Hunt (Mod 2) or Mike Bearpark (module 3).

'''The coursework hand-in times are fixed, there will be a penalty applied for every 24hrs after 5pm of the submit date.''' Any sections completed by the hand-in date will be assessed for full marks, additional material added after this will incur a penalty. If you are having problems, are ill or have extenuating circumstances please see [mailto:p.hunt@ic.ac.uk Dr Hunt] as early as possible, extensions may be granted and will be determined on a case-by-case basis.

----
See also: [[Mod:timetable|Timetable]], [[mod:laptop|Laptop use]], [[mod:programs|Programs]], [[mod:organic|Module 1]], [[Mod:inorganic|Module 2]], [[Mod:physical|Module 3]], [[Mod:writeup|Writing up]]

Mod:timetable

2013-01-14T14:26:28Z

Bw1911: /* Timetable for computational experiments */

See also: [[Mod:timetable|Timetable]],[[mod:laptop|Laptop use]], [[mod:programs|Programs]], [[mod:organic|Module 1]], [[Mod:inorganic|Module 2]], [[Mod:physical|Module 3]],[[Mod:writeup|Writing up]]

= Timetable for computational experiments =

The 2012-2013 list of groups are available {{pdf|Lab allocations 2013.pdf|here:}}. If for whatever reason you have swapped a course, please let us know so that we do not allocate zero marks for you. For each group, the course runs for four weeks, during which time you have to attempt '''TWO''' modules and submit '''TWO''' Wiki reports of your experiments. The first of these is due on the Friday at 17.00 at the end of the first two weeks, and the second on the Friday at 17.00 at the end of four weeks.

Dr Hunt, Dr Bearpark and Professor Rzepa will be available for personal discussion as follows and at other times by email or by arrangement with them. However, it is best if you direct your questions to a demonstrator first, as they are on hand and can solve most problems straight away.
*Module 1 [mailto:rzepa@imperial.ac.uk Henry Rzepa (169)] Monday afternoons, Weeks 1-4 of the course, and Friday afternoons, weeks 2 and 4. Paul Dingwall will be available as a demonstrator 12-1 and 3-4 Tuesdays.
*Module 2 [mailto:p.hunt@imperial.ac.uk Patricia Hunt (167)] or [mailto:richard.matthews@imperial.ac.uk Richard Matthews] Tuesday afternoons 2-3, Weeks 1-4 of the course, and Friday 12-1, weeks 2 and 4. Bryan Ward will be available as a demonstrator 12-1 and 4-5 on Thursdays
*Module 3 [mailto:m.bearpark@imperial.ac.uk Michael Bearpark (160a)]. Thursday afternoons, Weeks 1-4 of the course, and as needed throughout the course. Lee Thompson will be available as a demonstrator 12-1 and 3-4 on Mondays.

== Specific times ==

*Week 1 (Monday): Laptop sign-out (12.00-12.30) from Room 237A.
*Day 1 (Monday): Check-up (have you got started) in level 2 computer room, Henry Rzepa.
*Laptop return is four weeks later (Monday) again in Room 242, 11-12 during the study week following the course. '''THIS SESSION hand in will be Tuesday 11 Dec 11-12'''.

Although the schedule shows activity for only Mon, Tue, Thur and Fri of any week, you are of course free to use your laptop 24/7 and to work at times which best suit you. We strongly recommend you attend the first day's introductory sessions, these will tell set you up for the rest of the lab. The timetable above is a guideline. You should spend approximately 8 working lab-days per module, using your judgement on how you can make most effective use of your time (thus you might decide to interleave two modules concurrently). Previous groups have shown that '''time management''' is a skill that has to be cultivated, and you will get a chance to do so with this course! It is up to you to manage your time, not to do too much and not to do too little. Ask a staff member if you are at all unsure.

== Report submission ==

Submit the URL for your Wiki report from [https://vle.imperial.ac.uk/webct/logon/5047144695021 this address] by the appropriate deadline. These deadlines are on the Friday of the end of the second week of the course for the first module you attempt, and again on the Friday of the 4th week of the course, at 17.00 for the second module you attempt. You can do the modules in any order you wish provided you hand two reports in over the four week period at the times indicated.

If we do not receive the URL of your report (submitted via the Blackboard system, and '''NOT''' emailed to the individual members of the course team), we will attempt to contact you by email within one working day (Mon-Fri) of the deadline to check it has not gone missing. You should expect to get a grade on blackboard within 10 working days. If you have heard nothing and have not received a grade in blackboard, please contact the relevant member of staff for each module (Henry Rzepa for mod 1), Tricia Hunt (Mod 2) or Mike Bearpark (module 3).

'''The coursework hand-in times are fixed, there will be a penalty applied for every 24hrs after 5pm of the submit date.''' Any sections completed by the hand-in date will be assessed for full marks, additional material added after this will incur a penalty. If you are having problems, are ill or have extenuating circumstances please see [mailto:p.hunt@ic.ac.uk Dr Hunt] as early as possible, extensions may be granted and will be determined on a case-by-case basis.

----
See also: [[Mod:timetable|Timetable]], [[mod:laptop|Laptop use]], [[mod:programs|Programs]], [[mod:organic|Module 1]], [[Mod:inorganic|Module 2]], [[Mod:physical|Module 3]], [[Mod:writeup|Writing up]]

Mod:timetable

2013-01-14T14:26:10Z

Bw1911:

See also: [[Mod:timetable|Timetable]],[[mod:laptop|Laptop use]], [[mod:programs|Programs]], [[mod:organic|Module 1]], [[Mod:inorganic|Module 2]], [[Mod:physical|Module 3]],[[Mod:writeup|Writing up]]

= Timetable for computational experiments =

The 2012-2013 list of groups are available {{pdf|Lab allocations 2013.pdf|here:}}. If for whatever reason you have swapped a course, please let us know so that we do not allocate zero marks for you. For each group, the course runs for four weeks, during which time you have to attempt '''TWO''' modules and submit '''TWO''' Wiki reports of your experiments. The first of these is due on the Friday at 17.00 at the end of the first two weeks, and the second on the Friday at 17.00 at the end of four weeks.

Dr Hunt, Dr Bearpark and Professor Rzepa will be available for personal discussion as follows and at other times by email or by arrangement with them. However, it is best if you direct your questions to a demonstrator first, as they are on hand and can solve most problems straight away.
*Module 1 [mailto:rzepa@imperial.ac.uk Henry Rzepa (169)] Monday afternoons, Weeks 1-4 of the course, and Friday afternoons, weeks 2 and 4. Paul Dingwall will be available as a demonstrator 12-1 and 3-4 Tuesdays.
*Module 2 [mailto:p.hunt@imperial.ac.uk Patricia Hunt (167)] or [mailto:richard.matthews@imperial.ac.uk Richard Matthews] Tuesday afternoons 2-3, Weeks 1-4 of the course, and Friday 12-1, weeks 2 and 4. Bryan Ward will be available as a demonstrator 12-1 and 4-5 on Thursdays
*Module 3 [mailto:m.bearpark@imperial.ac.uk Michael Bearpark (160a)]. Thursday afternoons, Weeks 1-4 of the course, and as needed throughout the course. Lee Thompson will be available as a demonstrator 12-1 and 3-4on Mondays.

== Specific times ==

*Week 1 (Monday): Laptop sign-out (12.00-12.30) from Room 237A.
*Day 1 (Monday): Check-up (have you got started) in level 2 computer room, Henry Rzepa.
*Laptop return is four weeks later (Monday) again in Room 242, 11-12 during the study week following the course. '''THIS SESSION hand in will be Tuesday 11 Dec 11-12'''.

Although the schedule shows activity for only Mon, Tue, Thur and Fri of any week, you are of course free to use your laptop 24/7 and to work at times which best suit you. We strongly recommend you attend the first day's introductory sessions, these will tell set you up for the rest of the lab. The timetable above is a guideline. You should spend approximately 8 working lab-days per module, using your judgement on how you can make most effective use of your time (thus you might decide to interleave two modules concurrently). Previous groups have shown that '''time management''' is a skill that has to be cultivated, and you will get a chance to do so with this course! It is up to you to manage your time, not to do too much and not to do too little. Ask a staff member if you are at all unsure.

== Report submission ==

Submit the URL for your Wiki report from [https://vle.imperial.ac.uk/webct/logon/5047144695021 this address] by the appropriate deadline. These deadlines are on the Friday of the end of the second week of the course for the first module you attempt, and again on the Friday of the 4th week of the course, at 17.00 for the second module you attempt. You can do the modules in any order you wish provided you hand two reports in over the four week period at the times indicated.

If we do not receive the URL of your report (submitted via the Blackboard system, and '''NOT''' emailed to the individual members of the course team), we will attempt to contact you by email within one working day (Mon-Fri) of the deadline to check it has not gone missing. You should expect to get a grade on blackboard within 10 working days. If you have heard nothing and have not received a grade in blackboard, please contact the relevant member of staff for each module (Henry Rzepa for mod 1), Tricia Hunt (Mod 2) or Mike Bearpark (module 3).

'''The coursework hand-in times are fixed, there will be a penalty applied for every 24hrs after 5pm of the submit date.''' Any sections completed by the hand-in date will be assessed for full marks, additional material added after this will incur a penalty. If you are having problems, are ill or have extenuating circumstances please see [mailto:p.hunt@ic.ac.uk Dr Hunt] as early as possible, extensions may be granted and will be determined on a case-by-case basis.

----
See also: [[Mod:timetable|Timetable]], [[mod:laptop|Laptop use]], [[mod:programs|Programs]], [[mod:organic|Module 1]], [[Mod:inorganic|Module 2]], [[Mod:physical|Module 3]], [[Mod:writeup|Writing up]]

Mod:Hunt Research Group/calendar

2012-12-14T11:11:45Z

Bw1911:

== Calendar ==

*Tricia (Done)
*Abdihakim Hassan (Done)
*Bryan Ward (Done)
*Claire Ashworth (Done)
*Matthew Clough (Done)
*Dimitrios Katsikadakos (Not done)
*Ling Ge (Done)
*Precious Ugbomah (done)
*Richard Matthews (Done)
*Wendy Kuo (Not done)
*Vincent Chen (Done)
*Gabriel Lau (Done)
*Sarah Smith (Done)

 
<table border="1" cellpadding="5">
<tr bgcolor="#66CCFF">
<th width="115px">Mon</th>
<th width="115px">Tues</th>
<th width="115px">Wed</th>
<th width="115px">Thur</th>
<th width="115px">Fri</th>
<th width="115px" bgcolor="#CCCCCC">Sat</th>
<th width="115px" bgcolor="#CCCCCC">Sun</th>
<tr valign="top">
<td>26th November </td>
<td>27th </td>
<td>28th </td>
<td>29th </td>
<td>30th </td>
<td bgcolor="#4357CFF">1st December </td>
<td bgcolor="#CCCCCC">2nd </td>
</tr>
<tr valign="top">
<td>3rd </td>
<td>4th </td>
<td>5th </td>
<td>6th Matthew Away </td>
<td>7th Matthew Away </td>
<td bgcolor="#CCCCCC">8th </td>
<td bgcolor="#CCCCCC">9th </td>
</tr>
<tr valign="top">
<td>10th </td>
<td>11th </td>
<td>12th </td>
<td>13th </td>
<td bgcolor="#FFCCFF">14th End of Autumn Term </td>
<td bgcolor="#CCCCCC">15th </td>
<td bgcolor="#CCCCCC">16th </td>
</tr>
<tr valign="top">
<td>17th Tricia-CDT away day Bryan @ Oxford</td>
<td>18th Tricia-CDT away day Bryan @ Oxford '''{{fontcolor|red|Christmas dinner 6pm}}'''</td>
<td>19th Tricia-Home </td>
<td>20th Tricia-holdiay,Precious home</td>
<td>21st Tricia-holiday</td>
<td bgcolor="#2E8B57">22nd ''College Closed'' </td>
<td bgcolor="#2E8B57">23rd ''College Closed'' </td>
</tr>
<tr valign="top">
<td bgcolor="#2E8B57">24th ''College Closed'' </td>
<td bgcolor="#2E8B57">25th ''College Closed'' '''Christmas Day''' </td>
<td bgcolor="#2E8B57">26th ''College Closed'' '''Boxing Day''' </td>
<td bgcolor="#2E8B57">27th ''College Closed'' </td>
<td bgcolor="#2E8B57">28th ''College Closed'' </td>
<td bgcolor="#2E8B57">29th ''College Closed'' </td>
<td bgcolor="#2E8B57">30th ''College Closed'' </td>
</tr>
<tr valign="top">
<td bgcolor="#2E8B57">31st ''College Closed'' '''New Year's Eve''' </td>
<td bgcolor="#4357CFF">1st January ''College Closed'' '''New Year's Day''' </td>
<td>2nd Tricia, Claire, Sarah, Richard, Bryan Home, Precious home</td>
<td>3rd Tricia, Sarah, Bryan Home, precious home</td>
<td>4th Tricia, Matthew, Bryan Home, precious home </td>
<td bgcolor="#FFCCFF">5th Start of Spring Term</td>
<td bgcolor="#CCCCCC">6th </td>
</tr>
<tr valign="top">
<td>7th </td>
<td>8th </td>
<td>9th </td>
<td>10th </td>
<td>11th </td>
<td bgcolor="#CCCCCC">12th </td>
<td bgcolor="#CCCCCC">13th </td>
</tr>
<tr valign="top">
<td>14th </td>
<td>15th </td>
<td>16th </td>
<td>17th </td>
<td>18th </td>
<td bgcolor="#CCCCCC"> 19th </td>
<td bgcolor="#CCCCCC"> 20th </td>
</tr>
<tr valign="top">
<td>21st </td>
<td>22nd </td>
<td>23rd Claire Away</td>
<td>24th Claire Away</td>
<td>25th Claire Away</td>
<td bgcolor="#CCCCCC">26th Claire Away</td>
<td bgcolor="#CCCCCC">27th Claire Away </td>
</tr>
<tr valign="top">
<td>28th Claire Away</td>
<td>29th Claire Away</td>
<td>30th Claire Away</td>
<td>31st Claire Away</td>
<td bgcolor="#4357CFF">1st February Claire Away</td>
<td bgcolor="#CCCCCC">2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
</tr>
<tr valign="top">
<td>4th </td>
<td>5th </td>
<td>6th </td>
<td>7th </td>
<td>8th </td>
<td bgcolor="#CCCCCC">9th </td>
<td bgcolor="#CCCCCC">10th </td>
</tr>
<tr valign="top">
<td>11th </td>
<td>12th </td>
<td>13th </td>
<td>14th </td>
<td>15th </td>
<td bgcolor="#CCCCCC">16th </td>
<td bgcolor="#CCCCCC">17th </td>
</tr>
<tr valign="top">
<td>18th </td>
<td>19th</td>
<td>20th </td>
<td>21st </td>
<td>22nd </td>
<td bgcolor="#CCCCCC">23rd </td>
<td bgcolor="#CCCCCC">24th </td>
</tr>
<tr valign="top">
<td>25th </td>
<td>26th </td>
<td>27th </td>
<td>28th </td>
<td bgcolor="#4357CFF">1st March </td>
<td bgcolor="#CCCCCC">2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
</tr>
<tr valign="top">
<td >4th </td>
<td>5th </td>
<td>6th </td>
<td>7th </td>
<td>8th </td>
<td bgcolor="#CCCCCC">9th </td>
<td bgcolor="#CCCCCC">10th </td>
</tr>
<tr valign="top">
<td>11th </td>
<td>12th </td>
<td>13th </td>
<td>14th </td>
<td>15th </td>
<td bgcolor="#CCCCCC">16th </td>
<td bgcolor="#CCCCCC">17th </td>
</tr>
<tr valign="top">
<td>18th </td>
<td>19th </td>
<td>20th </td>
<td>21st </td>
<td bgcolor="#FFCCFF">22nd End of Spring Term</td>
<td bgcolor="#CCCCCC">23rd </td>
<td bgcolor="#CCCCCC">24th </td>
</tr>
<tr valign="top">
<td> 25th</td>
<td>26th </td>
<td>27th </td>
<td bgcolor="#2E8B57">28th College Closed</td>
<td bgcolor="#2E8B57">29th College Closed '''Good Friday'''</td>
<td bgcolor="#2E8B57">30th College Closed</td>
<td bgcolor="#2E8B57">31st College Closed '''Easter Sunday'''</td>
</tr>

<tr valign="top">
<td bgcolor="#4357CFF">1st April College Closed '''Easter Monday'''</td>
<td bgcolor="#2E8B57">2nd College Closed</td>
<td>3rd </td>
<td>4th </td>
<td>5th </td>
<td bgcolor="#CCCCCC">6th </td>
<td bgcolor="#CCCCCC">7th </td>
</tr>
</table>

Mod:Hunt Research Group/calendar

2012-11-22T10:39:59Z

Bw1911:

== Calendar ==

*Tricia (Done)
*Abdihakim Hassan (Not done)
*Bryan Ward (Done)
*Claire Ashworth (Done)
*Matthew Clough (Done)
*Dimitrios Katsikadakos (Not done)
*Ling Ge (Done)
*Precious Ugbomah (Not done)
*Richard Matthews (Not done)
*Wendy Kuo (Not done)
*Vincent Chen (Done)
*Gabriel Lau (Not done)
*Sarah Smith (Not done)

 
<table border="1" cellpadding="5">
<tr bgcolor="#66CCFF">
<th width="115px">Mon</th>
<th width="115px">Tues</th>
<th width="115px">Wed</th>
<th width="115px">Thur</th>
<th width="115px">Fri</th>
<th width="115px" bgcolor="#CCCCCC">Sat</th>
<th width="115px" bgcolor="#CCCCCC">Sun</th>
<tr valign="top">
<td>26th November </td>
<td>27th </td>
<td>28th </td>
<td>29th </td>
<td>30th </td>
<td bgcolor="#4357CFF">1st December </td>
<td bgcolor="#CCCCCC">2nd </td>
</tr>
<tr valign="top">
<td>3rd </td>
<td>4th </td>
<td>5th </td>
<td>6th </td>
<td>7th Matthew Away </td>
<td bgcolor="#CCCCCC">8th </td>
<td bgcolor="#CCCCCC">9th </td>
</tr>
<tr valign="top">
<td>10th </td>
<td>11th </td>
<td>12th </td>
<td>13th </td>
<td bgcolor="#FFCCFF">14th End of Autumn Term </td>
<td bgcolor="#CCCCCC">15th </td>
<td bgcolor="#CCCCCC">16th </td>
</tr>
<tr valign="top">
<td>17th Tricia-CDT away day </td>
<td>18th Tricia-CDT away day </td>
<td>19th Tricia-Home </td>
<td>20th Tricia-holdiay</td>
<td>21st Tricia-holiday</td>
<td bgcolor="#2E8B57">22nd ''College Closed'' </td>
<td bgcolor="#2E8B57">23rd ''College Closed'' </td>
</tr>
<tr valign="top">
<td bgcolor="#2E8B57">24th ''College Closed'' </td>
<td bgcolor="#2E8B57">25th ''College Closed'' '''Christmas Day''' </td>
<td bgcolor="#2E8B57">26th ''College Closed'' '''Boxing Day''' </td>
<td bgcolor="#2E8B57">27th ''College Closed'' </td>
<td bgcolor="#2E8B57">28th ''College Closed'' </td>
<td bgcolor="#2E8B57">29th ''College Closed'' </td>
<td bgcolor="#2E8B57">30th ''College Closed'' </td>
</tr>
<tr valign="top">
<td bgcolor="#2E8B57">31st ''College Closed'' '''New Year's Eve''' </td>
<td bgcolor="#4357CFF">1st January ''College Closed'' '''New Year's Day''' </td>
<td>2nd Tricia, Claire, Sarah, Bryan Home</td>
<td>3rd Tricia, Sarah, Bryan Home</td>
<td>4th Tricia, Matthew, Bryan Home </td>
<td bgcolor="#FFCCFF">5th Start of Spring Term</td>
<td bgcolor="#CCCCCC">6th </td>
</tr>
<tr valign="top">
<td>7th </td>
<td>8th </td>
<td>9th </td>
<td>10th </td>
<td>11th </td>
<td bgcolor="#CCCCCC">12th </td>
<td bgcolor="#CCCCCC">13th </td>
</tr>
<tr valign="top">
<td>14th </td>
<td>15th </td>
<td>16th </td>
<td>17th </td>
<td>18th </td>
<td bgcolor="#CCCCCC"> 19th </td>
<td bgcolor="#CCCCCC"> 20th </td>
</tr>
<tr valign="top">
<td>21st </td>
<td>22nd </td>
<td>23rd Claire Away</td>
<td>24th Claire Away</td>
<td>25th Claire Away</td>
<td bgcolor="#CCCCCC">26th Claire Away</td>
<td bgcolor="#CCCCCC">27th Claire Away </td>
</tr>
<tr valign="top">
<td>28th Claire Away</td>
<td>29th Claire Away</td>
<td>30th Claire Away</td>
<td>31st Claire Away</td>
<td bgcolor="#4357CFF">1st February Claire Away</td>
<td bgcolor="#CCCCCC">2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
</tr>
<tr valign="top">
<td>4th </td>
<td>5th </td>
<td>6th </td>
<td>7th </td>
<td>8th </td>
<td bgcolor="#CCCCCC">9th </td>
<td bgcolor="#CCCCCC">10th </td>
</tr>
<tr valign="top">
<td>11th </td>
<td>12th </td>
<td>13th </td>
<td>14th </td>
<td>15th </td>
<td bgcolor="#CCCCCC">16th </td>
<td bgcolor="#CCCCCC">17th </td>
</tr>
<tr valign="top">
<td>18th </td>
<td>19th</td>
<td>20th </td>
<td>21st </td>
<td>22nd </td>
<td bgcolor="#CCCCCC">23rd </td>
<td bgcolor="#CCCCCC">24th </td>
</tr>
<tr valign="top">
<td>25th </td>
<td>26th </td>
<td>27th </td>
<td>28th </td>
<td bgcolor="#4357CFF">1st March </td>
<td bgcolor="#CCCCCC">2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
</tr>
<tr valign="top">
<td >4th </td>
<td>5th </td>
<td>6th </td>
<td>7th </td>
<td>8th </td>
<td bgcolor="#CCCCCC">9th </td>
<td bgcolor="#CCCCCC">10th </td>
</tr>
<tr valign="top">
<td>11th </td>
<td>12th </td>
<td>13th </td>
<td>14th </td>
<td>15th </td>
<td bgcolor="#CCCCCC">16th </td>
<td bgcolor="#CCCCCC">17th </td>
</tr>
<tr valign="top">
<td>18th </td>
<td>19th </td>
<td>20th </td>
<td>21st </td>
<td bgcolor="#FFCCFF">22nd End of Spring Term</td>
<td bgcolor="#CCCCCC">23rd </td>
<td bgcolor="#CCCCCC">24th </td>
</tr>
<tr valign="top">
<td> 25th</td>
<td>26th </td>
<td>27th </td>
<td bgcolor="#2E8B57">28th College Closed</td>
<td bgcolor="#2E8B57">29th College Closed '''Good Friday'''</td>
<td bgcolor="#2E8B57">30th College Closed</td>
<td bgcolor="#2E8B57">31st College Closed '''Easter Sunday'''</td>
</tr>

<tr valign="top">
<td bgcolor="#4357CFF">1st April College Closed '''Easter Monday'''</td>
<td bgcolor="#2E8B57">2nd College Closed</td>
<td>3rd </td>
<td>4th </td>
<td>5th </td>
<td bgcolor="#CCCCCC">6th </td>
<td bgcolor="#CCCCCC">7th </td>
</tr>
</table>

Mod:Hunt Research Group/calendar

2012-11-22T10:39:49Z

Bw1911:

== Calendar ==

*Tricia (Done)
*Abdihakim Hassan (Not done)
*Bryan Ward (Not done)
*Claire Ashworth (Done)
*Matthew Clough (Done)
*Dimitrios Katsikadakos (Not done)
*Ling Ge (Done)
*Precious Ugbomah (Not done)
*Richard Matthews (Not done)
*Wendy Kuo (Not done)
*Vincent Chen (Done)
*Gabriel Lau (Not done)
*Sarah Smith (Not done)

 
<table border="1" cellpadding="5">
<tr bgcolor="#66CCFF">
<th width="115px">Mon</th>
<th width="115px">Tues</th>
<th width="115px">Wed</th>
<th width="115px">Thur</th>
<th width="115px">Fri</th>
<th width="115px" bgcolor="#CCCCCC">Sat</th>
<th width="115px" bgcolor="#CCCCCC">Sun</th>
<tr valign="top">
<td>26th November </td>
<td>27th </td>
<td>28th </td>
<td>29th </td>
<td>30th </td>
<td bgcolor="#4357CFF">1st December </td>
<td bgcolor="#CCCCCC">2nd </td>
</tr>
<tr valign="top">
<td>3rd </td>
<td>4th </td>
<td>5th </td>
<td>6th </td>
<td>7th Matthew Away </td>
<td bgcolor="#CCCCCC">8th </td>
<td bgcolor="#CCCCCC">9th </td>
</tr>
<tr valign="top">
<td>10th </td>
<td>11th </td>
<td>12th </td>
<td>13th </td>
<td bgcolor="#FFCCFF">14th End of Autumn Term </td>
<td bgcolor="#CCCCCC">15th </td>
<td bgcolor="#CCCCCC">16th </td>
</tr>
<tr valign="top">
<td>17th Tricia-CDT away day </td>
<td>18th Tricia-CDT away day </td>
<td>19th Tricia-Home </td>
<td>20th Tricia-holdiay</td>
<td>21st Tricia-holiday</td>
<td bgcolor="#2E8B57">22nd ''College Closed'' </td>
<td bgcolor="#2E8B57">23rd ''College Closed'' </td>
</tr>
<tr valign="top">
<td bgcolor="#2E8B57">24th ''College Closed'' </td>
<td bgcolor="#2E8B57">25th ''College Closed'' '''Christmas Day''' </td>
<td bgcolor="#2E8B57">26th ''College Closed'' '''Boxing Day''' </td>
<td bgcolor="#2E8B57">27th ''College Closed'' </td>
<td bgcolor="#2E8B57">28th ''College Closed'' </td>
<td bgcolor="#2E8B57">29th ''College Closed'' </td>
<td bgcolor="#2E8B57">30th ''College Closed'' </td>
</tr>
<tr valign="top">
<td bgcolor="#2E8B57">31st ''College Closed'' '''New Year's Eve''' </td>
<td bgcolor="#4357CFF">1st January ''College Closed'' '''New Year's Day''' </td>
<td>2nd Tricia, Claire, Sarah, Bryan Home</td>
<td>3rd Tricia, Sarah, Bryan Home</td>
<td>4th Tricia, Matthew, Bryan Home </td>
<td bgcolor="#FFCCFF">5th Start of Spring Term</td>
<td bgcolor="#CCCCCC">6th </td>
</tr>
<tr valign="top">
<td>7th </td>
<td>8th </td>
<td>9th </td>
<td>10th </td>
<td>11th </td>
<td bgcolor="#CCCCCC">12th </td>
<td bgcolor="#CCCCCC">13th </td>
</tr>
<tr valign="top">
<td>14th </td>
<td>15th </td>
<td>16th </td>
<td>17th </td>
<td>18th </td>
<td bgcolor="#CCCCCC"> 19th </td>
<td bgcolor="#CCCCCC"> 20th </td>
</tr>
<tr valign="top">
<td>21st </td>
<td>22nd </td>
<td>23rd Claire Away</td>
<td>24th Claire Away</td>
<td>25th Claire Away</td>
<td bgcolor="#CCCCCC">26th Claire Away</td>
<td bgcolor="#CCCCCC">27th Claire Away </td>
</tr>
<tr valign="top">
<td>28th Claire Away</td>
<td>29th Claire Away</td>
<td>30th Claire Away</td>
<td>31st Claire Away</td>
<td bgcolor="#4357CFF">1st February Claire Away</td>
<td bgcolor="#CCCCCC">2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
</tr>
<tr valign="top">
<td>4th </td>
<td>5th </td>
<td>6th </td>
<td>7th </td>
<td>8th </td>
<td bgcolor="#CCCCCC">9th </td>
<td bgcolor="#CCCCCC">10th </td>
</tr>
<tr valign="top">
<td>11th </td>
<td>12th </td>
<td>13th </td>
<td>14th </td>
<td>15th </td>
<td bgcolor="#CCCCCC">16th </td>
<td bgcolor="#CCCCCC">17th </td>
</tr>
<tr valign="top">
<td>18th </td>
<td>19th</td>
<td>20th </td>
<td>21st </td>
<td>22nd </td>
<td bgcolor="#CCCCCC">23rd </td>
<td bgcolor="#CCCCCC">24th </td>
</tr>
<tr valign="top">
<td>25th </td>
<td>26th </td>
<td>27th </td>
<td>28th </td>
<td bgcolor="#4357CFF">1st March </td>
<td bgcolor="#CCCCCC">2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
</tr>
<tr valign="top">
<td >4th </td>
<td>5th </td>
<td>6th </td>
<td>7th </td>
<td>8th </td>
<td bgcolor="#CCCCCC">9th </td>
<td bgcolor="#CCCCCC">10th </td>
</tr>
<tr valign="top">
<td>11th </td>
<td>12th </td>
<td>13th </td>
<td>14th </td>
<td>15th </td>
<td bgcolor="#CCCCCC">16th </td>
<td bgcolor="#CCCCCC">17th </td>
</tr>
<tr valign="top">
<td>18th </td>
<td>19th </td>
<td>20th </td>
<td>21st </td>
<td bgcolor="#FFCCFF">22nd End of Spring Term</td>
<td bgcolor="#CCCCCC">23rd </td>
<td bgcolor="#CCCCCC">24th </td>
</tr>
<tr valign="top">
<td> 25th</td>
<td>26th </td>
<td>27th </td>
<td bgcolor="#2E8B57">28th College Closed</td>
<td bgcolor="#2E8B57">29th College Closed '''Good Friday'''</td>
<td bgcolor="#2E8B57">30th College Closed</td>
<td bgcolor="#2E8B57">31st College Closed '''Easter Sunday'''</td>
</tr>

<tr valign="top">
<td bgcolor="#4357CFF">1st April College Closed '''Easter Monday'''</td>
<td bgcolor="#2E8B57">2nd College Closed</td>
<td>3rd </td>
<td>4th </td>
<td>5th </td>
<td bgcolor="#CCCCCC">6th </td>
<td bgcolor="#CCCCCC">7th </td>
</tr>
</table>

Mod:basic jmol instructions

2012-11-20T12:34:38Z

Bw1911: /* Incorporating Jmol with MOs into your wiki */

==Adding Jmol files of your molecule to your wiki==

===Creating the molecule coordinates file for Jmol===

To include a Jmol image of your molecule in your wiki page you need to create a file containing the coordinates of the molecule. The two simplest options to create the file are, one, to use gaussview to save a copy of your molecule as a .mol file or, two, to make a .xyz file. One benefit using the .xyz format is that the files tend to be smaller however they are less convenient to create than .mol files.

:'''Using Gaussview'''
::Open your molecule in gaussview
::Navigate to File>>Save
::In the options choose Save As a .mdl file which will default save as a .mol file
::Here is what Gaussview saved for my Mo(CO)(H2)(PH3)4 file:
<pre>
Title Card Required

Created by GaussView 5.0.8
21 18 0 0 0 0 0 0 0 0 0 0
0.0000 0.0001 -0.2759 Mo 0 0 0 0 0 0 0 0 0 0 0 0
-1.0114 -2.2089 -0.2905 P 0 0 0 0 0 0 0 0 0 0 0 0
-0.3724 -3.3206 0.3305 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.3233 -2.9082 -1.4928 H 0 0 0 0 0 0 0 0 0 0 0 0
2.2110 -1.0100 -0.1928 P 0 0 0 0 0 0 0 0 0 0 0 0
2.4180 -2.2493 0.4785 H 0 0 0 0 0 0 0 0 0 0 0 0
2.9665 -1.3716 -1.3435 H 0 0 0 0 0 0 0 0 0 0 0 0
1.0119 2.2095 -0.2895 P 0 0 0 0 0 0 0 0 0 0 0 0
0.3724 3.3212 0.3310 H 0 0 0 0 0 0 0 0 0 0 0 0
1.3254 2.9092 -1.4910 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.2110 1.0100 -0.1928 P 0 0 0 0 0 0 0 0 0 0 0 0
-2.4189 2.2495 0.4779 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.9666 1.3708 -1.3438 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.0004 -0.0005 1.6924 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.0008 -0.0015 2.8595 O 0 0 0 0 0 0 0 0 0 0 0 0
0.3612 -0.1679 -2.2213 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.3616 0.1688 -2.2210 H 0 0 0 0 0 0 0 0 0 0 0 0
3.2908 -0.3410 0.4520 H 0 0 0 0 0 0 0 0 0 0 0 0
2.2782 2.4471 0.3189 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.2786 -2.4473 0.3161 H 0 0 0 0 0 0 0 0 0 0 0 0
-3.2906 0.3408 0.4522 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 5 1 0 0 0 0
1 8 1 0 0 0 0
1 11 1 0 0 0 0
1 14 1 0 0 0 0
2 3 1 0 0 0 0
2 4 1 0 0 0 0
2 20 1 0 0 0 0
5 6 1 0 0 0 0
5 7 1 0 0 0 0
5 18 1 0 0 0 0
8 9 1 0 0 0 0
8 10 1 0 0 0 0
8 19 1 0 0 0 0
11 12 1 0 0 0 0
11 13 1 0 0 0 0
11 21 1 0 0 0 0
14 15 2 0 0 0 0

</pre>

:'''Making a .xyz file manually'''
:: You need to make this file yourself in a text editor
::A .xyz file has 3 sections
:::#First line: number of atoms in the molecule
:::#Second line: comments or title
:::#Following lines: atomic symbol followed by xyz coordiantes
::here is my Mo(CO)(H2)(PH3)4 file:
<pre>
21
Mo(CO)(H2)(PH3)4 molecule
Mo 0.000045 0.000102 -0.275893 27.797760
P -1.011401 -2.208947 -0.290536 -0.223504
H -0.372372 -3.320581 0.330463 0.085105
H -1.323285 -2.908209 -1.492765 0.082766
P 2.211020 -1.009990 -0.192847 -0.228591
H 2.418011 -2.249283 0.478494 0.087153
H 2.966565 -1.371591 -1.343488 0.086278
P 1.011822 2.209531 -0.289514 -0.223545
H 0.372347 3.321200 0.330959 0.085111
H 1.325404 2.909252 -1.491038 0.082797
P -2.211044 1.010021 -0.192849 -0.228575
H -2.418954 2.249487 0.477851 0.087149
H -2.966577 1.370804 -1.343808 0.086292
C -0.000389 -0.000536 1.692395 0.257683
O -0.000758 -0.001484 2.859470 -0.335269
H 0.361190 -0.167921 -2.221343 0.079092
H -0.361610 0.168783 -2.220950 0.079020
H 3.290813 -0.341001 0.452049 0.086821
H 2.278178 2.447165 0.318854 0.084820
H -2.278543 -2.447297 0.316108 0.084741
H -3.290613 0.340775 0.452167 0.086826
</pre>

:'''Making a .xyz file using Molden'''
::Alternatively you can create a .xyz file using a program called Molden (providing you have access to, and are familiar with, Molden)
:::#Open your molecule in Molden (this will require typing molden file_name.log)
:::#Navigate to the Molden Control window and select Write
:::#Select XYZ from the drop down menu - this will prompt the Molden Query Box to open
:::#Enter the file name you wish to use in the grey panel (ensuring there are no spaces - use underscores) and end with .xyz then select apply
:::#Click the Skull button to quit Molden
::Note: You should only use this method if you are familiar with Molden or have consulted the Molden Basics wiki page (coming soon).

===Load your file===
Load your file containing the molecule coordinates onto the wiki (as you would an image!)
:Load your molecule to the wiki, eg choose "upload file" from the menu to the left and follow the instructions

===How to add a Jmol to your wiki===
:There are two options to add a Jmol of your molecule.
::One method would be to add a button that will open a separate window with a Jmol molecule in it. This is the preferred option.
::Alternatively you can have the Jmol embedded directly into your wiki page. Use this option SPARINGLY!! Too many Jmol images will slow down the loading of your wiki page

'''Adding a button for your Jmol'''
:Add the following text to your wiki page replacing "MoCOH2PH3_4.xyz" with your file name as a .mol or .xyz file

:'''for a button that will open a new window'''
<pre>
<jmol>
<jmolAppletButton>
<uploadedFileContents>MoCOH2PH3_4.xyz</uploadedFileContents>
<text>Mo(CO)(H2)(PH3)4</text>
</jmolAppletButton>
</jmol>
</pre>
::this will produce the following:

<jmol>
<jmolAppletButton>
<uploadedFileContents>MoCOH2PH3_4.xyz</uploadedFileContents>
<text>Mo(CO)(H2)(PH3)4</text>
</jmolAppletButton>
</jmol>

:'''Embedding an image on your wiki page'''
<pre><jmol><jmolApplet>
<title>Mo(CO)(H2)(PH3)4</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>MoCOH2PH3_4.xyz</uploadedFileContents>
</jmolApplet></jmol></pre>

:This will produce the following:
<jmol><jmolApplet>
<title>test molecule</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>MoCOH2PH3_4.xyz</uploadedFileContents>
</jmolApplet></jmol>
::The title tag is self explanatory
::The colour tag sets the background colour to white
::The size tag sets the size of the Jmol image to display
::The uploadfile tag determines the file to load

'''Beware!''' You can corrupt your wiki if you type the Jmol XML incorrectly. Recovering from such an error is difficult! You should save your wiki before inserting any Jmol molecules and be careful that you put in the text exactly as it is here. It is advisable to copy then paste the text directly into your wiki then manually edit the appropriate file name and title, as well as any other changes you may wish to make such as background colour or window size.

More information on backing up and fixing your report after a crash can be found here:
[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:writeup#Backing_up_your_report fixing wiki problems]

==Visualising MOs using Jmol==

It is possible to superimpose MOs over the skeletal framework of your molecule. To do this you must first generate a cube (.cub) file for each MO of interest using Gaussview.

===How to generate .cub files===

This procedure assumes two things:

::#The geometry of your molecule has been properly optimised
::#You have performed a single point energy calculation with the key words pop=(full,nbo)

Using Gaussview, double click the .fchk file corresponding to your molecule and navigate to Edit>>MOs

Visualise however many MOs you require. Take note of the index numbers corresponding to the MOs of interest.

In Gaussview navigate to Results>>Surfaces/Contours. In the Cubes Available box select the first MO of interest and then from the drop down box Cube Actions select Save Cube. Repeat as necessary until you have saved all of the cube files corresponding to the MOs of interest.

Alternatively, instead of using Gaussview, the cubegen utility can be used (this is, of course, dependent on whether you have accessto computer with cubegen installed on it). If you do have access, then proceed by typing the following command in the command line:

<pre>./cubegen 0 MO=41 filename.fchk filename_mo41.cub 0
./cubegen 0 MO=35 filename.fchk filename_mo35.cub 0</pre>

where filename.fchk is the original name of the .fchk file.
The cube files generated (i.e. filename_mo41.cub) are likely to be quite large (a few megabytes in size). These files can be used to visualise the MOs over the molecular framework however owing to their size this will cause impossible webpage loading times. It is therefore advisable to reduce the size of the .cub file by processing it using Jmol, creating a .jvxl file.

===Creating .jvxl files from .cub files===

The .jvxl file is around 100 to 150 times smaller than the original .cub therefore it is strongly advisable to follow this procedure!!

There are a couple of ways to convert a .cub file to a .jvxl file

:One method is as follows:
::# Open Jmol (Jmol.jar). If you do not have Jmol, it can be obtained from [http://http://jmol.sourceforge.net/download/ here]
::# Navigate to File>>Open and select your .xyz or .mol file for your molecule framework
::# Once your molecule has loaded, navigate to File>>Open and select your first .cub file corresponding to an MO. This will load the MO on to the framework.
::# Right click on the Jmol display window prompting a floating menu bar to appear. Navigate to File>>Save JVXL isosurface in the floating menu. This will allow you to save a jvxl file.
::# You can then open another .cub file by selecting File>>Open in the menu at the top of the display window which will overwrite the first MO.
::# Repeat the saving procedure as necessary

:Note: I know this is time consuming - I will try and identify an alternative method

:Alternative method (number 1) for creating a .jvxl file
# Navigate to [http://www.ch.ic.ac.uk/rzepa/cub2jvxl/ this page] where you will be able press a button prompting you to select your cube file.
# This will be followed by three file save dialogs, one for the coordinates (.xyz), one for the MO surface (.jvxl) and a shrink-wrapped bundle (.pngj).

It is possible to reduce the size of the .jvxl file further by compressing it using gzip (Jmol will automatically detect and decompress this). You will end up with something that looks like name.jvxl.gz and you can safely rename this file to the original name.jvxl

===Incorporating Jmol with MOs into your wiki===

This method is very similar to the instructions outlined above for loading your Jmol molecule into your wiki page however, the Jmol XML script has been modified slightly to include the molecular orbital.

First, you will need to insert the following code into your Wiki, replacing the file name in between the <nowiki><uploadedFileContents></uploadedFileContents></nowiki> tags with the .xyz or .mol file, corresponding to your molecule from earlier.

<pre><nowiki><jmol>
<jmolApplet>
<title>Orbital</title><color>white</color><size>300</size>
<script>isosurface color orange purple "images/f/f3/MoCOH2PH3_4_mo23.jvxl" translucent;</script>
<uploadedFileContents>MoCOH2PH3_4.xyz</uploadedFileContents>
</jmolApplet>
</jmol></nowiki>
</pre>

In a new window, upload the .jvxl files on to the wiki using the [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Special:MultipleUpload/ Upload multiple files] link. Once uploaded, keep this window open and select the link to the first MO.

The browser window should now look like the image below. Click on the link as indicated by the red arrow.

[[File:File_upload_for_MOs_in_jvxl_format.png|900px]]

The browser window should now display the contents of the .jvxl file (in XML format). You will need to find the absolute path for the .jvxl file. Luckily this is displayed in the address bar at the top of the browser. This will appear as something like:

<pre>https://wiki.ch.ic.ac.uk/wiki/images/f/f3/MoCOH2PH3_4_mo23.jvxl</pre>

You will need to copy the equivalent text to:

<pre>images/f/f3/MoCOH2PH3_4_mo23.jvxl</pre>

This should be pasted into the Jmol code on your wiki page. This text should be pasted in between the <nowiki><script></script></nowiki> tags

Hopefully if all goes well you should get something similar to this:

<jmol>
<jmolApplet>
<title>Orbital</title><color>white</color><size>300</size>
<script>isosurface color orange purple "images/f/f3/MoCOH2PH3_4_mo23.jvxl" translucent;</script>
<uploadedFileContents>MoCOH2PH3_4.xyz</uploadedFileContents>
</jmolApplet>
</jmol>

=== An alternative way of loading surfaces ===
This method avoids the need to specify paths to files as seen above. Instead uses the '''.pngj''' bundle which contains all necessary information and can be invoked by
<pre><nowiki><jmolFile text="link to MO23">MoCOH2PH3_test_mo23.cub.pngj</jmolFile></nowiki></pre> which produces a <jmolFile text="link to MO23">MoCOH2PH3_test_mo23.cub.pngj</jmolFile>. This method is not as flexible as the above.

===Making your Jmol more awesome===
Section coming soon

Mod:basic jmol instructions

2012-11-20T12:32:51Z

Bw1911: /* Incorporating Jmol with MOs into your wiki */

==Adding Jmol files of your molecule to your wiki==

===Creating the molecule coordinates file for Jmol===

To include a Jmol image of your molecule in your wiki page you need to create a file containing the coordinates of the molecule. The two simplest options to create the file are, one, to use gaussview to save a copy of your molecule as a .mol file or, two, to make a .xyz file. One benefit using the .xyz format is that the files tend to be smaller however they are less convenient to create than .mol files.

:'''Using Gaussview'''
::Open your molecule in gaussview
::Navigate to File>>Save
::In the options choose Save As a .mdl file which will default save as a .mol file
::Here is what Gaussview saved for my Mo(CO)(H2)(PH3)4 file:
<pre>
Title Card Required

Created by GaussView 5.0.8
21 18 0 0 0 0 0 0 0 0 0 0
0.0000 0.0001 -0.2759 Mo 0 0 0 0 0 0 0 0 0 0 0 0
-1.0114 -2.2089 -0.2905 P 0 0 0 0 0 0 0 0 0 0 0 0
-0.3724 -3.3206 0.3305 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.3233 -2.9082 -1.4928 H 0 0 0 0 0 0 0 0 0 0 0 0
2.2110 -1.0100 -0.1928 P 0 0 0 0 0 0 0 0 0 0 0 0
2.4180 -2.2493 0.4785 H 0 0 0 0 0 0 0 0 0 0 0 0
2.9665 -1.3716 -1.3435 H 0 0 0 0 0 0 0 0 0 0 0 0
1.0119 2.2095 -0.2895 P 0 0 0 0 0 0 0 0 0 0 0 0
0.3724 3.3212 0.3310 H 0 0 0 0 0 0 0 0 0 0 0 0
1.3254 2.9092 -1.4910 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.2110 1.0100 -0.1928 P 0 0 0 0 0 0 0 0 0 0 0 0
-2.4189 2.2495 0.4779 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.9666 1.3708 -1.3438 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.0004 -0.0005 1.6924 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.0008 -0.0015 2.8595 O 0 0 0 0 0 0 0 0 0 0 0 0
0.3612 -0.1679 -2.2213 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.3616 0.1688 -2.2210 H 0 0 0 0 0 0 0 0 0 0 0 0
3.2908 -0.3410 0.4520 H 0 0 0 0 0 0 0 0 0 0 0 0
2.2782 2.4471 0.3189 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.2786 -2.4473 0.3161 H 0 0 0 0 0 0 0 0 0 0 0 0
-3.2906 0.3408 0.4522 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 5 1 0 0 0 0
1 8 1 0 0 0 0
1 11 1 0 0 0 0
1 14 1 0 0 0 0
2 3 1 0 0 0 0
2 4 1 0 0 0 0
2 20 1 0 0 0 0
5 6 1 0 0 0 0
5 7 1 0 0 0 0
5 18 1 0 0 0 0
8 9 1 0 0 0 0
8 10 1 0 0 0 0
8 19 1 0 0 0 0
11 12 1 0 0 0 0
11 13 1 0 0 0 0
11 21 1 0 0 0 0
14 15 2 0 0 0 0

</pre>

:'''Making a .xyz file manually'''
:: You need to make this file yourself in a text editor
::A .xyz file has 3 sections
:::#First line: number of atoms in the molecule
:::#Second line: comments or title
:::#Following lines: atomic symbol followed by xyz coordiantes
::here is my Mo(CO)(H2)(PH3)4 file:
<pre>
21
Mo(CO)(H2)(PH3)4 molecule
Mo 0.000045 0.000102 -0.275893 27.797760
P -1.011401 -2.208947 -0.290536 -0.223504
H -0.372372 -3.320581 0.330463 0.085105
H -1.323285 -2.908209 -1.492765 0.082766
P 2.211020 -1.009990 -0.192847 -0.228591
H 2.418011 -2.249283 0.478494 0.087153
H 2.966565 -1.371591 -1.343488 0.086278
P 1.011822 2.209531 -0.289514 -0.223545
H 0.372347 3.321200 0.330959 0.085111
H 1.325404 2.909252 -1.491038 0.082797
P -2.211044 1.010021 -0.192849 -0.228575
H -2.418954 2.249487 0.477851 0.087149
H -2.966577 1.370804 -1.343808 0.086292
C -0.000389 -0.000536 1.692395 0.257683
O -0.000758 -0.001484 2.859470 -0.335269
H 0.361190 -0.167921 -2.221343 0.079092
H -0.361610 0.168783 -2.220950 0.079020
H 3.290813 -0.341001 0.452049 0.086821
H 2.278178 2.447165 0.318854 0.084820
H -2.278543 -2.447297 0.316108 0.084741
H -3.290613 0.340775 0.452167 0.086826
</pre>

:'''Making a .xyz file using Molden'''
::Alternatively you can create a .xyz file using a program called Molden (providing you have access to, and are familiar with, Molden)
:::#Open your molecule in Molden (this will require typing molden file_name.log)
:::#Navigate to the Molden Control window and select Write
:::#Select XYZ from the drop down menu - this will prompt the Molden Query Box to open
:::#Enter the file name you wish to use in the grey panel (ensuring there are no spaces - use underscores) and end with .xyz then select apply
:::#Click the Skull button to quit Molden
::Note: You should only use this method if you are familiar with Molden or have consulted the Molden Basics wiki page (coming soon).

===Load your file===
Load your file containing the molecule coordinates onto the wiki (as you would an image!)
:Load your molecule to the wiki, eg choose "upload file" from the menu to the left and follow the instructions

===How to add a Jmol to your wiki===
:There are two options to add a Jmol of your molecule.
::One method would be to add a button that will open a separate window with a Jmol molecule in it. This is the preferred option.
::Alternatively you can have the Jmol embedded directly into your wiki page. Use this option SPARINGLY!! Too many Jmol images will slow down the loading of your wiki page

'''Adding a button for your Jmol'''
:Add the following text to your wiki page replacing "MoCOH2PH3_4.xyz" with your file name as a .mol or .xyz file

:'''for a button that will open a new window'''
<pre>
<jmol>
<jmolAppletButton>
<uploadedFileContents>MoCOH2PH3_4.xyz</uploadedFileContents>
<text>Mo(CO)(H2)(PH3)4</text>
</jmolAppletButton>
</jmol>
</pre>
::this will produce the following:

<jmol>
<jmolAppletButton>
<uploadedFileContents>MoCOH2PH3_4.xyz</uploadedFileContents>
<text>Mo(CO)(H2)(PH3)4</text>
</jmolAppletButton>
</jmol>

:'''Embedding an image on your wiki page'''
<pre><jmol><jmolApplet>
<title>Mo(CO)(H2)(PH3)4</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>MoCOH2PH3_4.xyz</uploadedFileContents>
</jmolApplet></jmol></pre>

:This will produce the following:
<jmol><jmolApplet>
<title>test molecule</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>MoCOH2PH3_4.xyz</uploadedFileContents>
</jmolApplet></jmol>
::The title tag is self explanatory
::The colour tag sets the background colour to white
::The size tag sets the size of the Jmol image to display
::The uploadfile tag determines the file to load

'''Beware!''' You can corrupt your wiki if you type the Jmol XML incorrectly. Recovering from such an error is difficult! You should save your wiki before inserting any Jmol molecules and be careful that you put in the text exactly as it is here. It is advisable to copy then paste the text directly into your wiki then manually edit the appropriate file name and title, as well as any other changes you may wish to make such as background colour or window size.

More information on backing up and fixing your report after a crash can be found here:
[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:writeup#Backing_up_your_report fixing wiki problems]

==Visualising MOs using Jmol==

It is possible to superimpose MOs over the skeletal framework of your molecule. To do this you must first generate a cube (.cub) file for each MO of interest using Gaussview.

===How to generate .cub files===

This procedure assumes two things:

::#The geometry of your molecule has been properly optimised
::#You have performed a single point energy calculation with the key words pop=(full,nbo)

Using Gaussview, double click the .fchk file corresponding to your molecule and navigate to Edit>>MOs

Visualise however many MOs you require. Take note of the index numbers corresponding to the MOs of interest.

In Gaussview navigate to Results>>Surfaces/Contours. In the Cubes Available box select the first MO of interest and then from the drop down box Cube Actions select Save Cube. Repeat as necessary until you have saved all of the cube files corresponding to the MOs of interest.

Alternatively, instead of using Gaussview, the cubegen utility can be used (this is, of course, dependent on whether you have accessto computer with cubegen installed on it). If you do have access, then proceed by typing the following command in the command line:

<pre>./cubegen 0 MO=41 filename.fchk filename_mo41.cub 0
./cubegen 0 MO=35 filename.fchk filename_mo35.cub 0</pre>

where filename.fchk is the original name of the .fchk file.
The cube files generated (i.e. filename_mo41.cub) are likely to be quite large (a few megabytes in size). These files can be used to visualise the MOs over the molecular framework however owing to their size this will cause impossible webpage loading times. It is therefore advisable to reduce the size of the .cub file by processing it using Jmol, creating a .jvxl file.

===Creating .jvxl files from .cub files===

The .jvxl file is around 100 to 150 times smaller than the original .cub therefore it is strongly advisable to follow this procedure!!

There are a couple of ways to convert a .cub file to a .jvxl file

:One method is as follows:
::# Open Jmol (Jmol.jar). If you do not have Jmol, it can be obtained from [http://http://jmol.sourceforge.net/download/ here]
::# Navigate to File>>Open and select your .xyz or .mol file for your molecule framework
::# Once your molecule has loaded, navigate to File>>Open and select your first .cub file corresponding to an MO. This will load the MO on to the framework.
::# Right click on the Jmol display window prompting a floating menu bar to appear. Navigate to File>>Save JVXL isosurface in the floating menu. This will allow you to save a jvxl file.
::# You can then open another .cub file by selecting File>>Open in the menu at the top of the display window which will overwrite the first MO.
::# Repeat the saving procedure as necessary

:Note: I know this is time consuming - I will try and identify an alternative method

:Alternative method (number 1) for creating a .jvxl file
# Navigate to [http://www.ch.ic.ac.uk/rzepa/cub2jvxl/ this page] where you will be able press a button prompting you to select your cube file.
# This will be followed by three file save dialogs, one for the coordinates (.xyz), one for the MO surface (.jvxl) and a shrink-wrapped bundle (.pngj).

It is possible to reduce the size of the .jvxl file further by compressing it using gzip (Jmol will automatically detect and decompress this). You will end up with something that looks like name.jvxl.gz and you can safely rename this file to the original name.jvxl

===Incorporating Jmol with MOs into your wiki===

This method is very similar to the instructions outlined above for loading your Jmol molecule into your wiki page however, the Jmol XML script has been modified slightly to include the molecular orbital.

First, you will need to insert the following code into your Wiki, replacing the file name in between the <nowiki><uploadedFileContents></uploadedFileContents></nowiki> tags with the .xyz or .mol file, corresponding to your molecule from earlier.

<pre><nowiki><jmol>
<jmolApplet>
<title>Orbital</title><color>white</color><size>300</size>
<script>isosurface color orange purple "images/f/f3/MoCOH2PH3_4_mo23.jvxl" translucent;</script>
<uploadedFileContents>MoCOH2PH3_4.xyz</uploadedFileContents>
</jmolApplet>
</jmol></nowiki>
</pre>

In a new window, upload the .jvxl files on to the wiki using the [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Special:MultipleUpload/ Upload multiple files] link. Once uploaded, keep this window open and select the link to the first MO.

The browser window should now look like the image below. Click on the link as indicated by the red arrow.

[[File:File_upload_for_MOs_in_jvxl_format.png|900px]]

The browser window should now display the contents of the .jvxl file (in XML format). You will need to find the absolute path for the .jvxl file. Luckily this is displayed in the address bar at the top of the browser. This will appear as something like:

<pre>https://wiki.ch.ic.ac.uk/wiki/images/f/f3/MoCOH2PH3_4_mo23.jvxl</pre>

You will need to copy the equivalent text to:

<pre>images/f/f3/MoCOH2PH3_4_mo23.jvxl</pre>

This should be pasted into the Jmol code on your wiki page. This text should be pasted in between the <nowiki><script></script></nowiki> tags

Hopefully if all goes well you should get something similar to this:

<jmol>
<jmolApplet>
<title>Orbital</title><color>white</color><size>300</size>
<script>isosurface color orange purple "images/f/f3/MoCOH2PH3_4_mo23.jvxl" translucent;</script>
<uploadedFileContents>MoCOH2PH3_4.xyz</uploadedFileContents>
</jmolApplet>
</jmol>

<jmol>
<jmolAppletButton>
<uploadedFileContents>MoCOH2PH3_4.xyz</uploadedFileContents>
<text>Mo(CO)(H2)(PH3)4 MO73</text>
<color>white</color>
<script>isosurface color orange purple "images/6/61/MoCOH2PH3_4_mo73.jvxl" translucent;</script>
</jmolAppletButton>
</jmol>

=== An alternative way of loading surfaces ===
This method avoids the need to specify paths to files as seen above. Instead uses the '''.pngj''' bundle which contains all necessary information and can be invoked by
<pre><nowiki><jmolFile text="link to MO23">MoCOH2PH3_test_mo23.cub.pngj</jmolFile></nowiki></pre> which produces a <jmolFile text="link to MO23">MoCOH2PH3_test_mo23.cub.pngj</jmolFile>. This method is not as flexible as the above.

===Making your Jmol more awesome===
Section coming soon

Mod:basic jmol instructions

2012-11-20T12:31:16Z

Bw1911: /* Incorporating Jmol with MOs into your wiki */

==Adding Jmol files of your molecule to your wiki==

===Creating the molecule coordinates file for Jmol===

To include a Jmol image of your molecule in your wiki page you need to create a file containing the coordinates of the molecule. The two simplest options to create the file are, one, to use gaussview to save a copy of your molecule as a .mol file or, two, to make a .xyz file. One benefit using the .xyz format is that the files tend to be smaller however they are less convenient to create than .mol files.

:'''Using Gaussview'''
::Open your molecule in gaussview
::Navigate to File>>Save
::In the options choose Save As a .mdl file which will default save as a .mol file
::Here is what Gaussview saved for my Mo(CO)(H2)(PH3)4 file:
<pre>
Title Card Required

Created by GaussView 5.0.8
21 18 0 0 0 0 0 0 0 0 0 0
0.0000 0.0001 -0.2759 Mo 0 0 0 0 0 0 0 0 0 0 0 0
-1.0114 -2.2089 -0.2905 P 0 0 0 0 0 0 0 0 0 0 0 0
-0.3724 -3.3206 0.3305 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.3233 -2.9082 -1.4928 H 0 0 0 0 0 0 0 0 0 0 0 0
2.2110 -1.0100 -0.1928 P 0 0 0 0 0 0 0 0 0 0 0 0
2.4180 -2.2493 0.4785 H 0 0 0 0 0 0 0 0 0 0 0 0
2.9665 -1.3716 -1.3435 H 0 0 0 0 0 0 0 0 0 0 0 0
1.0119 2.2095 -0.2895 P 0 0 0 0 0 0 0 0 0 0 0 0
0.3724 3.3212 0.3310 H 0 0 0 0 0 0 0 0 0 0 0 0
1.3254 2.9092 -1.4910 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.2110 1.0100 -0.1928 P 0 0 0 0 0 0 0 0 0 0 0 0
-2.4189 2.2495 0.4779 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.9666 1.3708 -1.3438 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.0004 -0.0005 1.6924 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.0008 -0.0015 2.8595 O 0 0 0 0 0 0 0 0 0 0 0 0
0.3612 -0.1679 -2.2213 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.3616 0.1688 -2.2210 H 0 0 0 0 0 0 0 0 0 0 0 0
3.2908 -0.3410 0.4520 H 0 0 0 0 0 0 0 0 0 0 0 0
2.2782 2.4471 0.3189 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.2786 -2.4473 0.3161 H 0 0 0 0 0 0 0 0 0 0 0 0
-3.2906 0.3408 0.4522 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 5 1 0 0 0 0
1 8 1 0 0 0 0
1 11 1 0 0 0 0
1 14 1 0 0 0 0
2 3 1 0 0 0 0
2 4 1 0 0 0 0
2 20 1 0 0 0 0
5 6 1 0 0 0 0
5 7 1 0 0 0 0
5 18 1 0 0 0 0
8 9 1 0 0 0 0
8 10 1 0 0 0 0
8 19 1 0 0 0 0
11 12 1 0 0 0 0
11 13 1 0 0 0 0
11 21 1 0 0 0 0
14 15 2 0 0 0 0

</pre>

:'''Making a .xyz file manually'''
:: You need to make this file yourself in a text editor
::A .xyz file has 3 sections
:::#First line: number of atoms in the molecule
:::#Second line: comments or title
:::#Following lines: atomic symbol followed by xyz coordiantes
::here is my Mo(CO)(H2)(PH3)4 file:
<pre>
21
Mo(CO)(H2)(PH3)4 molecule
Mo 0.000045 0.000102 -0.275893 27.797760
P -1.011401 -2.208947 -0.290536 -0.223504
H -0.372372 -3.320581 0.330463 0.085105
H -1.323285 -2.908209 -1.492765 0.082766
P 2.211020 -1.009990 -0.192847 -0.228591
H 2.418011 -2.249283 0.478494 0.087153
H 2.966565 -1.371591 -1.343488 0.086278
P 1.011822 2.209531 -0.289514 -0.223545
H 0.372347 3.321200 0.330959 0.085111
H 1.325404 2.909252 -1.491038 0.082797
P -2.211044 1.010021 -0.192849 -0.228575
H -2.418954 2.249487 0.477851 0.087149
H -2.966577 1.370804 -1.343808 0.086292
C -0.000389 -0.000536 1.692395 0.257683
O -0.000758 -0.001484 2.859470 -0.335269
H 0.361190 -0.167921 -2.221343 0.079092
H -0.361610 0.168783 -2.220950 0.079020
H 3.290813 -0.341001 0.452049 0.086821
H 2.278178 2.447165 0.318854 0.084820
H -2.278543 -2.447297 0.316108 0.084741
H -3.290613 0.340775 0.452167 0.086826
</pre>

:'''Making a .xyz file using Molden'''
::Alternatively you can create a .xyz file using a program called Molden (providing you have access to, and are familiar with, Molden)
:::#Open your molecule in Molden (this will require typing molden file_name.log)
:::#Navigate to the Molden Control window and select Write
:::#Select XYZ from the drop down menu - this will prompt the Molden Query Box to open
:::#Enter the file name you wish to use in the grey panel (ensuring there are no spaces - use underscores) and end with .xyz then select apply
:::#Click the Skull button to quit Molden
::Note: You should only use this method if you are familiar with Molden or have consulted the Molden Basics wiki page (coming soon).

===Load your file===
Load your file containing the molecule coordinates onto the wiki (as you would an image!)
:Load your molecule to the wiki, eg choose "upload file" from the menu to the left and follow the instructions

===How to add a Jmol to your wiki===
:There are two options to add a Jmol of your molecule.
::One method would be to add a button that will open a separate window with a Jmol molecule in it. This is the preferred option.
::Alternatively you can have the Jmol embedded directly into your wiki page. Use this option SPARINGLY!! Too many Jmol images will slow down the loading of your wiki page

'''Adding a button for your Jmol'''
:Add the following text to your wiki page replacing "MoCOH2PH3_4.xyz" with your file name as a .mol or .xyz file

:'''for a button that will open a new window'''
<pre>
<jmol>
<jmolAppletButton>
<uploadedFileContents>MoCOH2PH3_4.xyz</uploadedFileContents>
<text>Mo(CO)(H2)(PH3)4</text>
</jmolAppletButton>
</jmol>
</pre>
::this will produce the following:

<jmol>
<jmolAppletButton>
<uploadedFileContents>MoCOH2PH3_4.xyz</uploadedFileContents>
<text>Mo(CO)(H2)(PH3)4</text>
</jmolAppletButton>
</jmol>

:'''Embedding an image on your wiki page'''
<pre><jmol><jmolApplet>
<title>Mo(CO)(H2)(PH3)4</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>MoCOH2PH3_4.xyz</uploadedFileContents>
</jmolApplet></jmol></pre>

:This will produce the following:
<jmol><jmolApplet>
<title>test molecule</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>MoCOH2PH3_4.xyz</uploadedFileContents>
</jmolApplet></jmol>
::The title tag is self explanatory
::The colour tag sets the background colour to white
::The size tag sets the size of the Jmol image to display
::The uploadfile tag determines the file to load

'''Beware!''' You can corrupt your wiki if you type the Jmol XML incorrectly. Recovering from such an error is difficult! You should save your wiki before inserting any Jmol molecules and be careful that you put in the text exactly as it is here. It is advisable to copy then paste the text directly into your wiki then manually edit the appropriate file name and title, as well as any other changes you may wish to make such as background colour or window size.

More information on backing up and fixing your report after a crash can be found here:
[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:writeup#Backing_up_your_report fixing wiki problems]

==Visualising MOs using Jmol==

It is possible to superimpose MOs over the skeletal framework of your molecule. To do this you must first generate a cube (.cub) file for each MO of interest using Gaussview.

===How to generate .cub files===

This procedure assumes two things:

::#The geometry of your molecule has been properly optimised
::#You have performed a single point energy calculation with the key words pop=(full,nbo)

Using Gaussview, double click the .fchk file corresponding to your molecule and navigate to Edit>>MOs

Visualise however many MOs you require. Take note of the index numbers corresponding to the MOs of interest.

In Gaussview navigate to Results>>Surfaces/Contours. In the Cubes Available box select the first MO of interest and then from the drop down box Cube Actions select Save Cube. Repeat as necessary until you have saved all of the cube files corresponding to the MOs of interest.

Alternatively, instead of using Gaussview, the cubegen utility can be used (this is, of course, dependent on whether you have accessto computer with cubegen installed on it). If you do have access, then proceed by typing the following command in the command line:

<pre>./cubegen 0 MO=41 filename.fchk filename_mo41.cub 0
./cubegen 0 MO=35 filename.fchk filename_mo35.cub 0</pre>

where filename.fchk is the original name of the .fchk file.
The cube files generated (i.e. filename_mo41.cub) are likely to be quite large (a few megabytes in size). These files can be used to visualise the MOs over the molecular framework however owing to their size this will cause impossible webpage loading times. It is therefore advisable to reduce the size of the .cub file by processing it using Jmol, creating a .jvxl file.

===Creating .jvxl files from .cub files===

The .jvxl file is around 100 to 150 times smaller than the original .cub therefore it is strongly advisable to follow this procedure!!

There are a couple of ways to convert a .cub file to a .jvxl file

:One method is as follows:
::# Open Jmol (Jmol.jar). If you do not have Jmol, it can be obtained from [http://http://jmol.sourceforge.net/download/ here]
::# Navigate to File>>Open and select your .xyz or .mol file for your molecule framework
::# Once your molecule has loaded, navigate to File>>Open and select your first .cub file corresponding to an MO. This will load the MO on to the framework.
::# Right click on the Jmol display window prompting a floating menu bar to appear. Navigate to File>>Save JVXL isosurface in the floating menu. This will allow you to save a jvxl file.
::# You can then open another .cub file by selecting File>>Open in the menu at the top of the display window which will overwrite the first MO.
::# Repeat the saving procedure as necessary

:Note: I know this is time consuming - I will try and identify an alternative method

:Alternative method (number 1) for creating a .jvxl file
# Navigate to [http://www.ch.ic.ac.uk/rzepa/cub2jvxl/ this page] where you will be able press a button prompting you to select your cube file.
# This will be followed by three file save dialogs, one for the coordinates (.xyz), one for the MO surface (.jvxl) and a shrink-wrapped bundle (.pngj).

It is possible to reduce the size of the .jvxl file further by compressing it using gzip (Jmol will automatically detect and decompress this). You will end up with something that looks like name.jvxl.gz and you can safely rename this file to the original name.jvxl

===Incorporating Jmol with MOs into your wiki===

This method is very similar to the instructions outlined above for loading your Jmol molecule into your wiki page however, the Jmol XML script has been modified slightly to include the molecular orbital.

First, you will need to insert the following code into your Wiki, replacing the file name in between the <nowiki><uploadedFileContents></uploadedFileContents></nowiki> tags with the .xyz or .mol file, corresponding to your molecule from earlier.

<pre><nowiki><jmol>
<jmolApplet>
<title>Orbital</title><color>white</color><size>300</size>
<script>isosurface color orange purple "images/f/f3/MoCOH2PH3_4_mo23.jvxl" translucent;</script>
<uploadedFileContents>MoCOH2PH3_4.xyz</uploadedFileContents>
</jmolApplet>
</jmol></nowiki>
</pre>

In a new window, upload the .jvxl files on to the wiki using the [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Special:MultipleUpload/ Upload multiple files] link. Once uploaded, keep this window open and select the link to the first MO.

The browser window should now look like the image below. Click on the link as indicated by the red arrow.

[[File:File_upload_for_MOs_in_jvxl_format.png|900px]]

The browser window should now display the contents of the .jvxl file (in XML format). You will need to find the absolute path for the .jvxl file. Luckily this is displayed in the address bar at the top of the browser. This will appear as something like:

<pre>https://wiki.ch.ic.ac.uk/wiki/images/f/f3/MoCOH2PH3_4_mo23.jvxl</pre>

You will need to copy the equivalent text to:

<pre>images/f/f3/MoCOH2PH3_4_mo23.jvxl</pre>

This should be pasted into the Jmol code on your wiki page. This text should be pasted in between the <nowiki><script></script></nowiki> tags

Hopefully if all goes well you should get something similar to this:

<jmol>
<jmolApplet>
<title>Orbital</title><color>white</color><size>300</size>
<script>isosurface color orange purple "images/f/f3/MoCOH2PH3_4_mo23.jvxl" translucent;</script>
<uploadedFileContents>MoCOH2PH3_4.xyz</uploadedFileContents>
</jmolApplet>
</jmol>

<jmol>
<jmolButton>
<uploadedFileContents>MoCOH2PH3_4.xyz</uploadedFileContents>
<text>Mo(CO)(H2)(PH3)4 MO73</text>
<color>white</color>
<script>isosurface color orange purple "images/6/61/MoCOH2PH3_4_mo73.jvxl" translucent;</script>
</jmolButton>
</jmol>

=== An alternative way of loading surfaces ===
This method avoids the need to specify paths to files as seen above. Instead uses the '''.pngj''' bundle which contains all necessary information and can be invoked by
<pre><nowiki><jmolFile text="link to MO23">MoCOH2PH3_test_mo23.cub.pngj</jmolFile></nowiki></pre> which produces a <jmolFile text="link to MO23">MoCOH2PH3_test_mo23.cub.pngj</jmolFile>. This method is not as flexible as the above.

===Making your Jmol more awesome===
Section coming soon

Mod:basic jmol instructions

2012-11-20T12:27:44Z

Bw1911: /* Incorporating Jmol with MOs into your wiki */

==Adding Jmol files of your molecule to your wiki==

===Creating the molecule coordinates file for Jmol===

To include a Jmol image of your molecule in your wiki page you need to create a file containing the coordinates of the molecule. The two simplest options to create the file are, one, to use gaussview to save a copy of your molecule as a .mol file or, two, to make a .xyz file. One benefit using the .xyz format is that the files tend to be smaller however they are less convenient to create than .mol files.

:'''Using Gaussview'''
::Open your molecule in gaussview
::Navigate to File>>Save
::In the options choose Save As a .mdl file which will default save as a .mol file
::Here is what Gaussview saved for my Mo(CO)(H2)(PH3)4 file:
<pre>
Title Card Required

Created by GaussView 5.0.8
21 18 0 0 0 0 0 0 0 0 0 0
0.0000 0.0001 -0.2759 Mo 0 0 0 0 0 0 0 0 0 0 0 0
-1.0114 -2.2089 -0.2905 P 0 0 0 0 0 0 0 0 0 0 0 0
-0.3724 -3.3206 0.3305 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.3233 -2.9082 -1.4928 H 0 0 0 0 0 0 0 0 0 0 0 0
2.2110 -1.0100 -0.1928 P 0 0 0 0 0 0 0 0 0 0 0 0
2.4180 -2.2493 0.4785 H 0 0 0 0 0 0 0 0 0 0 0 0
2.9665 -1.3716 -1.3435 H 0 0 0 0 0 0 0 0 0 0 0 0
1.0119 2.2095 -0.2895 P 0 0 0 0 0 0 0 0 0 0 0 0
0.3724 3.3212 0.3310 H 0 0 0 0 0 0 0 0 0 0 0 0
1.3254 2.9092 -1.4910 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.2110 1.0100 -0.1928 P 0 0 0 0 0 0 0 0 0 0 0 0
-2.4189 2.2495 0.4779 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.9666 1.3708 -1.3438 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.0004 -0.0005 1.6924 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.0008 -0.0015 2.8595 O 0 0 0 0 0 0 0 0 0 0 0 0
0.3612 -0.1679 -2.2213 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.3616 0.1688 -2.2210 H 0 0 0 0 0 0 0 0 0 0 0 0
3.2908 -0.3410 0.4520 H 0 0 0 0 0 0 0 0 0 0 0 0
2.2782 2.4471 0.3189 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.2786 -2.4473 0.3161 H 0 0 0 0 0 0 0 0 0 0 0 0
-3.2906 0.3408 0.4522 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 5 1 0 0 0 0
1 8 1 0 0 0 0
1 11 1 0 0 0 0
1 14 1 0 0 0 0
2 3 1 0 0 0 0
2 4 1 0 0 0 0
2 20 1 0 0 0 0
5 6 1 0 0 0 0
5 7 1 0 0 0 0
5 18 1 0 0 0 0
8 9 1 0 0 0 0
8 10 1 0 0 0 0
8 19 1 0 0 0 0
11 12 1 0 0 0 0
11 13 1 0 0 0 0
11 21 1 0 0 0 0
14 15 2 0 0 0 0

</pre>

:'''Making a .xyz file manually'''
:: You need to make this file yourself in a text editor
::A .xyz file has 3 sections
:::#First line: number of atoms in the molecule
:::#Second line: comments or title
:::#Following lines: atomic symbol followed by xyz coordiantes
::here is my Mo(CO)(H2)(PH3)4 file:
<pre>
21
Mo(CO)(H2)(PH3)4 molecule
Mo 0.000045 0.000102 -0.275893 27.797760
P -1.011401 -2.208947 -0.290536 -0.223504
H -0.372372 -3.320581 0.330463 0.085105
H -1.323285 -2.908209 -1.492765 0.082766
P 2.211020 -1.009990 -0.192847 -0.228591
H 2.418011 -2.249283 0.478494 0.087153
H 2.966565 -1.371591 -1.343488 0.086278
P 1.011822 2.209531 -0.289514 -0.223545
H 0.372347 3.321200 0.330959 0.085111
H 1.325404 2.909252 -1.491038 0.082797
P -2.211044 1.010021 -0.192849 -0.228575
H -2.418954 2.249487 0.477851 0.087149
H -2.966577 1.370804 -1.343808 0.086292
C -0.000389 -0.000536 1.692395 0.257683
O -0.000758 -0.001484 2.859470 -0.335269
H 0.361190 -0.167921 -2.221343 0.079092
H -0.361610 0.168783 -2.220950 0.079020
H 3.290813 -0.341001 0.452049 0.086821
H 2.278178 2.447165 0.318854 0.084820
H -2.278543 -2.447297 0.316108 0.084741
H -3.290613 0.340775 0.452167 0.086826
</pre>

:'''Making a .xyz file using Molden'''
::Alternatively you can create a .xyz file using a program called Molden (providing you have access to, and are familiar with, Molden)
:::#Open your molecule in Molden (this will require typing molden file_name.log)
:::#Navigate to the Molden Control window and select Write
:::#Select XYZ from the drop down menu - this will prompt the Molden Query Box to open
:::#Enter the file name you wish to use in the grey panel (ensuring there are no spaces - use underscores) and end with .xyz then select apply
:::#Click the Skull button to quit Molden
::Note: You should only use this method if you are familiar with Molden or have consulted the Molden Basics wiki page (coming soon).

===Load your file===
Load your file containing the molecule coordinates onto the wiki (as you would an image!)
:Load your molecule to the wiki, eg choose "upload file" from the menu to the left and follow the instructions

===How to add a Jmol to your wiki===
:There are two options to add a Jmol of your molecule.
::One method would be to add a button that will open a separate window with a Jmol molecule in it. This is the preferred option.
::Alternatively you can have the Jmol embedded directly into your wiki page. Use this option SPARINGLY!! Too many Jmol images will slow down the loading of your wiki page

'''Adding a button for your Jmol'''
:Add the following text to your wiki page replacing "MoCOH2PH3_4.xyz" with your file name as a .mol or .xyz file

:'''for a button that will open a new window'''
<pre>
<jmol>
<jmolAppletButton>
<uploadedFileContents>MoCOH2PH3_4.xyz</uploadedFileContents>
<text>Mo(CO)(H2)(PH3)4</text>
</jmolAppletButton>
</jmol>
</pre>
::this will produce the following:

<jmol>
<jmolAppletButton>
<uploadedFileContents>MoCOH2PH3_4.xyz</uploadedFileContents>
<text>Mo(CO)(H2)(PH3)4</text>
</jmolAppletButton>
</jmol>

:'''Embedding an image on your wiki page'''
<pre><jmol><jmolApplet>
<title>Mo(CO)(H2)(PH3)4</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>MoCOH2PH3_4.xyz</uploadedFileContents>
</jmolApplet></jmol></pre>

:This will produce the following:
<jmol><jmolApplet>
<title>test molecule</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>MoCOH2PH3_4.xyz</uploadedFileContents>
</jmolApplet></jmol>
::The title tag is self explanatory
::The colour tag sets the background colour to white
::The size tag sets the size of the Jmol image to display
::The uploadfile tag determines the file to load

'''Beware!''' You can corrupt your wiki if you type the Jmol XML incorrectly. Recovering from such an error is difficult! You should save your wiki before inserting any Jmol molecules and be careful that you put in the text exactly as it is here. It is advisable to copy then paste the text directly into your wiki then manually edit the appropriate file name and title, as well as any other changes you may wish to make such as background colour or window size.

More information on backing up and fixing your report after a crash can be found here:
[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:writeup#Backing_up_your_report fixing wiki problems]

==Visualising MOs using Jmol==

It is possible to superimpose MOs over the skeletal framework of your molecule. To do this you must first generate a cube (.cub) file for each MO of interest using Gaussview.

===How to generate .cub files===

This procedure assumes two things:

::#The geometry of your molecule has been properly optimised
::#You have performed a single point energy calculation with the key words pop=(full,nbo)

Using Gaussview, double click the .fchk file corresponding to your molecule and navigate to Edit>>MOs

Visualise however many MOs you require. Take note of the index numbers corresponding to the MOs of interest.

In Gaussview navigate to Results>>Surfaces/Contours. In the Cubes Available box select the first MO of interest and then from the drop down box Cube Actions select Save Cube. Repeat as necessary until you have saved all of the cube files corresponding to the MOs of interest.

Alternatively, instead of using Gaussview, the cubegen utility can be used (this is, of course, dependent on whether you have accessto computer with cubegen installed on it). If you do have access, then proceed by typing the following command in the command line:

<pre>./cubegen 0 MO=41 filename.fchk filename_mo41.cub 0
./cubegen 0 MO=35 filename.fchk filename_mo35.cub 0</pre>

where filename.fchk is the original name of the .fchk file.
The cube files generated (i.e. filename_mo41.cub) are likely to be quite large (a few megabytes in size). These files can be used to visualise the MOs over the molecular framework however owing to their size this will cause impossible webpage loading times. It is therefore advisable to reduce the size of the .cub file by processing it using Jmol, creating a .jvxl file.

===Creating .jvxl files from .cub files===

The .jvxl file is around 100 to 150 times smaller than the original .cub therefore it is strongly advisable to follow this procedure!!

There are a couple of ways to convert a .cub file to a .jvxl file

:One method is as follows:
::# Open Jmol (Jmol.jar). If you do not have Jmol, it can be obtained from [http://http://jmol.sourceforge.net/download/ here]
::# Navigate to File>>Open and select your .xyz or .mol file for your molecule framework
::# Once your molecule has loaded, navigate to File>>Open and select your first .cub file corresponding to an MO. This will load the MO on to the framework.
::# Right click on the Jmol display window prompting a floating menu bar to appear. Navigate to File>>Save JVXL isosurface in the floating menu. This will allow you to save a jvxl file.
::# You can then open another .cub file by selecting File>>Open in the menu at the top of the display window which will overwrite the first MO.
::# Repeat the saving procedure as necessary

:Note: I know this is time consuming - I will try and identify an alternative method

:Alternative method (number 1) for creating a .jvxl file
# Navigate to [http://www.ch.ic.ac.uk/rzepa/cub2jvxl/ this page] where you will be able press a button prompting you to select your cube file.
# This will be followed by three file save dialogs, one for the coordinates (.xyz), one for the MO surface (.jvxl) and a shrink-wrapped bundle (.pngj).

It is possible to reduce the size of the .jvxl file further by compressing it using gzip (Jmol will automatically detect and decompress this). You will end up with something that looks like name.jvxl.gz and you can safely rename this file to the original name.jvxl

===Incorporating Jmol with MOs into your wiki===

This method is very similar to the instructions outlined above for loading your Jmol molecule into your wiki page however, the Jmol XML script has been modified slightly to include the molecular orbital.

First, you will need to insert the following code into your Wiki, replacing the file name in between the <nowiki><uploadedFileContents></uploadedFileContents></nowiki> tags with the .xyz or .mol file, corresponding to your molecule from earlier.

<pre><nowiki><jmol>
<jmolApplet>
<title>Orbital</title><color>white</color><size>300</size>
<script>isosurface color orange purple "images/f/f3/MoCOH2PH3_4_mo23.jvxl" translucent;</script>
<uploadedFileContents>MoCOH2PH3_4.xyz</uploadedFileContents>
</jmolApplet>
</jmol></nowiki>
</pre>

In a new window, upload the .jvxl files on to the wiki using the [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Special:MultipleUpload/ Upload multiple files] link. Once uploaded, keep this window open and select the link to the first MO.

The browser window should now look like the image below. Click on the link as indicated by the red arrow.

[[File:File_upload_for_MOs_in_jvxl_format.png|900px]]

The browser window should now display the contents of the .jvxl file (in XML format). You will need to find the absolute path for the .jvxl file. Luckily this is displayed in the address bar at the top of the browser. This will appear as something like:

<pre>https://wiki.ch.ic.ac.uk/wiki/images/f/f3/MoCOH2PH3_4_mo23.jvxl</pre>

You will need to copy the equivalent text to:

<pre>images/f/f3/MoCOH2PH3_4_mo23.jvxl</pre>

This should be pasted into the Jmol code on your wiki page. This text should be pasted in between the <nowiki><script></script></nowiki> tags

Hopefully if all goes well you should get something similar to this:

<jmol>
<jmolApplet>
<title>Orbital</title><color>white</color><size>300</size>
<script>isosurface color orange purple "images/f/f3/MoCOH2PH3_4_mo23.jvxl" translucent;</script>
<uploadedFileContents>MoCOH2PH3_4.xyz</uploadedFileContents>
</jmolApplet>
</jmol>

<jmol>
<jmolAppletLink>
<uploadedFileContents>MoCOH2PH3_4.xyz</uploadedFileContents>
<text>Mo(CO)(H2)(PH3)4 MO73</text>
<color>white</color>
</jmolAppletLink>
</jmol>

=== An alternative way of loading surfaces ===
This method avoids the need to specify paths to files as seen above. Instead uses the '''.pngj''' bundle which contains all necessary information and can be invoked by
<pre><nowiki><jmolFile text="link to MO23">MoCOH2PH3_test_mo23.cub.pngj</jmolFile></nowiki></pre> which produces a <jmolFile text="link to MO23">MoCOH2PH3_test_mo23.cub.pngj</jmolFile>. This method is not as flexible as the above.

===Making your Jmol more awesome===
Section coming soon

Mod:basic jmol instructions

2012-11-20T12:27:13Z

Bw1911: /* Incorporating Jmol with MOs into your wiki */

==Adding Jmol files of your molecule to your wiki==

===Creating the molecule coordinates file for Jmol===

To include a Jmol image of your molecule in your wiki page you need to create a file containing the coordinates of the molecule. The two simplest options to create the file are, one, to use gaussview to save a copy of your molecule as a .mol file or, two, to make a .xyz file. One benefit using the .xyz format is that the files tend to be smaller however they are less convenient to create than .mol files.

:'''Using Gaussview'''
::Open your molecule in gaussview
::Navigate to File>>Save
::In the options choose Save As a .mdl file which will default save as a .mol file
::Here is what Gaussview saved for my Mo(CO)(H2)(PH3)4 file:
<pre>
Title Card Required

Created by GaussView 5.0.8
21 18 0 0 0 0 0 0 0 0 0 0
0.0000 0.0001 -0.2759 Mo 0 0 0 0 0 0 0 0 0 0 0 0
-1.0114 -2.2089 -0.2905 P 0 0 0 0 0 0 0 0 0 0 0 0
-0.3724 -3.3206 0.3305 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.3233 -2.9082 -1.4928 H 0 0 0 0 0 0 0 0 0 0 0 0
2.2110 -1.0100 -0.1928 P 0 0 0 0 0 0 0 0 0 0 0 0
2.4180 -2.2493 0.4785 H 0 0 0 0 0 0 0 0 0 0 0 0
2.9665 -1.3716 -1.3435 H 0 0 0 0 0 0 0 0 0 0 0 0
1.0119 2.2095 -0.2895 P 0 0 0 0 0 0 0 0 0 0 0 0
0.3724 3.3212 0.3310 H 0 0 0 0 0 0 0 0 0 0 0 0
1.3254 2.9092 -1.4910 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.2110 1.0100 -0.1928 P 0 0 0 0 0 0 0 0 0 0 0 0
-2.4189 2.2495 0.4779 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.9666 1.3708 -1.3438 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.0004 -0.0005 1.6924 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.0008 -0.0015 2.8595 O 0 0 0 0 0 0 0 0 0 0 0 0
0.3612 -0.1679 -2.2213 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.3616 0.1688 -2.2210 H 0 0 0 0 0 0 0 0 0 0 0 0
3.2908 -0.3410 0.4520 H 0 0 0 0 0 0 0 0 0 0 0 0
2.2782 2.4471 0.3189 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.2786 -2.4473 0.3161 H 0 0 0 0 0 0 0 0 0 0 0 0
-3.2906 0.3408 0.4522 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 5 1 0 0 0 0
1 8 1 0 0 0 0
1 11 1 0 0 0 0
1 14 1 0 0 0 0
2 3 1 0 0 0 0
2 4 1 0 0 0 0
2 20 1 0 0 0 0
5 6 1 0 0 0 0
5 7 1 0 0 0 0
5 18 1 0 0 0 0
8 9 1 0 0 0 0
8 10 1 0 0 0 0
8 19 1 0 0 0 0
11 12 1 0 0 0 0
11 13 1 0 0 0 0
11 21 1 0 0 0 0
14 15 2 0 0 0 0

</pre>

:'''Making a .xyz file manually'''
:: You need to make this file yourself in a text editor
::A .xyz file has 3 sections
:::#First line: number of atoms in the molecule
:::#Second line: comments or title
:::#Following lines: atomic symbol followed by xyz coordiantes
::here is my Mo(CO)(H2)(PH3)4 file:
<pre>
21
Mo(CO)(H2)(PH3)4 molecule
Mo 0.000045 0.000102 -0.275893 27.797760
P -1.011401 -2.208947 -0.290536 -0.223504
H -0.372372 -3.320581 0.330463 0.085105
H -1.323285 -2.908209 -1.492765 0.082766
P 2.211020 -1.009990 -0.192847 -0.228591
H 2.418011 -2.249283 0.478494 0.087153
H 2.966565 -1.371591 -1.343488 0.086278
P 1.011822 2.209531 -0.289514 -0.223545
H 0.372347 3.321200 0.330959 0.085111
H 1.325404 2.909252 -1.491038 0.082797
P -2.211044 1.010021 -0.192849 -0.228575
H -2.418954 2.249487 0.477851 0.087149
H -2.966577 1.370804 -1.343808 0.086292
C -0.000389 -0.000536 1.692395 0.257683
O -0.000758 -0.001484 2.859470 -0.335269
H 0.361190 -0.167921 -2.221343 0.079092
H -0.361610 0.168783 -2.220950 0.079020
H 3.290813 -0.341001 0.452049 0.086821
H 2.278178 2.447165 0.318854 0.084820
H -2.278543 -2.447297 0.316108 0.084741
H -3.290613 0.340775 0.452167 0.086826
</pre>

:'''Making a .xyz file using Molden'''
::Alternatively you can create a .xyz file using a program called Molden (providing you have access to, and are familiar with, Molden)
:::#Open your molecule in Molden (this will require typing molden file_name.log)
:::#Navigate to the Molden Control window and select Write
:::#Select XYZ from the drop down menu - this will prompt the Molden Query Box to open
:::#Enter the file name you wish to use in the grey panel (ensuring there are no spaces - use underscores) and end with .xyz then select apply
:::#Click the Skull button to quit Molden
::Note: You should only use this method if you are familiar with Molden or have consulted the Molden Basics wiki page (coming soon).

===Load your file===
Load your file containing the molecule coordinates onto the wiki (as you would an image!)
:Load your molecule to the wiki, eg choose "upload file" from the menu to the left and follow the instructions

===How to add a Jmol to your wiki===
:There are two options to add a Jmol of your molecule.
::One method would be to add a button that will open a separate window with a Jmol molecule in it. This is the preferred option.
::Alternatively you can have the Jmol embedded directly into your wiki page. Use this option SPARINGLY!! Too many Jmol images will slow down the loading of your wiki page

'''Adding a button for your Jmol'''
:Add the following text to your wiki page replacing "MoCOH2PH3_4.xyz" with your file name as a .mol or .xyz file

:'''for a button that will open a new window'''
<pre>
<jmol>
<jmolAppletButton>
<uploadedFileContents>MoCOH2PH3_4.xyz</uploadedFileContents>
<text>Mo(CO)(H2)(PH3)4</text>
</jmolAppletButton>
</jmol>
</pre>
::this will produce the following:

<jmol>
<jmolAppletButton>
<uploadedFileContents>MoCOH2PH3_4.xyz</uploadedFileContents>
<text>Mo(CO)(H2)(PH3)4</text>
</jmolAppletButton>
</jmol>

:'''Embedding an image on your wiki page'''
<pre><jmol><jmolApplet>
<title>Mo(CO)(H2)(PH3)4</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>MoCOH2PH3_4.xyz</uploadedFileContents>
</jmolApplet></jmol></pre>

:This will produce the following:
<jmol><jmolApplet>
<title>test molecule</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>MoCOH2PH3_4.xyz</uploadedFileContents>
</jmolApplet></jmol>
::The title tag is self explanatory
::The colour tag sets the background colour to white
::The size tag sets the size of the Jmol image to display
::The uploadfile tag determines the file to load

'''Beware!''' You can corrupt your wiki if you type the Jmol XML incorrectly. Recovering from such an error is difficult! You should save your wiki before inserting any Jmol molecules and be careful that you put in the text exactly as it is here. It is advisable to copy then paste the text directly into your wiki then manually edit the appropriate file name and title, as well as any other changes you may wish to make such as background colour or window size.

More information on backing up and fixing your report after a crash can be found here:
[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:writeup#Backing_up_your_report fixing wiki problems]

==Visualising MOs using Jmol==

It is possible to superimpose MOs over the skeletal framework of your molecule. To do this you must first generate a cube (.cub) file for each MO of interest using Gaussview.

===How to generate .cub files===

This procedure assumes two things:

::#The geometry of your molecule has been properly optimised
::#You have performed a single point energy calculation with the key words pop=(full,nbo)

Using Gaussview, double click the .fchk file corresponding to your molecule and navigate to Edit>>MOs

Visualise however many MOs you require. Take note of the index numbers corresponding to the MOs of interest.

In Gaussview navigate to Results>>Surfaces/Contours. In the Cubes Available box select the first MO of interest and then from the drop down box Cube Actions select Save Cube. Repeat as necessary until you have saved all of the cube files corresponding to the MOs of interest.

Alternatively, instead of using Gaussview, the cubegen utility can be used (this is, of course, dependent on whether you have accessto computer with cubegen installed on it). If you do have access, then proceed by typing the following command in the command line:

<pre>./cubegen 0 MO=41 filename.fchk filename_mo41.cub 0
./cubegen 0 MO=35 filename.fchk filename_mo35.cub 0</pre>

where filename.fchk is the original name of the .fchk file.
The cube files generated (i.e. filename_mo41.cub) are likely to be quite large (a few megabytes in size). These files can be used to visualise the MOs over the molecular framework however owing to their size this will cause impossible webpage loading times. It is therefore advisable to reduce the size of the .cub file by processing it using Jmol, creating a .jvxl file.

===Creating .jvxl files from .cub files===

The .jvxl file is around 100 to 150 times smaller than the original .cub therefore it is strongly advisable to follow this procedure!!

There are a couple of ways to convert a .cub file to a .jvxl file

:One method is as follows:
::# Open Jmol (Jmol.jar). If you do not have Jmol, it can be obtained from [http://http://jmol.sourceforge.net/download/ here]
::# Navigate to File>>Open and select your .xyz or .mol file for your molecule framework
::# Once your molecule has loaded, navigate to File>>Open and select your first .cub file corresponding to an MO. This will load the MO on to the framework.
::# Right click on the Jmol display window prompting a floating menu bar to appear. Navigate to File>>Save JVXL isosurface in the floating menu. This will allow you to save a jvxl file.
::# You can then open another .cub file by selecting File>>Open in the menu at the top of the display window which will overwrite the first MO.
::# Repeat the saving procedure as necessary

:Note: I know this is time consuming - I will try and identify an alternative method

:Alternative method (number 1) for creating a .jvxl file
# Navigate to [http://www.ch.ic.ac.uk/rzepa/cub2jvxl/ this page] where you will be able press a button prompting you to select your cube file.
# This will be followed by three file save dialogs, one for the coordinates (.xyz), one for the MO surface (.jvxl) and a shrink-wrapped bundle (.pngj).

It is possible to reduce the size of the .jvxl file further by compressing it using gzip (Jmol will automatically detect and decompress this). You will end up with something that looks like name.jvxl.gz and you can safely rename this file to the original name.jvxl

===Incorporating Jmol with MOs into your wiki===

This method is very similar to the instructions outlined above for loading your Jmol molecule into your wiki page however, the Jmol XML script has been modified slightly to include the molecular orbital.

First, you will need to insert the following code into your Wiki, replacing the file name in between the <nowiki><uploadedFileContents></uploadedFileContents></nowiki> tags with the .xyz or .mol file, corresponding to your molecule from earlier.

<pre><nowiki><jmol>
<jmolApplet>
<title>Orbital</title><color>white</color><size>300</size>
<script>isosurface color orange purple "images/f/f3/MoCOH2PH3_4_mo23.jvxl" translucent;</script>
<uploadedFileContents>MoCOH2PH3_4.xyz</uploadedFileContents>
</jmolApplet>
</jmol></nowiki>
</pre>

In a new window, upload the .jvxl files on to the wiki using the [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Special:MultipleUpload/ Upload multiple files] link. Once uploaded, keep this window open and select the link to the first MO.

The browser window should now look like the image below. Click on the link as indicated by the red arrow.

[[File:File_upload_for_MOs_in_jvxl_format.png|900px]]

The browser window should now display the contents of the .jvxl file (in XML format). You will need to find the absolute path for the .jvxl file. Luckily this is displayed in the address bar at the top of the browser. This will appear as something like:

<pre>https://wiki.ch.ic.ac.uk/wiki/images/f/f3/MoCOH2PH3_4_mo23.jvxl</pre>

You will need to copy the equivalent text to:

<pre>images/f/f3/MoCOH2PH3_4_mo23.jvxl</pre>

This should be pasted into the Jmol code on your wiki page. This text should be pasted in between the <nowiki><script></script></nowiki> tags

Hopefully if all goes well you should get something similar to this:

<jmol>
<jmolApplet>
<title>Orbital</title><color>white</color><size>300</size>
<script>isosurface color orange purple "images/f/f3/MoCOH2PH3_4_mo23.jvxl" translucent;</script>
<uploadedFileContents>MoCOH2PH3_4.xyz</uploadedFileContents>
</jmolApplet>
</jmol>

<jmol>
<jmolAppletLink>
<uploadedFileContents>MoCOH2PH3_4.xyz</uploadedFileContents>
<text>Mo(CO)(H2)(PH3)4 MO73</text>
<color>white</color>
<script>isosurface color orange purple "images/6/61/MoCOH2PH3_4_mo73.jvxl" translucent;</script>
</jmolAppletLink>
</jmol>

=== An alternative way of loading surfaces ===
This method avoids the need to specify paths to files as seen above. Instead uses the '''.pngj''' bundle which contains all necessary information and can be invoked by
<pre><nowiki><jmolFile text="link to MO23">MoCOH2PH3_test_mo23.cub.pngj</jmolFile></nowiki></pre> which produces a <jmolFile text="link to MO23">MoCOH2PH3_test_mo23.cub.pngj</jmolFile>. This method is not as flexible as the above.

===Making your Jmol more awesome===
Section coming soon

Mod:basic jmol instructions

2012-11-20T12:21:37Z

Bw1911: /* Incorporating Jmol with MOs into your wiki */

==Adding Jmol files of your molecule to your wiki==

===Creating the molecule coordinates file for Jmol===

To include a Jmol image of your molecule in your wiki page you need to create a file containing the coordinates of the molecule. The two simplest options to create the file are, one, to use gaussview to save a copy of your molecule as a .mol file or, two, to make a .xyz file. One benefit using the .xyz format is that the files tend to be smaller however they are less convenient to create than .mol files.

:'''Using Gaussview'''
::Open your molecule in gaussview
::Navigate to File>>Save
::In the options choose Save As a .mdl file which will default save as a .mol file
::Here is what Gaussview saved for my Mo(CO)(H2)(PH3)4 file:
<pre>
Title Card Required

Created by GaussView 5.0.8
21 18 0 0 0 0 0 0 0 0 0 0
0.0000 0.0001 -0.2759 Mo 0 0 0 0 0 0 0 0 0 0 0 0
-1.0114 -2.2089 -0.2905 P 0 0 0 0 0 0 0 0 0 0 0 0
-0.3724 -3.3206 0.3305 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.3233 -2.9082 -1.4928 H 0 0 0 0 0 0 0 0 0 0 0 0
2.2110 -1.0100 -0.1928 P 0 0 0 0 0 0 0 0 0 0 0 0
2.4180 -2.2493 0.4785 H 0 0 0 0 0 0 0 0 0 0 0 0
2.9665 -1.3716 -1.3435 H 0 0 0 0 0 0 0 0 0 0 0 0
1.0119 2.2095 -0.2895 P 0 0 0 0 0 0 0 0 0 0 0 0
0.3724 3.3212 0.3310 H 0 0 0 0 0 0 0 0 0 0 0 0
1.3254 2.9092 -1.4910 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.2110 1.0100 -0.1928 P 0 0 0 0 0 0 0 0 0 0 0 0
-2.4189 2.2495 0.4779 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.9666 1.3708 -1.3438 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.0004 -0.0005 1.6924 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.0008 -0.0015 2.8595 O 0 0 0 0 0 0 0 0 0 0 0 0
0.3612 -0.1679 -2.2213 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.3616 0.1688 -2.2210 H 0 0 0 0 0 0 0 0 0 0 0 0
3.2908 -0.3410 0.4520 H 0 0 0 0 0 0 0 0 0 0 0 0
2.2782 2.4471 0.3189 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.2786 -2.4473 0.3161 H 0 0 0 0 0 0 0 0 0 0 0 0
-3.2906 0.3408 0.4522 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 5 1 0 0 0 0
1 8 1 0 0 0 0
1 11 1 0 0 0 0
1 14 1 0 0 0 0
2 3 1 0 0 0 0
2 4 1 0 0 0 0
2 20 1 0 0 0 0
5 6 1 0 0 0 0
5 7 1 0 0 0 0
5 18 1 0 0 0 0
8 9 1 0 0 0 0
8 10 1 0 0 0 0
8 19 1 0 0 0 0
11 12 1 0 0 0 0
11 13 1 0 0 0 0
11 21 1 0 0 0 0
14 15 2 0 0 0 0

</pre>

:'''Making a .xyz file manually'''
:: You need to make this file yourself in a text editor
::A .xyz file has 3 sections
:::#First line: number of atoms in the molecule
:::#Second line: comments or title
:::#Following lines: atomic symbol followed by xyz coordiantes
::here is my Mo(CO)(H2)(PH3)4 file:
<pre>
21
Mo(CO)(H2)(PH3)4 molecule
Mo 0.000045 0.000102 -0.275893 27.797760
P -1.011401 -2.208947 -0.290536 -0.223504
H -0.372372 -3.320581 0.330463 0.085105
H -1.323285 -2.908209 -1.492765 0.082766
P 2.211020 -1.009990 -0.192847 -0.228591
H 2.418011 -2.249283 0.478494 0.087153
H 2.966565 -1.371591 -1.343488 0.086278
P 1.011822 2.209531 -0.289514 -0.223545
H 0.372347 3.321200 0.330959 0.085111
H 1.325404 2.909252 -1.491038 0.082797
P -2.211044 1.010021 -0.192849 -0.228575
H -2.418954 2.249487 0.477851 0.087149
H -2.966577 1.370804 -1.343808 0.086292
C -0.000389 -0.000536 1.692395 0.257683
O -0.000758 -0.001484 2.859470 -0.335269
H 0.361190 -0.167921 -2.221343 0.079092
H -0.361610 0.168783 -2.220950 0.079020
H 3.290813 -0.341001 0.452049 0.086821
H 2.278178 2.447165 0.318854 0.084820
H -2.278543 -2.447297 0.316108 0.084741
H -3.290613 0.340775 0.452167 0.086826
</pre>

:'''Making a .xyz file using Molden'''
::Alternatively you can create a .xyz file using a program called Molden (providing you have access to, and are familiar with, Molden)
:::#Open your molecule in Molden (this will require typing molden file_name.log)
:::#Navigate to the Molden Control window and select Write
:::#Select XYZ from the drop down menu - this will prompt the Molden Query Box to open
:::#Enter the file name you wish to use in the grey panel (ensuring there are no spaces - use underscores) and end with .xyz then select apply
:::#Click the Skull button to quit Molden
::Note: You should only use this method if you are familiar with Molden or have consulted the Molden Basics wiki page (coming soon).

===Load your file===
Load your file containing the molecule coordinates onto the wiki (as you would an image!)
:Load your molecule to the wiki, eg choose "upload file" from the menu to the left and follow the instructions

===How to add a Jmol to your wiki===
:There are two options to add a Jmol of your molecule.
::One method would be to add a button that will open a separate window with a Jmol molecule in it. This is the preferred option.
::Alternatively you can have the Jmol embedded directly into your wiki page. Use this option SPARINGLY!! Too many Jmol images will slow down the loading of your wiki page

'''Adding a button for your Jmol'''
:Add the following text to your wiki page replacing "MoCOH2PH3_4.xyz" with your file name as a .mol or .xyz file

:'''for a button that will open a new window'''
<pre>
<jmol>
<jmolAppletButton>
<uploadedFileContents>MoCOH2PH3_4.xyz</uploadedFileContents>
<text>Mo(CO)(H2)(PH3)4</text>
</jmolAppletButton>
</jmol>
</pre>
::this will produce the following:

<jmol>
<jmolAppletButton>
<uploadedFileContents>MoCOH2PH3_4.xyz</uploadedFileContents>
<text>Mo(CO)(H2)(PH3)4</text>
</jmolAppletButton>
</jmol>

:'''Embedding an image on your wiki page'''
<pre><jmol><jmolApplet>
<title>Mo(CO)(H2)(PH3)4</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>MoCOH2PH3_4.xyz</uploadedFileContents>
</jmolApplet></jmol></pre>

:This will produce the following:
<jmol><jmolApplet>
<title>test molecule</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>MoCOH2PH3_4.xyz</uploadedFileContents>
</jmolApplet></jmol>
::The title tag is self explanatory
::The colour tag sets the background colour to white
::The size tag sets the size of the Jmol image to display
::The uploadfile tag determines the file to load

'''Beware!''' You can corrupt your wiki if you type the Jmol XML incorrectly. Recovering from such an error is difficult! You should save your wiki before inserting any Jmol molecules and be careful that you put in the text exactly as it is here. It is advisable to copy then paste the text directly into your wiki then manually edit the appropriate file name and title, as well as any other changes you may wish to make such as background colour or window size.

More information on backing up and fixing your report after a crash can be found here:
[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:writeup#Backing_up_your_report fixing wiki problems]

==Visualising MOs using Jmol==

It is possible to superimpose MOs over the skeletal framework of your molecule. To do this you must first generate a cube (.cub) file for each MO of interest using Gaussview.

===How to generate .cub files===

This procedure assumes two things:

::#The geometry of your molecule has been properly optimised
::#You have performed a single point energy calculation with the key words pop=(full,nbo)

Using Gaussview, double click the .fchk file corresponding to your molecule and navigate to Edit>>MOs

Visualise however many MOs you require. Take note of the index numbers corresponding to the MOs of interest.

In Gaussview navigate to Results>>Surfaces/Contours. In the Cubes Available box select the first MO of interest and then from the drop down box Cube Actions select Save Cube. Repeat as necessary until you have saved all of the cube files corresponding to the MOs of interest.

Alternatively, instead of using Gaussview, the cubegen utility can be used (this is, of course, dependent on whether you have accessto computer with cubegen installed on it). If you do have access, then proceed by typing the following command in the command line:

<pre>./cubegen 0 MO=41 filename.fchk filename_mo41.cub 0
./cubegen 0 MO=35 filename.fchk filename_mo35.cub 0</pre>

where filename.fchk is the original name of the .fchk file.
The cube files generated (i.e. filename_mo41.cub) are likely to be quite large (a few megabytes in size). These files can be used to visualise the MOs over the molecular framework however owing to their size this will cause impossible webpage loading times. It is therefore advisable to reduce the size of the .cub file by processing it using Jmol, creating a .jvxl file.

===Creating .jvxl files from .cub files===

The .jvxl file is around 100 to 150 times smaller than the original .cub therefore it is strongly advisable to follow this procedure!!

There are a couple of ways to convert a .cub file to a .jvxl file

:One method is as follows:
::# Open Jmol (Jmol.jar). If you do not have Jmol, it can be obtained from [http://http://jmol.sourceforge.net/download/ here]
::# Navigate to File>>Open and select your .xyz or .mol file for your molecule framework
::# Once your molecule has loaded, navigate to File>>Open and select your first .cub file corresponding to an MO. This will load the MO on to the framework.
::# Right click on the Jmol display window prompting a floating menu bar to appear. Navigate to File>>Save JVXL isosurface in the floating menu. This will allow you to save a jvxl file.
::# You can then open another .cub file by selecting File>>Open in the menu at the top of the display window which will overwrite the first MO.
::# Repeat the saving procedure as necessary

:Note: I know this is time consuming - I will try and identify an alternative method

:Alternative method (number 1) for creating a .jvxl file
# Navigate to [http://www.ch.ic.ac.uk/rzepa/cub2jvxl/ this page] where you will be able press a button prompting you to select your cube file.
# This will be followed by three file save dialogs, one for the coordinates (.xyz), one for the MO surface (.jvxl) and a shrink-wrapped bundle (.pngj).

It is possible to reduce the size of the .jvxl file further by compressing it using gzip (Jmol will automatically detect and decompress this). You will end up with something that looks like name.jvxl.gz and you can safely rename this file to the original name.jvxl

===Incorporating Jmol with MOs into your wiki===

This method is very similar to the instructions outlined above for loading your Jmol molecule into your wiki page however, the Jmol XML script has been modified slightly to include the molecular orbital.

First, you will need to insert the following code into your Wiki, replacing the file name in between the <nowiki><uploadedFileContents></uploadedFileContents></nowiki> tags with the .xyz or .mol file, corresponding to your molecule from earlier.

<pre><nowiki><jmol>
<jmolApplet>
<title>Orbital</title><color>white</color><size>300</size>
<script>isosurface color orange purple "images/f/f3/MoCOH2PH3_4_mo23.jvxl" translucent;</script>
<uploadedFileContents>MoCOH2PH3_4.xyz</uploadedFileContents>
</jmolApplet>
</jmol></nowiki>
</pre>

In a new window, upload the .jvxl files on to the wiki using the [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Special:MultipleUpload/ Upload multiple files] link. Once uploaded, keep this window open and select the link to the first MO.

The browser window should now look like the image below. Click on the link as indicated by the red arrow.

[[File:File_upload_for_MOs_in_jvxl_format.png|900px]]

The browser window should now display the contents of the .jvxl file (in XML format). You will need to find the absolute path for the .jvxl file. Luckily this is displayed in the address bar at the top of the browser. This will appear as something like:

<pre>https://wiki.ch.ic.ac.uk/wiki/images/f/f3/MoCOH2PH3_4_mo23.jvxl</pre>

You will need to copy the equivalent text to:

<pre>images/f/f3/MoCOH2PH3_4_mo23.jvxl</pre>

This should be pasted into the Jmol code on your wiki page. This text should be pasted in between the <nowiki><script></script></nowiki> tags

Hopefully if all goes well you should get something similar to this:

<jmol>
<jmolApplet>
<title>Orbital</title><color>white</color><size>300</size>
<script>isosurface color orange purple "images/f/f3/MoCOH2PH3_4_mo23.jvxl" translucent;</script>
<uploadedFileContents>MoCOH2PH3_4.xyz</uploadedFileContents>
</jmolApplet>
</jmol>

<jmol>
<jmolAppletLink>
<uploadedFileContents>MoCOH2PH3_4.xyz</uploadedFileContents>
<text>Mo(CO)(H2)(PH3)4 MO73</text>
<script>isosurface color orange purple "images/6/61/MoCOH2PH3_4_mo73.jvxl" translucent;</script>
</jmolAppletLink>
</jmol>

=== An alternative way of loading surfaces ===
This method avoids the need to specify paths to files as seen above. Instead uses the '''.pngj''' bundle which contains all necessary information and can be invoked by
<pre><nowiki><jmolFile text="link to MO23">MoCOH2PH3_test_mo23.cub.pngj</jmolFile></nowiki></pre> which produces a <jmolFile text="link to MO23">MoCOH2PH3_test_mo23.cub.pngj</jmolFile>. This method is not as flexible as the above.

===Making your Jmol more awesome===
Section coming soon

Mod:basic jmol instructions

2012-11-20T12:20:01Z

Bw1911: /* Incorporating Jmol with MOs into your wiki */

==Adding Jmol files of your molecule to your wiki==

===Creating the molecule coordinates file for Jmol===

To include a Jmol image of your molecule in your wiki page you need to create a file containing the coordinates of the molecule. The two simplest options to create the file are, one, to use gaussview to save a copy of your molecule as a .mol file or, two, to make a .xyz file. One benefit using the .xyz format is that the files tend to be smaller however they are less convenient to create than .mol files.

:'''Using Gaussview'''
::Open your molecule in gaussview
::Navigate to File>>Save
::In the options choose Save As a .mdl file which will default save as a .mol file
::Here is what Gaussview saved for my Mo(CO)(H2)(PH3)4 file:
<pre>
Title Card Required

Created by GaussView 5.0.8
21 18 0 0 0 0 0 0 0 0 0 0
0.0000 0.0001 -0.2759 Mo 0 0 0 0 0 0 0 0 0 0 0 0
-1.0114 -2.2089 -0.2905 P 0 0 0 0 0 0 0 0 0 0 0 0
-0.3724 -3.3206 0.3305 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.3233 -2.9082 -1.4928 H 0 0 0 0 0 0 0 0 0 0 0 0
2.2110 -1.0100 -0.1928 P 0 0 0 0 0 0 0 0 0 0 0 0
2.4180 -2.2493 0.4785 H 0 0 0 0 0 0 0 0 0 0 0 0
2.9665 -1.3716 -1.3435 H 0 0 0 0 0 0 0 0 0 0 0 0
1.0119 2.2095 -0.2895 P 0 0 0 0 0 0 0 0 0 0 0 0
0.3724 3.3212 0.3310 H 0 0 0 0 0 0 0 0 0 0 0 0
1.3254 2.9092 -1.4910 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.2110 1.0100 -0.1928 P 0 0 0 0 0 0 0 0 0 0 0 0
-2.4189 2.2495 0.4779 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.9666 1.3708 -1.3438 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.0004 -0.0005 1.6924 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.0008 -0.0015 2.8595 O 0 0 0 0 0 0 0 0 0 0 0 0
0.3612 -0.1679 -2.2213 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.3616 0.1688 -2.2210 H 0 0 0 0 0 0 0 0 0 0 0 0
3.2908 -0.3410 0.4520 H 0 0 0 0 0 0 0 0 0 0 0 0
2.2782 2.4471 0.3189 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.2786 -2.4473 0.3161 H 0 0 0 0 0 0 0 0 0 0 0 0
-3.2906 0.3408 0.4522 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 5 1 0 0 0 0
1 8 1 0 0 0 0
1 11 1 0 0 0 0
1 14 1 0 0 0 0
2 3 1 0 0 0 0
2 4 1 0 0 0 0
2 20 1 0 0 0 0
5 6 1 0 0 0 0
5 7 1 0 0 0 0
5 18 1 0 0 0 0
8 9 1 0 0 0 0
8 10 1 0 0 0 0
8 19 1 0 0 0 0
11 12 1 0 0 0 0
11 13 1 0 0 0 0
11 21 1 0 0 0 0
14 15 2 0 0 0 0

</pre>

:'''Making a .xyz file manually'''
:: You need to make this file yourself in a text editor
::A .xyz file has 3 sections
:::#First line: number of atoms in the molecule
:::#Second line: comments or title
:::#Following lines: atomic symbol followed by xyz coordiantes
::here is my Mo(CO)(H2)(PH3)4 file:
<pre>
21
Mo(CO)(H2)(PH3)4 molecule
Mo 0.000045 0.000102 -0.275893 27.797760
P -1.011401 -2.208947 -0.290536 -0.223504
H -0.372372 -3.320581 0.330463 0.085105
H -1.323285 -2.908209 -1.492765 0.082766
P 2.211020 -1.009990 -0.192847 -0.228591
H 2.418011 -2.249283 0.478494 0.087153
H 2.966565 -1.371591 -1.343488 0.086278
P 1.011822 2.209531 -0.289514 -0.223545
H 0.372347 3.321200 0.330959 0.085111
H 1.325404 2.909252 -1.491038 0.082797
P -2.211044 1.010021 -0.192849 -0.228575
H -2.418954 2.249487 0.477851 0.087149
H -2.966577 1.370804 -1.343808 0.086292
C -0.000389 -0.000536 1.692395 0.257683
O -0.000758 -0.001484 2.859470 -0.335269
H 0.361190 -0.167921 -2.221343 0.079092
H -0.361610 0.168783 -2.220950 0.079020
H 3.290813 -0.341001 0.452049 0.086821
H 2.278178 2.447165 0.318854 0.084820
H -2.278543 -2.447297 0.316108 0.084741
H -3.290613 0.340775 0.452167 0.086826
</pre>

:'''Making a .xyz file using Molden'''
::Alternatively you can create a .xyz file using a program called Molden (providing you have access to, and are familiar with, Molden)
:::#Open your molecule in Molden (this will require typing molden file_name.log)
:::#Navigate to the Molden Control window and select Write
:::#Select XYZ from the drop down menu - this will prompt the Molden Query Box to open
:::#Enter the file name you wish to use in the grey panel (ensuring there are no spaces - use underscores) and end with .xyz then select apply
:::#Click the Skull button to quit Molden
::Note: You should only use this method if you are familiar with Molden or have consulted the Molden Basics wiki page (coming soon).

===Load your file===
Load your file containing the molecule coordinates onto the wiki (as you would an image!)
:Load your molecule to the wiki, eg choose "upload file" from the menu to the left and follow the instructions

===How to add a Jmol to your wiki===
:There are two options to add a Jmol of your molecule.
::One method would be to add a button that will open a separate window with a Jmol molecule in it. This is the preferred option.
::Alternatively you can have the Jmol embedded directly into your wiki page. Use this option SPARINGLY!! Too many Jmol images will slow down the loading of your wiki page

'''Adding a button for your Jmol'''
:Add the following text to your wiki page replacing "MoCOH2PH3_4.xyz" with your file name as a .mol or .xyz file

:'''for a button that will open a new window'''
<pre>
<jmol>
<jmolAppletButton>
<uploadedFileContents>MoCOH2PH3_4.xyz</uploadedFileContents>
<text>Mo(CO)(H2)(PH3)4</text>
</jmolAppletButton>
</jmol>
</pre>
::this will produce the following:

<jmol>
<jmolAppletButton>
<uploadedFileContents>MoCOH2PH3_4.xyz</uploadedFileContents>
<text>Mo(CO)(H2)(PH3)4</text>
</jmolAppletButton>
</jmol>

:'''Embedding an image on your wiki page'''
<pre><jmol><jmolApplet>
<title>Mo(CO)(H2)(PH3)4</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>MoCOH2PH3_4.xyz</uploadedFileContents>
</jmolApplet></jmol></pre>

:This will produce the following:
<jmol><jmolApplet>
<title>test molecule</title>
<color>white</color>
<size>200</size>
<uploadedFileContents>MoCOH2PH3_4.xyz</uploadedFileContents>
</jmolApplet></jmol>
::The title tag is self explanatory
::The colour tag sets the background colour to white
::The size tag sets the size of the Jmol image to display
::The uploadfile tag determines the file to load

'''Beware!''' You can corrupt your wiki if you type the Jmol XML incorrectly. Recovering from such an error is difficult! You should save your wiki before inserting any Jmol molecules and be careful that you put in the text exactly as it is here. It is advisable to copy then paste the text directly into your wiki then manually edit the appropriate file name and title, as well as any other changes you may wish to make such as background colour or window size.

More information on backing up and fixing your report after a crash can be found here:
[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:writeup#Backing_up_your_report fixing wiki problems]

==Visualising MOs using Jmol==

It is possible to superimpose MOs over the skeletal framework of your molecule. To do this you must first generate a cube (.cub) file for each MO of interest using Gaussview.

===How to generate .cub files===

This procedure assumes two things:

::#The geometry of your molecule has been properly optimised
::#You have performed a single point energy calculation with the key words pop=(full,nbo)

Using Gaussview, double click the .fchk file corresponding to your molecule and navigate to Edit>>MOs

Visualise however many MOs you require. Take note of the index numbers corresponding to the MOs of interest.

In Gaussview navigate to Results>>Surfaces/Contours. In the Cubes Available box select the first MO of interest and then from the drop down box Cube Actions select Save Cube. Repeat as necessary until you have saved all of the cube files corresponding to the MOs of interest.

Alternatively, instead of using Gaussview, the cubegen utility can be used (this is, of course, dependent on whether you have accessto computer with cubegen installed on it). If you do have access, then proceed by typing the following command in the command line:

<pre>./cubegen 0 MO=41 filename.fchk filename_mo41.cub 0
./cubegen 0 MO=35 filename.fchk filename_mo35.cub 0</pre>

where filename.fchk is the original name of the .fchk file.
The cube files generated (i.e. filename_mo41.cub) are likely to be quite large (a few megabytes in size). These files can be used to visualise the MOs over the molecular framework however owing to their size this will cause impossible webpage loading times. It is therefore advisable to reduce the size of the .cub file by processing it using Jmol, creating a .jvxl file.

===Creating .jvxl files from .cub files===

The .jvxl file is around 100 to 150 times smaller than the original .cub therefore it is strongly advisable to follow this procedure!!

There are a couple of ways to convert a .cub file to a .jvxl file

:One method is as follows:
::# Open Jmol (Jmol.jar). If you do not have Jmol, it can be obtained from [http://http://jmol.sourceforge.net/download/ here]
::# Navigate to File>>Open and select your .xyz or .mol file for your molecule framework
::# Once your molecule has loaded, navigate to File>>Open and select your first .cub file corresponding to an MO. This will load the MO on to the framework.
::# Right click on the Jmol display window prompting a floating menu bar to appear. Navigate to File>>Save JVXL isosurface in the floating menu. This will allow you to save a jvxl file.
::# You can then open another .cub file by selecting File>>Open in the menu at the top of the display window which will overwrite the first MO.
::# Repeat the saving procedure as necessary

:Note: I know this is time consuming - I will try and identify an alternative method

:Alternative method (number 1) for creating a .jvxl file
# Navigate to [http://www.ch.ic.ac.uk/rzepa/cub2jvxl/ this page] where you will be able press a button prompting you to select your cube file.
# This will be followed by three file save dialogs, one for the coordinates (.xyz), one for the MO surface (.jvxl) and a shrink-wrapped bundle (.pngj).

It is possible to reduce the size of the .jvxl file further by compressing it using gzip (Jmol will automatically detect and decompress this). You will end up with something that looks like name.jvxl.gz and you can safely rename this file to the original name.jvxl

===Incorporating Jmol with MOs into your wiki===

This method is very similar to the instructions outlined above for loading your Jmol molecule into your wiki page however, the Jmol XML script has been modified slightly to include the molecular orbital.

First, you will need to insert the following code into your Wiki, replacing the file name in between the <nowiki><uploadedFileContents></uploadedFileContents></nowiki> tags with the .xyz or .mol file, corresponding to your molecule from earlier.

<pre><nowiki><jmol>
<jmolApplet>
<title>Orbital</title><color>white</color><size>300</size>
<script>isosurface color orange purple "images/f/f3/MoCOH2PH3_4_mo23.jvxl" translucent;</script>
<uploadedFileContents>MoCOH2PH3_4.xyz</uploadedFileContents>
</jmolApplet>
</jmol></nowiki>
</pre>

In a new window, upload the .jvxl files on to the wiki using the [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Special:MultipleUpload/ Upload multiple files] link. Once uploaded, keep this window open and select the link to the first MO.

The browser window should now look like the image below. Click on the link as indicated by the red arrow.

[[File:File_upload_for_MOs_in_jvxl_format.png|900px]]

The browser window should now display the contents of the .jvxl file (in XML format). You will need to find the absolute path for the .jvxl file. Luckily this is displayed in the address bar at the top of the browser. This will appear as something like:

<pre>https://wiki.ch.ic.ac.uk/wiki/images/f/f3/MoCOH2PH3_4_mo23.jvxl</pre>

You will need to copy the equivalent text to:

<pre>images/f/f3/MoCOH2PH3_4_mo23.jvxl</pre>

This should be pasted into the Jmol code on your wiki page. This text should be pasted in between the <nowiki><script></script></nowiki> tags

Hopefully if all goes well you should get something similar to this:

<jmol>
<jmolApplet>
<title>Orbital</title><color>white</color><size>300</size>
<script>isosurface color orange purple "images/f/f3/MoCOH2PH3_4_mo23.jvxl" translucent;</script>
<uploadedFileContents>MoCOH2PH3_4.xyz</uploadedFileContents>
</jmolApplet>
</jmol>

<jmol>
<jmolAppletButton>
<uploadedFileContents>MoCOH2PH3_4.xyz</uploadedFileContents>
<text>Mo(CO)(H2)(PH3)4 MO73</text>
<script>isosurface color orange purple "images/6/61/MoCOH2PH3_4_mo73.jvxl" translucent;</script>
</jmolAppletButton>
</jmol>

=== An alternative way of loading surfaces ===
This method avoids the need to specify paths to files as seen above. Instead uses the '''.pngj''' bundle which contains all necessary information and can be invoked by
<pre><nowiki><jmolFile text="link to MO23">MoCOH2PH3_test_mo23.cub.pngj</jmolFile></nowiki></pre> which produces a <jmolFile text="link to MO23">MoCOH2PH3_test_mo23.cub.pngj</jmolFile>. This method is not as flexible as the above.

===Making your Jmol more awesome===
Section coming soon