ChemWiki - User contributions [en]

Mod:Hunt Research Group/calendar

2015-06-30T16:02:55Z

Ca307:

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 (Not Done)
|-
| Vincent Chen (Done)
| Gabriel Lau (Done)
| Rebecca Rowe (Done)
| Ken Watson (Done)
|-
| Aiswarya Prabha (Not Done)
| Richard Fogarty (Not Done)
| Christopher Sewell (Done)
| Chen Chen (Not Done)
|-
|Ziyun Zhang (Done)
|Julie Schmauck (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="#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 Bryan Away </td>
<td bgcolor="#cccccc">20th Bryan Away Gabriel Away (Boulder Conference) </td>
<td bgcolor="#cccccc">21st Bryan Away Gabriel Away (Boulder Conference) </td>
</tr>
<tr valign="top">
<td>22nd Bryan Away Gabriel Away (Boulder Conference) </td>
<td>23rd Bryan Away Gabriel Away (Boulder Conference) </td>
<td>24th Bryan Away Gabriel Away (Boulder Conference) </td>
<td>25th Bryan Away Richard F Exp Gabriel Away (Boulder Conference) </td>
<td>26th Bryan Away Gabriel Away (Boulder Conference) </td>
<td bgcolor="#cccccc">27th Bryan Away Gabriel Away </td>
<td bgcolor="#cccccc">28th Bryan Away Gabriel Away </td>
</tr>
<tr valign="top">
<td >29th Bryan Away Gabriel Away Chris Away </td>
<td>30th Chris Away </td>
<td bgcolor="#4357CFF">'''1st July''' Gabriel Away Chris Away </td>
<td>2nd Gabriel Away Chris Away </td>
<td>3rd Tricia Away Gabriel Away Chris Away Claire Away</td>
<td bgcolor="#cccccc">4th Tricia Away Gabriel Away </td>
<td bgcolor="#cccccc">5th Tricia Away Gabriel Away </td>
</tr>
<tr valign="top">
<td >6th Tricia Away Gabriel Away </td>
<td>7th Richard F Exp Gabriel Away </td>
<td>8th Richard F Exp Gabriel Away Ken Away </td>
<td>9th Richard F Exp Gabriel Away Ken Away </td>
<td>10th Richard F Exp Gabriel Away Ken Away </td>
<td bgcolor="#cccccc">11th Gabriel Away (FOMMS Conference) </td>
<td bgcolor="#cccccc">12th Gabriel Away (FOMMS Conference) </td>
</tr>
<tr valign="top">
<td>13th Richard F Away Gabriel Away (FOMMS Conference) Chris Away </td>
<td>14th Gabriel Away (FOMMS Conference) Chris Away </td>
<td>15th Gabriel Away (FOMMS Conference) Chris Away </td>
<td>16th Gabriel Away (FOMMS Conference) Chris Away </td>
<td>17th Gabriel Away (FOMMS Conference) Chris Away </td>
<td bgcolor="#cccccc">18th </td>
<td bgcolor="#cccccc">19th </td>
</tr>
<tr valign="top">
<td>20th </td>
<td>21st Claire Away Chris Away </td>
<td>22nd Claire Away</td>
<td>23rd Claire Away</td>
<td>24th Claire Away</td>
<td bgcolor="#cccccc">25th Claire Away</td>
<td bgcolor="#cccccc">26th </td>
</tr>
<tr valign="top">
<td>27th </td>
<td>28th </td>
<td>29th Tricia Away </td>
<td>30th Tricia Away </td>
<td>31st Tricia Away </td>
<td bgcolor="#4357CFF">'''1st August''' Tricia Away </td>
<td bgcolor="#cccccc">2nd Tricia Away </td>
</tr>
<tr valign="top">
<td>3rd Tricia Away Richard F Away </td>
<td>4th Tricia Away Richard F Away </td>
<td>5th Tricia Away Richard F Away </td>
<td>6th Tricia Away Richard F Away </td>
<td>7th Tricia Away Richard F Away </td>
<td bgcolor="#cccccc">8th Tricia Away </td>
<td bgcolor="#cccccc">9th Tricia Away </td>
</tr>
<tr valign="top">
<td>10th Tricia Away Richard F Away </td>
<td>11th Tricia Away Richard F Away </td>
<td>12th Tricia Away </td>
<td>13th Tricia Away </td>
<td>14th Tricia Away </td>
<td bgcolor="#cccccc">15th Tricia Away </td>
<td bgcolor="#cccccc">16th Tricia Away </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 </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="#33CC99">31st '''Bank Holiday'''</td>
<td bgcolor="#4357CFF">'''1st September''' </td>
<td>2nd </td>
<td>3rd </td>
<td>4th </td>
<td bgcolor="#cccccc">5th </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 Tricia Away </td>
<td bgcolor="#cccccc">13th Tricia Away </td>
</tr>
<tr valign="top">
<td>14th Tricia Away </td>
<td>15th Tricia Away </td>
<td>16th Tricia Away </td>
<td>17th Tricia Away </td>
<td>18th Tricia Away </td>
<td bgcolor="#cccccc">19th Tricia Away </td>
<td bgcolor="#cccccc">20th Tricia Away </td>
</tr>
<tr valign="top">
<td>21st Becky away </td>
<td>22nd Becky away </td>
<td>23rd Becky away </td>
<td>24th Becky away </td>
<td>25th Becky away </td>
<td bgcolor="#cccccc">26th </td>
<td bgcolor="#cccccc">27th </td>
</tr>
<tr valign="top">
<td>28th Becky away </td>
<td>29th Becky away </td>
<td>30th Becky away </td>
<td bgcolor="#4357CFF">'''1st October''' Becky away </td>
<td>2nd Becky away </td>
<td bgcolor="#ffff66">3rd '''TERM BEGINS'''</td>
<td bgcolor="#cccccc">4th </td>
</tr>
</table>

Mod:Hunt Research Group/calendar

2015-06-22T07:28:23Z

Ca307:

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 (Not Done)
|-
| Vincent Chen (Done)
| Gabriel Lau (Done)
| Rebecca Rowe (Not Done)
| Ken Watson (Not Done)
|-
| Aiswarya Prabha (Not Done)
| Richard Fogarty (Not Done)
| Christopher Sewell (Not Done)
| Chen Chen (Not Done)
|-
|Ziyun Zhang (Done)
|Julie Schmauck (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="#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 Bryan Away </td>
<td bgcolor="#cccccc">20th Bryan Away Gabriel Away (Boulder Conference) </td>
<td bgcolor="#cccccc">21st Bryan Away Gabriel Away (Boulder Conference) </td>
</tr>
<tr valign="top">
<td>22nd Bryan Away Gabriel Away (Boulder Conference) </td>
<td>23rd Bryan Away Gabriel Away (Boulder Conference) </td>
<td>24th Bryan Away Gabriel Away (Boulder Conference) </td>
<td>25th Bryan Away Richard F Exp Gabriel Away (Boulder Conference) </td>
<td>26th Bryan Away Gabriel Away (Boulder Conference) </td>
<td bgcolor="#cccccc">27th Bryan Away Gabriel Away </td>
<td bgcolor="#cccccc">28th Bryan Away Gabriel Away </td>
</tr>
<tr valign="top">
<td >29th Bryan Away Gabriel Away </td>
<td>30th </td>
<td bgcolor="#4357CFF">'''1st July''' Gabriel Away </td>
<td>2nd Gabriel Away </td>
<td>3rd Tricia Away Gabriel Away </td>
<td bgcolor="#cccccc">4th Tricia Away Gabriel Away </td>
<td bgcolor="#cccccc">5th Tricia Away Gabriel Away </td>
</tr>
<tr valign="top">
<td >6th Tricia Away Gabriel Away </td>
<td>7th Richard F Exp Gabriel Away </td>
<td>8th Richard F Exp Gabriel Away </td>
<td>9th Richard F Exp Gabriel Away </td>
<td>10th Richard F Exp Gabriel Away </td>
<td bgcolor="#cccccc">11th Gabriel Away (FOMMS Conference) </td>
<td bgcolor="#cccccc">12th Gabriel Away (FOMMS Conference) </td>
</tr>
<tr valign="top">
<td>13th Richard F Away Gabriel Away (FOMMS Conference) </td>
<td>14th Gabriel Away (FOMMS Conference) </td>
<td>15th Gabriel Away (FOMMS Conference) </td>
<td>16th Gabriel Away (FOMMS Conference) </td>
<td>17th Gabriel Away (FOMMS Conference) </td>
<td bgcolor="#cccccc">18th </td>
<td bgcolor="#cccccc">19th </td>
</tr>
<tr valign="top">
<td>20th </td>
<td>21st Claire Away</td>
<td>22nd Claire Away</td>
<td>23rd Claire Away</td>
<td>24th Claire Away</td>
<td bgcolor="#cccccc">25th Claire Away</td>
<td bgcolor="#cccccc">26th </td>
</tr>
<tr valign="top">
<td>27th </td>
<td>28th </td>
<td>29th Tricia Away </td>
<td>30th Tricia Away </td>
<td>31st Tricia Away </td>
<td bgcolor="#4357CFF">'''1st August''' Tricia Away </td>
<td bgcolor="#cccccc">2nd Tricia Away </td>
</tr>
<tr valign="top">
<td>3rd Tricia Away Richard F Away </td>
<td>4th Tricia Away Richard F Away </td>
<td>5th Tricia Away Richard F Away </td>
<td>6th Tricia Away Richard F Away </td>
<td>7th Tricia Away Richard F Away </td>
<td bgcolor="#cccccc">8th Tricia Away </td>
<td bgcolor="#cccccc">9th Tricia Away </td>
</tr>
<tr valign="top">
<td>10th Tricia Away Richard F Away </td>
<td>11th Tricia Away Richard F Away </td>
<td>12th Tricia Away </td>
<td>13th Tricia Away </td>
<td>14th Tricia Away </td>
<td bgcolor="#cccccc">15th Tricia Away </td>
<td bgcolor="#cccccc">16th Tricia Away </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 </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="#33CC99">31st '''Bank Holiday'''</td>
<td bgcolor="#4357CFF">'''1st September''' </td>
<td>2nd </td>
<td>3rd </td>
<td>4th </td>
<td bgcolor="#cccccc">5th </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 Tricia Away </td>
<td bgcolor="#cccccc">13th Tricia Away </td>
</tr>
<tr valign="top">
<td>14th Tricia Away </td>
<td>15th Tricia Away </td>
<td>16th Tricia Away </td>
<td>17th Tricia Away </td>
<td>18th Tricia Away </td>
<td bgcolor="#cccccc">19th Tricia Away </td>
<td bgcolor="#cccccc">20th Tricia Away </td>
</tr>
<tr valign="top">
<td>21st </td>
<td>22nd </td>
<td>23rd </td>
<td>24th </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 bgcolor="#4357CFF">'''1st October''' </td>
<td>2nd </td>
<td bgcolor="#ffff66">3rd '''TERM BEGINS'''</td>
<td bgcolor="#cccccc">4th </td>
</tr>
</table>

Mod:Hunt Research Group/calendar

2015-06-22T07:26:21Z

Ca307:

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 (Not Done)
|-
| Vincent Chen (Done)
| Gabriel Lau (Done)
| Rebecca Rowe (Not Done)
| Ken Watson (Not Done)
|-
| Aiswarya Prabha (Not Done)
| Richard Fogarty (Not Done)
| Christopher Sewell (Not Done)
| Chen Chen (Not Done)
|-
|Ziyun Zhang (Done)
|Julie Schmauck (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="#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 Bryan Away </td>
<td bgcolor="#cccccc">20th Bryan Away Gabriel Away (Boulder Conference) </td>
<td bgcolor="#cccccc">21st Bryan Away Gabriel Away (Boulder Conference) </td>
</tr>
<tr valign="top">
<td>22nd Bryan Away Gabriel Away (Boulder Conference) </td>
<td>23rd Bryan Away Gabriel Away (Boulder Conference) </td>
<td>24th Bryan Away Gabriel Away (Boulder Conference) </td>
<td>25th Bryan Away Richard F Exp Gabriel Away (Boulder Conference) </td>
<td>26th Bryan Away Gabriel Away (Boulder Conference) </td>
<td bgcolor="#cccccc">27th Bryan Away Gabriel Away </td>
<td bgcolor="#cccccc">28th Bryan Away Gabriel Away </td>
</tr>
<tr valign="top">
<td >29th Bryan Away Gabriel Away </td>
<td>30th </td>
<td bgcolor="#4357CFF">'''1st July''' Gabriel Away </td>
<td>2nd Gabriel Away </td>
<td>3rd Tricia Away Gabriel Away </td>
<td bgcolor="#cccccc">4th Tricia Away Gabriel Away </td>
<td bgcolor="#cccccc">5th Tricia Away Gabriel Away </td>
</tr>
<tr valign="top">
<td >6th Tricia Away Gabriel Away </td>
<td>7th Richard F Exp Gabriel Away </td>
<td>8th Richard F Exp Gabriel Away </td>
<td>9th Richard F Exp Gabriel Away </td>
<td>10th Richard F Exp Gabriel Away </td>
<td bgcolor="#cccccc">11th Gabriel Away (FOMMS Conference) </td>
<td bgcolor="#cccccc">12th Gabriel Away (FOMMS Conference) </td>
</tr>
<tr valign="top">
<td>13th Richard F Away Gabriel Away (FOMMS Conference) </td>
<td>14th Gabriel Away (FOMMS Conference) </td>
<td>15th Gabriel Away (FOMMS Conference) </td>
<td>16th Gabriel Away (FOMMS Conference) </td>
<td>17th Gabriel Away (FOMMS Conference) </td>
<td bgcolor="#cccccc">18th </td>
<td bgcolor="#cccccc">19th </td>
</tr>
<tr valign="top">
<td>20th </td>
<td>21st Claire Away</td>
<td>22nd Claire Away</td>
<td>23rd Claire Away</td>
<td>24th Claire Away</td>
<td bgcolor="#cccccc">25th Claire Away</td>
<td bgcolor="#cccccc">26th </td>
</tr>
<tr valign="top">
<td>27th </td>
<td>28th </td>
<td>29th Tricia Away </td>
<td>30th Tricia Away </td>
<td>31st Tricia Away </td>
<td bgcolor="#4357CFF">'''1st August''' Tricia Away </td>
<td bgcolor="#cccccc">2nd Tricia Away </td>
</tr>
<tr valign="top">
<td>3rd Tricia Away Richard F Away </td>
<td>4th Tricia Away Richard F Away </td>
<td>5th Tricia Away Richard F Away </td>
<td>6th Tricia Away Richard F Away </td>
<td>7th Tricia Away Richard F Away </td>
<td bgcolor="#cccccc">8th Tricia Away </td>
<td bgcolor="#cccccc">9th Tricia Away </td>
</tr>
<tr valign="top">
<td>10th Tricia Away Richard F Away </td>
<td>11th Tricia Away Richard F Away </td>
<td>12th Tricia Away </td>
<td>13th Tricia Away </td>
<td>14th Tricia Away </td>
<td bgcolor="#cccccc">15th Tricia Away </td>
<td bgcolor="#cccccc">16th Tricia Away </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 </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="#33CC99">31st '''Bank Holiday'''</td>
<td bgcolor="#4357CFF">'''1st September''' </td>
<td>2nd </td>
<td>3rd </td>
<td>4th </td>
<td bgcolor="#cccccc">5th </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 Tricia Away </td>
<td bgcolor="#cccccc">13th Tricia Away </td>
</tr>
<tr valign="top">
<td>14th Tricia Away </td>
<td>15th Tricia Away </td>
<td>16th Tricia Away </td>
<td>17th Tricia Away </td>
<td>18th Tricia Away </td>
<td bgcolor="#cccccc">19th Tricia Away </td>
<td bgcolor="#cccccc">20th Tricia Away </td>
</tr>
<tr valign="top">
<td>21st </td>
<td>22nd </td>
<td>23rd </td>
<td>24th </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 bgcolor="#4357CFF">'''1st October''' </td>
<td>2nd </td>
<td bgcolor="#cccccc">3rd </td>
<td bgcolor="#cccccc">4th </td>
</tr>
</table>

Mod:Hunt Research Group/calendar

2015-06-22T07:22:38Z

Ca307:

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 (Not Done)
| Precious Ugbomah (Not Done)
|-
| Vincent Chen (Done)
| Gabriel Lau (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 (Done)
|Richard Fogarty (Not Done)
|Julie Schmauck ( 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="#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 Bryan Away </td>
<td bgcolor="#cccccc">20th Bryan Away Gabriel Away (Boulder Conference) </td>
<td bgcolor="#cccccc">21st Bryan Away Gabriel Away (Boulder Conference) </td>
</tr>
<tr valign="top">
<td>22nd Bryan Away Gabriel Away (Boulder Conference) </td>
<td>23rd Bryan Away Gabriel Away (Boulder Conference) </td>
<td>24th Bryan Away Gabriel Away (Boulder Conference) </td>
<td>25th Bryan Away Richard F Exp Gabriel Away (Boulder Conference) </td>
<td>26th Bryan Away Gabriel Away (Boulder Conference) </td>
<td bgcolor="#cccccc">27th Bryan Away Gabriel Away </td>
<td bgcolor="#cccccc">28th Bryan Away Gabriel Away </td>
</tr>
<tr valign="top">
<td >29th Bryan Away Gabriel Away </td>
<td>30th </td>
<td bgcolor="#4357CFF">'''1st July''' Gabriel Away </td>
<td>2nd Gabriel Away </td>
<td>3rd Tricia Away Gabriel Away </td>
<td bgcolor="#cccccc">4th Tricia Away Gabriel Away </td>
<td bgcolor="#cccccc">5th Tricia Away Gabriel Away </td>
</tr>
<tr valign="top">
<td >6th Tricia Away Gabriel Away </td>
<td>7th Richard F Exp Gabriel Away </td>
<td>8th Richard F Exp Gabriel Away </td>
<td>9th Richard F Exp Gabriel Away </td>
<td>10th Richard F Exp Gabriel Away </td>
<td bgcolor="#cccccc">11th Gabriel Away (FOMMS Conference) </td>
<td bgcolor="#cccccc">12th Gabriel Away (FOMMS Conference) </td>
</tr>
<tr valign="top">
<td>13th Richard F Away Gabriel Away (FOMMS Conference) </td>
<td>14th Gabriel Away (FOMMS Conference) </td>
<td>15th Gabriel Away (FOMMS Conference) </td>
<td>16th Gabriel Away (FOMMS Conference) </td>
<td>17th Gabriel Away (FOMMS Conference) </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>27th </td>
<td>28th </td>
<td>29th Tricia Away </td>
<td>30th Tricia Away </td>
<td>31st Tricia Away </td>
<td bgcolor="#4357CFF">'''1st August''' Tricia Away </td>
<td bgcolor="#cccccc">2nd Tricia Away </td>
</tr>
<tr valign="top">
<td>3rd Tricia Away Richard F Away </td>
<td>4th Tricia Away Richard F Away </td>
<td>5th Tricia Away Richard F Away </td>
<td>6th Tricia Away Richard F Away </td>
<td>7th Tricia Away Richard F Away </td>
<td bgcolor="#cccccc">8th Tricia Away </td>
<td bgcolor="#cccccc">9th Tricia Away </td>
</tr>
<tr valign="top">
<td>10th Tricia Away Richard F Away </td>
<td>11th Tricia Away Richard F Away </td>
<td>12th Tricia Away </td>
<td>13th Tricia Away </td>
<td>14th Tricia Away </td>
<td bgcolor="#cccccc">15th Tricia Away </td>
<td bgcolor="#cccccc">16th Tricia Away </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 </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="#33CC99">31st '''Bank Holiday'''</td>
<td bgcolor="#4357CFF">'''1st September''' </td>
<td>2nd </td>
<td>3rd </td>
<td>4th </td>
<td bgcolor="#cccccc">5th </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 Tricia Away </td>
<td bgcolor="#cccccc">13th Tricia Away </td>
</tr>
<tr valign="top">
<td>14th Tricia Away </td>
<td>15th Tricia Away </td>
<td>16th Tricia Away </td>
<td>17th Tricia Away </td>
<td>18th Tricia Away </td>
<td bgcolor="#cccccc">19th Tricia Away </td>
<td bgcolor="#cccccc">20th Tricia Away </td>
</tr>
<tr valign="top">
<td>21st </td>
<td>22nd </td>
<td>23rd </td>
<td>24th </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 bgcolor="#4357CFF">'''1st October''' </td>
<td>2nd </td>
<td bgcolor="#cccccc">3rd </td>
<td bgcolor="#cccccc">4th </td>
</tr>
</table>

Mod:Hunt Research Group/calendar

2015-03-31T07:26:03Z

Ca307:

Mod:Hunt Research Group/calendar

2015-03-17T12:46:35Z

Ca307:

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)
|
|
|-
|-)
|}

<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>23rd </td>
<td>24th </td>
<td>25th </td>
<td>26th </td>
<td>27th </td>
<td bgcolor="#CCCCCC">28th </td>
<td bgcolor="#4357CFF">'''1st March''' </td>
</tr>
<tr valign="top">
<td>2nd </td>
<td>3rd </td>
<td>4th </td>
<td>5th </td>
<td>6th </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="#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 </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 </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

2015-03-17T12:41:29Z

Ca307:

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 (Not Done)
|-
| Precious Ugbomah (Not Done)
| Richard Matthews (Not Done)
| Vincent Chen (Not Done)
| Gabriel Lau (Not Done)
|-
| Rebecca Rowe (Not Done)
| Patricia Ho (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)
|-
|-)
|}

<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>23rd </td>
<td>24th </td>
<td>25th </td>
<td>26th </td>
<td>27th </td>
<td bgcolor="#CCCCCC">28th </td>
<td bgcolor="#4357CFF">'''1st March''' </td>
</tr>
<tr valign="top">
<td>2nd </td>
<td>3rd </td>
<td>4th </td>
<td>5th </td>
<td>6th </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="#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 </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 </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

2015-03-17T12:37:35Z

Ca307:

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 (Not Done)
|-
| Precious Ugbomah (Not Done)
| Richard Matthews (Not Done)
| Vincent Chen (Not Done)
| Gabriel Lau (Not Done)
|-
| Rebecca Rowe (Not Done)
| Patricia Ho (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)
|-
|-)
|}

<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>23rd </td>
<td>24th </td>
<td>25th </td>
<td>26th </td>
<td>27th </td>
<td bgcolor="#CCCCCC">28th </td>
<td bgcolor="#4357CFF">'''1st March''' </td>
</tr>
<tr valign="top">
<td>2nd </td>
<td>3rd </td>
<td>4th </td>
<td>5th </td>
<td>6th </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="#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 '''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 '''College closed'''</td>
<td bgcolor="#33CC99">7th '''College closed''' </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 </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>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>29th </td>
<td bgcolor="#CCCCCC">30th </td>
<td bgcolor="#CCCCCC">31st </td>
</tr>
</table>

Mod:Hunt Research Group/calendar

2015-03-17T12:29:24Z

Ca307:

Mod:Hunt Research Group/calendar

2015-03-17T12:26:27Z

Ca307:

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 (Not Done)
|-
| Precious Ugbomah (Not Done)
| Richard Matthews (Not Done)
| Vincent Chen (Not Done)
| Gabriel Lau (Not Done)
|-
| Rebecca Rowe (Not Done)
| Patricia Ho (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)
|-
|-)
|}

<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> </td>
<td> </td>
<td> </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 Precious Away Aiswarya Away Gabriel Away Chen Chen Away Rebecca Away </td>
<td>6th Aiswarya Away Gabriel Away Rebecca Away </td>
<td>7th Aiswarya Away Gabriel Away Rebecca Away </td>
<td>8th Aiswarya Away Gabriel Away Rebecca Away Richard F Away </td>
<td>9th Aiswarya Away Gabriel Away Rebecca Away </td>
<td bgcolor="#CCCCCC">10th </td>
<td bgcolor="#CCCCCC">11th </td>
</tr>
<tr valign="top">
<td bgcolor="#FFFF00">12th '''NEW TERM''' Aiswarya Away (P) </td>
<td>13th Aiswarya Away (P) </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 Richard F Away </td>
<td>22nd </td>
<td>23rd </td>
<td bgcolor="#CCCCCC">24th </td>
<td bgcolor="#CCCCCC">25th </td>
</tr>
<tr valign="top">
<td>26th Claire Away</td>
<td>27th Richard F Away Claire Away </td>
<td>28th Richard F Away </td>
<td>29th Richard F Away </td>
<td>30th Richard F Away </td>
<td bgcolor="#CCCCCC">31st </td>
<td bgcolor="#4357CFF">'''1st February''' </td>
</tr>
<tr valign="top">
<td>2nd </td>
<td>3rd </td>
<td>4th </td>
<td>5th </td>
<td>6th </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>
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<td bgcolor="#4357CFF">'''1st March''' </td>
</tr>
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</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 '''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 '''College closed'''</td>
<td bgcolor="#33CC99">7th '''College closed''' </td>
<td>8th </td>
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<td bgcolor="#CCCCCC">11th </td>
<td bgcolor="#CCCCCC">12th </td>
</tr>
</table>

Mod:Hunt Research Group/calendar

2015-03-17T12:23:07Z

Ca307:

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 (Not Done)
|-
| Precious Ugbomah (Not Done)
| Richard Matthews (Not Done)
| Vincent Chen (Not Done)
| Gabriel Lau (Not Done)
|-
| Rebecca Rowe (Not Done)
| Patricia Ho (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)
|-
|-)
|}

<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> </td>
<td> </td>
<td> </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 Precious Away Aiswarya Away Gabriel Away Chen Chen Away Rebecca Away </td>
<td>6th Aiswarya Away Gabriel Away Rebecca Away </td>
<td>7th Aiswarya Away Gabriel Away Rebecca Away </td>
<td>8th Aiswarya Away Gabriel Away Rebecca Away Richard F Away </td>
<td>9th Aiswarya Away Gabriel Away Rebecca Away </td>
<td bgcolor="#CCCCCC">10th </td>
<td bgcolor="#CCCCCC">11th </td>
</tr>
<tr valign="top">
<td bgcolor="#FFFF00">12th '''NEW TERM''' Aiswarya Away (P) </td>
<td>13th Aiswarya Away (P) </td>
<td>14th </td>
<td>15th </td>
<td>16th </td>
<td bgcolor="#CCCCCC">17th </td>
<td bgcolor="#CCCCCC">18th </td>
</tr>
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<td>19th </td>
<td>20th </td>
<td>21st Richard F Away </td>
<td>22nd </td>
<td>23rd </td>
<td bgcolor="#CCCCCC">24th </td>
<td bgcolor="#CCCCCC">25th </td>
</tr>
<tr valign="top">
<td>26th Claire Away</td>
<td>27th Richard F Away Claire Away </td>
<td>28th Richard F Away </td>
<td>29th Richard F Away </td>
<td>30th Richard F Away </td>
<td bgcolor="#CCCCCC">31st </td>
<td bgcolor="#4357CFF">'''1st February''' </td>
</tr>
<tr valign="top">
<td>2nd </td>
<td>3rd </td>
<td>4th </td>
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</tr>
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<td>24th </td>
<td>25th </td>
<td>26th </td>
<td>27th </td>
<td bgcolor="#CCCCCC">28th </td>
<td bgcolor="#4357CFF">'''1st March''' </td>
</tr>
<tr valign="top">
<td>2nd </td>
<td>3rd </td>
<td>4th </td>
<td>5th </td>
<td>6th </td>
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</tr>
<tr valign="top">
<td>30th </td>
<td>31st </td>
<td bgcolor="#4357CFF">'''1st April''' </td>
<td>2nd </td>
<td>3rd </td>
<td bgcolor="#CCCCCC">4th </td>
<td bgcolor="#CCCCCC">5th </td>
</tr>
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</tr>
</table>

Talk:Mod:Hunt Research Group/MolCluster

2015-01-23T18:41:01Z

Ca307:

===What is MolCluster?===
MolCluster is a tool (developed by Vincent and Gabriel) that can be used to cut clusters from MD trajectories and create the input files for ChemShell.

To use MolCluster, you will need:
* The latest version of MolCluster (available from Vincent).
* Python version 2.7.6, or above.
* The HISTORY file from which the clusters are to be cut, and the corresponding FIELD file. Note: these need to be in DL_POLY format. If you have used the 'restart' option in DL_POLY, the header of the HISTORY file may need to be amended. Additional transformations of the HISTORY and FIELD files, to convert atom labels into an acceptable format for MolCluster/ChemShell, may also be required (example given later).

===Using MolCluster: Basic Instructions===
'''Please note that these instructions relate to MolCluster v1-7. New instructions for MolCluster v1-8 will be created shortly.'''

1. Create a directory within the main MolCluster directory. Put the required HISTORY and FIELD files here.

2. Load MolCluster: ./MolCluster.py

3. Requests directory name to be specified (this is the location of the FIELD and HISTORY files). After specifying, the code will attempt to read and give an overview of the system.

4. Need to specify which configurations to cut a cluster from. Two options are currently available:
::*'''[n]''': Cut a cluster every "nth" configuration. N.B: numbering starts from 1 (i.e. 1st timestep). Therefore, if you request n=1000, clusters for configurations 1, 1001, 2001 etc. will be created.
::*'''[c]''': Select a custom set of configurations i.e. you can specify exactly which configurations you want.

5. Once the configurations have been extracted, you will be asked to choose how the origin will be defined in the clusters to be cut. Options are:
::*'''[AN]''': Atom number
::*'''[AT]''': Atom type
::*'''[MN]''': Molecule number
::*'''[MT]''': Molecule type
::*'''[C]''': Custom coordinates

You will then be asked to specify the specific atom number/type etc.

6. MolCluster will estimate the number of atoms within a region, for a range of radii with respect to your origin. Use this information to help you decide on the total radius (in Angstroms) of the clusters to be cut. You will be asked to specify this.

7. MolCluster has two options for deciding which molecules to include/exclude at the boundary of the clusters being cut:
::*'''[H]''': Hard boundary - all atoms of a molecule must be within the cutoff radius for the molecule to be included.
::*'''[S]''': Soft boundary - if the centre of mass of a molecule is within the cutoff radius, the molecule will be included.

8. Specify if the clusters are required to be neutral ('''Y/N''').

9. Decide on the output formats:
::*'''[C]''': Generates a ChemShell fragment input file, with accompanying .xyz co-ordinates file.
::*'''[X]''': Generates the .xyz co-ordinates file only.

If '''[X]''' selected, the clusters will be cut, .xyz files generated and MolCluster will terminate.

If '''[C]''' selected, you will be asked if you would also like to generate the necessary ChemShell input files for a QM/MM optimisation ('''Y/N''').

10. If your answer to step 9 was '''[C]''' (generate a ChemShell fragment input) and '''Y''' (generate ChemShell input files for a QM/MM optimisation), you will then be asked to define the QM region. Available options are:
::*'''[S]''': Spherical region (or threshold) centred about the defined origin (although not necessarily spherical??!!)
:::: If '''[S]''' selected, MolCluster will estimate the number of atoms in regions defined by a range of radii. Specify the QM radius. This must be specified (in Angstroms) and must, obviously, be less than, or equal to, the total radius of the cluster. Soft boundary conditions are implemented.
::*'''[M]''': By number of molecules. Molecules closest to the origin will be included.
::*'''[A]''': By an upper limit of atoms. Only whole molecules & those closest to the origin included.
::*'''[C]''': Custom region i.e. can select molecules individually to be in the QM region
::*'''[O]''': Spherical regions centred about one or more origins

If options '''[C]''' or '''[O]''' selected, MolCluster will go straight to steps 11 and 12. Once the active region and the directory/filenames have been defined, MolCluster will then ask for the custom QM regions to be defined ''per'' cluster (see step 14).

11. Once the QM region has been defined, the active region must be defined. MolCluster will estimate the number of atoms that would be in the active and frozen regions for a range of active radii. This information can be used to help decide upon an appropriate active radius. This must be specified (in Angstroms) and must, obviously, be less than, or equal to, the total radius of the cluster. If all atoms are to be included, simple enter "ALL". Soft boundary conditions are implemented.

12. Specify the output directory (i.e. where your final clusters and associated files will be saved) and specify the base-name for the output files (e.g. if you type "cluster" here, your clusters will be saved as cluster_1, cluster_2 etc.).

13. Unless options 10 '''[C'''] or '''[O]''' were selected (in that case, see point 14), MolCluster will generate the specified clusters and then terminate.

14. If option '''[C]''' selected in step 10, MolCluster will at this point list all the molecules in the first cluster, along with the distances to the origin. You will be asked to list all the molecules to be included in the QM region for this cluster. The same procedure is carried out for each cluster, before the clusters are generated and MolCluster terminates.

If option '''[O]''' selected in step 10, you will be asked to specify how many QM regions are to be defined and then specify the origin type and size of each QM region.

===The Output Files===
* Each cluster will have its own directory within the directory named in step 12. These subdirectories will be named: '''cluster_1''', '''cluster_2'''...'''cluster_n'''.
* Within the main directory one will also find a file called '''molcluster.log''' and a file called '''bulk_system_info.txt'''.
::*'''molcluster.log''' is a record of the user responses to each of the MolCluster options (look at this if you have forgotten, for example, the cluster radius).
::*'''bulk_system_info.txt''' summarises information relating to the system before clusters are cut (e.g. number and type of molecules, total number of atoms, total system charge, atom labels within a molecule, atomic charges).

*If option '''[X]''' selected in step 9, each subdirectory '''cluster_n''' will contain:
::*The '''cluster_n.xyz''' coordinates file
::*'''system_info.txt''': Summary of the cluster (e.g. total number of molecules, total number of atoms, total charge)

*If option '''[C]''', '''Y''' selected in step 9, each subdirectory '''cluster_n''' will contain:
::*The '''cluster_n.xyz''' coordinates file
::*'''system_info.txt''': Summary of the cluster (e.g. total number of molecules, total number of atoms, total charge)
::*The '''cluster_n.chm''' coordinates file. This will be used to create the '''cluster.pun''' ChemShell input file.
::*'''cluster_tiered.xyz''': xyz coordinates with the QM, active and frozen regions defined (all QM atoms listed as X1 (X=element symbol), active as X2 and frozen as X3). This file can be used to easily visualise the different regions in VMD.
::*'''conn.txt''' : the connectivity data needed by ChemShell
::*'''ff.dat''' : the forcefield in ChemShell format
::*'''opt.chm''': ChemShell input file. Options for the ChemShell optimisation specified here.

===Step-By-Step Example: Ionic Liquid Clusters===

Our example system:
* 256 ion pairs of [C4C1im][MeSO4]
* In total, the production run is 20ns in length; 4 lots of 5ns employing the "restart" keyword in DL_Poly.
* Our aim is to cut clusters from the last 5ns of the trajectory and create the input files for a ChemShell optimisation.

1). Create a directory within the main MolCluster directory and put the '''HISTORY''' and '''FIELD''' files here. Our directory will be called: '''BMIM_MESO4_EXAMPLE'''.

2). We now need to check to see if the HISTORY and FIELD files are in the correct format.

*As the ''restart'' keyword has been employed, two lines are missing from the header of the HISTORY file, '''Figure 1a''' and '''1b'''. MolCluster does not like this. Therefore, we need to add in the two lines that it is expecting to see, '''Figure 1c'''.

[[Image:MolCluster-HISTORY-header.png|frame|center|850px|'''Figure 1'''. Headers from selected HISTORY files '''(a)''' first 5ns of our simulation, without the use of the restart keyword, '''(b)''' last 5ns of our simulation with the restart keyword and '''(c)''' same HISTORY file as in (b), with missing lines added in. ]]

*The second problem we need to address is the atom labelling. The original atom labelling for [C4C1im][MeSO4], as used in the DL_Poly simulation, is shown in '''Figure 2a'''. Unfortunately, ChemShell has issues with this. To keep ChemShell happy, we have to change the atom labels in the HISTORY and FIELD files to the format ''elementsymbolnumber'' e.g. C2 rather than CR. Thankfully, this is quite easy to do using a script ('''sub_script.sh''', see below) written by Vincent. Firstly, however, we need to decide upon the new atom labelling. This is shown in '''Figure 2b''' for our example system. '''sub_script.sh''' requires that we have defined the atom label mappings in a file called '''sub_map.txt''' (also shown below for this system).

[[Image:BMIM-MESO4-numbering.png|thumb|center|850px|'''Figure 2'''. Original atom labelling (as used in DL_POLY MD simulation) shown in '''(a)''' and new atom labelling (suitable for MolCluster) shown in '''(b)'''. Within '''(b)''', atom labels that already had the correct format are in red. ]]

'''sub_script.sh''':

<pre>#!/bin/bash

while read line

do

#echo $line

s1=$(echo $line | awk '{ print $1 }')

s2=$(echo $line | awk '{ print $2 }')

echo "$s1 $s2"

gsed -i_bu2 "s|\<$s1\>|$s2|g" FIELD

gsed -i_bu2 "s|\<$s1\>|$s2|g" HISTORY

done < sub_map.txt</pre>

'''sub_map.txt''':
<pre>CR C3

NA N1

CW C4

HCR H2

HCW H3

HC H4

CT C6

OS4 O4

OC4 O5

HS4 H5

CS C5

CS4 C7</pre>

*Run '''./sub_script.sh'''
Note: this process may take a while, depending on the size of the file. Progress can be seen in the terminal (example shown in '''Figure 3'''), with each of the mappings specified in sub_map.txt considered in turn. The first few lines of the HISTORY file, before, and after, the relabelling can be seen in '''Figure 4'''.

[[Image:sub_map_mappings.png|thumb|center|800px|'''Figure 3'''. Example terminal output whilst running sub_script.sh ]]

[[Image:HISTORY-before-after.png|thumb|center|1000px|'''Figure 4'''. First few lines of the HISTORY file before '''(a)''' and after '''(b)''' the relabelling. ]]

3). Now our files are in the correct format, we can run MolCluster: '''./MolCluster.py'''

4). The first thing MolCluster does is to ask us to specify the directory containing the FIELD and HISTORY files. Our directory is called BMIM_MESO4_EXAMPLE. Once this has been specified, MolCluster will attempt to read the files and generate a summary of the system (from timestep 1 of the trajectory). This is shown in '''Figure 5''' for our system, and it can be seen that the information summarised by MolCluster is correct.

[[Image:MC-read-files-annotate.png|thumb|center|800px|'''Figure 5'''. After specifying the directory for the FIELD and HISTORY files, MolCluster summarises the bulk system information. ]]

5). MolCluster works out how many configurations in the HISTORY file (5000 in our example) and then asks us to specify the configurations we would like to cut a cluster from. In this case, we are going to select the '''[n]''' option (cut a cluster from every 'nth' configuration) and then specify n as an integer, in this case 1000 (i.e. n=1000, therefore cut a cluster every 1000th time step), '''Figure 6'''.

[[Image:MC-specify-config.png|thumb|center|800px|'''Figure 6'''. Specifying the configurations to create clusters for. ]]

6). We must now select how we would like to define the origin of the clusters to be cut. We are going to select option '''[AN]''' (atom number) and choose atom 1 to be the origin (for reference, in our case this is a C3 atom), '''Figure 7'''.

[[Image:origin-define.png|thumb|center|800px|'''Figure 7'''. Defining the cluster origin. ]]

7). An estimate of the number of atoms in regions with varying radii (with respect to our defined origin) is provided by MolCluster. We need to cut a cluster large enough to incorporate a reasonable number of ion pairs (bearing in mind that our cation alone, in all trans form, is over 9 Angstroms in width), but not so large that the calculation is unfeasible. The ideal size is still being investigated, but for now, let us specify a cluster radius of 15 Angstroms, '''Figure 8'''.

[[Image:cluster-radius-cut.png|thumb|center|900px|'''Figure 8'''. Choosing the cluster radius. ]]

8). MolCluster now asks us to tell it which boundary condition to use when cutting the clusters (essentially this is just how MolCluster will decide whether or not to include a molecule in the cluster for molecules at the boundary). We will select '''[S]''' (soft boundary) here. We are then asked to specify if the cluster needs to be neutral. Obviously this is only really applicable to charged systems (with counter ions), such as ionic liquids . We will select yes here, '''[Y]''', so that all our clusters have the same total charge, '''Figure 9'''.

[[Image:boundary-neutral.png|thumb|center|850px|'''Figure 9'''. Selecting boundary conditions. ]]

9). We now need to decide on the output file type. As the ultimate aim is to run QM/MM optimisations of our clusters, we need to select the options that will generate the ChemShell input files: '''[C]''', '''[Y]''', '''Figure 10'''.

[[Image:output-filetype.png|thumb|center|850px| ]]

10). A decision on how the QM region will be defined is now made. We are going to select '''[S]''' (spherical region). MolCluster then estimates the number of atoms in regions of varying radii with respect to our origin. Again, as with step 7, the optimum size has not yet been deduced. However, from previous tests, a QM radius of 7 Angstroms results in a manageable number of ions and is large enough to observe local structural features. Therefore, we shall specify a radius of 7 Angstroms in this example, '''Figure 11'''.

[[Image:QM-define.png|thumb|center|800px|'''Figure 11'''. QM region defined. ]]

11). After defining the QM region, we then need to define the size of the active region. Again MolCluster helps us by estimating the number of atoms for a range of radii. Molecules not included in the active region, will be in the Frozen region. Fir this example, we shall define the specify active region to have a radius of 11 Angstroms, '''Figure 12'''.

[[Image:Active-region .png|thumb|center|800px|'''Figure 12'''. Radius of active region specified. ]]

12). Finally, we are asked to specify the output directory where all our files will be placed, and the basename for each of our clusters. In this example the output directory will be ''BMIM_MESO4_EXAMPLE/example'' and the base name will be ''cluster'', '''Figure 13'''.

[[Image:Ouput-filenames.png|thumb|center|800px| ]]

13). MolCluster then sets about creating the clusters according to our specifications. The terminal output for the first cluster (cluster_1) is shown in '''Figure 14'''. After creating all the clusters, MolCluster will terminate.

[[Image:cluster_1.png|thumb|center|800px|'''Figure 14'''. Cluster_1 created. ]]

14). Within the named output directory, each cluster has it's own subdirectory: cluster_1, cluster_2 etc. Within each of the subdirectories can be found the requested output files, '''Figure 15'''.

[[Image:directory-files.png|thumb|center|1100px|'''Figure 15'''. Output files. ]]

15). The file called system_info.txt summarises key information relating to the cluster. This is shown in '''Figure 16''' for cluster 1. We can see that in total there are 72 molecules (36 cations and 36 anions) and that, as requested, the total charge of the system is zero.

[[Image:system-info-cluster_1.png|thumb|center|800px|'''Figure 16'''. Total system information for cluster 1. ]]

*To find out how many molecules in the QM and active regions, we can open the file called ''molcluster.log'' in the parent directory. This is a record of all the options we selected. By scrolling through we can find the information relating to cluster 1, '''Figure 17''', and can see that there are 9 molecules in the QM region; 4 cations and 5 anions, resulting in a total charge of -1. There are 35 molecules in the active region.

[[Image:molcluster-log-cluster1-annot.png|thumb|center|800px|'''Figure 17'''. Information about cluster 1, found in the output file molcluster.log. ]]

*Returning to the files in our subdirectory ''cluster_1'', we can open ''cluster.xyz'' (or ''cluster_tiered.xyz'') in VMD to visualise the cut cluster, '''Figure 18''' for our cluster 1. ''cluster_tiered.xyz'' is particularly useful, as it allows us to visualise each of the distinct regions. All of the atoms in the QM region are labelled with a 1 (active labelled with 2 and frozen labelled with 3), therefore we can choose to visualise the QM region only, '''Figure 19a'''. In '''Figure 19b''', all the regions are shown in different colours.

[[Image:full-cluster-1.png|thumb|center|800px|'''Figure 18'''. Cluster 1 visualised in VMD. ]]

[[Image:cluster_tiered-edit.png|thumb|center|800px|'''Figure 19'''. '''(a)''' QM region visualised in VMD. '''(b)''' All regions, visualised in different colours. ]]

Mod:Hunt Research Group/calendar

2015-01-23T13:22:16Z

Ca307:

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 (Not Done)
|-
| Precious Ugbomah (Not Done)
| Richard Matthews (Not Done)
| Vincent Chen (Not Done)
| Gabriel Lau (Not Done)
|-
| Rebecca Rowe (Not Done)
| Patricia Ho (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)
|-
|-)
|}

<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> </td>
<td> </td>
<td> </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 Precious Away Aiswarya Away Gabriel Away Chen Chen Away Rebecca Away </td>
<td>6th Aiswarya Away Gabriel Away Rebecca Away </td>
<td>7th Aiswarya Away Gabriel Away Rebecca Away </td>
<td>8th Aiswarya Away Gabriel Away Rebecca Away Richard F Away </td>
<td>9th Aiswarya Away Gabriel Away Rebecca Away </td>
<td bgcolor="#CCCCCC">10th </td>
<td bgcolor="#CCCCCC">11th </td>
</tr>
<tr valign="top">
<td bgcolor="#FFFF00">12th '''NEW TERM''' Aiswarya Away (P) </td>
<td>13th Aiswarya Away (P) </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 Richard F Away </td>
<td>22nd </td>
<td>23rd </td>
<td bgcolor="#CCCCCC">24th </td>
<td bgcolor="#CCCCCC">25th </td>
</tr>
<tr valign="top">
<td>26th Claire Away</td>
<td>27th Richard F Away Claire Away </td>
<td>28th Richard F Away </td>
<td>29th Richard F Away </td>
<td>30th Richard F Away </td>
<td bgcolor="#CCCCCC">31st </td>
<td bgcolor="#4357CFF">'''1st February''' </td>
</tr>
<tr valign="top">
<td>2nd </td>
<td>3rd </td>
<td>4th </td>
<td>5th </td>
<td>6th </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>27th </td>
<td bgcolor="#CCCCCC">28th </td>
<td bgcolor="#4357CFF">'''1st March''' </td>
</tr>
</table>

Mod:Hunt Research Group/calendar

2015-01-23T13:21:08Z

Ca307:

Mod:Hunt Research Group/calendar

2015-01-23T13:17:44Z

Ca307:

Talk:Mod:Hunt Research Group/MolCluster

2014-12-19T18:03:03Z

Ca307: /* Step-By-Step Example: Ionic Liquid Clusters */

===What is MolCluster?===
MolCluster is a tool (developed by Vincent and Gabriel) that can be used to cut clusters from MD trajectories and create the input files for ChemShell.

To use MolCluster, you will need:
* The latest version of MolCluster (available from Vincent).
* Python version 2.7.6, or above.
* The HISTORY file from which the clusters are to be cut, and the corresponding FIELD file. Note: these need to be in DL_POLY format. If you have used the 'restart' option in DL_POLY, the header of the HISTORY file may need to be amended. Additional transformations of the HISTORY and FIELD files, to convert atom labels into an acceptable format for MolCluster/ChemShell, may also be required (example given later).

===Using MolCluster: Basic Instructions===

1. Create a directory within the main MolCluster directory. Put the required HISTORY and FIELD files here.

2. Load MolCluster: ./MolCluster.py

3. Requests directory name to be specified (this is the location of the FIELD and HISTORY files). After specifying, the code will attempt to read and give an overview of the system.

4. Need to specify which configurations to cut a cluster from. Two options are currently available:
::*'''[n]''': Cut a cluster every "nth" configuration. N.B: numbering starts from 1 (i.e. 1st timestep). Therefore, if you request n=1000, clusters for configurations 1, 1001, 2001 etc. will be created.
::*'''[c]''': Select a custom set of configurations i.e. you can specify exactly which configurations you want.

5. Once the configurations have been extracted, you will be asked to choose how the origin will be defined in the clusters to be cut. Options are:
::*'''[AN]''': Atom number
::*'''[AT]''': Atom type
::*'''[MN]''': Molecule number
::*'''[MT]''': Molecule type
::*'''[C]''': Custom coordinates

You will then be asked to specify the specific atom number/type etc.

6. MolCluster will estimate the number of atoms within a region, for a range of radii with respect to your origin. Use this information to help you decide on the total radius (in Angstroms) of the clusters to be cut. You will be asked to specify this.

7. MolCluster has two options for deciding which molecules to include/exclude at the boundary of the clusters being cut:
::*'''[H]''': Hard boundary - all atoms of a molecule must be within the cutoff radius for the molecule to be included.
::*'''[S]''': Soft boundary - if the centre of mass of a molecule is within the cutoff radius, the molecule will be included.

8. Specify if the clusters are required to be neutral ('''Y/N''').

9. Decide on the output formats:
::*'''[C]''': Generates a ChemShell fragment input file, with accompanying .xyz co-ordinates file.
::*'''[X]''': Generates the .xyz co-ordinates file only.

If '''[X]''' selected, the clusters will be cut, .xyz files generated and MolCluster will terminate.

If '''[C]''' selected, you will be asked if you would also like to generate the necessary ChemShell input files for a QM/MM optimisation ('''Y/N''').

10. If your answer to step 9 was '''[C]''' (generate a ChemShell fragment input) and '''Y''' (generate ChemShell input files for a QM/MM optimisation), you will then be asked to define the QM region. Available options are:
::*'''[S]''': Spherical region (or threshold) centred about the defined origin (although not necessarily spherical??!!)
:::: If '''[S]''' selected, MolCluster will estimate the number of atoms in regions defined by a range of radii. Specify the QM radius. This must be specified (in Angstroms) and must, obviously, be less than, or equal to, the total radius of the cluster. Soft boundary conditions are implemented.
::*'''[M]''': By number of molecules. Molecules closest to the origin will be included.
::*'''[A]''': By an upper limit of atoms. Only whole molecules & those closest to the origin included.
::*'''[C]''': Custom region i.e. can select molecules individually to be in the QM region
::*'''[O]''': Spherical regions centred about one or more origins

If options '''[C]''' or '''[O]''' selected, MolCluster will go straight to steps 11 and 12. Once the active region and the directory/filenames have been defined, MolCluster will then ask for the custom QM regions to be defined ''per'' cluster (see step 14).

11. Once the QM region has been defined, the active region must be defined. MolCluster will estimate the number of atoms that would be in the active and frozen regions for a range of active radii. This information can be used to help decide upon an appropriate active radius. This must be specified (in Angstroms) and must, obviously, be less than, or equal to, the total radius of the cluster. If all atoms are to be included, simple enter "ALL". Soft boundary conditions are implemented.

12. Specify the output directory (i.e. where your final clusters and associated files will be saved) and specify the base-name for the output files (e.g. if you type "cluster" here, your clusters will be saved as cluster_1, cluster_2 etc.).

13. Unless options 10 '''[C'''] or '''[O]''' were selected (in that case, see point 14), MolCluster will generate the specified clusters and then terminate.

14. If option '''[C]''' selected in step 10, MolCluster will at this point list all the molecules in the first cluster, along with the distances to the origin. You will be asked to list all the molecules to be included in the QM region for this cluster. The same procedure is carried out for each cluster, before the clusters are generated and MolCluster terminates.

If option '''[O]''' selected in step 10, you will be asked to specify how many QM regions are to be defined and then specify the origin type and size of each QM region.

===The Output Files===
* Each cluster will have its own directory within the directory named in step 12. These subdirectories will be named: '''cluster_1''', '''cluster_2'''...'''cluster_n'''.
* Within the main directory one will also find a file called '''molcluster.log''' and a file called '''bulk_system_info.txt'''.
::*'''molcluster.log''' is a record of the user responses to each of the MolCluster options (look at this if you have forgotten, for example, the cluster radius).
::*'''bulk_system_info.txt''' summarises information relating to the system before clusters are cut (e.g. number and type of molecules, total number of atoms, total system charge, atom labels within a molecule, atomic charges).

*If option '''[X]''' selected in step 9, each subdirectory '''cluster_n''' will contain:
::*The '''cluster_n.xyz''' coordinates file
::*'''system_info.txt''': Summary of the cluster (e.g. total number of molecules, total number of atoms, total charge)

*If option '''[C]''', '''Y''' selected in step 9, each subdirectory '''cluster_n''' will contain:
::*The '''cluster_n.xyz''' coordinates file
::*'''system_info.txt''': Summary of the cluster (e.g. total number of molecules, total number of atoms, total charge)
::*The '''cluster_n.chm''' coordinates file. This will be used to create the '''cluster.pun''' ChemShell input file.
::*'''cluster_tiered.xyz''': xyz coordinates with the QM, active and frozen regions defined (all QM atoms listed as X1 (X=element symbol), active as X2 and frozen as X3). This file can be used to easily visualise the different regions in VMD.
::*'''conn.txt''' : the connectivity data needed by ChemShell
::*'''ff.dat''' : the forcefield in ChemShell format
::*'''opt.chm''': ChemShell input file. Options for the ChemShell optimisation specified here.

===Step-By-Step Example: Ionic Liquid Clusters===

Our example system:
* 256 ion pairs of [C4C1im][MeSO4]
* In total, the production run is 20ns in length; 4 lots of 5ns employing the "restart" keyword in DL_Poly.
* Our aim is to cut clusters from the last 5ns of the trajectory and create the input files for a ChemShell optimisation.

1). Create a directory within the main MolCluster directory and put the '''HISTORY''' and '''FIELD''' files here. Our directory will be called: '''BMIM_MESO4_EXAMPLE'''.

2). We now need to check to see if the HISTORY and FIELD files are in the correct format.

*As the ''restart'' keyword has been employed, two lines are missing from the header of the HISTORY file, '''Figure 1a''' and '''1b'''. MolCluster does not like this. Therefore, we need to add in the two lines that it is expecting to see, '''Figure 1c'''.

[[Image:MolCluster-HISTORY-header.png|frame|center|850px|'''Figure 1'''. Headers from selected HISTORY files '''(a)''' first 5ns of our simulation, without the use of the restart keyword, '''(b)''' last 5ns of our simulation with the restart keyword and '''(c)''' same HISTORY file as in (b), with missing lines added in. ]]

*The second problem we need to address is the atom labelling. The original atom labelling for [C4C1im][MeSO4], as used in the DL_Poly simulation, is shown in '''Figure 2a'''. Unfortunately, ChemShell has issues with this. To keep ChemShell happy, we have to change the atom labels in the HISTORY and FIELD files to the format ''elementsymbolnumber'' e.g. C2 rather than CR. Thankfully, this is quite easy to do using a script ('''sub_script.sh''', see below) written by Vincent. Firstly, however, we need to decide upon the new atom labelling. This is shown in '''Figure 2b''' for our example system. '''sub_script.sh''' requires that we have defined the atom label mappings in a file called '''sub_map.txt''' (also shown below for this system).

[[Image:BMIM-MESO4-numbering.png|thumb|center|850px|'''Figure 2'''. Original atom labelling (as used in DL_POLY MD simulation) shown in '''(a)''' and new atom labelling (suitable for MolCluster) shown in '''(b)'''. Within '''(b)''', atom labels that already had the correct format are in red. ]]

'''sub_script.sh''':

<pre>#!/bin/bash

while read line

do

#echo $line

s1=$(echo $line | awk '{ print $1 }')

s2=$(echo $line | awk '{ print $2 }')

echo "$s1 $s2"

gsed -i_bu2 "s|\<$s1\>|$s2|g" FIELD

gsed -i_bu2 "s|\<$s1\>|$s2|g" HISTORY

done < sub_map.txt</pre>

'''sub_map.txt''':
<pre>CR C3

NA N1

CW C4

HCR H2

HCW H3

HC H4

CT C6

OS4 O4

OC4 O5

HS4 H5

CS C5

CS4 C7</pre>

*Run '''./sub_script.sh'''
Note: this process may take a while, depending on the size of the file. Progress can be seen in the terminal (example shown in '''Figure 3'''), with each of the mappings specified in sub_map.txt considered in turn. The first few lines of the HISTORY file, before, and after, the relabelling can be seen in '''Figure 4'''.

[[Image:sub_map_mappings.png|thumb|center|800px|'''Figure 3'''. Example terminal output whilst running sub_script.sh ]]

[[Image:HISTORY-before-after.png|thumb|center|1000px|'''Figure 4'''. First few lines of the HISTORY file before '''(a)''' and after '''(b)''' the relabelling. ]]

3). Now our files are in the correct format, we can run MolCluster: '''./MolCluster.py'''

4). The first thing MolCluster does is to ask us to specify the directory containing the FIELD and HISTORY files. Our directory is called BMIM_MESO4_EXAMPLE. Once this has been specified, MolCluster will attempt to read the files and generate a summary of the system (from timestep 1 of the trajectory). This is shown in '''Figure 5''' for our system, and it can be seen that the information summarised by MolCluster is correct.

[[Image:MC-read-files-annotate.png|thumb|center|800px|'''Figure 5'''. After specifying the directory for the FIELD and HISTORY files, MolCluster summarises the bulk system information. ]]

5). MolCluster works out how many configurations in the HISTORY file (5000 in our example) and then asks us to specify the configurations we would like to cut a cluster from. In this case, we are going to select the '''[n]''' option (cut a cluster from every 'nth' configuration) and then specify n as an integer, in this case 1000 (i.e. n=1000, therefore cut a cluster every 1000th time step), '''Figure 6'''.

[[Image:MC-specify-config.png|thumb|center|800px|'''Figure 6'''. Specifying the configurations to create clusters for. ]]

6). We must now select how we would like to define the origin of the clusters to be cut. We are going to select option '''[AN]''' (atom number) and choose atom 1 to be the origin (for reference, in our case this is a C3 atom), '''Figure 7'''.

[[Image:origin-define.png|thumb|center|800px|'''Figure 7'''. Defining the cluster origin. ]]

7). An estimate of the number of atoms in regions with varying radii (with respect to our defined origin) is provided by MolCluster. We need to cut a cluster large enough to incorporate a reasonable number of ion pairs (bearing in mind that our cation alone, in all trans form, is over 9 Angstroms in width), but not so large that the calculation is unfeasible. The ideal size is still being investigated, but for now, let us specify a cluster radius of 15 Angstroms, '''Figure 8'''.

[[Image:cluster-radius-cut.png|thumb|center|900px|'''Figure 8'''. Choosing the cluster radius. ]]

8). MolCluster now asks us to tell it which boundary condition to use when cutting the clusters (essentially this is just how MolCluster will decide whether or not to include a molecule in the cluster for molecules at the boundary). We will select '''[S]''' (soft boundary) here. We are then asked to specify if the cluster needs to be neutral. Obviously this is only really applicable to charged systems (with counter ions), such as ionic liquids . We will select yes here, '''[Y]''', so that all our clusters have the same total charge, '''Figure 9'''.

[[Image:boundary-neutral.png|thumb|center|850px|'''Figure 9'''. Selecting boundary conditions. ]]

9). We now need to decide on the output file type. As the ultimate aim is to run QM/MM optimisations of our clusters, we need to select the options that will generate the ChemShell input files: '''[C]''', '''[Y]''', '''Figure 10'''.

[[Image:output-filetype.png|thumb|center|850px| ]]

10). A decision on how the QM region will be defined is now made. We are going to select '''[S]''' (spherical region). MolCluster then estimates the number of atoms in regions of varying radii with respect to our origin. Again, as with step 7, the optimum size has not yet been deduced. However, from previous tests, a QM radius of 7 Angstroms results in a manageable number of ions and is large enough to observe local structural features. Therefore, we shall specify a radius of 7 Angstroms in this example, '''Figure 11'''.

[[Image:QM-define.png|thumb|center|800px|'''Figure 11'''. QM region defined. ]]

11). After defining the QM region, we then need to define the size of the active region. Again MolCluster helps us by estimating the number of atoms for a range of radii. Molecules not included in the active region, will be in the Frozen region. Fir this example, we shall define the specify active region to have a radius of 11 Angstroms, '''Figure 12'''.

[[Image:Active-region .png|thumb|center|800px|'''Figure 12'''. Radius of active region specified. ]]

12). Finally, we are asked to specify the output directory where all our files will be placed, and the basename for each of our clusters. In this example the output directory will be ''BMIM_MESO4_EXAMPLE/example'' and the base name will be ''cluster'', '''Figure 13'''.

[[Image:Ouput-filenames.png|thumb|center|800px| ]]

13). MolCluster then sets about creating the clusters according to our specifications. The terminal output for the first cluster (cluster_1) is shown in '''Figure 14'''. After creating all the clusters, MolCluster will terminate.

[[Image:cluster_1.png|thumb|center|800px|'''Figure 14'''. Cluster_1 created. ]]

14). Within the named output directory, each cluster has it's own subdirectory: cluster_1, cluster_2 etc. Within each of the subdirectories can be found the requested output files, '''Figure 15'''.

[[Image:directory-files.png|thumb|center|1100px|'''Figure 15'''. Output files. ]]

15). The file called system_info.txt summarises key information relating to the cluster. This is shown in '''Figure 16''' for cluster 1. We can see that in total there are 72 molecules (36 cations and 36 anions) and that, as requested, the total charge of the system is zero.

[[Image:system-info-cluster_1.png|thumb|center|800px|'''Figure 16'''. Total system information for cluster 1. ]]

*To find out how many molecules in the QM and active regions, we can open the file called ''molcluster.log'' in the parent directory. This is a record of all the options we selected. By scrolling through we can find the information relating to cluster 1, '''Figure 17''', and can see that there are 9 molecules in the QM region; 4 cations and 5 anions, resulting in a total charge of -1. There are 35 molecules in the active region.

[[Image:molcluster-log-cluster1-annot.png|thumb|center|800px|'''Figure 17'''. Information about cluster 1, found in the output file molcluster.log. ]]

*Returning to the files in our subdirectory ''cluster_1'', we can open ''cluster.xyz'' (or ''cluster_tiered.xyz'') in VMD to visualise the cut cluster, '''Figure 18''' for our cluster 1. ''cluster_tiered.xyz'' is particularly useful, as it allows us to visualise each of the distinct regions. All of the atoms in the QM region are labelled with a 1 (active labelled with 2 and frozen labelled with 3), therefore we can choose to visualise the QM region only, '''Figure 19a'''. In '''Figure 19b''', all the regions are shown in different colours.

[[Image:full-cluster-1.png|thumb|center|800px|'''Figure 18'''. Cluster 1 visualised in VMD. ]]

[[Image:cluster_tiered-edit.png|thumb|center|800px|'''Figure 19'''. '''(a)''' QM region visualised in VMD. '''(b)''' All regions, visualised in different colours. ]]

Talk:Mod:Hunt Research Group/MolCluster

2014-12-19T18:01:17Z

Ca307: /* Step-By-Step Example: Ionic Liquid Clusters */

===What is MolCluster?===
MolCluster is a tool (developed by Vincent and Gabriel) that can be used to cut clusters from MD trajectories and create the input files for ChemShell.

To use MolCluster, you will need:
* The latest version of MolCluster (available from Vincent).
* Python version 2.7.6, or above.
* The HISTORY file from which the clusters are to be cut, and the corresponding FIELD file. Note: these need to be in DL_POLY format. If you have used the 'restart' option in DL_POLY, the header of the HISTORY file may need to be amended. Additional transformations of the HISTORY and FIELD files, to convert atom labels into an acceptable format for MolCluster/ChemShell, may also be required (example given later).

===Using MolCluster: Basic Instructions===

1. Create a directory within the main MolCluster directory. Put the required HISTORY and FIELD files here.

2. Load MolCluster: ./MolCluster.py

3. Requests directory name to be specified (this is the location of the FIELD and HISTORY files). After specifying, the code will attempt to read and give an overview of the system.

4. Need to specify which configurations to cut a cluster from. Two options are currently available:
::*'''[n]''': Cut a cluster every "nth" configuration. N.B: numbering starts from 1 (i.e. 1st timestep). Therefore, if you request n=1000, clusters for configurations 1, 1001, 2001 etc. will be created.
::*'''[c]''': Select a custom set of configurations i.e. you can specify exactly which configurations you want.

5. Once the configurations have been extracted, you will be asked to choose how the origin will be defined in the clusters to be cut. Options are:
::*'''[AN]''': Atom number
::*'''[AT]''': Atom type
::*'''[MN]''': Molecule number
::*'''[MT]''': Molecule type
::*'''[C]''': Custom coordinates

You will then be asked to specify the specific atom number/type etc.

6. MolCluster will estimate the number of atoms within a region, for a range of radii with respect to your origin. Use this information to help you decide on the total radius (in Angstroms) of the clusters to be cut. You will be asked to specify this.

7. MolCluster has two options for deciding which molecules to include/exclude at the boundary of the clusters being cut:
::*'''[H]''': Hard boundary - all atoms of a molecule must be within the cutoff radius for the molecule to be included.
::*'''[S]''': Soft boundary - if the centre of mass of a molecule is within the cutoff radius, the molecule will be included.

8. Specify if the clusters are required to be neutral ('''Y/N''').

9. Decide on the output formats:
::*'''[C]''': Generates a ChemShell fragment input file, with accompanying .xyz co-ordinates file.
::*'''[X]''': Generates the .xyz co-ordinates file only.

If '''[X]''' selected, the clusters will be cut, .xyz files generated and MolCluster will terminate.

If '''[C]''' selected, you will be asked if you would also like to generate the necessary ChemShell input files for a QM/MM optimisation ('''Y/N''').

10. If your answer to step 9 was '''[C]''' (generate a ChemShell fragment input) and '''Y''' (generate ChemShell input files for a QM/MM optimisation), you will then be asked to define the QM region. Available options are:
::*'''[S]''': Spherical region (or threshold) centred about the defined origin (although not necessarily spherical??!!)
:::: If '''[S]''' selected, MolCluster will estimate the number of atoms in regions defined by a range of radii. Specify the QM radius. This must be specified (in Angstroms) and must, obviously, be less than, or equal to, the total radius of the cluster. Soft boundary conditions are implemented.
::*'''[M]''': By number of molecules. Molecules closest to the origin will be included.
::*'''[A]''': By an upper limit of atoms. Only whole molecules & those closest to the origin included.
::*'''[C]''': Custom region i.e. can select molecules individually to be in the QM region
::*'''[O]''': Spherical regions centred about one or more origins

If options '''[C]''' or '''[O]''' selected, MolCluster will go straight to steps 11 and 12. Once the active region and the directory/filenames have been defined, MolCluster will then ask for the custom QM regions to be defined ''per'' cluster (see step 14).

11. Once the QM region has been defined, the active region must be defined. MolCluster will estimate the number of atoms that would be in the active and frozen regions for a range of active radii. This information can be used to help decide upon an appropriate active radius. This must be specified (in Angstroms) and must, obviously, be less than, or equal to, the total radius of the cluster. If all atoms are to be included, simple enter "ALL". Soft boundary conditions are implemented.

12. Specify the output directory (i.e. where your final clusters and associated files will be saved) and specify the base-name for the output files (e.g. if you type "cluster" here, your clusters will be saved as cluster_1, cluster_2 etc.).

13. Unless options 10 '''[C'''] or '''[O]''' were selected (in that case, see point 14), MolCluster will generate the specified clusters and then terminate.

14. If option '''[C]''' selected in step 10, MolCluster will at this point list all the molecules in the first cluster, along with the distances to the origin. You will be asked to list all the molecules to be included in the QM region for this cluster. The same procedure is carried out for each cluster, before the clusters are generated and MolCluster terminates.

If option '''[O]''' selected in step 10, you will be asked to specify how many QM regions are to be defined and then specify the origin type and size of each QM region.

===The Output Files===
* Each cluster will have its own directory within the directory named in step 12. These subdirectories will be named: '''cluster_1''', '''cluster_2'''...'''cluster_n'''.
* Within the main directory one will also find a file called '''molcluster.log''' and a file called '''bulk_system_info.txt'''.
::*'''molcluster.log''' is a record of the user responses to each of the MolCluster options (look at this if you have forgotten, for example, the cluster radius).
::*'''bulk_system_info.txt''' summarises information relating to the system before clusters are cut (e.g. number and type of molecules, total number of atoms, total system charge, atom labels within a molecule, atomic charges).

*If option '''[X]''' selected in step 9, each subdirectory '''cluster_n''' will contain:
::*The '''cluster_n.xyz''' coordinates file
::*'''system_info.txt''': Summary of the cluster (e.g. total number of molecules, total number of atoms, total charge)

*If option '''[C]''', '''Y''' selected in step 9, each subdirectory '''cluster_n''' will contain:
::*The '''cluster_n.xyz''' coordinates file
::*'''system_info.txt''': Summary of the cluster (e.g. total number of molecules, total number of atoms, total charge)
::*The '''cluster_n.chm''' coordinates file. This will be used to create the '''cluster.pun''' ChemShell input file.
::*'''cluster_tiered.xyz''': xyz coordinates with the QM, active and frozen regions defined (all QM atoms listed as X1 (X=element symbol), active as X2 and frozen as X3). This file can be used to easily visualise the different regions in VMD.
::*'''conn.txt''' : the connectivity data needed by ChemShell
::*'''ff.dat''' : the forcefield in ChemShell format
::*'''opt.chm''': ChemShell input file. Options for the ChemShell optimisation specified here.

===Step-By-Step Example: Ionic Liquid Clusters===

Our example system:
* 256 ion pairs of [C4C1im][MeSO4]
* In total, the production run is 20ns in length; 4 lots of 5ns employing the "restart" keyword in DL_Poly.
* Our aim is to cut clusters from the last 5ns of the trajectory and create the input files for a ChemShell optimisation.

1). Create a directory within the main MolCluster directory and put the '''HISTORY''' and '''FIELD''' files here. Our directory will be called: '''BMIM_MESO4_EXAMPLE'''.

2). We now need to check to see if the HISTORY and FIELD files are in the correct format.

*As the ''restart'' keyword has been employed, two lines are missing from the header of the HISTORY file, '''Figure 1a''' and '''1b'''. MolCluster does not like this. Therefore, we need to add in the two lines that it is expecting to see, '''Figure 1c'''.

[[Image:MolCluster-HISTORY-header.png|frame|center|850px|'''Figure 1'''. Headers from selected HISTORY files '''(a)''' first 5ns of our simulation, without the use of the restart keyword, '''(b)''' last 5ns of our simulation with the restart keyword and '''(c)''' same HISTORY file as in (b), with missing lines added in. ]]

*The second problem we need to address is the atom labelling. The original atom labelling for [C4C1im][MeSO4], as used in the DL_Poly simulation, is shown in '''Figure 2a'''. Unfortunately, ChemShell has issues with this. To keep ChemShell happy, we have to change the atom labels in the HISTORY and FIELD files to the format ''elementsymbolnumber'' e.g. C2 rather than CR. Thankfully, this is quite easy to do using a script ('''sub_script.sh''', see below) written by Vincent. Firstly, however, we need to decide upon the new atom labelling. This is shown in '''Figure 2b''' for our example system. '''sub_script.sh''' requires that we have defined the atom label mappings in a file called '''sub_map.txt''' (also shown below for this system).

[[Image:BMIM-MESO4-numbering.png|thumb|center|850px|'''Figure 2'''. Original atom labelling (as used in DL_POLY MD simulation) shown in '''(a)''' and new atom labelling (suitable for MolCluster) shown in '''(b)'''. Within '''(b)''', atom labels that already had the correct format are in red. ]]

'''sub_script.sh''':

<pre>#!/bin/bash

while read line

do

#echo $line

s1=$(echo $line | awk '{ print $1 }')

s2=$(echo $line | awk '{ print $2 }')

echo "$s1 $s2"

gsed -i_bu2 "s|\<$s1\>|$s2|g" FIELD

gsed -i_bu2 "s|\<$s1\>|$s2|g" HISTORY

done < sub_map.txt</pre>

'''sub_map.txt''':
<pre>CR C3

NA N1

CW C4

HCR H2

HCW H3

HC H4

CT C6

OS4 O4

OC4 O5

HS4 H5

CS C5

CS4 C7</pre>

*Run '''./sub_script.sh'''
Note: this process may take a while, depending on the size of the file. Progress can be seen in the terminal (example shown in '''Figure 3'''), with each of the mappings specified in sub_map.txt considered in turn. The first few lines of the HISTORY file, before, and after, the relabelling can be seen in '''Figure 4'''.

[[Image:sub_map_mappings.png|thumb|center|800px|'''Figure 3'''. Example terminal output whilst running sub_script.sh ]]

[[Image:HISTORY-before-after.png|thumb|center|1000px|'''Figure 4'''. First few lines of the HISTORY file before '''(a)''' and after '''(b)''' the relabelling. ]]

3). Now our files are in the correct format, we can run MolCluster: '''./MolCluster.py'''

4). The first thing MolCluster does is to ask us to specify the directory containing the FIELD and HISTORY files. Our directory is called BMIM_MESO4_EXAMPLE. Once this has been specified, MolCluster will attempt to read the files and generate a summary of the system (from timestep 1 of the trajectory). This is shown in '''Figure 5''' for our system, and it can be seen that the information summarised by MolCluster is correct.

[[Image:MC-read-files-annotate.png|thumb|center|800px|'''Figure 5'''. After specifying the directory for the FIELD and HISTORY files, MolCluster summarises the bulk system information. ]]

5). MolCluster works out how many configurations in the HISTORY file (5000 in our example) and then asks us to specify the configurations we would like to cut a cluster from. In this case, we are going to select the '''[n]''' option (cut a cluster from every 'nth' configuration) and then specify n as an integer, in this case 1000 (i.e. n=1000, therefore cut a cluster every 1000th time step), '''Figure 6'''.

[[Image:MC-specify-config.png|thumb|center|800px|'''Figure 6'''. Specifying the configurations to create clusters for. ]]

6). We must now select how we would like to define the origin of the clusters to be cut. We are going to select option '''[AN]''' (atom number) and choose atom 1 to be the origin (for reference, in our case this is a C3 atom), '''Figure 7'''.

[[Image:origin-define.png|thumb|center|800px|'''Figure 7'''. Defining the cluster origin. ]]

7). An estimate of the number of atoms in regions with varying radii (with respect to our defined origin) is provided by MolCluster. We need to cut a cluster large enough to incorporate a reasonable number of ion pairs (bearing in mind that our cation alone, in all trans form, is over 9 Angstroms in width), but not so large that the calculation is unfeasible. The ideal size is still being investigated, but for now, let us specify a cluster radius of 15 Angstroms, '''Figure 8'''.

[[Image:cluster-radius-cut.png|thumb|center|900px|'''Figure 8'''. Choosing the cluster radius. ]]

8). MolCluster now asks us to tell it which boundary condition to use when cutting the clusters (essentially this is just how MolCluster will decide whether or not to include a molecule in the cluster for molecules at the boundary). We will select '''[S]''' (soft boundary) here. We are then asked to specify if the cluster needs to be neutral. Obviously this is only really applicable to charged systems (with counter ions), such as ionic liquids . We will select yes here, '''[Y]''', so that all our clusters have the same total charge, '''Figure 9'''.

[[Image:boundary-neutral.png|thumb|center|850px|'''Figure 9'''. Selecting boundary conditions. ]]

9). We now need to decide on the output file type. As the ultimate aim is to run QM/MM optimisations of our clusters, we need to select the options that will generate the ChemShell input files: '''[C]''', '''[Y]''', '''Figure 10'''.

[[Image:output-filetype.png|thumb|center|850px| ]]

10). A decision on how the QM region will be defined is now made. We are going to select '''[S]''' (spherical region). MolCluster then estimates the number of atoms in regions of varying radii with respect to our origin. Again, as with step 7, the optimum size has not yet been deduced. However, from previous tests, a QM radius of 7 Angstroms results in a manageable number of ions and is large enough to observe local structural features. Therefore, we shall specify a radius of 7 Angstroms in this example, '''Figure 11'''.

[[Image:QM-define.png|thumb|center|800px|'''Figure 11'''. QM region defined. ]]

11). After defining the QM region, we then need to define the size of the active region. Again MolCluster helps us by estimating the number of atoms for a range of radii. Molecules not included in the active region, will be in the Frozen region. Fir this example, we shall define the specify active region to have a radius of 11 Angstroms, '''Figure 12'''.

[[Image:Active-region .png|thumb|center|800px|'''Figure 12'''. Radius of active region specified. ]]

12). Finally, we are asked to specify the output directory where all our files will be placed, and the basename for each of our clusters. In this example the output directory will be ''BMIM_MESO4_EXAMPLE/example'' and the base name will be ''cluster'', '''Figure 13'''.

[[Image:Ouput-filenames.png|thumb|center|800px| ]]

13). MolCluster then sets about creating the clusters according to our specifications. The terminal output for the first cluster (cluster_1) is shown in '''Figure 14'''. After creating all the clusters, MolCluster will terminate.

[[Image:cluster_1.png|thumb|center|800px|'''Figure 14'''. Cluster_1 created. ]]

14). Within the named output directory, each cluster has it's own subdirectory: cluster_1, cluster_2 etc. Within each of the subdirectories can be found the requested output files, '''Figure 15'''.

[[Image:directory-files.png|thumb|center|1100px|'''Figure 15'''. Output files. ]]

15). The file called system_info.txt summarises key information relating to the cluster. This is shown in '''Figure 16''' for cluster 1. We can see that in total there are 72 molecules (36 cations and 36 anions) and that, as requested, the total charge of the system is zero.

[[Image:system-info-cluster_1.png|thumb|center|800px|'''Figure 16'''. Total system information for cluster 1. ]]

*To find out how many atoms in the QM and active regions, we can open the file called ''molcluster.log'' in the parent directory. This is a record of all the options we selected. By scrolling through we can find the information relating to cluster 1, '''Figure 17''', and can see that there are 9 molecules in the QM region; 4 cations and 5 anions, resulting in a total charge of -1. There are 35 molecules in the active region.

[[Image:molcluster-log-cluster1-annot.png|thumb|center|800px|'''Figure 17'''. Information about cluster 1, found in the output file molcluster.log. ]]

*Returning to the files in our subdirectory ''cluster_1'', we can open ''cluster.xyz'' (or ''cluster_tiered.xyz'') in VMD to visualise the cut cluster, '''Figure 18''' for our cluster 1. ''cluster_tiered.xyz'' is particularly useful, as it allows us to visualise each of the distinct regions. All of the atoms in the QM region are labelled with a 1 (active labelled with 2 and frozen labelled with 3), therefore we can choose to visualise the QM region only, '''Figure 19a'''. In '''Figure 19b''', all the regions are shown in different colours.

[[Image:full-cluster-1.png|thumb|center|800px|'''Figure 18'''. Cluster 1 visualised in VMD. ]]

[[Image:cluster_tiered-edit.png|thumb|center|800px|'''Figure 19'''. '''(a)''' QM region visualised in VMD. '''(b)''' All regions, visualised in different colours. ]]

File:Cluster tiered-edit.png

2014-12-19T17:56:57Z

Ca307:

File:Full-cluster-1.png

2014-12-19T17:54:28Z

Ca307:

Talk:Mod:Hunt Research Group/MolCluster

2014-12-19T17:46:54Z

Ca307: /* Step-By-Step Example: Ionic Liquid Clusters */

===What is MolCluster?===
MolCluster is a tool (developed by Vincent and Gabriel) that can be used to cut clusters from MD trajectories and create the input files for ChemShell.

To use MolCluster, you will need:
* The latest version of MolCluster (available from Vincent).
* Python version 2.7.6, or above.
* The HISTORY file from which the clusters are to be cut, and the corresponding FIELD file. Note: these need to be in DL_POLY format. If you have used the 'restart' option in DL_POLY, the header of the HISTORY file may need to be amended. Additional transformations of the HISTORY and FIELD files, to convert atom labels into an acceptable format for MolCluster/ChemShell, may also be required (example given later).

===Using MolCluster: Basic Instructions===

1. Create a directory within the main MolCluster directory. Put the required HISTORY and FIELD files here.

2. Load MolCluster: ./MolCluster.py

3. Requests directory name to be specified (this is the location of the FIELD and HISTORY files). After specifying, the code will attempt to read and give an overview of the system.

4. Need to specify which configurations to cut a cluster from. Two options are currently available:
::*'''[n]''': Cut a cluster every "nth" configuration. N.B: numbering starts from 1 (i.e. 1st timestep). Therefore, if you request n=1000, clusters for configurations 1, 1001, 2001 etc. will be created.
::*'''[c]''': Select a custom set of configurations i.e. you can specify exactly which configurations you want.

5. Once the configurations have been extracted, you will be asked to choose how the origin will be defined in the clusters to be cut. Options are:
::*'''[AN]''': Atom number
::*'''[AT]''': Atom type
::*'''[MN]''': Molecule number
::*'''[MT]''': Molecule type
::*'''[C]''': Custom coordinates

You will then be asked to specify the specific atom number/type etc.

6. MolCluster will estimate the number of atoms within a region, for a range of radii with respect to your origin. Use this information to help you decide on the total radius (in Angstroms) of the clusters to be cut. You will be asked to specify this.

7. MolCluster has two options for deciding which molecules to include/exclude at the boundary of the clusters being cut:
::*'''[H]''': Hard boundary - all atoms of a molecule must be within the cutoff radius for the molecule to be included.
::*'''[S]''': Soft boundary - if the centre of mass of a molecule is within the cutoff radius, the molecule will be included.

8. Specify if the clusters are required to be neutral ('''Y/N''').

9. Decide on the output formats:
::*'''[C]''': Generates a ChemShell fragment input file, with accompanying .xyz co-ordinates file.
::*'''[X]''': Generates the .xyz co-ordinates file only.

If '''[X]''' selected, the clusters will be cut, .xyz files generated and MolCluster will terminate.

If '''[C]''' selected, you will be asked if you would also like to generate the necessary ChemShell input files for a QM/MM optimisation ('''Y/N''').

10. If your answer to step 9 was '''[C]''' (generate a ChemShell fragment input) and '''Y''' (generate ChemShell input files for a QM/MM optimisation), you will then be asked to define the QM region. Available options are:
::*'''[S]''': Spherical region (or threshold) centred about the defined origin (although not necessarily spherical??!!)
:::: If '''[S]''' selected, MolCluster will estimate the number of atoms in regions defined by a range of radii. Specify the QM radius. This must be specified (in Angstroms) and must, obviously, be less than, or equal to, the total radius of the cluster. Soft boundary conditions are implemented.
::*'''[M]''': By number of molecules. Molecules closest to the origin will be included.
::*'''[A]''': By an upper limit of atoms. Only whole molecules & those closest to the origin included.
::*'''[C]''': Custom region i.e. can select molecules individually to be in the QM region
::*'''[O]''': Spherical regions centred about one or more origins

If options '''[C]''' or '''[O]''' selected, MolCluster will go straight to steps 11 and 12. Once the active region and the directory/filenames have been defined, MolCluster will then ask for the custom QM regions to be defined ''per'' cluster (see step 14).

11. Once the QM region has been defined, the active region must be defined. MolCluster will estimate the number of atoms that would be in the active and frozen regions for a range of active radii. This information can be used to help decide upon an appropriate active radius. This must be specified (in Angstroms) and must, obviously, be less than, or equal to, the total radius of the cluster. If all atoms are to be included, simple enter "ALL". Soft boundary conditions are implemented.

12. Specify the output directory (i.e. where your final clusters and associated files will be saved) and specify the base-name for the output files (e.g. if you type "cluster" here, your clusters will be saved as cluster_1, cluster_2 etc.).

13. Unless options 10 '''[C'''] or '''[O]''' were selected (in that case, see point 14), MolCluster will generate the specified clusters and then terminate.

14. If option '''[C]''' selected in step 10, MolCluster will at this point list all the molecules in the first cluster, along with the distances to the origin. You will be asked to list all the molecules to be included in the QM region for this cluster. The same procedure is carried out for each cluster, before the clusters are generated and MolCluster terminates.

If option '''[O]''' selected in step 10, you will be asked to specify how many QM regions are to be defined and then specify the origin type and size of each QM region.

===The Output Files===
* Each cluster will have its own directory within the directory named in step 12. These subdirectories will be named: '''cluster_1''', '''cluster_2'''...'''cluster_n'''.
* Within the main directory one will also find a file called '''molcluster.log''' and a file called '''bulk_system_info.txt'''.
::*'''molcluster.log''' is a record of the user responses to each of the MolCluster options (look at this if you have forgotten, for example, the cluster radius).
::*'''bulk_system_info.txt''' summarises information relating to the system before clusters are cut (e.g. number and type of molecules, total number of atoms, total system charge, atom labels within a molecule, atomic charges).

*If option '''[X]''' selected in step 9, each subdirectory '''cluster_n''' will contain:
::*The '''cluster_n.xyz''' coordinates file
::*'''system_info.txt''': Summary of the cluster (e.g. total number of molecules, total number of atoms, total charge)

*If option '''[C]''', '''Y''' selected in step 9, each subdirectory '''cluster_n''' will contain:
::*The '''cluster_n.xyz''' coordinates file
::*'''system_info.txt''': Summary of the cluster (e.g. total number of molecules, total number of atoms, total charge)
::*The '''cluster_n.chm''' coordinates file. This will be used to create the '''cluster.pun''' ChemShell input file.
::*'''cluster_tiered.xyz''': xyz coordinates with the QM, active and frozen regions defined (all QM atoms listed as X1 (X=element symbol), active as X2 and frozen as X3). This file can be used to easily visualise the different regions in VMD.
::*'''conn.txt''' : the connectivity data needed by ChemShell
::*'''ff.dat''' : the forcefield in ChemShell format
::*'''opt.chm''': ChemShell input file. Options for the ChemShell optimisation specified here.

===Step-By-Step Example: Ionic Liquid Clusters===

Our example system:
* 256 ion pairs of [C4C1im][MeSO4]
* In total, the production run is 20ns in length; 4 lots of 5ns employing the "restart" keyword in DL_Poly.
* Our aim is to cut clusters from the last 5ns of the trajectory and create the input files for a ChemShell optimisation.

1). Create a directory within the main MolCluster directory and put the '''HISTORY''' and '''FIELD''' files here. Our directory will be called: '''BMIM_MESO4_EXAMPLE'''.

2). We now need to check to see if the HISTORY and FIELD files are in the correct format.

*As the ''restart'' keyword has been employed, two lines are missing from the header of the HISTORY file, '''Figure 1a''' and '''1b'''. MolCluster does not like this. Therefore, we need to add in the two lines that it is expecting to see, '''Figure 1c'''.

[[Image:MolCluster-HISTORY-header.png|frame|center|850px|'''Figure 1'''. Headers from selected HISTORY files '''(a)''' first 5ns of our simulation, without the use of the restart keyword, '''(b)''' last 5ns of our simulation with the restart keyword and '''(c)''' same HISTORY file as in (b), with missing lines added in. ]]

*The second problem we need to address is the atom labelling. The original atom labelling for [C4C1im][MeSO4], as used in the DL_Poly simulation, is shown in '''Figure 2a'''. Unfortunately, ChemShell has issues with this. To keep ChemShell happy, we have to change the atom labels in the HISTORY and FIELD files to the format ''elementsymbolnumber'' e.g. C2 rather than CR. Thankfully, this is quite easy to do using a script ('''sub_script.sh''', see below) written by Vincent. Firstly, however, we need to decide upon the new atom labelling. This is shown in '''Figure 2b''' for our example system. '''sub_script.sh''' requires that we have defined the atom label mappings in a file called '''sub_map.txt''' (also shown below for this system).

[[Image:BMIM-MESO4-numbering.png|thumb|center|850px|'''Figure 2'''. Original atom labelling (as used in DL_POLY MD simulation) shown in '''(a)''' and new atom labelling (suitable for MolCluster) shown in '''(b)'''. Within '''(b)''', atom labels that already had the correct format are in red. ]]

'''sub_script.sh''':

<pre>#!/bin/bash

while read line

do

#echo $line

s1=$(echo $line | awk '{ print $1 }')

s2=$(echo $line | awk '{ print $2 }')

echo "$s1 $s2"

gsed -i_bu2 "s|\<$s1\>|$s2|g" FIELD

gsed -i_bu2 "s|\<$s1\>|$s2|g" HISTORY

done < sub_map.txt</pre>

'''sub_map.txt''':
<pre>CR C3

NA N1

CW C4

HCR H2

HCW H3

HC H4

CT C6

OS4 O4

OC4 O5

HS4 H5

CS C5

CS4 C7</pre>

*Run '''./sub_script.sh'''
Note: this process may take a while, depending on the size of the file. Progress can be seen in the terminal (example shown in '''Figure 3'''), with each of the mappings specified in sub_map.txt considered in turn. The first few lines of the HISTORY file, before, and after, the relabelling can be seen in '''Figure 4'''.

[[Image:sub_map_mappings.png|thumb|center|800px|'''Figure 3'''. Example terminal output whilst running sub_script.sh ]]

[[Image:HISTORY-before-after.png|thumb|center|1000px|'''Figure 4'''. First few lines of the HISTORY file before '''(a)''' and after '''(b)''' the relabelling. ]]

3). Now our files are in the correct format, we can run MolCluster: '''./MolCluster.py'''

4). The first thing MolCluster does is to ask us to specify the directory containing the FIELD and HISTORY files. Our directory is called BMIM_MESO4_EXAMPLE. Once this has been specified, MolCluster will attempt to read the files and generate a summary of the system (from timestep 1 of the trajectory). This is shown in '''Figure 5''' for our system, and it can be seen that the information summarised by MolCluster is correct.

[[Image:MC-read-files-annotate.png|thumb|center|800px|'''Figure 5'''. After specifying the directory for the FIELD and HISTORY files, MolCluster summarises the bulk system information. ]]

5). MolCluster works out how many configurations in the HISTORY file (5000 in our example) and then asks us to specify the configurations we would like to cut a cluster from. In this case, we are going to select the '''[n]''' option (cut a cluster from every 'nth' configuration) and then specify n as an integer, in this case 1000 (i.e. n=1000, therefore cut a cluster every 1000th time step), '''Figure 6'''.

[[Image:MC-specify-config.png|thumb|center|800px|'''Figure 6'''. Specifying the configurations to create clusters for. ]]

6). We must now select how we would like to define the origin of the clusters to be cut. We are going to select option '''[AN]''' (atom number) and choose atom 1 to be the origin (for reference, in our case this is a C3 atom), '''Figure 7'''.

[[Image:origin-define.png|thumb|center|800px|'''Figure 7'''. Defining the cluster origin. ]]

7). An estimate of the number of atoms in regions with varying radii (with respect to our defined origin) is provided by MolCluster. We need to cut a cluster large enough to incorporate a reasonable number of ion pairs (bearing in mind that our cation alone, in all trans form, is over 9 Angstroms in width), but not so large that the calculation is unfeasible. The ideal size is still being investigated, but for now, let us specify a cluster radius of 15 Angstroms, '''Figure 8'''.

[[Image:cluster-radius-cut.png|thumb|center|900px|'''Figure 8'''. Choosing the cluster radius. ]]

8). MolCluster now asks us to tell it which boundary condition to use when cutting the clusters (essentially this is just how MolCluster will decide whether or not to include a molecule in the cluster for molecules at the boundary). We will select '''[S]''' (soft boundary) here. We are then asked to specify if the cluster needs to be neutral. Obviously this is only really applicable to charged systems (with counter ions), such as ionic liquids . We will select yes here, '''[Y]''', so that all our clusters have the same total charge, '''Figure 9'''.

[[Image:boundary-neutral.png|thumb|center|850px|'''Figure 9'''. Selecting boundary conditions. ]]

9). We now need to decide on the output file type. As the ultimate aim is to run QM/MM optimisations of our clusters, we need to select the options that will generate the ChemShell input files: '''[C]''', '''[Y]''', '''Figure 10'''.

[[Image:output-filetype.png|thumb|center|850px| ]]

10). A decision on how the QM region will be defined is now made. We are going to select '''[S]''' (spherical region). MolCluster then estimates the number of atoms in regions of varying radii with respect to our origin. Again, as with step 7, the optimum size has not yet been deduced. However, from previous tests, a QM radius of 7 Angstroms results in a manageable number of ions and is large enough to observe local structural features. Therefore, we shall specify a radius of 7 Angstroms in this example, '''Figure 11'''.

[[Image:QM-define.png|thumb|center|800px|'''Figure 11'''. QM region defined. ]]

11). After defining the QM region, we then need to define the size of the active region. Again MolCluster helps us by estimating the number of atoms for a range of radii. Molecules not included in the active region, will be in the Frozen region. Fir this example, we shall define the specify active region to have a radius of 11 Angstroms, '''Figure 12'''.

[[Image:Active-region .png|thumb|center|800px|'''Figure 12'''. Radius of active region specified. ]]

12). Finally, we are asked to specify the output directory where all our files will be placed, and the basename for each of our clusters. In this example the output directory will be ''BMIM_MESO4_EXAMPLE/example'' and the base name will be ''cluster'', '''Figure 13'''.

[[Image:Ouput-filenames.png|thumb|center|800px| ]]

13). MolCluster then sets about creating the clusters according to our specifications. The terminal output for the first cluster (cluster_1) is shown in '''Figure 14'''. After creating all the clusters, MolCluster will terminate.

[[Image:cluster_1.png|thumb|center|800px|'''Figure 14'''. Cluster_1 created. ]]

14). Within the named output directory, each cluster has it's own subdirectory: cluster_1, cluster_2 etc. Within each of the subdirectories can be found the requested output files, '''Figure 15'''.

[[Image:directory-files.png|thumb|center|1100px|'''Figure 15'''. Output files. ]]

15). The file called system_info.txt summarises key information relating to the cluster. This is shown in '''Figure 16''' for cluster 1. We can see that in total there are 72 molecules (36 cations and 36 anions) and that, as requested, the total charge of the system is zero.

[[Image:system-info-cluster_1.png|thumb|center|800px|'''Figure 16'''. Total system information for cluster 1. ]]

To find out how many atoms in the QM and active regions, we can open the file called ''mol cluster.log'' in the parent directory. This is a record of all the options we selected. By scrolling through we can find the information relating to cluster 1, '''Figure 17''', and can see that there are 9 molecules in the QM region; 4 cations and 5 anions, resulting in a total charge of -1. There are 35 molecules in the active region.

[[Image:molcluster-log-cluster1-annot.png|thumb|center|800px|'''Figure 17'''. Information about cluster 1, found in the output file molcluster.log. ]]

File:Molcluster-log-cluster1-annot.png

2014-12-19T17:44:47Z

Ca307:

Talk:Mod:Hunt Research Group/MolCluster

2014-12-19T15:44:40Z

Ca307: /* Step-By-Step Example: Ionic Liquid Clusters */

===What is MolCluster?===
MolCluster is a tool (developed by Vincent and Gabriel) that can be used to cut clusters from MD trajectories and create the input files for ChemShell.

To use MolCluster, you will need:
* The latest version of MolCluster (available from Vincent).
* Python version 2.7.6, or above.
* The HISTORY file from which the clusters are to be cut, and the corresponding FIELD file. Note: these need to be in DL_POLY format. If you have used the 'restart' option in DL_POLY, the header of the HISTORY file may need to be amended. Additional transformations of the HISTORY and FIELD files, to convert atom labels into an acceptable format for MolCluster/ChemShell, may also be required (example given later).

===Using MolCluster: Basic Instructions===

1. Create a directory within the main MolCluster directory. Put the required HISTORY and FIELD files here.

2. Load MolCluster: ./MolCluster.py

3. Requests directory name to be specified (this is the location of the FIELD and HISTORY files). After specifying, the code will attempt to read and give an overview of the system.

4. Need to specify which configurations to cut a cluster from. Two options are currently available:
::*'''[n]''': Cut a cluster every "nth" configuration. N.B: numbering starts from 1 (i.e. 1st timestep). Therefore, if you request n=1000, clusters for configurations 1, 1001, 2001 etc. will be created.
::*'''[c]''': Select a custom set of configurations i.e. you can specify exactly which configurations you want.

5. Once the configurations have been extracted, you will be asked to choose how the origin will be defined in the clusters to be cut. Options are:
::*'''[AN]''': Atom number
::*'''[AT]''': Atom type
::*'''[MN]''': Molecule number
::*'''[MT]''': Molecule type
::*'''[C]''': Custom coordinates

You will then be asked to specify the specific atom number/type etc.

6. MolCluster will estimate the number of atoms within a region, for a range of radii with respect to your origin. Use this information to help you decide on the total radius (in Angstroms) of the clusters to be cut. You will be asked to specify this.

7. MolCluster has two options for deciding which molecules to include/exclude at the boundary of the clusters being cut:
::*'''[H]''': Hard boundary - all atoms of a molecule must be within the cutoff radius for the molecule to be included.
::*'''[S]''': Soft boundary - if the centre of mass of a molecule is within the cutoff radius, the molecule will be included.

8. Specify if the clusters are required to be neutral ('''Y/N''').

9. Decide on the output formats:
::*'''[C]''': Generates a ChemShell fragment input file, with accompanying .xyz co-ordinates file.
::*'''[X]''': Generates the .xyz co-ordinates file only.

If '''[X]''' selected, the clusters will be cut, .xyz files generated and MolCluster will terminate.

If '''[C]''' selected, you will be asked if you would also like to generate the necessary ChemShell input files for a QM/MM optimisation ('''Y/N''').

10. If your answer to step 9 was '''[C]''' (generate a ChemShell fragment input) and '''Y''' (generate ChemShell input files for a QM/MM optimisation), you will then be asked to define the QM region. Available options are:
::*'''[S]''': Spherical region (or threshold) centred about the defined origin (although not necessarily spherical??!!)
:::: If '''[S]''' selected, MolCluster will estimate the number of atoms in regions defined by a range of radii. Specify the QM radius. This must be specified (in Angstroms) and must, obviously, be less than, or equal to, the total radius of the cluster. Soft boundary conditions are implemented.
::*'''[M]''': By number of molecules. Molecules closest to the origin will be included.
::*'''[A]''': By an upper limit of atoms. Only whole molecules & those closest to the origin included.
::*'''[C]''': Custom region i.e. can select molecules individually to be in the QM region
::*'''[O]''': Spherical regions centred about one or more origins

If options '''[C]''' or '''[O]''' selected, MolCluster will go straight to steps 11 and 12. Once the active region and the directory/filenames have been defined, MolCluster will then ask for the custom QM regions to be defined ''per'' cluster (see step 14).

11. Once the QM region has been defined, the active region must be defined. MolCluster will estimate the number of atoms that would be in the active and frozen regions for a range of active radii. This information can be used to help decide upon an appropriate active radius. This must be specified (in Angstroms) and must, obviously, be less than, or equal to, the total radius of the cluster. If all atoms are to be included, simple enter "ALL". Soft boundary conditions are implemented.

12. Specify the output directory (i.e. where your final clusters and associated files will be saved) and specify the base-name for the output files (e.g. if you type "cluster" here, your clusters will be saved as cluster_1, cluster_2 etc.).

13. Unless options 10 '''[C'''] or '''[O]''' were selected (in that case, see point 14), MolCluster will generate the specified clusters and then terminate.

14. If option '''[C]''' selected in step 10, MolCluster will at this point list all the molecules in the first cluster, along with the distances to the origin. You will be asked to list all the molecules to be included in the QM region for this cluster. The same procedure is carried out for each cluster, before the clusters are generated and MolCluster terminates.

If option '''[O]''' selected in step 10, you will be asked to specify how many QM regions are to be defined and then specify the origin type and size of each QM region.

===The Output Files===
* Each cluster will have its own directory within the directory named in step 12. These subdirectories will be named: '''cluster_1''', '''cluster_2'''...'''cluster_n'''.
* Within the main directory one will also find a file called '''molcluster.log''' and a file called '''bulk_system_info.txt'''.
::*'''molcluster.log''' is a record of the user responses to each of the MolCluster options (look at this if you have forgotten, for example, the cluster radius).
::*'''bulk_system_info.txt''' summarises information relating to the system before clusters are cut (e.g. number and type of molecules, total number of atoms, total system charge, atom labels within a molecule, atomic charges).

*If option '''[X]''' selected in step 9, each subdirectory '''cluster_n''' will contain:
::*The '''cluster_n.xyz''' coordinates file
::*'''system_info.txt''': Summary of the cluster (e.g. total number of molecules, total number of atoms, total charge)

*If option '''[C]''', '''Y''' selected in step 9, each subdirectory '''cluster_n''' will contain:
::*The '''cluster_n.xyz''' coordinates file
::*'''system_info.txt''': Summary of the cluster (e.g. total number of molecules, total number of atoms, total charge)
::*The '''cluster_n.chm''' coordinates file. This will be used to create the '''cluster.pun''' ChemShell input file.
::*'''cluster_tiered.xyz''': xyz coordinates with the QM, active and frozen regions defined (all QM atoms listed as X1 (X=element symbol), active as X2 and frozen as X3). This file can be used to easily visualise the different regions in VMD.
::*'''conn.txt''' : the connectivity data needed by ChemShell
::*'''ff.dat''' : the forcefield in ChemShell format
::*'''opt.chm''': ChemShell input file. Options for the ChemShell optimisation specified here.

===Step-By-Step Example: Ionic Liquid Clusters===

Our example system:
* 256 ion pairs of [C4C1im][MeSO4]
* In total, the production run is 20ns in length; 4 lots of 5ns employing the "restart" keyword in DL_Poly.
* Our aim is to cut clusters from the last 5ns of the trajectory and create the input files for a ChemShell optimisation.

1). Create a directory within the main MolCluster directory and put the '''HISTORY''' and '''FIELD''' files here. Our directory will be called: '''BMIM_MESO4_EXAMPLE'''.

2). We now need to check to see if the HISTORY and FIELD files are in the correct format.

*As the ''restart'' keyword has been employed, two lines are missing from the header of the HISTORY file, '''Figure 1a''' and '''1b'''. MolCluster does not like this. Therefore, we need to add in the two lines that it is expecting to see, '''Figure 1c'''.

[[Image:MolCluster-HISTORY-header.png|frame|center|850px|'''Figure 1'''. Headers from selected HISTORY files '''(a)''' first 5ns of our simulation, without the use of the restart keyword, '''(b)''' last 5ns of our simulation with the restart keyword and '''(c)''' same HISTORY file as in (b), with missing lines added in. ]]

*The second problem we need to address is the atom labelling. The original atom labelling for [C4C1im][MeSO4], as used in the DL_Poly simulation, is shown in '''Figure 2a'''. Unfortunately, ChemShell has issues with this. To keep ChemShell happy, we have to change the atom labels in the HISTORY and FIELD files to the format ''elementsymbolnumber'' e.g. C2 rather than CR. Thankfully, this is quite easy to do using a script ('''sub_script.sh''', see below) written by Vincent. Firstly, however, we need to decide upon the new atom labelling. This is shown in '''Figure 2b''' for our example system. '''sub_script.sh''' requires that we have defined the atom label mappings in a file called '''sub_map.txt''' (also shown below for this system).

[[Image:BMIM-MESO4-numbering.png|thumb|center|850px|'''Figure 2'''. Original atom labelling (as used in DL_POLY MD simulation) shown in '''(a)''' and new atom labelling (suitable for MolCluster) shown in '''(b)'''. Within '''(b)''', atom labels that already had the correct format are in red. ]]

'''sub_script.sh''':

<pre>#!/bin/bash

while read line

do

#echo $line

s1=$(echo $line | awk '{ print $1 }')

s2=$(echo $line | awk '{ print $2 }')

echo "$s1 $s2"

gsed -i_bu2 "s|\<$s1\>|$s2|g" FIELD

gsed -i_bu2 "s|\<$s1\>|$s2|g" HISTORY

done < sub_map.txt</pre>

'''sub_map.txt''':
<pre>CR C3

NA N1

CW C4

HCR H2

HCW H3

HC H4

CT C6

OS4 O4

OC4 O5

HS4 H5

CS C5

CS4 C7</pre>

*Run '''./sub_script.sh'''
Note: this process may take a while, depending on the size of the file. Progress can be seen in the terminal (example shown in '''Figure 3'''), with each of the mappings specified in sub_map.txt considered in turn. The first few lines of the HISTORY file, before, and after, the relabelling can be seen in '''Figure 4'''.

[[Image:sub_map_mappings.png|thumb|center|800px|'''Figure 3'''. Example terminal output whilst running sub_script.sh ]]

[[Image:HISTORY-before-after.png|thumb|center|1000px|'''Figure 4'''. First few lines of the HISTORY file before '''(a)''' and after '''(b)''' the relabelling. ]]

3). Now our files are in the correct format, we can run MolCluster: '''./MolCluster.py'''

4). The first thing MolCluster does is to ask us to specify the directory containing the FIELD and HISTORY files. Our directory is called BMIM_MESO4_EXAMPLE. Once this has been specified, MolCluster will attempt to read the files and generate a summary of the system (from timestep 1 of the trajectory). This is shown in '''Figure 5''' for our system, and it can be seen that the information summarised by MolCluster is correct.

[[Image:MC-read-files-annotate.png|thumb|center|800px|'''Figure 5'''. After specifying the directory for the FIELD and HISTORY files, MolCluster summarises the bulk system information. ]]

5). MolCluster works out how many configurations in the HISTORY file (5000 in our example) and then asks us to specify the configurations we would like to cut a cluster from. In this case, we are going to select the '''[n]''' option (cut a cluster from every 'nth' configuration) and then specify n as an integer, in this case 1000 (i.e. n=1000, therefore cut a cluster every 1000th time step), '''Figure 6'''.

[[Image:MC-specify-config.png|thumb|center|800px|'''Figure 6'''. Specifying the configurations to create clusters for. ]]

6). We must now select how we would like to define the origin of the clusters to be cut. We are going to select option '''[AN]''' (atom number) and choose atom 1 to be the origin (for reference, in our case this is a C3 atom), '''Figure 7'''.

[[Image:origin-define.png|thumb|center|800px|'''Figure 7'''. Defining the cluster origin. ]]

7). An estimate of the number of atoms in regions with varying radii (with respect to our defined origin) is provided by MolCluster. We need to cut a cluster large enough to incorporate a reasonable number of ion pairs (bearing in mind that our cation alone, in all trans form, is over 9 Angstroms in width), but not so large that the calculation is unfeasible. The ideal size is still being investigated, but for now, let us specify a cluster radius of 15 Angstroms, '''Figure 8'''.

[[Image:cluster-radius-cut.png|thumb|center|900px|'''Figure 8'''. Choosing the cluster radius. ]]

8). MolCluster now asks us to tell it which boundary condition to use when cutting the clusters (essentially this is just how MolCluster will decide whether or not to include a molecule in the cluster for molecules at the boundary). We will select '''[S]''' (soft boundary) here. We are then asked to specify if the cluster needs to be neutral. Obviously this is only really applicable to charged systems (with counter ions), such as ionic liquids . We will select yes here, '''[Y]''', so that all our clusters have the same total charge, '''Figure 9'''.

[[Image:boundary-neutral.png|thumb|center|850px|'''Figure 9'''. Selecting boundary conditions. ]]

9). We now need to decide on the output file type. As the ultimate aim is to run QM/MM optimisations of our clusters, we need to select the options that will generate the ChemShell input files: '''[C]''', '''[Y]''', '''Figure 10'''.

[[Image:output-filetype.png|thumb|center|850px| ]]

10). A decision on how the QM region will be defined is now made. We are going to select '''[S]''' (spherical region). MolCluster then estimates the number of atoms in regions of varying radii with respect to our origin. Again, as with step 7, the optimum size has not yet been deduced. However, from previous tests, a QM radius of 7 Angstroms results in a manageable number of ions and is large enough to observe local structural features. Therefore, we shall specify a radius of 7 Angstroms in this example, '''Figure 11'''.

[[Image:QM-define.png|thumb|center|800px|'''Figure 11'''. QM region defined. ]]

11). After defining the QM region, we then need to define the size of the active region. Again MolCluster helps us by estimating the number of atoms for a range of radii. Molecules not included in the active region, will be in the Frozen region. Fir this example, we shall define the specify active region to have a radius of 11 Angstroms, '''Figure 12'''.

[[Image:Active-region .png|thumb|center|800px|'''Figure 12'''. Radius of active region specified. ]]

12). Finally, we are asked to specify the output directory where all our files will be placed, and the basename for each of our clusters. In this example the output directory will be ''BMIM_MESO4_EXAMPLE/example'' and the base name will be ''cluster'', '''Figure 13'''.

[[Image:Ouput-filenames.png|thumb|center|800px| ]]

13). MolCluster then sets about creating the clusters according to our specifications. The terminal output for the first cluster (cluster_1) is shown in '''Figure 14'''. After creating all the clusters, MolCluster will terminate.

[[Image:cluster_1.png|thumb|center|800px|'''Figure 14'''. Cluster_1 created. ]]

14). Within the named output directory, each cluster has it's own subdirectory: cluster_1, cluster_2 etc. Within each of the subdirectories can be found the requested output files, '''Figure 15'''.

[[Image:directory-files.png|thumb|center|1100px|'''Figure 15'''. Output files. ]]

15). The file called system_info.txt summarises key information relating to the cluster. This is shown in '''Figure 16''' for cluster 1. We can see that in total there are 72 molecules (36 cations and 36 anions) and that, as requested, the total charge of the system is zero.

[[Image:system-info-cluster_1.png|thumb|center|800px|'''Figure 16'''. Total system information for cluster 1. ]]

File:System-info-cluster 1.png

2014-12-19T15:42:34Z

Ca307:

Talk:Mod:Hunt Research Group/MolCluster

2014-12-19T10:30:10Z

Ca307: /* Step-By-Step Example: Ionic Liquid Clusters */

===What is MolCluster?===
MolCluster is a tool (developed by Vincent and Gabriel) that can be used to cut clusters from MD trajectories and create the input files for ChemShell.

To use MolCluster, you will need:
* The latest version of MolCluster (available from Vincent).
* Python version 2.7.6, or above.
* The HISTORY file from which the clusters are to be cut, and the corresponding FIELD file. Note: these need to be in DL_POLY format. If you have used the 'restart' option in DL_POLY, the header of the HISTORY file may need to be amended. Additional transformations of the HISTORY and FIELD files, to convert atom labels into an acceptable format for MolCluster/ChemShell, may also be required (example given later).

===Using MolCluster: Basic Instructions===

1. Create a directory within the main MolCluster directory. Put the required HISTORY and FIELD files here.

2. Load MolCluster: ./MolCluster.py

3. Requests directory name to be specified (this is the location of the FIELD and HISTORY files). After specifying, the code will attempt to read and give an overview of the system.

4. Need to specify which configurations to cut a cluster from. Two options are currently available:
::*'''[n]''': Cut a cluster every "nth" configuration. N.B: numbering starts from 1 (i.e. 1st timestep). Therefore, if you request n=1000, clusters for configurations 1, 1001, 2001 etc. will be created.
::*'''[c]''': Select a custom set of configurations i.e. you can specify exactly which configurations you want.

5. Once the configurations have been extracted, you will be asked to choose how the origin will be defined in the clusters to be cut. Options are:
::*'''[AN]''': Atom number
::*'''[AT]''': Atom type
::*'''[MN]''': Molecule number
::*'''[MT]''': Molecule type
::*'''[C]''': Custom coordinates

You will then be asked to specify the specific atom number/type etc.

6. MolCluster will estimate the number of atoms within a region, for a range of radii with respect to your origin. Use this information to help you decide on the total radius (in Angstroms) of the clusters to be cut. You will be asked to specify this.

7. MolCluster has two options for deciding which molecules to include/exclude at the boundary of the clusters being cut:
::*'''[H]''': Hard boundary - all atoms of a molecule must be within the cutoff radius for the molecule to be included.
::*'''[S]''': Soft boundary - if the centre of mass of a molecule is within the cutoff radius, the molecule will be included.

8. Specify if the clusters are required to be neutral ('''Y/N''').

9. Decide on the output formats:
::*'''[C]''': Generates a ChemShell fragment input file, with accompanying .xyz co-ordinates file.
::*'''[X]''': Generates the .xyz co-ordinates file only.

If '''[X]''' selected, the clusters will be cut, .xyz files generated and MolCluster will terminate.

If '''[C]''' selected, you will be asked if you would also like to generate the necessary ChemShell input files for a QM/MM optimisation ('''Y/N''').

10. If your answer to step 9 was '''[C]''' (generate a ChemShell fragment input) and '''Y''' (generate ChemShell input files for a QM/MM optimisation), you will then be asked to define the QM region. Available options are:
::*'''[S]''': Spherical region (or threshold) centred about the defined origin (although not necessarily spherical??!!)
:::: If '''[S]''' selected, MolCluster will estimate the number of atoms in regions defined by a range of radii. Specify the QM radius. This must be specified (in Angstroms) and must, obviously, be less than, or equal to, the total radius of the cluster. Soft boundary conditions are implemented.
::*'''[M]''': By number of molecules. Molecules closest to the origin will be included.
::*'''[A]''': By an upper limit of atoms. Only whole molecules & those closest to the origin included.
::*'''[C]''': Custom region i.e. can select molecules individually to be in the QM region
::*'''[O]''': Spherical regions centred about one or more origins

If options '''[C]''' or '''[O]''' selected, MolCluster will go straight to steps 11 and 12. Once the active region and the directory/filenames have been defined, MolCluster will then ask for the custom QM regions to be defined ''per'' cluster (see step 14).

11. Once the QM region has been defined, the active region must be defined. MolCluster will estimate the number of atoms that would be in the active and frozen regions for a range of active radii. This information can be used to help decide upon an appropriate active radius. This must be specified (in Angstroms) and must, obviously, be less than, or equal to, the total radius of the cluster. If all atoms are to be included, simple enter "ALL". Soft boundary conditions are implemented.

12. Specify the output directory (i.e. where your final clusters and associated files will be saved) and specify the base-name for the output files (e.g. if you type "cluster" here, your clusters will be saved as cluster_1, cluster_2 etc.).

13. Unless options 10 '''[C'''] or '''[O]''' were selected (in that case, see point 14), MolCluster will generate the specified clusters and then terminate.

14. If option '''[C]''' selected in step 10, MolCluster will at this point list all the molecules in the first cluster, along with the distances to the origin. You will be asked to list all the molecules to be included in the QM region for this cluster. The same procedure is carried out for each cluster, before the clusters are generated and MolCluster terminates.

If option '''[O]''' selected in step 10, you will be asked to specify how many QM regions are to be defined and then specify the origin type and size of each QM region.

===The Output Files===
* Each cluster will have its own directory within the directory named in step 12. These subdirectories will be named: '''cluster_1''', '''cluster_2'''...'''cluster_n'''.
* Within the main directory one will also find a file called '''molcluster.log''' and a file called '''bulk_system_info.txt'''.
::*'''molcluster.log''' is a record of the user responses to each of the MolCluster options (look at this if you have forgotten, for example, the cluster radius).
::*'''bulk_system_info.txt''' summarises information relating to the system before clusters are cut (e.g. number and type of molecules, total number of atoms, total system charge, atom labels within a molecule, atomic charges).

*If option '''[X]''' selected in step 9, each subdirectory '''cluster_n''' will contain:
::*The '''cluster_n.xyz''' coordinates file
::*'''system_info.txt''': Summary of the cluster (e.g. total number of molecules, total number of atoms, total charge)

*If option '''[C]''', '''Y''' selected in step 9, each subdirectory '''cluster_n''' will contain:
::*The '''cluster_n.xyz''' coordinates file
::*'''system_info.txt''': Summary of the cluster (e.g. total number of molecules, total number of atoms, total charge)
::*The '''cluster_n.chm''' coordinates file. This will be used to create the '''cluster.pun''' ChemShell input file.
::*'''cluster_tiered.xyz''': xyz coordinates with the QM, active and frozen regions defined (all QM atoms listed as X1 (X=element symbol), active as X2 and frozen as X3). This file can be used to easily visualise the different regions in VMD.
::*'''conn.txt''' : the connectivity data needed by ChemShell
::*'''ff.dat''' : the forcefield in ChemShell format
::*'''opt.chm''': ChemShell input file. Options for the ChemShell optimisation specified here.

===Step-By-Step Example: Ionic Liquid Clusters===

Our example system:
* 256 ion pairs of [C4C1im][MeSO4]
* In total, the production run is 20ns in length; 4 lots of 5ns employing the "restart" keyword in DL_Poly.
* Our aim is to cut clusters from the last 5ns of the trajectory and create the input files for a ChemShell optimisation.

1). Create a directory within the main MolCluster directory and put the '''HISTORY''' and '''FIELD''' files here. Our directory will be called: '''BMIM_MESO4_EXAMPLE'''.

2). We now need to check to see if the HISTORY and FIELD files are in the correct format.

*As the ''restart'' keyword has been employed, two lines are missing from the header of the HISTORY file, '''Figure 1a''' and '''1b'''. MolCluster does not like this. Therefore, we need to add in the two lines that it is expecting to see, '''Figure 1c'''.

[[Image:MolCluster-HISTORY-header.png|frame|center|850px|'''Figure 1'''. Headers from selected HISTORY files '''(a)''' first 5ns of our simulation, without the use of the restart keyword, '''(b)''' last 5ns of our simulation with the restart keyword and '''(c)''' same HISTORY file as in (b), with missing lines added in. ]]

*The second problem we need to address is the atom labelling. The original atom labelling for [C4C1im][MeSO4], as used in the DL_Poly simulation, is shown in '''Figure 2a'''. Unfortunately, ChemShell has issues with this. To keep ChemShell happy, we have to change the atom labels in the HISTORY and FIELD files to the format ''elementsymbolnumber'' e.g. C2 rather than CR. Thankfully, this is quite easy to do using a script ('''sub_script.sh''', see below) written by Vincent. Firstly, however, we need to decide upon the new atom labelling. This is shown in '''Figure 2b''' for our example system. '''sub_script.sh''' requires that we have defined the atom label mappings in a file called '''sub_map.txt''' (also shown below for this system).

[[Image:BMIM-MESO4-numbering.png|thumb|center|850px|'''Figure 2'''. Original atom labelling (as used in DL_POLY MD simulation) shown in '''(a)''' and new atom labelling (suitable for MolCluster) shown in '''(b)'''. Within '''(b)''', atom labels that already had the correct format are in red. ]]

'''sub_script.sh''':

<pre>#!/bin/bash

while read line

do

#echo $line

s1=$(echo $line | awk '{ print $1 }')

s2=$(echo $line | awk '{ print $2 }')

echo "$s1 $s2"

gsed -i_bu2 "s|\<$s1\>|$s2|g" FIELD

gsed -i_bu2 "s|\<$s1\>|$s2|g" HISTORY

done < sub_map.txt</pre>

'''sub_map.txt''':
<pre>CR C3

NA N1

CW C4

HCR H2

HCW H3

HC H4

CT C6

OS4 O4

OC4 O5

HS4 H5

CS C5

CS4 C7</pre>

*Run '''./sub_script.sh'''
Note: this process may take a while, depending on the size of the file. Progress can be seen in the terminal (example shown in '''Figure 3'''), with each of the mappings specified in sub_map.txt considered in turn. The first few lines of the HISTORY file, before, and after, the relabelling can be seen in '''Figure 4'''.

[[Image:sub_map_mappings.png|thumb|center|800px|'''Figure 3'''. Example terminal output whilst running sub_script.sh ]]

[[Image:HISTORY-before-after.png|thumb|center|1000px|'''Figure 4'''. First few lines of the HISTORY file before '''(a)''' and after '''(b)''' the relabelling. ]]

3). Now our files are in the correct format, we can run MolCluster: '''./MolCluster.py'''

4). The first thing MolCluster does is to ask us to specify the directory containing the FIELD and HISTORY files. Our directory is called BMIM_MESO4_EXAMPLE. Once this has been specified, MolCluster will attempt to read the files and generate a summary of the system (from timestep 1 of the trajectory). This is shown in '''Figure 5''' for our system, and it can be seen that the information summarised by MolCluster is correct.

[[Image:MC-read-files-annotate.png|thumb|center|800px|'''Figure 5'''. After specifying the directory for the FIELD and HISTORY files, MolCluster summarises the bulk system information. ]]

5). MolCluster works out how many configurations in the HISTORY file (5000 in our example) and then asks us to specify the configurations we would like to cut a cluster from. In this case, we are going to select the '''[n]''' option (cut a cluster from every 'nth' configuration) and then specify n as an integer, in this case 1000 (i.e. n=1000, therefore cut a cluster every 1000th time step), '''Figure 6'''.

[[Image:MC-specify-config.png|thumb|center|800px|'''Figure 6'''. Specifying the configurations to create clusters for. ]]

6). We must now select how we would like to define the origin of the clusters to be cut. We are going to select option '''[AN]''' (atom number) and choose atom 1 to be the origin (for reference, in our case this is a C3 atom), '''Figure 7'''.

[[Image:origin-define.png|thumb|center|800px|'''Figure 7'''. Defining the cluster origin. ]]

7). An estimate of the number of atoms in regions with varying radii (with respect to our defined origin) is provided by MolCluster. We need to cut a cluster large enough to incorporate a reasonable number of ion pairs (bearing in mind that our cation alone, in all trans form, is over 9 Angstroms in width), but not so large that the calculation is unfeasible. The ideal size is still being investigated, but for now, let us specify a cluster radius of 15 Angstroms, '''Figure 8'''.

[[Image:cluster-radius-cut.png|thumb|center|900px|'''Figure 8'''. Choosing the cluster radius. ]]

8). MolCluster now asks us to tell it which boundary condition to use when cutting the clusters (essentially this is just how MolCluster will decide whether or not to include a molecule in the cluster for molecules at the boundary). We will select '''[S]''' (soft boundary) here. We are then asked to specify if the cluster needs to be neutral. Obviously this is only really applicable to charged systems (with counter ions), such as ionic liquids . We will select yes here, '''[Y]''', so that all our clusters have the same total charge, '''Figure 9'''.

[[Image:boundary-neutral.png|thumb|center|850px|'''Figure 9'''. Selecting boundary conditions. ]]

9). We now need to decide on the output file type. As the ultimate aim is to run QM/MM optimisations of our clusters, we need to select the options that will generate the ChemShell input files: '''[C]''', '''[Y]''', '''Figure 10'''.

[[Image:output-filetype.png|thumb|center|850px| ]]

10). A decision on how the QM region will be defined is now made. We are going to select '''[S]''' (spherical region). MolCluster then estimates the number of atoms in regions of varying radii with respect to our origin. Again, as with step 7, the optimum size has not yet been deduced. However, from previous tests, a QM radius of 7 Angstroms results in a manageable number of ions and is large enough to observe local structural features. Therefore, we shall specify a radius of 7 Angstroms in this example, '''Figure 11'''.

[[Image:QM-define.png|thumb|center|800px|'''Figure 11'''. QM region defined. ]]

11). After defining the QM region, we then need to define the size of the active region. Again MolCluster helps us by estimating the number of atoms for a range of radii. Molecules not included in the active region, will be in the Frozen region. Fir this example, we shall define the specify active region to have a radius of 11 Angstroms, '''Figure 12'''.

[[Image:Active-region .png|thumb|center|800px|'''Figure 12'''. Radius of active region specified. ]]

12). Finally, we are asked to specify the output directory where all our files will be placed, and the basename for each of our clusters. In this example the output directory will be ''BMIM_MESO4_EXAMPLE/example'' and the base name will be ''cluster'', '''Figure 13'''.

[[Image:Ouput-filenames.png|thumb|center|800px| ]]

13). MolCluster then sets about creating the clusters according to our specifications. The terminal output for the first cluster (cluster_1) is shown in '''Figure 14'''. After creating all the clusters, MolCluster will terminate.

[[Image:cluster_1.png|thumb|center|800px|'''Figure 14'''. Cluster_1 created. ]]

14). Within the named output directory, each cluster has it's own subdirectory: cluster_1, cluster_2 etc. Within each of the subdirectories can be found the requested output files, '''Figure 15'''.

[[Image:directory-files.png|thumb|center|1100px| ]]

15). The file called system_info.txt summarises key information relating to the cluster. This is shown in '''Figure 16''' for cluster 1. We can see that in total there are 72 molecules (36 cations and 36 anions) and that, as requested, the total charge of the system is zero.

File:Directory-files.png

2014-12-19T10:13:46Z

Ca307:

File:Cluster 1.png

2014-12-19T10:09:04Z

Ca307:

Talk:Mod:Hunt Research Group/MolCluster

2014-12-19T09:39:29Z

Ca307: /* Step-By-Step Example: Ionic Liquid Clusters */

===What is MolCluster?===
MolCluster is a tool (developed by Vincent and Gabriel) that can be used to cut clusters from MD trajectories and create the input files for ChemShell.

To use MolCluster, you will need:
* The latest version of MolCluster (available from Vincent).
* Python version 2.7.6, or above.
* The HISTORY file from which the clusters are to be cut, and the corresponding FIELD file. Note: these need to be in DL_POLY format. If you have used the 'restart' option in DL_POLY, the header of the HISTORY file may need to be amended. Additional transformations of the HISTORY and FIELD files, to convert atom labels into an acceptable format for MolCluster/ChemShell, may also be required (example given later).

===Using MolCluster: Basic Instructions===

1. Create a directory within the main MolCluster directory. Put the required HISTORY and FIELD files here.

2. Load MolCluster: ./MolCluster.py

3. Requests directory name to be specified (this is the location of the FIELD and HISTORY files). After specifying, the code will attempt to read and give an overview of the system.

4. Need to specify which configurations to cut a cluster from. Two options are currently available:
::*'''[n]''': Cut a cluster every "nth" configuration. N.B: numbering starts from 1 (i.e. 1st timestep). Therefore, if you request n=1000, clusters for configurations 1, 1001, 2001 etc. will be created.
::*'''[c]''': Select a custom set of configurations i.e. you can specify exactly which configurations you want.

5. Once the configurations have been extracted, you will be asked to choose how the origin will be defined in the clusters to be cut. Options are:
::*'''[AN]''': Atom number
::*'''[AT]''': Atom type
::*'''[MN]''': Molecule number
::*'''[MT]''': Molecule type
::*'''[C]''': Custom coordinates

You will then be asked to specify the specific atom number/type etc.

6. MolCluster will estimate the number of atoms within a region, for a range of radii with respect to your origin. Use this information to help you decide on the total radius (in Angstroms) of the clusters to be cut. You will be asked to specify this.

7. MolCluster has two options for deciding which molecules to include/exclude at the boundary of the clusters being cut:
::*'''[H]''': Hard boundary - all atoms of a molecule must be within the cutoff radius for the molecule to be included.
::*'''[S]''': Soft boundary - if the centre of mass of a molecule is within the cutoff radius, the molecule will be included.

8. Specify if the clusters are required to be neutral ('''Y/N''').

9. Decide on the output formats:
::*'''[C]''': Generates a ChemShell fragment input file, with accompanying .xyz co-ordinates file.
::*'''[X]''': Generates the .xyz co-ordinates file only.

If '''[X]''' selected, the clusters will be cut, .xyz files generated and MolCluster will terminate.

If '''[C]''' selected, you will be asked if you would also like to generate the necessary ChemShell input files for a QM/MM optimisation ('''Y/N''').

10. If your answer to step 9 was '''[C]''' (generate a ChemShell fragment input) and '''Y''' (generate ChemShell input files for a QM/MM optimisation), you will then be asked to define the QM region. Available options are:
::*'''[S]''': Spherical region (or threshold) centred about the defined origin (although not necessarily spherical??!!)
:::: If '''[S]''' selected, MolCluster will estimate the number of atoms in regions defined by a range of radii. Specify the QM radius. This must be specified (in Angstroms) and must, obviously, be less than, or equal to, the total radius of the cluster. Soft boundary conditions are implemented.
::*'''[M]''': By number of molecules. Molecules closest to the origin will be included.
::*'''[A]''': By an upper limit of atoms. Only whole molecules & those closest to the origin included.
::*'''[C]''': Custom region i.e. can select molecules individually to be in the QM region
::*'''[O]''': Spherical regions centred about one or more origins

If options '''[C]''' or '''[O]''' selected, MolCluster will go straight to steps 11 and 12. Once the active region and the directory/filenames have been defined, MolCluster will then ask for the custom QM regions to be defined ''per'' cluster (see step 14).

11. Once the QM region has been defined, the active region must be defined. MolCluster will estimate the number of atoms that would be in the active and frozen regions for a range of active radii. This information can be used to help decide upon an appropriate active radius. This must be specified (in Angstroms) and must, obviously, be less than, or equal to, the total radius of the cluster. If all atoms are to be included, simple enter "ALL". Soft boundary conditions are implemented.

12. Specify the output directory (i.e. where your final clusters and associated files will be saved) and specify the base-name for the output files (e.g. if you type "cluster" here, your clusters will be saved as cluster_1, cluster_2 etc.).

13. Unless options 10 '''[C'''] or '''[O]''' were selected (in that case, see point 14), MolCluster will generate the specified clusters and then terminate.

14. If option '''[C]''' selected in step 10, MolCluster will at this point list all the molecules in the first cluster, along with the distances to the origin. You will be asked to list all the molecules to be included in the QM region for this cluster. The same procedure is carried out for each cluster, before the clusters are generated and MolCluster terminates.

If option '''[O]''' selected in step 10, you will be asked to specify how many QM regions are to be defined and then specify the origin type and size of each QM region.

===The Output Files===
* Each cluster will have its own directory within the directory named in step 12. These subdirectories will be named: '''cluster_1''', '''cluster_2'''...'''cluster_n'''.
* Within the main directory one will also find a file called '''molcluster.log''' and a file called '''bulk_system_info.txt'''.
::*'''molcluster.log''' is a record of the user responses to each of the MolCluster options (look at this if you have forgotten, for example, the cluster radius).
::*'''bulk_system_info.txt''' summarises information relating to the system before clusters are cut (e.g. number and type of molecules, total number of atoms, total system charge, atom labels within a molecule, atomic charges).

*If option '''[X]''' selected in step 9, each subdirectory '''cluster_n''' will contain:
::*The '''cluster_n.xyz''' coordinates file
::*'''system_info.txt''': Summary of the cluster (e.g. total number of molecules, total number of atoms, total charge)

*If option '''[C]''', '''Y''' selected in step 9, each subdirectory '''cluster_n''' will contain:
::*The '''cluster_n.xyz''' coordinates file
::*'''system_info.txt''': Summary of the cluster (e.g. total number of molecules, total number of atoms, total charge)
::*The '''cluster_n.chm''' coordinates file. This will be used to create the '''cluster.pun''' ChemShell input file.
::*'''cluster_tiered.xyz''': xyz coordinates with the QM, active and frozen regions defined (all QM atoms listed as X1 (X=element symbol), active as X2 and frozen as X3). This file can be used to easily visualise the different regions in VMD.
::*'''conn.txt''' : the connectivity data needed by ChemShell
::*'''ff.dat''' : the forcefield in ChemShell format
::*'''opt.chm''': ChemShell input file. Options for the ChemShell optimisation specified here.

===Step-By-Step Example: Ionic Liquid Clusters===

Our example system:
* 256 ion pairs of [C4C1im][MeSO4]
* In total, the production run is 20ns in length; 4 lots of 5ns employing the "restart" keyword in DL_Poly.
* Our aim is to cut clusters from the last 5ns of the trajectory and create the input files for a ChemShell optimisation.

1). Create a directory within the main MolCluster directory and put the '''HISTORY''' and '''FIELD''' files here. Our directory will be called: '''BMIM_MESO4_EXAMPLE'''.

2). We now need to check to see if the HISTORY and FIELD files are in the correct format.

*As the ''restart'' keyword has been employed, two lines are missing from the header of the HISTORY file, '''Figure 1a''' and '''1b'''. MolCluster does not like this. Therefore, we need to add in the two lines that it is expecting to see, '''Figure 1c'''.

[[Image:MolCluster-HISTORY-header.png|frame|center|850px|'''Figure 1'''. Headers from selected HISTORY files '''(a)''' first 5ns of our simulation, without the use of the restart keyword, '''(b)''' last 5ns of our simulation with the restart keyword and '''(c)''' same HISTORY file as in (b), with missing lines added in. ]]

*The second problem we need to address is the atom labelling. The original atom labelling for [C4C1im][MeSO4], as used in the DL_Poly simulation, is shown in '''Figure 2a'''. Unfortunately, ChemShell has issues with this. To keep ChemShell happy, we have to change the atom labels in the HISTORY and FIELD files to the format ''elementsymbolnumber'' e.g. C2 rather than CR. Thankfully, this is quite easy to do using a script ('''sub_script.sh''', see below) written by Vincent. Firstly, however, we need to decide upon the new atom labelling. This is shown in '''Figure 2b''' for our example system. '''sub_script.sh''' requires that we have defined the atom label mappings in a file called '''sub_map.txt''' (also shown below for this system).

[[Image:BMIM-MESO4-numbering.png|thumb|center|850px|'''Figure 2'''. Original atom labelling (as used in DL_POLY MD simulation) shown in '''(a)''' and new atom labelling (suitable for MolCluster) shown in '''(b)'''. Within '''(b)''', atom labels that already had the correct format are in red. ]]

'''sub_script.sh''':

<pre>#!/bin/bash

while read line

do

#echo $line

s1=$(echo $line | awk '{ print $1 }')

s2=$(echo $line | awk '{ print $2 }')

echo "$s1 $s2"

gsed -i_bu2 "s|\<$s1\>|$s2|g" FIELD

gsed -i_bu2 "s|\<$s1\>|$s2|g" HISTORY

done < sub_map.txt</pre>

'''sub_map.txt''':
<pre>CR C3

NA N1

CW C4

HCR H2

HCW H3

HC H4

CT C6

OS4 O4

OC4 O5

HS4 H5

CS C5

CS4 C7</pre>

*Run '''./sub_script.sh'''
Note: this process may take a while, depending on the size of the file. Progress can be seen in the terminal (example shown in '''Figure 3'''), with each of the mappings specified in sub_map.txt considered in turn. The first few lines of the HISTORY file, before, and after, the relabelling can be seen in '''Figure 4'''.

[[Image:sub_map_mappings.png|thumb|center|800px|'''Figure 3'''. Example terminal output whilst running sub_script.sh ]]

[[Image:HISTORY-before-after.png|thumb|center|1000px|'''Figure 4'''. First few lines of the HISTORY file before '''(a)''' and after '''(b)''' the relabelling. ]]

3). Now our files are in the correct format, we can run MolCluster: '''./MolCluster.py'''

4). The first thing MolCluster does is to ask us to specify the directory containing the FIELD and HISTORY files. Our directory is called BMIM_MESO4_EXAMPLE. Once this has been specified, MolCluster will attempt to read the files and generate a summary of the system (from timestep 1 of the trajectory). This is shown in '''Figure 5''' for our system, and it can be seen that the information summarised by MolCluster is correct.

[[Image:MC-read-files-annotate.png|thumb|center|800px|'''Figure 5'''. After specifying the directory for the FIELD and HISTORY files, MolCluster summarises the bulk system information. ]]

5). MolCluster works out how many configurations in the HISTORY file (5000 in our example) and then asks us to specify the configurations we would like to cut a cluster from. In this case, we are going to select the '''[n]''' option (cut a cluster from every 'nth' configuration) and then specify n as an integer, in this case 1000 (i.e. n=1000, therefore cut a cluster every 1000th time step), '''Figure 6'''.

[[Image:MC-specify-config.png|thumb|center|800px|'''Figure 6'''. Specifying the configurations to create clusters for. ]]

6). We must now select how we would like to define the origin of the clusters to be cut. We are going to select option '''[AN]''' (atom number) and choose atom 1 to be the origin (for reference, in our case this is a C3 atom), '''Figure 7'''.

[[Image:origin-define.png|thumb|center|800px|'''Figure 7'''. Defining the cluster origin. ]]

7). An estimate of the number of atoms in regions with varying radii (with respect to our defined origin) is provided by MolCluster. We need to cut a cluster large enough to incorporate a reasonable number of ion pairs (bearing in mind that our cation alone, in all trans form, is over 9 Angstroms in width), but not so large that the calculation is unfeasible. The ideal size is still being investigated, but for now, let us specify a cluster radius of 15 Angstroms, '''Figure 8'''.

[[Image:cluster-radius-cut.png|thumb|center|900px|'''Figure 8'''. Choosing the cluster radius. ]]

8). MolCluster now asks us to tell it which boundary condition to use when cutting the clusters (essentially this is just how MolCluster will decide whether or not to include a molecule in the cluster for molecules at the boundary). We will select '''[S]''' (soft boundary) here. We are then asked to specify if the cluster needs to be neutral. Obviously this is only really applicable to charged systems (with counter ions), such as ionic liquids . We will select yes here, '''[Y]''', so that all our clusters have the same total charge, '''Figure 9'''.

[[Image:boundary-neutral.png|thumb|center|850px|'''Figure 9'''. Selecting boundary conditions. ]]

9). We now need to decide on the output file type. As the ultimate aim is to run QM/MM optimisations of our clusters, we need to select the options that will generate the ChemShell input files: '''[C]''', '''[Y]''', '''Figure 10'''.

[[Image:output-filetype.png|thumb|center|850px| ]]

10). A decision on how the QM region will be defined is now made. We are going to select '''[S]''' (spherical region). MolCluster then estimates the number of atoms in regions of varying radii with respect to our origin. Again, as with step 7, the optimum size has not yet been deduced. However, from previous tests, a QM radius of 7 Angstroms results in a manageable number of ions and is large enough to observe local structural features. Therefore, we shall specify a radius of 7 Angstroms in this example, '''Figure 11'''.

[[Image:QM-define.png|thumb|center|800px|'''Figure 11'''. QM region defined. ]]

11). After defining the QM region, we then need to define the size of the active region. Again MolCluster helps us by estimating the number of atoms for a range of radii. Molecules not included in the active region, will be in the Frozen region. Fir this example, we shall define the specify active region to have a radius of 11 Angstroms, '''Figure 12'''.

[[Image:Active-region .png|thumb|center|800px|'''Figure 12'''. Radius of active region specified. ]]

12). Finally, we are asked to specify the output directory where all our files will be placed, and the basename for each of our clusters. In this example the output directory will be ''BMIM_MESO4_EXAMPLE/example'' and the base name will be ''cluster'', '''Figure 13'''.

[[Image:Ouput-filenames.png|thumb|center|800px| ]]

13). MolCluster then sets about creating the clusters according to our specifications. The terminal output for the first cluster (cluster_1) is shown in '''Figure 14'''. After creating all the clusters, MolCluster will terminate.

File:Ouput-filenames.png

2014-12-19T09:36:06Z

Ca307:

Talk:Mod:Hunt Research Group/MolCluster

2014-12-19T09:24:28Z

Ca307: /* Step-By-Step Example: Ionic Liquid Clusters */

===What is MolCluster?===
MolCluster is a tool (developed by Vincent and Gabriel) that can be used to cut clusters from MD trajectories and create the input files for ChemShell.

To use MolCluster, you will need:
* The latest version of MolCluster (available from Vincent).
* Python version 2.7.6, or above.
* The HISTORY file from which the clusters are to be cut, and the corresponding FIELD file. Note: these need to be in DL_POLY format. If you have used the 'restart' option in DL_POLY, the header of the HISTORY file may need to be amended. Additional transformations of the HISTORY and FIELD files, to convert atom labels into an acceptable format for MolCluster/ChemShell, may also be required (example given later).

===Using MolCluster: Basic Instructions===

1. Create a directory within the main MolCluster directory. Put the required HISTORY and FIELD files here.

2. Load MolCluster: ./MolCluster.py

3. Requests directory name to be specified (this is the location of the FIELD and HISTORY files). After specifying, the code will attempt to read and give an overview of the system.

4. Need to specify which configurations to cut a cluster from. Two options are currently available:
::*'''[n]''': Cut a cluster every "nth" configuration. N.B: numbering starts from 1 (i.e. 1st timestep). Therefore, if you request n=1000, clusters for configurations 1, 1001, 2001 etc. will be created.
::*'''[c]''': Select a custom set of configurations i.e. you can specify exactly which configurations you want.

5. Once the configurations have been extracted, you will be asked to choose how the origin will be defined in the clusters to be cut. Options are:
::*'''[AN]''': Atom number
::*'''[AT]''': Atom type
::*'''[MN]''': Molecule number
::*'''[MT]''': Molecule type
::*'''[C]''': Custom coordinates

You will then be asked to specify the specific atom number/type etc.

6. MolCluster will estimate the number of atoms within a region, for a range of radii with respect to your origin. Use this information to help you decide on the total radius (in Angstroms) of the clusters to be cut. You will be asked to specify this.

7. MolCluster has two options for deciding which molecules to include/exclude at the boundary of the clusters being cut:
::*'''[H]''': Hard boundary - all atoms of a molecule must be within the cutoff radius for the molecule to be included.
::*'''[S]''': Soft boundary - if the centre of mass of a molecule is within the cutoff radius, the molecule will be included.

8. Specify if the clusters are required to be neutral ('''Y/N''').

9. Decide on the output formats:
::*'''[C]''': Generates a ChemShell fragment input file, with accompanying .xyz co-ordinates file.
::*'''[X]''': Generates the .xyz co-ordinates file only.

If '''[X]''' selected, the clusters will be cut, .xyz files generated and MolCluster will terminate.

If '''[C]''' selected, you will be asked if you would also like to generate the necessary ChemShell input files for a QM/MM optimisation ('''Y/N''').

10. If your answer to step 9 was '''[C]''' (generate a ChemShell fragment input) and '''Y''' (generate ChemShell input files for a QM/MM optimisation), you will then be asked to define the QM region. Available options are:
::*'''[S]''': Spherical region (or threshold) centred about the defined origin (although not necessarily spherical??!!)
:::: If '''[S]''' selected, MolCluster will estimate the number of atoms in regions defined by a range of radii. Specify the QM radius. This must be specified (in Angstroms) and must, obviously, be less than, or equal to, the total radius of the cluster. Soft boundary conditions are implemented.
::*'''[M]''': By number of molecules. Molecules closest to the origin will be included.
::*'''[A]''': By an upper limit of atoms. Only whole molecules & those closest to the origin included.
::*'''[C]''': Custom region i.e. can select molecules individually to be in the QM region
::*'''[O]''': Spherical regions centred about one or more origins

If options '''[C]''' or '''[O]''' selected, MolCluster will go straight to steps 11 and 12. Once the active region and the directory/filenames have been defined, MolCluster will then ask for the custom QM regions to be defined ''per'' cluster (see step 14).

11. Once the QM region has been defined, the active region must be defined. MolCluster will estimate the number of atoms that would be in the active and frozen regions for a range of active radii. This information can be used to help decide upon an appropriate active radius. This must be specified (in Angstroms) and must, obviously, be less than, or equal to, the total radius of the cluster. If all atoms are to be included, simple enter "ALL". Soft boundary conditions are implemented.

12. Specify the output directory (i.e. where your final clusters and associated files will be saved) and specify the base-name for the output files (e.g. if you type "cluster" here, your clusters will be saved as cluster_1, cluster_2 etc.).

13. Unless options 10 '''[C'''] or '''[O]''' were selected (in that case, see point 14), MolCluster will generate the specified clusters and then terminate.

14. If option '''[C]''' selected in step 10, MolCluster will at this point list all the molecules in the first cluster, along with the distances to the origin. You will be asked to list all the molecules to be included in the QM region for this cluster. The same procedure is carried out for each cluster, before the clusters are generated and MolCluster terminates.

If option '''[O]''' selected in step 10, you will be asked to specify how many QM regions are to be defined and then specify the origin type and size of each QM region.

===The Output Files===
* Each cluster will have its own directory within the directory named in step 12. These subdirectories will be named: '''cluster_1''', '''cluster_2'''...'''cluster_n'''.
* Within the main directory one will also find a file called '''molcluster.log''' and a file called '''bulk_system_info.txt'''.
::*'''molcluster.log''' is a record of the user responses to each of the MolCluster options (look at this if you have forgotten, for example, the cluster radius).
::*'''bulk_system_info.txt''' summarises information relating to the system before clusters are cut (e.g. number and type of molecules, total number of atoms, total system charge, atom labels within a molecule, atomic charges).

*If option '''[X]''' selected in step 9, each subdirectory '''cluster_n''' will contain:
::*The '''cluster_n.xyz''' coordinates file
::*'''system_info.txt''': Summary of the cluster (e.g. total number of molecules, total number of atoms, total charge)

*If option '''[C]''', '''Y''' selected in step 9, each subdirectory '''cluster_n''' will contain:
::*The '''cluster_n.xyz''' coordinates file
::*'''system_info.txt''': Summary of the cluster (e.g. total number of molecules, total number of atoms, total charge)
::*The '''cluster_n.chm''' coordinates file. This will be used to create the '''cluster.pun''' ChemShell input file.
::*'''cluster_tiered.xyz''': xyz coordinates with the QM, active and frozen regions defined (all QM atoms listed as X1 (X=element symbol), active as X2 and frozen as X3). This file can be used to easily visualise the different regions in VMD.
::*'''conn.txt''' : the connectivity data needed by ChemShell
::*'''ff.dat''' : the forcefield in ChemShell format
::*'''opt.chm''': ChemShell input file. Options for the ChemShell optimisation specified here.

===Step-By-Step Example: Ionic Liquid Clusters===

Our example system:
* 256 ion pairs of [C4C1im][MeSO4]
* In total, the production run is 20ns in length; 4 lots of 5ns employing the "restart" keyword in DL_Poly.
* Our aim is to cut clusters from the last 5ns of the trajectory and create the input files for a ChemShell optimisation.

1). Create a directory within the main MolCluster directory and put the '''HISTORY''' and '''FIELD''' files here. Our directory will be called: '''BMIM_MESO4_EXAMPLE'''.

2). We now need to check to see if the HISTORY and FIELD files are in the correct format.

*As the ''restart'' keyword has been employed, two lines are missing from the header of the HISTORY file, '''Figure 1a''' and '''1b'''. MolCluster does not like this. Therefore, we need to add in the two lines that it is expecting to see, '''Figure 1c'''.

[[Image:MolCluster-HISTORY-header.png|frame|center|850px|'''Figure 1'''. Headers from selected HISTORY files '''(a)''' first 5ns of our simulation, without the use of the restart keyword, '''(b)''' last 5ns of our simulation with the restart keyword and '''(c)''' same HISTORY file as in (b), with missing lines added in. ]]

*The second problem we need to address is the atom labelling. The original atom labelling for [C4C1im][MeSO4], as used in the DL_Poly simulation, is shown in '''Figure 2a'''. Unfortunately, ChemShell has issues with this. To keep ChemShell happy, we have to change the atom labels in the HISTORY and FIELD files to the format ''elementsymbolnumber'' e.g. C2 rather than CR. Thankfully, this is quite easy to do using a script ('''sub_script.sh''', see below) written by Vincent. Firstly, however, we need to decide upon the new atom labelling. This is shown in '''Figure 2b''' for our example system. '''sub_script.sh''' requires that we have defined the atom label mappings in a file called '''sub_map.txt''' (also shown below for this system).

[[Image:BMIM-MESO4-numbering.png|thumb|center|850px|'''Figure 2'''. Original atom labelling (as used in DL_POLY MD simulation) shown in '''(a)''' and new atom labelling (suitable for MolCluster) shown in '''(b)'''. Within '''(b)''', atom labels that already had the correct format are in red. ]]

'''sub_script.sh''':

<pre>#!/bin/bash

while read line

do

#echo $line

s1=$(echo $line | awk '{ print $1 }')

s2=$(echo $line | awk '{ print $2 }')

echo "$s1 $s2"

gsed -i_bu2 "s|\<$s1\>|$s2|g" FIELD

gsed -i_bu2 "s|\<$s1\>|$s2|g" HISTORY

done < sub_map.txt</pre>

'''sub_map.txt''':
<pre>CR C3

NA N1

CW C4

HCR H2

HCW H3

HC H4

CT C6

OS4 O4

OC4 O5

HS4 H5

CS C5

CS4 C7</pre>

*Run '''./sub_script.sh'''
Note: this process may take a while, depending on the size of the file. Progress can be seen in the terminal (example shown in '''Figure 3'''), with each of the mappings specified in sub_map.txt considered in turn. The first few lines of the HISTORY file, before, and after, the relabelling can be seen in '''Figure 4'''.

[[Image:sub_map_mappings.png|thumb|center|800px|'''Figure 3'''. Example terminal output whilst running sub_script.sh ]]

[[Image:HISTORY-before-after.png|thumb|center|1000px|'''Figure 4'''. First few lines of the HISTORY file before '''(a)''' and after '''(b)''' the relabelling. ]]

3). Now our files are in the correct format, we can run MolCluster: '''./MolCluster.py'''

4). The first thing MolCluster does is to ask us to specify the directory containing the FIELD and HISTORY files. Our directory is called BMIM_MESO4_EXAMPLE. Once this has been specified, MolCluster will attempt to read the files and generate a summary of the system (from timestep 1 of the trajectory). This is shown in '''Figure 5''' for our system, and it can be seen that the information summarised by MolCluster is correct.

[[Image:MC-read-files-annotate.png|thumb|center|800px|'''Figure 5'''. After specifying the directory for the FIELD and HISTORY files, MolCluster summarises the bulk system information. ]]

5). MolCluster works out how many configurations in the HISTORY file (5000 in our example) and then asks us to specify the configurations we would like to cut a cluster from. In this case, we are going to select the '''[n]''' option (cut a cluster from every 'nth' configuration) and then specify n as an integer, in this case 1000 (i.e. n=1000, therefore cut a cluster every 1000th time step), '''Figure 6'''.

[[Image:MC-specify-config.png|thumb|center|800px|'''Figure 6'''. Specifying the configurations to create clusters for. ]]

6). We must now select how we would like to define the origin of the clusters to be cut. We are going to select option '''[AN]''' (atom number) and choose atom 1 to be the origin (for reference, in our case this is a C3 atom), '''Figure 7'''.

[[Image:origin-define.png|thumb|center|800px|'''Figure 7'''. Defining the cluster origin. ]]

7). An estimate of the number of atoms in regions with varying radii (with respect to our defined origin) is provided by MolCluster. We need to cut a cluster large enough to incorporate a reasonable number of ion pairs (bearing in mind that our cation alone, in all trans form, is over 9 Angstroms in width), but not so large that the calculation is unfeasible. The ideal size is still being investigated, but for now, let us specify a cluster radius of 15 Angstroms, '''Figure 8'''.

[[Image:cluster-radius-cut.png|thumb|center|900px|'''Figure 8'''. Choosing the cluster radius. ]]

8). MolCluster now asks us to tell it which boundary condition to use when cutting the clusters (essentially this is just how MolCluster will decide whether or not to include a molecule in the cluster for molecules at the boundary). We will select '''[S]''' (soft boundary) here. We are then asked to specify if the cluster needs to be neutral. Obviously this is only really applicable to charged systems (with counter ions), such as ionic liquids . We will select yes here, '''[Y]''', so that all our clusters have the same total charge, '''Figure 9'''.

[[Image:boundary-neutral.png|thumb|center|850px|'''Figure 9'''. Selecting boundary conditions. ]]

9). We now need to decide on the output file type. As the ultimate aim is to run QM/MM optimisations of our clusters, we need to select the options that will generate the ChemShell input files: '''[C]''', '''[Y]''', '''Figure 10'''.

[[Image:output-filetype.png|thumb|center|850px| ]]

10). A decision on how the QM region will be defined is now made. We are going to select '''[S]''' (spherical region). MolCluster then estimates the number of atoms in regions of varying radii with respect to our origin. Again, as with step 7, the optimum size has not yet been deduced. However, from previous tests, a QM radius of 7 Angstroms results in a manageable number of ions and is large enough to observe local structural features. Therefore, we shall specify a radius of 7 Angstroms in this example, '''Figure 11'''.

[[Image:QM-define.png|thumb|center|800px|'''Figure 11'''. QM region defined. ]]

11). After defining the QM region, we then need to define the size of the active region. Again MolCluster helps us by estimating the number of atoms for a range of radii. Molecules not included in the active region, will be in the Frozen region. Fir this example, we shall define the specify active region to have a radius of 11 Angstroms, '''Figure 12'''.

[[Image:Active-region .png|thumb|center|800px|'''Figure 12'''. Radius of active region specified. ]]

File:Active-region .png

2014-12-19T09:22:53Z

Ca307:

File:QM-define.png

2014-12-19T09:09:43Z

Ca307:

Talk:Mod:Hunt Research Group/MolCluster

2014-12-19T09:04:52Z

Ca307: /* Step-By-Step Example: Ionic Liquid Clusters */

===What is MolCluster?===
MolCluster is a tool (developed by Vincent and Gabriel) that can be used to cut clusters from MD trajectories and create the input files for ChemShell.

To use MolCluster, you will need:
* The latest version of MolCluster (available from Vincent).
* Python version 2.7.6, or above.
* The HISTORY file from which the clusters are to be cut, and the corresponding FIELD file. Note: these need to be in DL_POLY format. If you have used the 'restart' option in DL_POLY, the header of the HISTORY file may need to be amended. Additional transformations of the HISTORY and FIELD files, to convert atom labels into an acceptable format for MolCluster/ChemShell, may also be required (example given later).

===Using MolCluster: Basic Instructions===

1. Create a directory within the main MolCluster directory. Put the required HISTORY and FIELD files here.

2. Load MolCluster: ./MolCluster.py

3. Requests directory name to be specified (this is the location of the FIELD and HISTORY files). After specifying, the code will attempt to read and give an overview of the system.

4. Need to specify which configurations to cut a cluster from. Two options are currently available:
::*'''[n]''': Cut a cluster every "nth" configuration. N.B: numbering starts from 1 (i.e. 1st timestep). Therefore, if you request n=1000, clusters for configurations 1, 1001, 2001 etc. will be created.
::*'''[c]''': Select a custom set of configurations i.e. you can specify exactly which configurations you want.

5. Once the configurations have been extracted, you will be asked to choose how the origin will be defined in the clusters to be cut. Options are:
::*'''[AN]''': Atom number
::*'''[AT]''': Atom type
::*'''[MN]''': Molecule number
::*'''[MT]''': Molecule type
::*'''[C]''': Custom coordinates

You will then be asked to specify the specific atom number/type etc.

6. MolCluster will estimate the number of atoms within a region, for a range of radii with respect to your origin. Use this information to help you decide on the total radius (in Angstroms) of the clusters to be cut. You will be asked to specify this.

7. MolCluster has two options for deciding which molecules to include/exclude at the boundary of the clusters being cut:
::*'''[H]''': Hard boundary - all atoms of a molecule must be within the cutoff radius for the molecule to be included.
::*'''[S]''': Soft boundary - if the centre of mass of a molecule is within the cutoff radius, the molecule will be included.

8. Specify if the clusters are required to be neutral ('''Y/N''').

9. Decide on the output formats:
::*'''[C]''': Generates a ChemShell fragment input file, with accompanying .xyz co-ordinates file.
::*'''[X]''': Generates the .xyz co-ordinates file only.

If '''[X]''' selected, the clusters will be cut, .xyz files generated and MolCluster will terminate.

If '''[C]''' selected, you will be asked if you would also like to generate the necessary ChemShell input files for a QM/MM optimisation ('''Y/N''').

10. If your answer to step 9 was '''[C]''' (generate a ChemShell fragment input) and '''Y''' (generate ChemShell input files for a QM/MM optimisation), you will then be asked to define the QM region. Available options are:
::*'''[S]''': Spherical region (or threshold) centred about the defined origin (although not necessarily spherical??!!)
:::: If '''[S]''' selected, MolCluster will estimate the number of atoms in regions defined by a range of radii. Specify the QM radius. This must be specified (in Angstroms) and must, obviously, be less than, or equal to, the total radius of the cluster. Soft boundary conditions are implemented.
::*'''[M]''': By number of molecules. Molecules closest to the origin will be included.
::*'''[A]''': By an upper limit of atoms. Only whole molecules & those closest to the origin included.
::*'''[C]''': Custom region i.e. can select molecules individually to be in the QM region
::*'''[O]''': Spherical regions centred about one or more origins

If options '''[C]''' or '''[O]''' selected, MolCluster will go straight to steps 11 and 12. Once the active region and the directory/filenames have been defined, MolCluster will then ask for the custom QM regions to be defined ''per'' cluster (see step 14).

11. Once the QM region has been defined, the active region must be defined. MolCluster will estimate the number of atoms that would be in the active and frozen regions for a range of active radii. This information can be used to help decide upon an appropriate active radius. This must be specified (in Angstroms) and must, obviously, be less than, or equal to, the total radius of the cluster. If all atoms are to be included, simple enter "ALL". Soft boundary conditions are implemented.

12. Specify the output directory (i.e. where your final clusters and associated files will be saved) and specify the base-name for the output files (e.g. if you type "cluster" here, your clusters will be saved as cluster_1, cluster_2 etc.).

13. Unless options 10 '''[C'''] or '''[O]''' were selected (in that case, see point 14), MolCluster will generate the specified clusters and then terminate.

14. If option '''[C]''' selected in step 10, MolCluster will at this point list all the molecules in the first cluster, along with the distances to the origin. You will be asked to list all the molecules to be included in the QM region for this cluster. The same procedure is carried out for each cluster, before the clusters are generated and MolCluster terminates.

If option '''[O]''' selected in step 10, you will be asked to specify how many QM regions are to be defined and then specify the origin type and size of each QM region.

===The Output Files===
* Each cluster will have its own directory within the directory named in step 12. These subdirectories will be named: '''cluster_1''', '''cluster_2'''...'''cluster_n'''.
* Within the main directory one will also find a file called '''molcluster.log''' and a file called '''bulk_system_info.txt'''.
::*'''molcluster.log''' is a record of the user responses to each of the MolCluster options (look at this if you have forgotten, for example, the cluster radius).
::*'''bulk_system_info.txt''' summarises information relating to the system before clusters are cut (e.g. number and type of molecules, total number of atoms, total system charge, atom labels within a molecule, atomic charges).

*If option '''[X]''' selected in step 9, each subdirectory '''cluster_n''' will contain:
::*The '''cluster_n.xyz''' coordinates file
::*'''system_info.txt''': Summary of the cluster (e.g. total number of molecules, total number of atoms, total charge)

*If option '''[C]''', '''Y''' selected in step 9, each subdirectory '''cluster_n''' will contain:
::*The '''cluster_n.xyz''' coordinates file
::*'''system_info.txt''': Summary of the cluster (e.g. total number of molecules, total number of atoms, total charge)
::*The '''cluster_n.chm''' coordinates file. This will be used to create the '''cluster.pun''' ChemShell input file.
::*'''cluster_tiered.xyz''': xyz coordinates with the QM, active and frozen regions defined (all QM atoms listed as X1 (X=element symbol), active as X2 and frozen as X3). This file can be used to easily visualise the different regions in VMD.
::*'''conn.txt''' : the connectivity data needed by ChemShell
::*'''ff.dat''' : the forcefield in ChemShell format
::*'''opt.chm''': ChemShell input file. Options for the ChemShell optimisation specified here.

===Step-By-Step Example: Ionic Liquid Clusters===

Our example system:
* 256 ion pairs of [C4C1im][MeSO4]
* In total, the production run is 20ns in length; 4 lots of 5ns employing the "restart" keyword in DL_Poly.
* Our aim is to cut clusters from the last 5ns of the trajectory and create the input files for a ChemShell optimisation.

1). Create a directory within the main MolCluster directory and put the '''HISTORY''' and '''FIELD''' files here. Our directory will be called: '''BMIM_MESO4_EXAMPLE'''.

2). We now need to check to see if the HISTORY and FIELD files are in the correct format.

*As the ''restart'' keyword has been employed, two lines are missing from the header of the HISTORY file, '''Figure 1a''' and '''1b'''. MolCluster does not like this. Therefore, we need to add in the two lines that it is expecting to see, '''Figure 1c'''.

[[Image:MolCluster-HISTORY-header.png|frame|center|850px|'''Figure 1'''. Headers from selected HISTORY files '''(a)''' first 5ns of our simulation, without the use of the restart keyword, '''(b)''' last 5ns of our simulation with the restart keyword and '''(c)''' same HISTORY file as in (b), with missing lines added in. ]]

*The second problem we need to address is the atom labelling. The original atom labelling for [C4C1im][MeSO4], as used in the DL_Poly simulation, is shown in '''Figure 2a'''. Unfortunately, ChemShell has issues with this. To keep ChemShell happy, we have to change the atom labels in the HISTORY and FIELD files to the format ''elementsymbolnumber'' e.g. C2 rather than CR. Thankfully, this is quite easy to do using a script ('''sub_script.sh''', see below) written by Vincent. Firstly, however, we need to decide upon the new atom labelling. This is shown in '''Figure 2b''' for our example system. '''sub_script.sh''' requires that we have defined the atom label mappings in a file called '''sub_map.txt''' (also shown below for this system).

[[Image:BMIM-MESO4-numbering.png|thumb|center|850px|'''Figure 2'''. Original atom labelling (as used in DL_POLY MD simulation) shown in '''(a)''' and new atom labelling (suitable for MolCluster) shown in '''(b)'''. Within '''(b)''', atom labels that already had the correct format are in red. ]]

'''sub_script.sh''':

<pre>#!/bin/bash

while read line

do

#echo $line

s1=$(echo $line | awk '{ print $1 }')

s2=$(echo $line | awk '{ print $2 }')

echo "$s1 $s2"

gsed -i_bu2 "s|\<$s1\>|$s2|g" FIELD

gsed -i_bu2 "s|\<$s1\>|$s2|g" HISTORY

done < sub_map.txt</pre>

'''sub_map.txt''':
<pre>CR C3

NA N1

CW C4

HCR H2

HCW H3

HC H4

CT C6

OS4 O4

OC4 O5

HS4 H5

CS C5

CS4 C7</pre>

*Run '''./sub_script.sh'''
Note: this process may take a while, depending on the size of the file. Progress can be seen in the terminal (example shown in '''Figure 3'''), with each of the mappings specified in sub_map.txt considered in turn. The first few lines of the HISTORY file, before, and after, the relabelling can be seen in '''Figure 4'''.

[[Image:sub_map_mappings.png|thumb|center|800px|'''Figure 3'''. Example terminal output whilst running sub_script.sh ]]

[[Image:HISTORY-before-after.png|thumb|center|1000px|'''Figure 4'''. First few lines of the HISTORY file before '''(a)''' and after '''(b)''' the relabelling. ]]

3). Now our files are in the correct format, we can run MolCluster: '''./MolCluster.py'''

4). The first thing MolCluster does is to ask us to specify the directory containing the FIELD and HISTORY files. Our directory is called BMIM_MESO4_EXAMPLE. Once this has been specified, MolCluster will attempt to read the files and generate a summary of the system (from timestep 1 of the trajectory). This is shown in '''Figure 5''' for our system, and it can be seen that the information summarised by MolCluster is correct.

[[Image:MC-read-files-annotate.png|thumb|center|800px|'''Figure 5'''. After specifying the directory for the FIELD and HISTORY files, MolCluster summarises the bulk system information. ]]

5). MolCluster works out how many configurations in the HISTORY file (5000 in our example) and then asks us to specify the configurations we would like to cut a cluster from. In this case, we are going to select the '''[n]''' option (cut a cluster from every 'nth' configuration) and then specify n as an integer, in this case 1000 (i.e. n=1000, therefore cut a cluster every 1000th time step), '''Figure 6'''.

[[Image:MC-specify-config.png|thumb|center|800px|'''Figure 6'''. Specifying the configurations to create clusters for. ]]

6). We must now select how we would like to define the origin of the clusters to be cut. We are going to select option '''[AN]''' (atom number) and choose atom 1 to be the origin (for reference, in our case this is a C3 atom), '''Figure 7'''.

[[Image:origin-define.png|thumb|center|800px|'''Figure 7'''. Defining the cluster origin. ]]

7). An estimate of the number of atoms in regions with varying radii (with respect to our defined origin) is provided by MolCluster. We need to cut a cluster large enough to incorporate a reasonable number of ion pairs (bearing in mind that our cation alone, in all trans form, is over 9 Angstroms in width), but not so large that the calculation is unfeasible. The ideal size is still being investigated, but for now, let us specify a cluster radius of 15 Angstroms, '''Figure 8'''.

[[Image:cluster-radius-cut.png|thumb|center|900px|'''Figure 8'''. Choosing the cluster radius. ]]

8). MolCluster now asks us to tell it which boundary condition to use when cutting the clusters (essentially this is just how MolCluster will decide whether or not to include a molecule in the cluster for molecules at the boundary). We will select '''[S]''' (soft boundary) here. We are then asked to specify if the cluster needs to be neutral. Obviously this is only really applicable to charged systems (with counter ions), such as ionic liquids . We will select yes here, '''[Y]''', so that all our clusters have the same total charge, '''Figure 9'''.

[[Image:boundary-neutral.png|thumb|center|850px|'''Figure 9'''. Selecting boundary conditions. ]]

9). We now need to decide on the output file type. As the ultimate aim is to run QM/MM optimisations of our clusters, we need to select the options that will generate the ChemShell input files: '''[C]''', '''[Y]''', '''Figure 10'''.

[[Image:output-filetype.png|thumb|center|850px| ]]

10). A decision on how the QM region will be defined is now made. We are going to select '''[S]''' (spherical region). MolCluster then estimates the number of atoms in regions of varying radii with respect to our origin. Again, as with step 7, the optimum size has not yet been deduced. However, from previous tests, a QM radius of 7 Angstroms results in a manageable number of ions and is large enough to observe local structural features. Therefore, we shall specify a radius of 7 Angstroms in this example, '''Figure 11'''.

File:Output-filetype.png

2014-12-19T08:57:02Z

Ca307:

Mod:Hunt Research Group/calendar

2014-12-18T11:25:02Z

Ca307:

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)
| Matthew Clough (Not Done)
| Bryan Ward (Done)
| Claire Ashworth (Done)
|-
| Precious Ugbomah (Done)
| Richard Matthews (Done)
| Vincent Chen (Done)
| Gabriel Lau (Done)
|-
| Rebecca Rowe (Not Done)
| Patricia Ho (Done)
| Ken Watson (Done)
| Laila Bana (Done)
|-
| Oliver Benton (Not Done)
|Christopher Sewell (Not Done)
|Chen Chen (Done)
|Aiswarya Prabha (Done)
|-
|-)
|}

<table border="1" cellpadding="5" width="1190">
<tr bgcolor="#66CCFF">
<th width="170px">Mon</th>
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<th width="170px">Wed</th>
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<th width="170px" bgcolor="#CCCCCC">Sat</th>
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</tr>
<tr valign="top">
<td bgcolor="#4357CFF">'''1st December''' </td>
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</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>
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</tr>
<tr valign="top">
<td>15th Richard M Away </td>
<td>16th Richard F Away Richard M Away </td>
<td>17th Richard F Away Richard M Away </td>
<td>18th Richard M Away </td>
<td bgcolor="#FFFF00">19th '''END OF TERM''' Bryan Away Precious Away Richard M Away </td>
<td bgcolor="#CCCCCC">20th </td>
<td bgcolor="#CCCCCC">21st </td>
</tr>
<tr valign="top">
<td>22nd Tricia Away Ken Away Bryan Away Claire Away Precious Away Richard M Away Aiswarya Away Gabriel Away </td>
<td>23rd Tricia Away Ken Away Bryan Away Claire Away Precious Away Richard M Away Aiswarya Away Gabriel 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 </td>
<td bgcolor="#CCCCCC">28th </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 Precious Away Aiswarya Away Gabriel Away Chen Chen Away</td>
<td>6th Aiswarya Away Gabriel Away </td>
<td>7th Aiswarya Away Gabriel Away </td>
<td>8th Aiswarya Away Gabriel Away </td>
<td>9th Aiswarya Away Gabriel Away </td>
<td bgcolor="#CCCCCC">10th </td>
<td bgcolor="#CCCCCC">11th </td>
</tr>
<tr valign="top">
<td bgcolor="#FFFF00">12th '''NEW TERM''' Aiswarya Away (P) </td>
<td>13th Aiswarya Away (P) </td>
<td>14th </td>
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<td bgcolor="#CCCCCC">17th </td>
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</tr>
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<td bgcolor="#4357CFF">'''1st February 2015''' </td>
</tr>
</table>

Talk:Mod:Hunt Research Group/MolCluster

2014-12-17T17:23:08Z

Ca307: /* Step-By-Step Example: Ionic Liquid Clusters */

===What is MolCluster?===
MolCluster is a tool (developed by Vincent and Gabriel) that can be used to cut clusters from MD trajectories and create the input files for ChemShell.

To use MolCluster, you will need:
* The latest version of MolCluster (available from Vincent).
* Python version 2.7.6, or above.
* The HISTORY file from which the clusters are to be cut, and the corresponding FIELD file. Note: these need to be in DL_POLY format. If you have used the 'restart' option in DL_POLY, the header of the HISTORY file may need to be amended. Additional transformations of the HISTORY and FIELD files, to convert atom labels into an acceptable format for MolCluster/ChemShell, may also be required (example given later).

===Using MolCluster: Basic Instructions===

1. Create a directory within the main MolCluster directory. Put the required HISTORY and FIELD files here.

2. Load MolCluster: ./MolCluster.py

3. Requests directory name to be specified (this is the location of the FIELD and HISTORY files). After specifying, the code will attempt to read and give an overview of the system.

4. Need to specify which configurations to cut a cluster from. Two options are currently available:
::*'''[n]''': Cut a cluster every "nth" configuration. N.B: numbering starts from 1 (i.e. 1st timestep). Therefore, if you request n=1000, clusters for configurations 1, 1001, 2001 etc. will be created.
::*'''[c]''': Select a custom set of configurations i.e. you can specify exactly which configurations you want.

5. Once the configurations have been extracted, you will be asked to choose how the origin will be defined in the clusters to be cut. Options are:
::*'''[AN]''': Atom number
::*'''[AT]''': Atom type
::*'''[MN]''': Molecule number
::*'''[MT]''': Molecule type
::*'''[C]''': Custom coordinates

You will then be asked to specify the specific atom number/type etc.

6. MolCluster will estimate the number of atoms within a region, for a range of radii with respect to your origin. Use this information to help you decide on the total radius (in Angstroms) of the clusters to be cut. You will be asked to specify this.

7. MolCluster has two options for deciding which molecules to include/exclude at the boundary of the clusters being cut:
::*'''[H]''': Hard boundary - all atoms of a molecule must be within the cutoff radius for the molecule to be included.
::*'''[S]''': Soft boundary - if the centre of mass of a molecule is within the cutoff radius, the molecule will be included.

8. Specify if the clusters are required to be neutral ('''Y/N''').

9. Decide on the output formats:
::*'''[C]''': Generates a ChemShell fragment input file, with accompanying .xyz co-ordinates file.
::*'''[X]''': Generates the .xyz co-ordinates file only.

If '''[X]''' selected, the clusters will be cut, .xyz files generated and MolCluster will terminate.

If '''[C]''' selected, you will be asked if you would also like to generate the necessary ChemShell input files for a QM/MM optimisation ('''Y/N''').

10. If your answer to step 9 was '''[C]''' (generate a ChemShell fragment input) and '''Y''' (generate ChemShell input files for a QM/MM optimisation), you will then be asked to define the QM region. Available options are:
::*'''[S]''': Spherical region (or threshold) centred about the defined origin (although not necessarily spherical??!!)
:::: If '''[S]''' selected, MolCluster will estimate the number of atoms in regions defined by a range of radii. Specify the QM radius. This must be specified (in Angstroms) and must, obviously, be less than, or equal to, the total radius of the cluster. Soft boundary conditions are implemented.
::*'''[M]''': By number of molecules. Molecules closest to the origin will be included.
::*'''[A]''': By an upper limit of atoms. Only whole molecules & those closest to the origin included.
::*'''[C]''': Custom region i.e. can select molecules individually to be in the QM region
::*'''[O]''': Spherical regions centred about one or more origins

If options '''[C]''' or '''[O]''' selected, MolCluster will go straight to steps 11 and 12. Once the active region and the directory/filenames have been defined, MolCluster will then ask for the custom QM regions to be defined ''per'' cluster (see step 14).

11. Once the QM region has been defined, the active region must be defined. MolCluster will estimate the number of atoms that would be in the active and frozen regions for a range of active radii. This information can be used to help decide upon an appropriate active radius. This must be specified (in Angstroms) and must, obviously, be less than, or equal to, the total radius of the cluster. If all atoms are to be included, simple enter "ALL". Soft boundary conditions are implemented.

12. Specify the output directory (i.e. where your final clusters and associated files will be saved) and specify the base-name for the output files (e.g. if you type "cluster" here, your clusters will be saved as cluster_1, cluster_2 etc.).

13. Unless options 10 '''[C'''] or '''[O]''' were selected (in that case, see point 14), MolCluster will generate the specified clusters and then terminate.

14. If option '''[C]''' selected in step 10, MolCluster will at this point list all the molecules in the first cluster, along with the distances to the origin. You will be asked to list all the molecules to be included in the QM region for this cluster. The same procedure is carried out for each cluster, before the clusters are generated and MolCluster terminates.

If option '''[O]''' selected in step 10, you will be asked to specify how many QM regions are to be defined and then specify the origin type and size of each QM region.

===The Output Files===
* Each cluster will have its own directory within the directory named in step 12. These subdirectories will be named: '''cluster_1''', '''cluster_2'''...'''cluster_n'''.
* Within the main directory one will also find a file called '''molcluster.log''' and a file called '''bulk_system_info.txt'''.
::*'''molcluster.log''' is a record of the user responses to each of the MolCluster options (look at this if you have forgotten, for example, the cluster radius).
::*'''bulk_system_info.txt''' summarises information relating to the system before clusters are cut (e.g. number and type of molecules, total number of atoms, total system charge, atom labels within a molecule, atomic charges).

*If option '''[X]''' selected in step 9, each subdirectory '''cluster_n''' will contain:
::*The '''cluster_n.xyz''' coordinates file
::*'''system_info.txt''': Summary of the cluster (e.g. total number of molecules, total number of atoms, total charge)

*If option '''[C]''', '''Y''' selected in step 9, each subdirectory '''cluster_n''' will contain:
::*The '''cluster_n.xyz''' coordinates file
::*'''system_info.txt''': Summary of the cluster (e.g. total number of molecules, total number of atoms, total charge)
::*The '''cluster_n.chm''' coordinates file. This will be used to create the '''cluster.pun''' ChemShell input file.
::*'''cluster_tiered.xyz''': xyz coordinates with the QM, active and frozen regions defined (all QM atoms listed as X1 (X=element symbol), active as X2 and frozen as X3). This file can be used to easily visualise the different regions in VMD.
::*'''conn.txt''' : the connectivity data needed by ChemShell
::*'''ff.dat''' : the forcefield in ChemShell format
::*'''opt.chm''': ChemShell input file. Options for the ChemShell optimisation specified here.

===Step-By-Step Example: Ionic Liquid Clusters===

Our example system:
* 256 ion pairs of [C4C1im][MeSO4]
* In total, the production run is 20ns in length; 4 lots of 5ns employing the "restart" keyword in DL_Poly.
* Our aim is to cut clusters from the last 5ns of the trajectory and create the input files for a ChemShell optimisation.

1). Create a directory within the main MolCluster directory and put the '''HISTORY''' and '''FIELD''' files here. Our directory will be called: '''BMIM_MESO4_EXAMPLE'''.

2). We now need to check to see if the HISTORY and FIELD files are in the correct format.

*As the ''restart'' keyword has been employed, two lines are missing from the header of the HISTORY file, '''Figure 1a''' and '''1b'''. MolCluster does not like this. Therefore, we need to add in the two lines that it is expecting to see, '''Figure 1c'''.

[[Image:MolCluster-HISTORY-header.png|frame|center|850px|'''Figure 1'''. Headers from selected HISTORY files '''(a)''' first 5ns of our simulation, without the use of the restart keyword, '''(b)''' last 5ns of our simulation with the restart keyword and '''(c)''' same HISTORY file as in (b), with missing lines added in. ]]

*The second problem we need to address is the atom labelling. The original atom labelling for [C4C1im][MeSO4], as used in the DL_Poly simulation, is shown in '''Figure 2a'''. Unfortunately, ChemShell has issues with this. To keep ChemShell happy, we have to change the atom labels in the HISTORY and FIELD files to the format ''elementsymbolnumber'' e.g. C2 rather than CR. Thankfully, this is quite easy to do using a script ('''sub_script.sh''', see below) written by Vincent. Firstly, however, we need to decide upon the new atom labelling. This is shown in '''Figure 2b''' for our example system. '''sub_script.sh''' requires that we have defined the atom label mappings in a file called '''sub_map.txt''' (also shown below for this system).

[[Image:BMIM-MESO4-numbering.png|thumb|center|850px|'''Figure 2'''. Original atom labelling (as used in DL_POLY MD simulation) shown in '''(a)''' and new atom labelling (suitable for MolCluster) shown in '''(b)'''. Within '''(b)''', atom labels that already had the correct format are in red. ]]

'''sub_script.sh''':

<pre>#!/bin/bash

while read line

do

#echo $line

s1=$(echo $line | awk '{ print $1 }')

s2=$(echo $line | awk '{ print $2 }')

echo "$s1 $s2"

gsed -i_bu2 "s|\<$s1\>|$s2|g" FIELD

gsed -i_bu2 "s|\<$s1\>|$s2|g" HISTORY

done < sub_map.txt</pre>

'''sub_map.txt''':
<pre>CR C3

NA N1

CW C4

HCR H2

HCW H3

HC H4

CT C6

OS4 O4

OC4 O5

HS4 H5

CS C5

CS4 C7</pre>

*Run '''./sub_script.sh'''
Note: this process may take a while, depending on the size of the file. Progress can be seen in the terminal (example shown in '''Figure 3'''), with each of the mappings specified in sub_map.txt considered in turn. The first few lines of the HISTORY file, before, and after, the relabelling can be seen in '''Figure 4'''.

[[Image:sub_map_mappings.png|thumb|center|800px|'''Figure 3'''. Example terminal output whilst running sub_script.sh ]]

[[Image:HISTORY-before-after.png|thumb|center|1000px|'''Figure 4'''. First few lines of the HISTORY file before '''(a)''' and after '''(b)''' the relabelling. ]]

3). Now our files are in the correct format, we can run MolCluster: '''./MolCluster.py'''

4). The first thing MolCluster does is to ask us to specify the directory containing the FIELD and HISTORY files. Our directory is called BMIM_MESO4_EXAMPLE. Once this has been specified, MolCluster will attempt to read the files and generate a summary of the system (from timestep 1 of the trajectory). This is shown in '''Figure 5''' for our system, and it can be seen that the information summarised by MolCluster is correct.

[[Image:MC-read-files-annotate.png|thumb|center|800px|'''Figure 5'''. After specifying the directory for the FIELD and HISTORY files, MolCluster summarises the bulk system information. ]]

5). MolCluster works out how many configurations in the HISTORY file (5000 in our example) and then asks us to specify the configurations we would like to cut a cluster from. In this case, we are going to select the '''[n]''' option (cut a cluster from every 'nth' configuration) and then specify n as an integer, in this case 1000 (i.e. n=1000, therefore cut a cluster every 1000th time step), '''Figure 6'''.

[[Image:MC-specify-config.png|thumb|center|800px|'''Figure 6'''. Specifying the configurations to create clusters for. ]]

6). We must now select how we would like to define the origin of the clusters to be cut. We are going to select option '''[AN]''' (atom number) and choose atom 1 to be the origin (for reference, in our case this is a C3 atom), '''Figure 7'''.

[[Image:origin-define.png|thumb|center|800px|'''Figure 7'''. Defining the cluster origin. ]]

7). An estimate of the number of atoms in regions with varying radii (with respect to our defined origin) is provided by MolCluster. We need to cut a cluster large enough to incorporate a reasonable number of ion pairs (bearing in mind that our cation alone, in all trans form, is over 9 Angstroms in width), but not so large that the calculation is unfeasible. The ideal size is still being investigated, but for now, let us specify a cluster radius of 15 Angstroms, '''Figure 8'''.

[[Image:cluster-radius-cut.png|thumb|center|900px|'''Figure 8'''. Choosing the cluster radius. ]]

8). MolCluster now asks us to tell it which boundary condition to use when cutting the clusters (essentially this is just how MolCluster will decide whether or not to include a molecule in the cluster for molecules at the boundary). We will select '''[S]''' (soft boundary) here. We are then asked to specify if the cluster needs to be neutral. Obviously this is only really applicable to charged systems (with counter ions), such as ionic liquids . We will select yes here, '''[Y]''', so that all our clusters have the same total charge, '''Figure 9'''.

[[Image:boundary-neutral.png|thumb|center|850px|'''Figure 9'''. Selecting boundary conditions. ]]

File:Boundary-neutral.png

2014-12-17T17:21:15Z

Ca307:

Talk:Mod:Hunt Research Group/MolCluster

2014-12-17T17:13:00Z

Ca307: /* Step-By-Step Example: Ionic Liquid Clusters */

===What is MolCluster?===
MolCluster is a tool (developed by Vincent and Gabriel) that can be used to cut clusters from MD trajectories and create the input files for ChemShell.

To use MolCluster, you will need:
* The latest version of MolCluster (available from Vincent).
* Python version 2.7.6, or above.
* The HISTORY file from which the clusters are to be cut, and the corresponding FIELD file. Note: these need to be in DL_POLY format. If you have used the 'restart' option in DL_POLY, the header of the HISTORY file may need to be amended. Additional transformations of the HISTORY and FIELD files, to convert atom labels into an acceptable format for MolCluster/ChemShell, may also be required (example given later).

===Using MolCluster: Basic Instructions===

1. Create a directory within the main MolCluster directory. Put the required HISTORY and FIELD files here.

2. Load MolCluster: ./MolCluster.py

3. Requests directory name to be specified (this is the location of the FIELD and HISTORY files). After specifying, the code will attempt to read and give an overview of the system.

4. Need to specify which configurations to cut a cluster from. Two options are currently available:
::*'''[n]''': Cut a cluster every "nth" configuration. N.B: numbering starts from 1 (i.e. 1st timestep). Therefore, if you request n=1000, clusters for configurations 1, 1001, 2001 etc. will be created.
::*'''[c]''': Select a custom set of configurations i.e. you can specify exactly which configurations you want.

5. Once the configurations have been extracted, you will be asked to choose how the origin will be defined in the clusters to be cut. Options are:
::*'''[AN]''': Atom number
::*'''[AT]''': Atom type
::*'''[MN]''': Molecule number
::*'''[MT]''': Molecule type
::*'''[C]''': Custom coordinates

You will then be asked to specify the specific atom number/type etc.

6. MolCluster will estimate the number of atoms within a region, for a range of radii with respect to your origin. Use this information to help you decide on the total radius (in Angstroms) of the clusters to be cut. You will be asked to specify this.

7. MolCluster has two options for deciding which molecules to include/exclude at the boundary of the clusters being cut:
::*'''[H]''': Hard boundary - all atoms of a molecule must be within the cutoff radius for the molecule to be included.
::*'''[S]''': Soft boundary - if the centre of mass of a molecule is within the cutoff radius, the molecule will be included.

8. Specify if the clusters are required to be neutral ('''Y/N''').

9. Decide on the output formats:
::*'''[C]''': Generates a ChemShell fragment input file, with accompanying .xyz co-ordinates file.
::*'''[X]''': Generates the .xyz co-ordinates file only.

If '''[X]''' selected, the clusters will be cut, .xyz files generated and MolCluster will terminate.

If '''[C]''' selected, you will be asked if you would also like to generate the necessary ChemShell input files for a QM/MM optimisation ('''Y/N''').

10. If your answer to step 9 was '''[C]''' (generate a ChemShell fragment input) and '''Y''' (generate ChemShell input files for a QM/MM optimisation), you will then be asked to define the QM region. Available options are:
::*'''[S]''': Spherical region (or threshold) centred about the defined origin (although not necessarily spherical??!!)
:::: If '''[S]''' selected, MolCluster will estimate the number of atoms in regions defined by a range of radii. Specify the QM radius. This must be specified (in Angstroms) and must, obviously, be less than, or equal to, the total radius of the cluster. Soft boundary conditions are implemented.
::*'''[M]''': By number of molecules. Molecules closest to the origin will be included.
::*'''[A]''': By an upper limit of atoms. Only whole molecules & those closest to the origin included.
::*'''[C]''': Custom region i.e. can select molecules individually to be in the QM region
::*'''[O]''': Spherical regions centred about one or more origins

If options '''[C]''' or '''[O]''' selected, MolCluster will go straight to steps 11 and 12. Once the active region and the directory/filenames have been defined, MolCluster will then ask for the custom QM regions to be defined ''per'' cluster (see step 14).

11. Once the QM region has been defined, the active region must be defined. MolCluster will estimate the number of atoms that would be in the active and frozen regions for a range of active radii. This information can be used to help decide upon an appropriate active radius. This must be specified (in Angstroms) and must, obviously, be less than, or equal to, the total radius of the cluster. If all atoms are to be included, simple enter "ALL". Soft boundary conditions are implemented.

12. Specify the output directory (i.e. where your final clusters and associated files will be saved) and specify the base-name for the output files (e.g. if you type "cluster" here, your clusters will be saved as cluster_1, cluster_2 etc.).

13. Unless options 10 '''[C'''] or '''[O]''' were selected (in that case, see point 14), MolCluster will generate the specified clusters and then terminate.

14. If option '''[C]''' selected in step 10, MolCluster will at this point list all the molecules in the first cluster, along with the distances to the origin. You will be asked to list all the molecules to be included in the QM region for this cluster. The same procedure is carried out for each cluster, before the clusters are generated and MolCluster terminates.

If option '''[O]''' selected in step 10, you will be asked to specify how many QM regions are to be defined and then specify the origin type and size of each QM region.

===The Output Files===
* Each cluster will have its own directory within the directory named in step 12. These subdirectories will be named: '''cluster_1''', '''cluster_2'''...'''cluster_n'''.
* Within the main directory one will also find a file called '''molcluster.log''' and a file called '''bulk_system_info.txt'''.
::*'''molcluster.log''' is a record of the user responses to each of the MolCluster options (look at this if you have forgotten, for example, the cluster radius).
::*'''bulk_system_info.txt''' summarises information relating to the system before clusters are cut (e.g. number and type of molecules, total number of atoms, total system charge, atom labels within a molecule, atomic charges).

*If option '''[X]''' selected in step 9, each subdirectory '''cluster_n''' will contain:
::*The '''cluster_n.xyz''' coordinates file
::*'''system_info.txt''': Summary of the cluster (e.g. total number of molecules, total number of atoms, total charge)

*If option '''[C]''', '''Y''' selected in step 9, each subdirectory '''cluster_n''' will contain:
::*The '''cluster_n.xyz''' coordinates file
::*'''system_info.txt''': Summary of the cluster (e.g. total number of molecules, total number of atoms, total charge)
::*The '''cluster_n.chm''' coordinates file. This will be used to create the '''cluster.pun''' ChemShell input file.
::*'''cluster_tiered.xyz''': xyz coordinates with the QM, active and frozen regions defined (all QM atoms listed as X1 (X=element symbol), active as X2 and frozen as X3). This file can be used to easily visualise the different regions in VMD.
::*'''conn.txt''' : the connectivity data needed by ChemShell
::*'''ff.dat''' : the forcefield in ChemShell format
::*'''opt.chm''': ChemShell input file. Options for the ChemShell optimisation specified here.

===Step-By-Step Example: Ionic Liquid Clusters===

Our example system:
* 256 ion pairs of [C4C1im][MeSO4]
* In total, the production run is 20ns in length; 4 lots of 5ns employing the "restart" keyword in DL_Poly.
* Our aim is to cut clusters from the last 5ns of the trajectory and create the input files for a ChemShell optimisation.

1). Create a directory within the main MolCluster directory and put the '''HISTORY''' and '''FIELD''' files here. Our directory will be called: '''BMIM_MESO4_EXAMPLE'''.

2). We now need to check to see if the HISTORY and FIELD files are in the correct format.

*As the ''restart'' keyword has been employed, two lines are missing from the header of the HISTORY file, '''Figure 1a''' and '''1b'''. MolCluster does not like this. Therefore, we need to add in the two lines that it is expecting to see, '''Figure 1c'''.

[[Image:MolCluster-HISTORY-header.png|frame|center|850px|'''Figure 1'''. Headers from selected HISTORY files '''(a)''' first 5ns of our simulation, without the use of the restart keyword, '''(b)''' last 5ns of our simulation with the restart keyword and '''(c)''' same HISTORY file as in (b), with missing lines added in. ]]

*The second problem we need to address is the atom labelling. The original atom labelling for [C4C1im][MeSO4], as used in the DL_Poly simulation, is shown in '''Figure 2a'''. Unfortunately, ChemShell has issues with this. To keep ChemShell happy, we have to change the atom labels in the HISTORY and FIELD files to the format ''elementsymbolnumber'' e.g. C2 rather than CR. Thankfully, this is quite easy to do using a script ('''sub_script.sh''', see below) written by Vincent. Firstly, however, we need to decide upon the new atom labelling. This is shown in '''Figure 2b''' for our example system. '''sub_script.sh''' requires that we have defined the atom label mappings in a file called '''sub_map.txt''' (also shown below for this system).

[[Image:BMIM-MESO4-numbering.png|thumb|center|850px|'''Figure 2'''. Original atom labelling (as used in DL_POLY MD simulation) shown in '''(a)''' and new atom labelling (suitable for MolCluster) shown in '''(b)'''. Within '''(b)''', atom labels that already had the correct format are in red. ]]

'''sub_script.sh''':

<pre>#!/bin/bash

while read line

do

#echo $line

s1=$(echo $line | awk '{ print $1 }')

s2=$(echo $line | awk '{ print $2 }')

echo "$s1 $s2"

gsed -i_bu2 "s|\<$s1\>|$s2|g" FIELD

gsed -i_bu2 "s|\<$s1\>|$s2|g" HISTORY

done < sub_map.txt</pre>

'''sub_map.txt''':
<pre>CR C3

NA N1

CW C4

HCR H2

HCW H3

HC H4

CT C6

OS4 O4

OC4 O5

HS4 H5

CS C5

CS4 C7</pre>

*Run '''./sub_script.sh'''
Note: this process may take a while, depending on the size of the file. Progress can be seen in the terminal (example shown in '''Figure 3'''), with each of the mappings specified in sub_map.txt considered in turn. The first few lines of the HISTORY file, before, and after, the relabelling can be seen in '''Figure 4'''.

[[Image:sub_map_mappings.png|thumb|center|800px|'''Figure 3'''. Example terminal output whilst running sub_script.sh ]]

[[Image:HISTORY-before-after.png|thumb|center|1000px|'''Figure 4'''. First few lines of the HISTORY file before '''(a)''' and after '''(b)''' the relabelling. ]]

3). Now our files are in the correct format, we can run MolCluster: '''./MolCluster.py'''

4). The first thing MolCluster does is to ask us to specify the directory containing the FIELD and HISTORY files. Our directory is called BMIM_MESO4_EXAMPLE. Once this has been specified, MolCluster will attempt to read the files and generate a summary of the system (from timestep 1 of the trajectory). This is shown in '''Figure 5''' for our system, and it can be seen that the information summarised by MolCluster is correct.

[[Image:MC-read-files-annotate.png|thumb|center|800px|'''Figure 5'''. After specifying the directory for the FIELD and HISTORY files, MolCluster summarises the bulk system information. ]]

5). MolCluster works out how many configurations in the HISTORY file (5000 in our example) and then asks us to specify the configurations we would like to cut a cluster from. In this case, we are going to select the '''[n]''' option (cut a cluster from every 'nth' configuration) and then specify n as an integer, in this case 1000 (i.e. n=1000, therefore cut a cluster every 1000th time step), '''Figure 6'''.

[[Image:MC-specify-config.png|thumb|center|800px|'''Figure 6'''. Specifying the configurations to create clusters for. ]]

6). We must now select how we would like to define the origin of the clusters to be cut. We are going to select option '''[AN]''' (atom number) and choose atom 1 to be the origin (for reference, in our case this is a C3 atom), '''Figure 7'''.

[[Image:origin-define.png|thumb|center|800px|'''Figure 7'''. Defining the cluster origin. ]]

7). An estimate of the number of atoms in regions with varying radii (with respect to our defined origin) is provided by MolCluster. We need to cut a cluster large enough to incorporate a reasonable number of ion pairs (bearing in mind that our cation alone, in all trans form, is over 9 Angstroms in width), but not so large that the calculation is unfeasible. The ideal size is still being investigated, but for now, let us specify a cluster radius of 15 Angstroms, '''Figure 8'''.

[[Image:cluster-radius-cut.png|thumb|center|900px|'''Figure 8'''. Choosing the cluster radius. ]]

8). MolCluster now asks us to tell it which boundary condition to use when cutting the clusters (essentially this is just how MolCluster will decide whether or not to include a molecule in the cluster for molecules at the boundary). We will select '''[S]''' (soft boundary) here. We are then asked to specify if the cluster needs to be neutral. Obviously this is only really applicable to charged systems (with counter ions), such as ionic liquids . We will select yes here, '''[Y]''', so that all our clusters have the same total charge, '''Figure 9'''.

Talk:Mod:Hunt Research Group/MolCluster

2014-12-17T17:05:37Z

Ca307: /* Step-By-Step Example: Ionic Liquid Clusters */

===What is MolCluster?===
MolCluster is a tool (developed by Vincent and Gabriel) that can be used to cut clusters from MD trajectories and create the input files for ChemShell.

To use MolCluster, you will need:
* The latest version of MolCluster (available from Vincent).
* Python version 2.7.6, or above.
* The HISTORY file from which the clusters are to be cut, and the corresponding FIELD file. Note: these need to be in DL_POLY format. If you have used the 'restart' option in DL_POLY, the header of the HISTORY file may need to be amended. Additional transformations of the HISTORY and FIELD files, to convert atom labels into an acceptable format for MolCluster/ChemShell, may also be required (example given later).

===Using MolCluster: Basic Instructions===

1. Create a directory within the main MolCluster directory. Put the required HISTORY and FIELD files here.

2. Load MolCluster: ./MolCluster.py

3. Requests directory name to be specified (this is the location of the FIELD and HISTORY files). After specifying, the code will attempt to read and give an overview of the system.

4. Need to specify which configurations to cut a cluster from. Two options are currently available:
::*'''[n]''': Cut a cluster every "nth" configuration. N.B: numbering starts from 1 (i.e. 1st timestep). Therefore, if you request n=1000, clusters for configurations 1, 1001, 2001 etc. will be created.
::*'''[c]''': Select a custom set of configurations i.e. you can specify exactly which configurations you want.

5. Once the configurations have been extracted, you will be asked to choose how the origin will be defined in the clusters to be cut. Options are:
::*'''[AN]''': Atom number
::*'''[AT]''': Atom type
::*'''[MN]''': Molecule number
::*'''[MT]''': Molecule type
::*'''[C]''': Custom coordinates

You will then be asked to specify the specific atom number/type etc.

6. MolCluster will estimate the number of atoms within a region, for a range of radii with respect to your origin. Use this information to help you decide on the total radius (in Angstroms) of the clusters to be cut. You will be asked to specify this.

7. MolCluster has two options for deciding which molecules to include/exclude at the boundary of the clusters being cut:
::*'''[H]''': Hard boundary - all atoms of a molecule must be within the cutoff radius for the molecule to be included.
::*'''[S]''': Soft boundary - if the centre of mass of a molecule is within the cutoff radius, the molecule will be included.

8. Specify if the clusters are required to be neutral ('''Y/N''').

9. Decide on the output formats:
::*'''[C]''': Generates a ChemShell fragment input file, with accompanying .xyz co-ordinates file.
::*'''[X]''': Generates the .xyz co-ordinates file only.

If '''[X]''' selected, the clusters will be cut, .xyz files generated and MolCluster will terminate.

If '''[C]''' selected, you will be asked if you would also like to generate the necessary ChemShell input files for a QM/MM optimisation ('''Y/N''').

10. If your answer to step 9 was '''[C]''' (generate a ChemShell fragment input) and '''Y''' (generate ChemShell input files for a QM/MM optimisation), you will then be asked to define the QM region. Available options are:
::*'''[S]''': Spherical region (or threshold) centred about the defined origin (although not necessarily spherical??!!)
:::: If '''[S]''' selected, MolCluster will estimate the number of atoms in regions defined by a range of radii. Specify the QM radius. This must be specified (in Angstroms) and must, obviously, be less than, or equal to, the total radius of the cluster. Soft boundary conditions are implemented.
::*'''[M]''': By number of molecules. Molecules closest to the origin will be included.
::*'''[A]''': By an upper limit of atoms. Only whole molecules & those closest to the origin included.
::*'''[C]''': Custom region i.e. can select molecules individually to be in the QM region
::*'''[O]''': Spherical regions centred about one or more origins

If options '''[C]''' or '''[O]''' selected, MolCluster will go straight to steps 11 and 12. Once the active region and the directory/filenames have been defined, MolCluster will then ask for the custom QM regions to be defined ''per'' cluster (see step 14).

11. Once the QM region has been defined, the active region must be defined. MolCluster will estimate the number of atoms that would be in the active and frozen regions for a range of active radii. This information can be used to help decide upon an appropriate active radius. This must be specified (in Angstroms) and must, obviously, be less than, or equal to, the total radius of the cluster. If all atoms are to be included, simple enter "ALL". Soft boundary conditions are implemented.

12. Specify the output directory (i.e. where your final clusters and associated files will be saved) and specify the base-name for the output files (e.g. if you type "cluster" here, your clusters will be saved as cluster_1, cluster_2 etc.).

13. Unless options 10 '''[C'''] or '''[O]''' were selected (in that case, see point 14), MolCluster will generate the specified clusters and then terminate.

14. If option '''[C]''' selected in step 10, MolCluster will at this point list all the molecules in the first cluster, along with the distances to the origin. You will be asked to list all the molecules to be included in the QM region for this cluster. The same procedure is carried out for each cluster, before the clusters are generated and MolCluster terminates.

If option '''[O]''' selected in step 10, you will be asked to specify how many QM regions are to be defined and then specify the origin type and size of each QM region.

===The Output Files===
* Each cluster will have its own directory within the directory named in step 12. These subdirectories will be named: '''cluster_1''', '''cluster_2'''...'''cluster_n'''.
* Within the main directory one will also find a file called '''molcluster.log''' and a file called '''bulk_system_info.txt'''.
::*'''molcluster.log''' is a record of the user responses to each of the MolCluster options (look at this if you have forgotten, for example, the cluster radius).
::*'''bulk_system_info.txt''' summarises information relating to the system before clusters are cut (e.g. number and type of molecules, total number of atoms, total system charge, atom labels within a molecule, atomic charges).

*If option '''[X]''' selected in step 9, each subdirectory '''cluster_n''' will contain:
::*The '''cluster_n.xyz''' coordinates file
::*'''system_info.txt''': Summary of the cluster (e.g. total number of molecules, total number of atoms, total charge)

*If option '''[C]''', '''Y''' selected in step 9, each subdirectory '''cluster_n''' will contain:
::*The '''cluster_n.xyz''' coordinates file
::*'''system_info.txt''': Summary of the cluster (e.g. total number of molecules, total number of atoms, total charge)
::*The '''cluster_n.chm''' coordinates file. This will be used to create the '''cluster.pun''' ChemShell input file.
::*'''cluster_tiered.xyz''': xyz coordinates with the QM, active and frozen regions defined (all QM atoms listed as X1 (X=element symbol), active as X2 and frozen as X3). This file can be used to easily visualise the different regions in VMD.
::*'''conn.txt''' : the connectivity data needed by ChemShell
::*'''ff.dat''' : the forcefield in ChemShell format
::*'''opt.chm''': ChemShell input file. Options for the ChemShell optimisation specified here.

===Step-By-Step Example: Ionic Liquid Clusters===

Our example system:
* 256 ion pairs of [C4C1im][MeSO4]
* In total, the production run is 20ns in length; 4 lots of 5ns employing the "restart" keyword in DL_Poly.
* Our aim is to cut clusters from the last 5ns of the trajectory and create the input files for a ChemShell optimisation.

1). Create a directory within the main MolCluster directory and put the '''HISTORY''' and '''FIELD''' files here. Our directory will be called: '''BMIM_MESO4_EXAMPLE'''.

2). We now need to check to see if the HISTORY and FIELD files are in the correct format.

*As the ''restart'' keyword has been employed, two lines are missing from the header of the HISTORY file, '''Figure 1a''' and '''1b'''. MolCluster does not like this. Therefore, we need to add in the two lines that it is expecting to see, '''Figure 1c'''.

[[Image:MolCluster-HISTORY-header.png|frame|center|850px|'''Figure 1'''. Headers from selected HISTORY files '''(a)''' first 5ns of our simulation, without the use of the restart keyword, '''(b)''' last 5ns of our simulation with the restart keyword and '''(c)''' same HISTORY file as in (b), with missing lines added in. ]]

*The second problem we need to address is the atom labelling. The original atom labelling for [C4C1im][MeSO4], as used in the DL_Poly simulation, is shown in '''Figure 2a'''. Unfortunately, ChemShell has issues with this. To keep ChemShell happy, we have to change the atom labels in the HISTORY and FIELD files to the format ''elementsymbolnumber'' e.g. C2 rather than CR. Thankfully, this is quite easy to do using a script ('''sub_script.sh''', see below) written by Vincent. Firstly, however, we need to decide upon the new atom labelling. This is shown in '''Figure 2b''' for our example system. '''sub_script.sh''' requires that we have defined the atom label mappings in a file called '''sub_map.txt''' (also shown below for this system).

[[Image:BMIM-MESO4-numbering.png|thumb|center|850px|'''Figure 2'''. Original atom labelling (as used in DL_POLY MD simulation) shown in '''(a)''' and new atom labelling (suitable for MolCluster) shown in '''(b)'''. Within '''(b)''', atom labels that already had the correct format are in red. ]]

'''sub_script.sh''':

<pre>#!/bin/bash

while read line

do

#echo $line

s1=$(echo $line | awk '{ print $1 }')

s2=$(echo $line | awk '{ print $2 }')

echo "$s1 $s2"

gsed -i_bu2 "s|\<$s1\>|$s2|g" FIELD

gsed -i_bu2 "s|\<$s1\>|$s2|g" HISTORY

done < sub_map.txt</pre>

'''sub_map.txt''':
<pre>CR C3

NA N1

CW C4

HCR H2

HCW H3

HC H4

CT C6

OS4 O4

OC4 O5

HS4 H5

CS C5

CS4 C7</pre>

*Run '''./sub_script.sh'''
Note: this process may take a while, depending on the size of the file. Progress can be seen in the terminal (example shown in '''Figure 3'''), with each of the mappings specified in sub_map.txt considered in turn. The first few lines of the HISTORY file, before, and after, the relabelling can be seen in '''Figure 4'''.

[[Image:sub_map_mappings.png|thumb|center|800px|'''Figure 3'''. Example terminal output whilst running sub_script.sh ]]

[[Image:HISTORY-before-after.png|thumb|center|1000px|'''Figure 4'''. First few lines of the HISTORY file before '''(a)''' and after '''(b)''' the relabelling. ]]

3). Now our files are in the correct format, we can run MolCluster: '''./MolCluster.py'''

4). The first thing MolCluster does is to ask us to specify the directory containing the FIELD and HISTORY files. Our directory is called BMIM_MESO4_EXAMPLE. Once this has been specified, MolCluster will attempt to read the files and generate a summary of the system (from timestep 1 of the trajectory). This is shown in '''Figure 5''' for our system, and it can be seen that the information summarised by MolCluster is correct.

[[Image:MC-read-files-annotate.png|thumb|center|800px|'''Figure 5'''. After specifying the directory for the FIELD and HISTORY files, MolCluster summarises the bulk system information. ]]

5). MolCluster works out how many configurations in the HISTORY file (5000 in our example) and then asks us to specify the configurations we would like to cut a cluster from. In this case, we are going to select the '''[n]''' option (cut a cluster from every 'nth' configuration) and then specify n as an integer, in this case 1000 (i.e. n=1000, therefore cut a cluster every 1000th time step), '''Figure 6'''.

[[Image:MC-specify-config.png|thumb|center|800px|'''Figure 6'''. Specifying the configurations to create clusters for. ]]

6). We must now select how we would like to define the origin of the clusters to be cut. We are going to select option '''[AN]''' (atom number) and choose atom 1 to be the origin (for reference, in our case this is a C3 atom), '''Figure 7'''.

[[Image:origin-define.png|thumb|center|800px|'''Figure 7'''. Defining the cluster origin. ]]

7). An estimate of the number of atoms in regions with varying radii (with respect to our defined origin) is provided by MolCluster. We need to cut a cluster large enough to incorporate a reasonable number of ion pairs (bearing in mind that our cation alone, in all trans form, is over 9 Angstroms in width), but not so large that the calculation is unfeasible. The ideal size is still being investigated, but for now, let us specify a cluster radius of 15 Angstroms, '''Figure 8'''.

[[Image:cluster-radius-cut.png|thumb|center|900px|'''Figure 8'''. Choosing the cluster radius. ]]

8). MolCluster now asks us to tell it which boundary condition to use when cutting the clusters (essentially this is just how MolCluster will decide whether or not to include a molecule in the cluster for molecules at the boundary). We will select '''[S]''' (soft boundary) here.

Talk:Mod:Hunt Research Group/MolCluster

2014-12-17T16:57:16Z

Ca307: /* Step-By-Step Example: Ionic Liquid Clusters */

===What is MolCluster?===
MolCluster is a tool (developed by Vincent and Gabriel) that can be used to cut clusters from MD trajectories and create the input files for ChemShell.

To use MolCluster, you will need:
* The latest version of MolCluster (available from Vincent).
* Python version 2.7.6, or above.
* The HISTORY file from which the clusters are to be cut, and the corresponding FIELD file. Note: these need to be in DL_POLY format. If you have used the 'restart' option in DL_POLY, the header of the HISTORY file may need to be amended. Additional transformations of the HISTORY and FIELD files, to convert atom labels into an acceptable format for MolCluster/ChemShell, may also be required (example given later).

===Using MolCluster: Basic Instructions===

1. Create a directory within the main MolCluster directory. Put the required HISTORY and FIELD files here.

2. Load MolCluster: ./MolCluster.py

3. Requests directory name to be specified (this is the location of the FIELD and HISTORY files). After specifying, the code will attempt to read and give an overview of the system.

4. Need to specify which configurations to cut a cluster from. Two options are currently available:
::*'''[n]''': Cut a cluster every "nth" configuration. N.B: numbering starts from 1 (i.e. 1st timestep). Therefore, if you request n=1000, clusters for configurations 1, 1001, 2001 etc. will be created.
::*'''[c]''': Select a custom set of configurations i.e. you can specify exactly which configurations you want.

5. Once the configurations have been extracted, you will be asked to choose how the origin will be defined in the clusters to be cut. Options are:
::*'''[AN]''': Atom number
::*'''[AT]''': Atom type
::*'''[MN]''': Molecule number
::*'''[MT]''': Molecule type
::*'''[C]''': Custom coordinates

You will then be asked to specify the specific atom number/type etc.

6. MolCluster will estimate the number of atoms within a region, for a range of radii with respect to your origin. Use this information to help you decide on the total radius (in Angstroms) of the clusters to be cut. You will be asked to specify this.

7. MolCluster has two options for deciding which molecules to include/exclude at the boundary of the clusters being cut:
::*'''[H]''': Hard boundary - all atoms of a molecule must be within the cutoff radius for the molecule to be included.
::*'''[S]''': Soft boundary - if the centre of mass of a molecule is within the cutoff radius, the molecule will be included.

8. Specify if the clusters are required to be neutral ('''Y/N''').

9. Decide on the output formats:
::*'''[C]''': Generates a ChemShell fragment input file, with accompanying .xyz co-ordinates file.
::*'''[X]''': Generates the .xyz co-ordinates file only.

If '''[X]''' selected, the clusters will be cut, .xyz files generated and MolCluster will terminate.

If '''[C]''' selected, you will be asked if you would also like to generate the necessary ChemShell input files for a QM/MM optimisation ('''Y/N''').

10. If your answer to step 9 was '''[C]''' (generate a ChemShell fragment input) and '''Y''' (generate ChemShell input files for a QM/MM optimisation), you will then be asked to define the QM region. Available options are:
::*'''[S]''': Spherical region (or threshold) centred about the defined origin (although not necessarily spherical??!!)
:::: If '''[S]''' selected, MolCluster will estimate the number of atoms in regions defined by a range of radii. Specify the QM radius. This must be specified (in Angstroms) and must, obviously, be less than, or equal to, the total radius of the cluster. Soft boundary conditions are implemented.
::*'''[M]''': By number of molecules. Molecules closest to the origin will be included.
::*'''[A]''': By an upper limit of atoms. Only whole molecules & those closest to the origin included.
::*'''[C]''': Custom region i.e. can select molecules individually to be in the QM region
::*'''[O]''': Spherical regions centred about one or more origins

If options '''[C]''' or '''[O]''' selected, MolCluster will go straight to steps 11 and 12. Once the active region and the directory/filenames have been defined, MolCluster will then ask for the custom QM regions to be defined ''per'' cluster (see step 14).

11. Once the QM region has been defined, the active region must be defined. MolCluster will estimate the number of atoms that would be in the active and frozen regions for a range of active radii. This information can be used to help decide upon an appropriate active radius. This must be specified (in Angstroms) and must, obviously, be less than, or equal to, the total radius of the cluster. If all atoms are to be included, simple enter "ALL". Soft boundary conditions are implemented.

12. Specify the output directory (i.e. where your final clusters and associated files will be saved) and specify the base-name for the output files (e.g. if you type "cluster" here, your clusters will be saved as cluster_1, cluster_2 etc.).

13. Unless options 10 '''[C'''] or '''[O]''' were selected (in that case, see point 14), MolCluster will generate the specified clusters and then terminate.

14. If option '''[C]''' selected in step 10, MolCluster will at this point list all the molecules in the first cluster, along with the distances to the origin. You will be asked to list all the molecules to be included in the QM region for this cluster. The same procedure is carried out for each cluster, before the clusters are generated and MolCluster terminates.

If option '''[O]''' selected in step 10, you will be asked to specify how many QM regions are to be defined and then specify the origin type and size of each QM region.

===The Output Files===
* Each cluster will have its own directory within the directory named in step 12. These subdirectories will be named: '''cluster_1''', '''cluster_2'''...'''cluster_n'''.
* Within the main directory one will also find a file called '''molcluster.log''' and a file called '''bulk_system_info.txt'''.
::*'''molcluster.log''' is a record of the user responses to each of the MolCluster options (look at this if you have forgotten, for example, the cluster radius).
::*'''bulk_system_info.txt''' summarises information relating to the system before clusters are cut (e.g. number and type of molecules, total number of atoms, total system charge, atom labels within a molecule, atomic charges).

*If option '''[X]''' selected in step 9, each subdirectory '''cluster_n''' will contain:
::*The '''cluster_n.xyz''' coordinates file
::*'''system_info.txt''': Summary of the cluster (e.g. total number of molecules, total number of atoms, total charge)

*If option '''[C]''', '''Y''' selected in step 9, each subdirectory '''cluster_n''' will contain:
::*The '''cluster_n.xyz''' coordinates file
::*'''system_info.txt''': Summary of the cluster (e.g. total number of molecules, total number of atoms, total charge)
::*The '''cluster_n.chm''' coordinates file. This will be used to create the '''cluster.pun''' ChemShell input file.
::*'''cluster_tiered.xyz''': xyz coordinates with the QM, active and frozen regions defined (all QM atoms listed as X1 (X=element symbol), active as X2 and frozen as X3). This file can be used to easily visualise the different regions in VMD.
::*'''conn.txt''' : the connectivity data needed by ChemShell
::*'''ff.dat''' : the forcefield in ChemShell format
::*'''opt.chm''': ChemShell input file. Options for the ChemShell optimisation specified here.

===Step-By-Step Example: Ionic Liquid Clusters===

Our example system:
* 256 ion pairs of [C4C1im][MeSO4]
* In total, the production run is 20ns in length; 4 lots of 5ns employing the "restart" keyword in DL_Poly.
* Our aim is to cut clusters from the last 5ns of the trajectory and create the input files for a ChemShell optimisation.

1). Create a directory within the main MolCluster directory and put the '''HISTORY''' and '''FIELD''' files here. Our directory will be called: '''BMIM_MESO4_EXAMPLE'''.

2). We now need to check to see if the HISTORY and FIELD files are in the correct format.

*As the ''restart'' keyword has been employed, two lines are missing from the header of the HISTORY file, '''Figure 1a''' and '''1b'''. MolCluster does not like this. Therefore, we need to add in the two lines that it is expecting to see, '''Figure 1c'''.

[[Image:MolCluster-HISTORY-header.png|frame|center|850px|'''Figure 1'''. Headers from selected HISTORY files '''(a)''' first 5ns of our simulation, without the use of the restart keyword, '''(b)''' last 5ns of our simulation with the restart keyword and '''(c)''' same HISTORY file as in (b), with missing lines added in. ]]

*The second problem we need to address is the atom labelling. The original atom labelling for [C4C1im][MeSO4], as used in the DL_Poly simulation, is shown in '''Figure 2a'''. Unfortunately, ChemShell has issues with this. To keep ChemShell happy, we have to change the atom labels in the HISTORY and FIELD files to the format ''elementsymbolnumber'' e.g. C2 rather than CR. Thankfully, this is quite easy to do using a script ('''sub_script.sh''', see below) written by Vincent. Firstly, however, we need to decide upon the new atom labelling. This is shown in '''Figure 2b''' for our example system. '''sub_script.sh''' requires that we have defined the atom label mappings in a file called '''sub_map.txt''' (also shown below for this system).

[[Image:BMIM-MESO4-numbering.png|thumb|center|850px|'''Figure 2'''. Original atom labelling (as used in DL_POLY MD simulation) shown in '''(a)''' and new atom labelling (suitable for MolCluster) shown in '''(b)'''. Within '''(b)''', atom labels that already had the correct format are in red. ]]

'''sub_script.sh''':

<pre>#!/bin/bash

while read line

do

#echo $line

s1=$(echo $line | awk '{ print $1 }')

s2=$(echo $line | awk '{ print $2 }')

echo "$s1 $s2"

gsed -i_bu2 "s|\<$s1\>|$s2|g" FIELD

gsed -i_bu2 "s|\<$s1\>|$s2|g" HISTORY

done < sub_map.txt</pre>

'''sub_map.txt''':
<pre>CR C3

NA N1

CW C4

HCR H2

HCW H3

HC H4

CT C6

OS4 O4

OC4 O5

HS4 H5

CS C5

CS4 C7</pre>

*Run '''./sub_script.sh'''
Note: this process may take a while, depending on the size of the file. Progress can be seen in the terminal (example shown in '''Figure 3'''), with each of the mappings specified in sub_map.txt considered in turn. The first few lines of the HISTORY file, before, and after, the relabelling can be seen in '''Figure 4'''.

[[Image:sub_map_mappings.png|thumb|center|800px|'''Figure 3'''. Example terminal output whilst running sub_script.sh ]]

[[Image:HISTORY-before-after.png|thumb|center|1000px|'''Figure 4'''. First few lines of the HISTORY file before '''(a)''' and after '''(b)''' the relabelling. ]]

3). Now our files are in the correct format, we can run MolCluster: '''./MolCluster.py'''

4). The first thing MolCluster does is to ask us to specify the directory containing the FIELD and HISTORY files. Our directory is called BMIM_MESO4_EXAMPLE. Once this has been specified, MolCluster will attempt to read the files and generate a summary of the system (from timestep 1 of the trajectory). This is shown in '''Figure 5''' for our system, and it can be seen that the information summarised by MolCluster is correct.

[[Image:MC-read-files-annotate.png|thumb|center|800px|'''Figure 5'''. After specifying the directory for the FIELD and HISTORY files, MolCluster summarises the bulk system information. ]]

5). MolCluster works out how many configurations in the HISTORY file (5000 in our example) and then asks us to specify the configurations we would like to cut a cluster from. In this case, we are going to select the '''[n]''' option (cut a cluster from every 'nth' configuration) and then specify n as an integer, in this case 1000 (i.e. n=1000, therefore cut a cluster every 1000th time step), '''Figure 6'''.

[[Image:MC-specify-config.png|thumb|center|800px|'''Figure 6'''. Specifying the configurations to create clusters for. ]]

6). We must now select how we would like to define the origin of the clusters to be cut. We are going to select option '''[AN]''' (atom number) and choose atom 1 to be the origin (for reference, in our case this is a C3 atom), '''Figure 7'''.

[[Image:origin-define.png|thumb|center|800px|'''Figure 7'''. Defining the cluster origin. ]]

7). An estimate of the number of atoms in regions with varying radii (with respect to our defined origin) is provided by MolCluster. We need to cut a cluster large enough to incorporate a reasonable number of ion pairs (bearing in mind that our cation alone, in all trans form, is over 9 Angstroms in width), but not so large that the calculation is unfeasible. The ideal size is still being investigated, but for now, let us specify a cluster radius of 15 Angstroms, '''Figure 8'''.

[[Image:cluster-radius-cut.png|thumb|center|900px|'''Figure 8'''. Choosing the cluster radius. ]]

File:Cluster-radius-cut.png

2014-12-17T16:54:54Z

Ca307:

Talk:Mod:Hunt Research Group/MolCluster

2014-12-17T16:28:24Z

Ca307: /* Step-By-Step Example: Ionic Liquid Clusters */

===What is MolCluster?===
MolCluster is a tool (developed by Vincent and Gabriel) that can be used to cut clusters from MD trajectories and create the input files for ChemShell.

To use MolCluster, you will need:
* The latest version of MolCluster (available from Vincent).
* Python version 2.7.6, or above.
* The HISTORY file from which the clusters are to be cut, and the corresponding FIELD file. Note: these need to be in DL_POLY format. If you have used the 'restart' option in DL_POLY, the header of the HISTORY file may need to be amended. Additional transformations of the HISTORY and FIELD files, to convert atom labels into an acceptable format for MolCluster/ChemShell, may also be required (example given later).

===Using MolCluster: Basic Instructions===

1. Create a directory within the main MolCluster directory. Put the required HISTORY and FIELD files here.

2. Load MolCluster: ./MolCluster.py

3. Requests directory name to be specified (this is the location of the FIELD and HISTORY files). After specifying, the code will attempt to read and give an overview of the system.

4. Need to specify which configurations to cut a cluster from. Two options are currently available:
::*'''[n]''': Cut a cluster every "nth" configuration. N.B: numbering starts from 1 (i.e. 1st timestep). Therefore, if you request n=1000, clusters for configurations 1, 1001, 2001 etc. will be created.
::*'''[c]''': Select a custom set of configurations i.e. you can specify exactly which configurations you want.

5. Once the configurations have been extracted, you will be asked to choose how the origin will be defined in the clusters to be cut. Options are:
::*'''[AN]''': Atom number
::*'''[AT]''': Atom type
::*'''[MN]''': Molecule number
::*'''[MT]''': Molecule type
::*'''[C]''': Custom coordinates

You will then be asked to specify the specific atom number/type etc.

6. MolCluster will estimate the number of atoms within a region, for a range of radii with respect to your origin. Use this information to help you decide on the total radius (in Angstroms) of the clusters to be cut. You will be asked to specify this.

7. MolCluster has two options for deciding which molecules to include/exclude at the boundary of the clusters being cut:
::*'''[H]''': Hard boundary - all atoms of a molecule must be within the cutoff radius for the molecule to be included.
::*'''[S]''': Soft boundary - if the centre of mass of a molecule is within the cutoff radius, the molecule will be included.

8. Specify if the clusters are required to be neutral ('''Y/N''').

9. Decide on the output formats:
::*'''[C]''': Generates a ChemShell fragment input file, with accompanying .xyz co-ordinates file.
::*'''[X]''': Generates the .xyz co-ordinates file only.

If '''[X]''' selected, the clusters will be cut, .xyz files generated and MolCluster will terminate.

If '''[C]''' selected, you will be asked if you would also like to generate the necessary ChemShell input files for a QM/MM optimisation ('''Y/N''').

10. If your answer to step 9 was '''[C]''' (generate a ChemShell fragment input) and '''Y''' (generate ChemShell input files for a QM/MM optimisation), you will then be asked to define the QM region. Available options are:
::*'''[S]''': Spherical region (or threshold) centred about the defined origin (although not necessarily spherical??!!)
:::: If '''[S]''' selected, MolCluster will estimate the number of atoms in regions defined by a range of radii. Specify the QM radius. This must be specified (in Angstroms) and must, obviously, be less than, or equal to, the total radius of the cluster. Soft boundary conditions are implemented.
::*'''[M]''': By number of molecules. Molecules closest to the origin will be included.
::*'''[A]''': By an upper limit of atoms. Only whole molecules & those closest to the origin included.
::*'''[C]''': Custom region i.e. can select molecules individually to be in the QM region
::*'''[O]''': Spherical regions centred about one or more origins

If options '''[C]''' or '''[O]''' selected, MolCluster will go straight to steps 11 and 12. Once the active region and the directory/filenames have been defined, MolCluster will then ask for the custom QM regions to be defined ''per'' cluster (see step 14).

11. Once the QM region has been defined, the active region must be defined. MolCluster will estimate the number of atoms that would be in the active and frozen regions for a range of active radii. This information can be used to help decide upon an appropriate active radius. This must be specified (in Angstroms) and must, obviously, be less than, or equal to, the total radius of the cluster. If all atoms are to be included, simple enter "ALL". Soft boundary conditions are implemented.

12. Specify the output directory (i.e. where your final clusters and associated files will be saved) and specify the base-name for the output files (e.g. if you type "cluster" here, your clusters will be saved as cluster_1, cluster_2 etc.).

13. Unless options 10 '''[C'''] or '''[O]''' were selected (in that case, see point 14), MolCluster will generate the specified clusters and then terminate.

14. If option '''[C]''' selected in step 10, MolCluster will at this point list all the molecules in the first cluster, along with the distances to the origin. You will be asked to list all the molecules to be included in the QM region for this cluster. The same procedure is carried out for each cluster, before the clusters are generated and MolCluster terminates.

If option '''[O]''' selected in step 10, you will be asked to specify how many QM regions are to be defined and then specify the origin type and size of each QM region.

===The Output Files===
* Each cluster will have its own directory within the directory named in step 12. These subdirectories will be named: '''cluster_1''', '''cluster_2'''...'''cluster_n'''.
* Within the main directory one will also find a file called '''molcluster.log''' and a file called '''bulk_system_info.txt'''.
::*'''molcluster.log''' is a record of the user responses to each of the MolCluster options (look at this if you have forgotten, for example, the cluster radius).
::*'''bulk_system_info.txt''' summarises information relating to the system before clusters are cut (e.g. number and type of molecules, total number of atoms, total system charge, atom labels within a molecule, atomic charges).

*If option '''[X]''' selected in step 9, each subdirectory '''cluster_n''' will contain:
::*The '''cluster_n.xyz''' coordinates file
::*'''system_info.txt''': Summary of the cluster (e.g. total number of molecules, total number of atoms, total charge)

*If option '''[C]''', '''Y''' selected in step 9, each subdirectory '''cluster_n''' will contain:
::*The '''cluster_n.xyz''' coordinates file
::*'''system_info.txt''': Summary of the cluster (e.g. total number of molecules, total number of atoms, total charge)
::*The '''cluster_n.chm''' coordinates file. This will be used to create the '''cluster.pun''' ChemShell input file.
::*'''cluster_tiered.xyz''': xyz coordinates with the QM, active and frozen regions defined (all QM atoms listed as X1 (X=element symbol), active as X2 and frozen as X3). This file can be used to easily visualise the different regions in VMD.
::*'''conn.txt''' : the connectivity data needed by ChemShell
::*'''ff.dat''' : the forcefield in ChemShell format
::*'''opt.chm''': ChemShell input file. Options for the ChemShell optimisation specified here.

===Step-By-Step Example: Ionic Liquid Clusters===

Our example system:
* 256 ion pairs of [C4C1im][MeSO4]
* In total, the production run is 20ns in length; 4 lots of 5ns employing the "restart" keyword in DL_Poly.
* Our aim is to cut clusters from the last 5ns of the trajectory and create the input files for a ChemShell optimisation.

1). Create a directory within the main MolCluster directory and put the '''HISTORY''' and '''FIELD''' files here. Our directory will be called: '''BMIM_MESO4_EXAMPLE'''.

2). We now need to check to see if the HISTORY and FIELD files are in the correct format.

*As the ''restart'' keyword has been employed, two lines are missing from the header of the HISTORY file, '''Figure 1a''' and '''1b'''. MolCluster does not like this. Therefore, we need to add in the two lines that it is expecting to see, '''Figure 1c'''.

[[Image:MolCluster-HISTORY-header.png|frame|center|850px|'''Figure 1'''. Headers from selected HISTORY files '''(a)''' first 5ns of our simulation, without the use of the restart keyword, '''(b)''' last 5ns of our simulation with the restart keyword and '''(c)''' same HISTORY file as in (b), with missing lines added in. ]]

*The second problem we need to address is the atom labelling. The original atom labelling for [C4C1im][MeSO4], as used in the DL_Poly simulation, is shown in '''Figure 2a'''. Unfortunately, ChemShell has issues with this. To keep ChemShell happy, we have to change the atom labels in the HISTORY and FIELD files to the format ''elementsymbolnumber'' e.g. C2 rather than CR. Thankfully, this is quite easy to do using a script ('''sub_script.sh''', see below) written by Vincent. Firstly, however, we need to decide upon the new atom labelling. This is shown in '''Figure 2b''' for our example system. '''sub_script.sh''' requires that we have defined the atom label mappings in a file called '''sub_map.txt''' (also shown below for this system).

[[Image:BMIM-MESO4-numbering.png|thumb|center|800px|'''Figure 2'''. Original atom labelling (as used in DL_POLY MD simulation) shown in '''(a)''' and new atom labelling (suitable for MolCluster) shown in '''(b)'''. Within '''(b)''', atom labels that already had the correct format are in red. ]]

'''sub_script.sh''':

<pre>#!/bin/bash

while read line

do

#echo $line

s1=$(echo $line | awk '{ print $1 }')

s2=$(echo $line | awk '{ print $2 }')

echo "$s1 $s2"

gsed -i_bu2 "s|\<$s1\>|$s2|g" FIELD

gsed -i_bu2 "s|\<$s1\>|$s2|g" HISTORY

done < sub_map.txt</pre>

'''sub_map.txt''':
<pre>CR C3

NA N1

CW C4

HCR H2

HCW H3

HC H4

CT C6

OS4 O4

OC4 O5

HS4 H5

CS C5

CS4 C7</pre>

*Run '''./sub_script.sh'''
Note: this process may take a while, depending on the size of the file. Progress can be seen in the terminal (example shown in '''Figure 3'''), with each of the mappings specified in sub_map.txt considered in turn. The first few lines of the HISTORY file, before, and after, the relabelling can be seen in '''Figure 4'''.

[[Image:sub_map_mappings.png|thumb|center|800px|'''Figure 3'''. Example terminal output whilst running sub_script.sh ]]

[[Image:HISTORY-before-after.png|thumb|center|1000px|'''Figure 4'''. First few lines of the HISTORY file before '''(a)''' and after '''(b)''' the relabelling. ]]

3). Now our files are in the correct format, we can run MolCluster: '''./MolCluster.py'''

4). The first thing MolCluster does is to ask us to specify the directory containing the FIELD and HISTORY files. Our directory is called BMIM_MESO4_EXAMPLE. Once this has been specified, MolCluster will attempt to read the files and generate a summary of the system (from timestep 1 of the trajectory). This is shown in '''Figure 5''' for our system, and it can be seen that the information summarised by MolCluster is correct.

[[Image:MC-read-files-annotate.png|thumb|center|800px|'''Figure 5'''. After specifying the directory for the FIELD and HISTORY files, MolCluster summarises the bulk system information. ]]

5). MolCluster works out how many configurations in the HISTORY file (5000 in our example) and then asks us to specify the configurations we would like to cut a cluster from. In this case, we are going to select the '''[n]''' option (cut a cluster from every 'nth' configuration) and then specify n as an integer, in this case 1000 (i.e. n=1000, therefore cut a cluster every 1000th time step), '''Figure 6'''.

[[Image:MC-specify-config.png|thumb|center|800px|'''Figure 6'''. Specifying the configurations to create clusters for. ]]

6). We must now select how we would like to define the origin of the clusters to be cut. We are going to select option '''[AN]''' (atom number) and choose atom 1 to be the origin (for reference, in our case this is a C3 atom), '''Figure 7'''.

[[Image:origin-define.png|thumb|center|800px|'''Figure 7'''. Defining the cluster origin. ]]

7). An estimate of the number of atoms in regions with varying radii (with respect to our defined origin) is provided by MolCluster. We need to cut a cluster large enough to incorporate a reasonable number of ion pairs (bearing in mind that our cation alone, in all trans form, is over 9 Angstroms in width), but not so large that the calculation is unfeasible. The ideal size is still being investigated, but for now, let us specify a cluster radius of 15 Angstroms, '''Figure 8'''.

File:Origin-define.png

2014-12-17T16:06:56Z

Ca307:

File:MC-specify-config.png

2014-12-17T15:43:21Z

Ca307:

Talk:Mod:Hunt Research Group/MolCluster

2014-12-17T15:32:17Z

Ca307: /* Step-By-Step Example: Ionic Liquid Clusters */

Talk:Mod:Hunt Research Group/MolCluster

2014-12-17T15:02:42Z

Ca307: /* Step-By-Step Example: Ionic Liquid Clusters */

File:MC-read-files-annotate.png

2014-12-17T14:58:56Z

Ca307:

Talk:Mod:Hunt Research Group/MolCluster

2014-12-17T14:24:22Z

Ca307: /* Step-By-Step Example: Ionic Liquid Clusters */

File:HISTORY-before-after.png

2014-12-17T14:15:09Z

Ca307:

Talk:Mod:Hunt Research Group/MolCluster

2014-12-17T13:56:03Z

Ca307: /* Using MolCluster: Basic Instructions */

Talk:Mod:Hunt Research Group/MolCluster

2014-12-17T12:26:26Z

Ca307: /* Step-By-Step Example: Ionic Liquid Clusters */