[CP2K:5151] FES

Taha Salavati-fard t.salav... at gmail.com
Wed Mar 26 15:15:14 UTC 2014


here it is


On Wed, Mar 26, 2014 at 10:53 AM, Teodoro Laino <teodor... at gmail.com>wrote:

> please, post that file.
>
> On 26 Mar 2014, at 14:21, Taha Salavati-fard <t.salav... at gmail.com>
> wrote:
>
> Thanks Teo.
> Problem might be due to old linux on the cluster I am using. I am going to
> try it again on my laptop and will let you know.
> Thanks for great helps.
>
>
>
> On Wed, Mar 26, 2014 at 1:09 AM, Teodoro Laino <teodor... at gmail.com>
> wrote:
>
>> On my laptop, when I run:
>>
>> fes.sopt -cpmd -ndim 2
>>
>> I get the fes.dat file attached. Which is everything but not zero.
>> Can you please attach your fes.dat output file generated by fes.sopt ?
>>
>> Teo
>>
>>
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>>
>> On 25 Mar 2014, at 16:25, Taha Salavati-fard <t.salav... at gmail.com>
>> wrote:
>>
>> Yes of course,
>> Here they are!
>>
>>
>> On Tue, Mar 25, 2014 at 11:16 AM, Teodoro Laino <teodor... at gmail.com>
>>  wrote:
>>
>>> can you post your files?
>>>
>>> On 25 Mar 2014, at 16:10, Taha Salavati-fard <t.salav... at gmail.com>
>>> wrote:
>>>
>>> Dear Teo,
>>>
>>> I've tried that but still zeros!
>>>
>>> FES|  Parsing file:   <colvar_mtd>
>>>
>>> **********************************************************************
>>> FES|  Parameters for FES:
>>>
>>> FES|  NDIM         ::           2
>>> FES|  NWD          ::           2
>>> FES|  HILLS        ::        2156
>>> FES|  COLVAR #   1 ::     (  2.294 , 10.688)               (   MAPPED)
>>> FES|  COLVAR #   2 ::     (  2.278 , 10.693)               (   MAPPED)
>>> FES|  NGRID        ::         100    100
>>> FES|  DX           ::       0.085  0.085
>>> FES|  CUTOFF       ::     .10000E-06
>>> **********************************************************************
>>>
>>>
>>> FES|  Computing Free Energy Surface
>>> FES|  Mapping Gaussians ::  10 %
>>> FES|  Mapping Gaussians ::  20 %
>>> FES|  Mapping Gaussians ::  30 %
>>> FES|  Mapping Gaussians ::  40 %
>>> FES|  Mapping Gaussians ::  50 %
>>> FES|  Mapping Gaussians ::  60 %
>>> FES|  Mapping Gaussians ::  70 %
>>> FES|  Mapping Gaussians ::  80 %
>>> FES|  Mapping Gaussians ::  90 %
>>> FES|  Mapping Gaussians :: 100 %
>>> FES|  Dumping FES structure in file: < fes.dat >
>>>
>>> FES| NORMAL FES TERMINATION.
>>>
>>>
>>>
>>> On Tue, Mar 25, 2014 at 3:13 AM, Teodoro Laino <teodor... at gmail.com>
>>>  wrote:
>>>
>>>> fes.sopt -help
>>>>
>>>> will give you an help.. Try to go though it.
>>>>
>>>> You'll have to specify -ndim and also -ndw (if I remember correctly).
>>>>
>>>> Teo
>>>>
>>>> On 25 Mar 2014, at 00:50, T. Salavati fard <t.salav... at gmail.com>
>>>> wrote:
>>>>
>>>> Thanks all for your reply.
>>>> I've compiled fes and it seems working. But the problem is when I use
>>>> it, in fes.dat all values are zero.
>>>> I've used following synatax:
>>>> fes.sopt [-cpmd] in a folder which contains colvar and parvar files.
>>>> any ideas?
>>>> Thanks in advance--
>>>>
>>>> On Monday, March 24, 2014 2:36:48 AM UTC-4, Teo wrote:
>>>>>
>>>>>
>>>>> On 24 Mar 2014, at 00:00, Ole Schütt <o.... at schuett.name> wrote:
>>>>>
>>>>>
>>>>> Actually, if you are using the latest svn version you now have to type
>>>>> "make graph", because the names of the make-targets now match the names of
>>>>> the executables. Alternatively, you can just call make without any targets,
>>>>> which will build all executables including the fes tool.
>>>>>
>>>>>
>>>>> Not entirely true - using the SVN version, one can still compile FES,
>>>>> by typing
>>>>>
>>>>> > make fes
>>>>>
>>>>> alternatively also
>>>>>
>>>>> > make graph
>>>>>
>>>>> works..
>>>>>
>>>>> Teo
>>>>>
>>>>>
>>>>>
>>>>> -Ole
>>>>>
>>>>>
>>>>>
>>>>> On 2014-03-23 22:39, Ari Paavo Seitsonen wrote:
>>>>>
>>>>> Dear T. Salavati fard,
>>>>>   In <cp2k-root>/src/metadyn_tools/, if you are using the latest
>>>>> version? It used to be in <cp2k-root>/tools/metadyn/ earlier. One
>>>>> compiles by typing "make fes" in '<cp2k-root>/makefiles'.
>>>>>     Greetings from Zurich,
>>>>>        apsi
>>>>> 2014-03-23 21:52 GMT+01:00 T. Salavati fard
>>>>> <t.sal... at gmail.com>:
>>>>>
>>>>> Dear all
>>>>> I am CPMD user. I am doing metadynamics calculations and I need to
>>>>> reconstruct FES. I know there is a code by Teo to reconstruct free
>>>>> energy surface using colvar and parvar files.
>>>>> My problem is finding FES program source!! I couldn't find that code
>>>>> to compile and try..
>>>>> I appreciate your helps--Thanks
>>>>> --
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>>>>> --
>>>>> -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=
>>>>> -=*=-=*=-=*=-=*=-
>>>>>   Ari Paavo Seitsonen / Ari.P... at iki.fi /
>>>>> http://www.iki.fi/~apsi/ [3]
>>>>>   Institut für Chemie der Universität Zürich
>>>>>   Tel: +41 44 63 55 44 97  /  Mobile: +41 79 71 90 935
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>>>
>>>
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>>
>>
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>> <colvar_mtd><parvar_mtd>
>>
>>
>>
>>
>
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