[CP2K:5107] FES

Teodoro Laino teodor... at gmail.com
Wed Mar 26 15:32:48 UTC 2014


mmm… strange..  it could really be some issue with the compiler..

Teo

On 26 Mar 2014, at 16:15, Taha Salavati-fard <t.salav... at gmail.com> wrote:

> 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
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>>> 
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>>> <colvar_mtd><parvar_mtd>
>> 
>> 
>> 
>> 
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> <fes.dat>

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