[CP2K:5110] FES
Teodoro Laino
teodor... at gmail.com
Wed Mar 26 19:42:48 UTC 2014
which compiler ?
On 26 Mar 2014, at 18:26, Taha Salavati-fard <t.salav... at gmail.com> wrote:
> Dear Teo,
>
> I've compiled it again on different machine with latest ubuntu.
> fes.dat this time contains zeros and NaNs !!
> I used exactly same files that I have sent to you!
>
>
>
> On Wed, Mar 26, 2014 at 11:32 AM, Teodoro Laino <teodor... at gmail.com> wrote:
> 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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>>
>>
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>> <fes.dat>
>
>
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