[CP2K:5156] FES
Taha Salavati-fard
t.salav... at gmail.com
Wed Mar 26 19:45:25 UTC 2014
I guess it is gfortran
On Wed, Mar 26, 2014 at 3:42 PM, Teodoro Laino <teodor... at gmail.com>wrote:
> 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
>>>>>>> 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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>>
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>> <fes.dat>
>>
>>
>>
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>
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