[CP2K:5153] FES
Taha Salavati-fard
t.salav... at gmail.com
Wed Mar 26 17:26:58 UTC 2014
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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> <fes.dat>
>
>
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