[CP2K-user] [CP2K:20730] Re: Plotting Metadynamics Colvar with graph.psmp

[Saurabh Negi]

Hii Liam H

I hope you are doing good.
I tried this and I am getting only 8 points in mep.data

*How can we increase number of points in mep.data?*
Thank you 

On Friday, June 30, 2023 at 9:25:06 PM UTC+5:30 Liam H wrote:

> Hi Marcella,
>
> Thank you that makes sense, I see the number of CVs do matter, I've 
> replotted using only 2 ndim=ndw and the data looks much better. I can find 
> the minima as well using -find-minima. 
>
> I also figured out how to make use of the -find-path option by pasting the 
> minima floats obtained from the -find-minima output for -point-a and 
> -point-b, so I'll post it here incase anyone else is wondering.
>
> input:
>
> FES|  Mapping Gaussians :: 100 %
> FES|  Dumping FES structure in file: < fes.dat >
>  Iteration nr.           1  1.504066111949192E-002
>
> graph.psmp -cp2k -file input.restart -ndim 2 -ndw 1 2 -out fes.dat 
> -find-minima
>
> output:
>
> FES|  Dumping FES structure in file: < fes.dat >
> FES| Trust hyper-radius     10    10 which is equivalent to:     0.191530 
>    0.483382
> FES| Minimum found (    2.727613    2.186932 ). FES value =    -0.001262 
> Hartree. Number of Iter:    102
> FES| Minimum found (    3.017643    2.627451 ). FES value =    -0.019981 
> Hartree. Number of Iter:    101
>
>
> then taking 2 relevant minima and pasting one after another with exact 
> same digits
>
> graph.psmp -cp2k -file input.restart -ndim 2 -ndw 1 2 -out fes.dat 
> -find-path -point-a  2.727613    2.186932 -point-b 3.017643    2.627451
>
> FES|  Mapping Gaussians :: 100 %
> FES|  Dumping FES structure in file: < fes.dat >
>  Iteration nr.           1  1.504066111949192E-002
> ...
> ..
>  MEP saved on <mep.data> file.
>
> FES| NORMAL FES TERMINATION.
>
> Best regards,
> Liam
>
> On Wednesday, June 28, 2023 at 6:02:03 AM UTC-2:30 Marcella Iannuzzi wrote:
>
>>
>> Dear ...
>>
>> The search of minima using "graph" is possible only considering the whole 
>> metadynamics space, no for projections of it to lower dimension.
>> ndw=ndim  and ndim should be the actual dimension of the space, otherwise 
>> whatever you get is wrong.
>> Regards
>> Marcella
>>
>>
>> On Wednesday, June 28, 2023 at 1:44:11 AM UTC+2 Liam H wrote:
>>
>>> More importantly though, since I do have the minima, I'd like to figure 
>>> how to use the -find-path option.
>>>
>>> graph.psmp -cp2k -file input.restart -find-path -ndim 2 -ndw 1  2  -out 
>>> fes.dat
>>>
>>> gives the output:
>>>  ABORT in metadyn_tools/graph.F:362 -find-path requires the 
>>> specification of -po
>>>  int-a and -point-b !
>>>
>>> So i've attempted a few combinations
>>> graph.psmp -cp2k -file input.restart -find-path -point-a -point-b -ndim 
>>> 2 -ndw 1  2  -out fes.dat
>>>
>>> But I haven't been able to find any examples of the particular format 
>>> for specifying -point-a and -point-b
>>>
>>> ive tried in the format of the COLVAR , specifying XY -point-a  2.070, 
>>>  6.416 -point-b 0.248,  3.076
>>> ive tried XYZ, ive tried without comma, ive tried line number
>>>
>>> If anyone has any information on the format of the -find-path -point-a 
>>> -point-b function it would be very much appreciated!
>>>
>>>
>>> On Tuesday, June 27, 2023 at 4:15:45 PM UTC-2:30 Liam H wrote:
>>>
>>>> Yes that's right although it seems to work even though I sampled 6 it 
>>>> will work with  -ndim 2 or  -ndim 3,
>>>>
>>>> However, the issue i'm having now.. when using the -find-minima command:
>>>>
>>>> Also this example is with only 3 CV to simplify, still the same issue 
>>>> with 6.
>>>>
>>>> it works perfectly when using 
>>>>
>>>> graph.psmp -cp2k -file input.restart -find-minima -ndim 2 -ndw 1  2  
>>>> -out fes.dat
>>>>
>>>> however if I try the same thing even with the same two CV with -ndim 3, 
>>>> it fails for both -ndw 1 2 and -ndw 1 3
>>>> Here is an example with the output.
>>>>
>>>> The data gets plotted but the -find-minima fails, it works when i use 
>>>> -ndim 2 , it finds 9 minima, but in this case then i cannot access CV3 -ndw 
>>>> 1 3
>>>>
>>>>
>>>> graph.psmp -cp2k -file input.restart -find-minima -ndim 3 -ndw 1  2  
>>>> -out fes.dat
>>>>
>>>> FES|  Parsing file:   <input.restart>
>>>>
>>>> **********************************************************************
>>>> FES|  Parameters for FES:
>>>>
>>>> FES|  NDIM         ::           3
>>>> FES|  NWD          ::           2
>>>> FES|  HILLS        ::         120
>>>> FES|  COLVAR #   1 ::     (  2.070 ,  6.416)               (   MAPPED)
>>>> FES|  COLVAR #   3 ::     (  0.248 ,  3.076)               (   MAPPED)
>>>> FES|  COLVAR #   2 ::     (  1.784 ,  3.636)               (NO MAPPED)
>>>> FES|  NGRID        ::         100    100
>>>> FES|  DX           ::       0.044  0.029
>>>> FES|  CUTOFF       ::     .10000E-05
>>>> **********************************************************************
>>>>
>>>>
>>>> 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 ::  70 %
>>>> FES|  Mapping Gaussians ::  80 %
>>>> FES|  Mapping Gaussians ::  90 %
>>>> FES|  Mapping Gaussians :: 100 %
>>>> FES|  Mapping Gaussians :: 100 %
>>>> FES|  Dumping FES structure in file: < FES10.dat >
>>>>  ABORT in metadyn_tools/graph_methods.F:279 Not implemented for 
>>>> projected FES!
>>>> forrtl: error (76): Abort trap signal
>>>>
>>>> On Tuesday, June 27, 2023 at 1:55:32 PM UTC-2:30 Marcella Iannuzzi 
>>>> wrote:
>>>>
>>>>>
>>>>> Hello,
>>>>>
>>>>> Both are wrong, the dimension of the sampled space is 6 therefore 
>>>>> -ndim 6 is the correct input.
>>>>> Regards
>>>>> Marcella
>>>>>
>>>>> On Tuesday, June 27, 2023 at 6:01:50 PM UTC+2 Liam H wrote:
>>>>>
>>>>>> My concern now is that the plot I get using
>>>>>>
>>>>>> graph.psmp -cp2k -file input.restart -ndim 2 -ndw 1  2  -out fes.dat
>>>>>>
>>>>>> Is not identical when doing -ndim 3 and only mapping the first two CV
>>>>>>
>>>>>> graph.psmp -cp2k -file input.restart -ndim 3 -ndw 1  2  -out fes.dat
>>>>>>
>>>>>> I am not sure how this could be, raw data itself looks correct but 
>>>>>> when plotting the surface it isn't the same the minimums and saddlepoint 
>>>>>> are completely different when plotting the same CV
>>>>>>
>>>>>> On Tuesday, June 27, 2023 at 1:23:39 PM UTC-2:30 Liam H wrote:
>>>>>>
>>>>>>> Nevermind I figured it out, by changing the -ndim to a higher number 
>>>>>>> , it still allows you to map COLVAR -ndw 1 3
>>>>>>>
>>>>>>> graph.psmp -cp2k -file input.restart -ndim 2 -ndw 1  3  -out fes.dat 
>>>>>>> Doesnt work
>>>>>>>
>>>>>>> graph.psmp -cp2k -file input.restart -ndim 3 -ndw 1  3  -out fes.dat
>>>>>>> works
>>>>>>> On Tuesday, June 27, 2023 at 12:21:45 PM UTC-2:30 Liam H wrote:
>>>>>>>
>>>>>>>> Hello.
>>>>>>>>
>>>>>>>> I have been running metadynamics simulations with multiple colvar, 
>>>>>>>> 6 in this case.
>>>>>>>>
>>>>>>>> This is because I want to be able to plot different surfaces with 
>>>>>>>> different colvar, because I can't visualize a 6 dimensional surface.
>>>>>>>>
>>>>>>>> graph.psmp -cp2k -file input.restart -ndim 2 -ndw 1 2 -out fes.dat
>>>>>>>>
>>>>>>>> This works fine to give me the 3D surface, (cv1,cv2,energy)
>>>>>>>> I would like to plot (cv1,cv3,energy) 
>>>>>>>>
>>>>>>>> but running the command:
>>>>>>>> graph.psmp -cp2k -file input.restart -ndim 2 -ndw 1 3 -out fes.dat
>>>>>>>>
>>>>>>>> Does not work.
>>>>>>>>
>>>>>>>> graph.psmp -cp2k -file input.restart -ndim 6 -ndw 1 2 3 4 5 6 -out 
>>>>>>>> fes.dat
>>>>>>>>
>>>>>>>> This works but produces such a massive file its not practical to 
>>>>>>>> try and plot the 2d surface..
>>>>>>>> Is there any way to specify which cvs to be used in the plot, 
>>>>>>>> without plotting them all at once?
>>>>>>>>
>>>>>>>>
>>>>>>>>

-- 
You received this message because you are subscribed to the Google Groups "cp2k" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+unsubscribe at googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/9e4819d7-6bc1-4286-8962-739f30bff0a4n%40googlegroups.com.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20240926/9cf23997/attachment.htm>