[CP2K-user] [CP2K:19008] Re: Plotting Metadynamics Colvar with graph.psmp

[Marcella Iannuzzi]

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?
>>>>>>
>>>>>>
>>>>>>

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