[CP2K-user] [CP2K:19001] Re: Plotting Metadynamics Colvar with graph.psmp

[Liam H]

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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