[CP2K-user] [CP2K:18998] Re: Plotting Metadynamics Colvar with graph.psmp

[Liam H]

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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