plumed
PRINT grid files may benefit from a FLAG to ensure one is printing a grid
@gtribello what do you think?
(I attach your conversation in the mailing list)
Hello,
Thank you very much for your answer.
I think I might have found a tiny bug in the parser. I get a .grid file if I do this:
PRINT FILE=fes.grid
But if I do:
PRINT FILE=./myfolder/fes.grid or PRINT FILE=./fes.grid
I don't get a grid file, I get what I described above. I don't know if its worth fixing but it is worth knowing at least.
Best Sergio
On Monday, May 6, 2019 at 7:47:49 PM UTC+2, Gareth Tribello wrote: Hello
You need to make sure you have a .grid at the end of the file name that you are printing to.
Gareth
On 4 May 2019, at 14:56, Sergio Perez-Conesa [email protected] wrote:
Hello,
I tried using a script similar to the one I used some time ago and I am getting some problems in the printing. It does not print it out in a grid format but rather something like:
#! FIELDS time tds.1.1 tds.2.1 tds.3.1 tds.4.1 tds.5.1 tds.6.1 tds.7.1 ...
I tried using DUMPGRID but it doesn't seem to use this keyword anymore.
Thank you!
Sergio On Friday, July 13, 2018 at 12:32:12 PM UTC+2, Sergio Perez-Conesa wrote: By the way if anyone else is interested in using it. You can also do 2D grids using ARG1=X ARG2=Y and GRID=300,300 etc. It would be nice if these ACTIONS would make it to the main branch.
On Monday, July 9, 2018 at 3:12:39 PM UTC+2, Sergio Perez-Conesa wrote: The final script is:
#READ Variable ee: READ FILE=COLVAR IGNORE_TIME VALUES=ener s2: READ FILE=COLVAR IGNORE_TIME VALUES=s2
#If it is a METAD simulation: metad: READ FILE=COLVAR IGNORE_TIME VALUES=metad.rbias www: REWEIGHT_BIAS ARG=metad.rbias TEMP=300
Build the numerator of our weighted average. If the simulation is unbiased remove LOGWEIGHTS
enumer_kde: KDE ARG1=s2 HEIGHTS=ee GRID_MIN=-8. GRID_MAX=0. GRID_BIN=100 KERNEL=DISCRETE UNORMALIZED UPDATE_FROM=400000 enumer: AVERAGE ARG=enumer_kde STRIDE=1 LOGWEIGHTS=www
And the denominator. If the simulation is unbiased remove LOGWEIGHTS
edenom_kde: KDE ARG1=s2 GRID_MIN=-8. GRID_MAX=0. GRID_BIN=100 KERNEL=DISCRETE UNORMALIZED UPDATE_FROM=400000 edenom: AVERAGE ARG=edenom_kde LOGWEIGHTS=www
And the average energy on the grid
av_eng: MATHEVAL ARG1=enumer ARG2=edenom FUNC=x/y PERIODIC=NO
Free energy
free_e: CONVERT_TO_FES ARG=edenom TEMP=300.
And the T\Delta S
tds: MATHEVAL ARG1=free_e ARG2=av_eng FUNC=x-y PERIODIC=NO
Print average energy
PRINT ARG=av_eng FILE=average_energy.grid
Print free energy
PRINT ARG=free_e FILE=fes.grid
Print entropy
PRINT ARG=tds FILE=tds.grid
Gaussian Kernels can be used removing KERNEL=DISCRETE and add a BANDWIDTH=0.1.
Thank you! Sergio
On Tuesday, July 3, 2018 at 1:32:51 PM UTC+2, Gareth Tribello wrote: Ok can you send me some input off list so I can take a look please? I am about to take off on a flight currently so I won't be able to respond immediately.
Sorry about that. Gareth
On Tue, 3 Jul 2018, 12:28 Sergio Perez-Conesa, [email protected] wrote: Yes that is the case. They are both equal. It seems to be doing a regular histogram ignoring HEIGHTS.
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@gtribello in general I think that relying on file extensions is very old style.. we can keep that but I would also add flags