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| This is part of the cltools module |
sum_hills is a tool that allows one to to use plumed to post-process an existing hills/colvar file
--help/-h | ( default=off ) print this help |
--help-debug | ( default=off ) print special options that can be used to create regtests |
--negbias | ( default=off ) print the negative bias instead of the free energy (only needed with well tempered runs and flexible hills) |
--nohistory | ( default=off ) to be used with –stride: it splits the bias/histogram in pieces without previous history |
--mintozero | ( default=off ) it translate all the minimum value in bias/histogram to zero (useful to compare results) |
--hills | specify the name of the hills file |
--histo | specify the name of the file for histogram a colvar/hills file is good |
--stride | specify the stride for integrating hills file (default 0=never) |
--min | the lower bounds for the grid |
--max | the upper bounds for the grid |
--bin | the number of bins for the grid |
--spacing | grid spacing, alternative to the number of bins |
--idw | specify the variables to be used for the free-energy/histogram (default is all). With –hills the other variables will be integrated out, with –histo the other variables won't be considered |
--outfile | specify the output file for sumhills |
--outhisto | specify the output file for the histogram |
--kt | specify temperature in energy units for integrating out variables |
--sigma | a vector that specify the sigma for binning (only needed when doing histogram |
--fmt | specify the output format |
a typical case is about the integration of a hills file:
plumed sum_hills --hills PATHTOMYHILLSFILE
The default name for the output file will be fes.dat Note that starting from this version plumed will automatically detect the number of the variables you have and their periodicity. Additionally, if you use flexible hills (multivariate Gaussian kernels), plumed will understand it from the HILLS file.
The sum_hills tool will also accept multiple files that will be integrated one after the other
plumed sum_hills --hills PATHTOMYHILLSFILE1,PATHTOMYHILLSFILE2,PATHTOMYHILLSFILE3
if you want to integrate out some variable you do
plumed sum_hills --hills PATHTOMYHILLSFILE --idw t1 --kt 0.6
where with –idw you define the variables that you want all the others will be integrated out. –kt defines the temperature of the system in energy units. (be consistent with the units you have in your hills: plumed will not check this for you) If you need more variables then you may use a comma separated syntax
plumed sum_hills --hills PATHTOMYHILLSFILE --idw t1,t2 --kt 0.6
You can define the output grid only with the number of bins you want while min/max will be detected for you
plumed sum_hills --bin 99,99 --hills PATHTOMYHILLSFILE
or full grid specification
plumed sum_hills --bin 99,99 --min -pi,-pi --max pi,pi --hills PATHTOMYHILLSFILE
You can of course use numbers instead of -pi/pi.
You can use a –stride keyword to have a dump each bunch of hills you read
plumed sum_hills --stride 300 --hills PATHTOMYHILLSFILE
You can also have, in case of well tempered metadynamics, only the negative bias instead of the free energy through the keyword –negbias
plumed sum_hills --negbias --hills PATHTOMYHILLSFILE
Here the default name will be negativebias.dat
From time to time you might need to use HILLS or a COLVAR file as it was just a simple set of points from which you want to build a free energy by using -(1/beta)log(P) then you use –histo
plumed sum_hills --histo PATHTOMYCOLVARORHILLSFILE --sigma 0.2,0.2 --kt 0.6
in this case you need a –kt to do the reweighting and then you need also some width (with the –sigma keyword) for the histogram calculation (actually will be done with Gaussian kernels, so it will be a continuous histogram) Here the default output will be histo.dat. Note that also here you can have multiple input files separated by a comma.
Additionally, if you want to do histogram and hills from the same file you can do as this
plumed sum_hills --hills --histo PATHTOMYCOLVARORHILLSFILE --sigma 0.2,0.2 --kt 0.6
The two files can be eventually the same
Another interesting thing one can do is monitor the difference in blocks as a metadynamics goes on. When the bias deposited is constant over the whole domain one can consider to be at convergence. This can be done with the –nohistory keyword
plumed sum_hills --stride 300 --hills PATHTOMYHILLSFILE --nohistory
and similarly one can do the same for an histogram file
plumed sum_hills --histo PATHTOMYCOLVARORHILLSFILE --sigma 0.2,0.2 --kt 0.6 --nohistory
just to check the hypothetical free energy calculated in single blocks of time during a simulation and not in a cumulative way
Output format can be controlled via the –fmt field
plumed sum_hills --hills PATHTOMYHILLSFILE --fmt %8.3f
where here we chose a float with length of 8 and 3 digits
The output can be named in a arbitrary way :
plumed sum_hills --hills PATHTOMYHILLSFILE --outfile myfes.dat
will produce a file myfes.dat which contains the free energy.
If you use stride, this keyword is the suffix
plumed sum_hills --hills PATHTOMYHILLSFILE --outfile myfes_ --stride 100
will produce myfes_0.dat, myfes_1.dat, myfes_2.dat etc.
The same is true for the output coming from histogram
plumed sum_hills --histo HILLS --kt 2.5 --sigma 0.01 --outhisto myhisto.dat
is producing a file myhisto.dat while, when using stride, this is the suffix
plumed sum_hills --histo HILLS --kt 2.5 --sigma 0.01 --outhisto myhisto_ --stride 100
that gives myhisto_0.dat, myhisto_1.dat, myhisto_3.dat etc..
1.8.14