PLUMED
This is part of the generic module

Embed a separate PLUMED instance.

This command can be used to embed a separate PLUMED instance. Only required atoms will be passed to that instance, using an interface that is similar to the one used when calling PLUMED from the NAMD engine.

Notice that the two instances are running in the same UNIX process, so that they cannot be perfectly isolated. However, most of the features are expected to work correctly.

Notes:

  • The LOAD action will not work correctly since registers will be shared among the two instances. In particular, the loaded actions will be visible to both guest and host irrespective of where they are loaded from. This can be fixed and will probably be fixed in a later version.
  • CHDIR is not thread safe. However, in most implementations there will be a single process running PLUMED, with perhaps multiple OpenMP threads spawn in order to parallelize the calculation of individual variables. So, this is likely not a problem.
  • MPI is working correctly. However, notice that the guest PLUMED will always run with a single process. Multiple replicas should be handled correctly.

As an advanced feature, one can use the option KERNEL to select the version of the guest PLUMED instance. In particular, an empty KERNEL (default) implies that the guest PLUMED instance is the same as the host one (no library is loaded). On the other hand, KERNEL=/path/to/libplumedKernel.so will allow specifying a library to be loaded for the guest instance. In addition to those mentioned above, this feature has limitations mostly related to clashes in the symbols defined in the different instances of the PLUMED library. Clashes might be due by synonymous symbols from the PLUMED library or synonymous symbols from libraries linked to PLUMED, and would differ depending on the operating system you are using:

  • On OSX:
    • Symbols from the PLUMED library would clash. The only way to avoid is to load PLUMED dynamically:
      • If you are are using PLUMED with an MD code, it should be patched with --runtime.
      • If you are using PLUMED driver, you should launch the plumed-runtime executable (contained in the prefix/lib/plumed/ directory) and export PLUMED_KERNEL equal to the path of the host kernel library (as usual in runtime loading). Notice that as of PLUMED 2.10 we load kernels with RTLD_LOCAL by default.
      • Symbols from dependent libraries should not clash since, as of version 2.5, we are using two-level namespace. Problems when loading previous versions should anyway be solved using runtime mode as explained above.
  • On Linux, any KERNEL should in principle work correctly. To achieve namespace separation we are loading the guest kernel with RTLD_DEEPBIND. However, this might create difficult to track problems in other linked libraries.
  • On Unix systems where RTLD_DEEPBIND is not available kernels will not load correctly.

  • In general, there might be unexpected crashes. Particularly difficult are situations where different kernels were compiled with different libraries.

    Todo:
Examples

Here an example plumed file:

Click on the labels of the actions for more information on what each action computes
tested on master
# plumed.dat
p: PLUMED 
FILE
input file for the guest PLUMED instance 
=plumed2.dat 
PRINT 
ARG
compulsory keyword 
the labels of the values that you would like to print to the file 
=p.bias 
FILE
the name of the file on which to output these quantities 
=COLVAR

plumed2.dat can be an arbitrary plumed input file, for instance

Click on the labels of the actions for more information on what each action computes
tested on master





Now a more useful example. Imagine that you ran simulations using two different PLUMED input files. The files are long and complex and there are some clashes in the name of the variables (that is: same names are used in both files, same files are written, etc). In addition, files might have been written using different units (see UNITS`). If you want to run a single simulation with a bias potential that is the sum of the two bias potentials, you can:
    

  • Place the two input files, as well as all the files required by plumed, in separate directories directory1 and directory2.
    • 

  • Run with the following input file in the parent directory: 

     Click on the labels of the actions for more information on what each action computes 
    

    tested on master
    # plumed.dat
PLUMED 
    FILE
    input file for the guest PLUMED instance 
    =plumed.dat 
    CHDIR
    run guest in a separate directory 
    =directory1 
PLUMED 
    FILE
    input file for the guest PLUMED instance 
    =plumed.dat 
    CHDIR
    run guest in a separate directory 
    =directory2 

    

    • 



Glossary of keywords and components


Description of components


By default this Action calculates the following quantities. These quantities can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the quantity required from the list below.





 Quantity    Description    



 bias  the instantaneous value of the bias potential   




Compulsory keywords





 STRIDE  ( default=1 ) stride different from 1 are not supported yet   




Options





 NOREPLICAS  
( default=off ) run multiple replicas as isolated ones, without letting them know that the host has multiple replicas  







 FILE  input file for the guest PLUMED instance   



 KERNEL  kernel to be used for the guest PLUMED instance (USE WITH CAUTION!)   



 LOG  log file for the guest PLUMED instance. By default the host log is used   



 CHDIR  run guest in a separate directory