- ::mbtools::utils::setup_outputdir : [outputdir] -paramsfile.arg -tabdir.arg -tabnames.arg -startf.arg -ntabs.arg
- outputdir Complete path of the directory to be setup. At least the parent of the directory must exist
- paramfile [] Name of a file to be copied to the output directory
- tabdir [] Full path name of the directory where forcetables are kept
- tabnames [] Complete list of forcetables to be used in the simulation. These will be copied to the output directory
This routine is designed to setup a directory for simulation
output. It copies forcetables and the parameter file to the
directory after creating it if necessary.
- ::mbtools::utils::read_startfile : [file]
- file Complete path of the file to be read. Should be an espresso blockfile
Read in particle configuration from an existing file or simulation snapshot
- ::mbtools::utils::read_checkpoint : [dir]
- dir Directory containing the checkpoint file which must be called checkpoint.latest.gz
Read in a checkpoint and check for success. Warn if the checkpoint does not exist.
- ::mbtools::utils::read_topology : [file]
- file Complete path of the file that contains the topology information
Read in the topology from a file and then execute the analyze set "topo_part_sync" command of espresso
- ::mbtools::utils::set_topology : [topo]
Set the given topology and then execute the analyze set "topo_part_sync" command of espresso
- ::mbtools::utils::set_bonded_interactions : [bonded_parms]
- bonded_parms A list of bonded
interactions. Each element of this list should contain all
the appropriate arguments in their correct order for a
particular call to the espresso inter
command. See the espresso inter command for a list of
possible bonded interactions and correct syntax.
Set all the bonded interactions
- ::mbtools::utils::set_nb_interactions : [nb_parms]
- nb_parms A list of
interactions. Each element of this list should contain all
the appropriate arguments in their correct order for a
particular call to the espresso inter
command. See the espresso inter command for a list of
possible non-bonded interactions and correct syntax.
Set all the bonded interactions
- ::mbtools::utils::init_random : [n_procs]
- n_procs The number of processors used in this job
Initialize the random number generators on each processor based
on the current time with a fixed increment to the time seed used
for each proc.
- ::mbtools::utils::initialize_vmd : [flag] [outputdir] [ident] -extracommands.arg
- flag Depending on the value of this parameter initialize vmd to one of its possible states:
- interactive : VMD is started and a connection to espresso
established for immediate viewing of the current
espresso process. With some luck this might even work
sometimes!!! If VMD doesn't get a proper connection
to espresso then it will crash.
- offline : Just constructs the appropriate psf and
vmd_animation.script files and writes them to the
output directory so that pdb files generated with
writepdb can be viewed with vmd -e
vmd_animation.script
- default : Any value other than those above for flag will just result
in vmd not being initialized.
- outputdir The directory where vmd output will be written
- ident A basename to be be given to vmd files
- extracommands [] A list of strings each of which will be written to the end of the vmd_animationscript. Use this to give additional commands to vmd
Prepare for vmd output