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# interface to beus.namd (bias-exchange umbrella sampling script)
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# running on most supercomuters available with namd runscript:
# ./run <configfile> <logfile> <total_num_nodes> +replicas <num_replicas> +stdout <logfile>.%d
# <total_num_nodes> must be a multiple of <num_replicas>
# example: ./runbatch_cuda job0.conf job0.log 20 +replicas 20 +stdout output/job0.log.%d

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# job id (always start with 0 then increment by 1)
set job_id 0
# (default: 0)

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# beus-specific parameters

set runUS 500
# (default: 500)
#exchange will be attemped every <runUS> steps

set runs 1000
# (required) total simulation time = <runs> * <runUS>

set runs_per_restart 1
# (default: 1) checkpoints every <runs_per_restart> * <steps_per_run> steps

set nc 5
# (default: 1)
# if greater than 1, each image will be represented by <num_of_copies> replicas
# total number of replicas must be a multiple of <num_of_copies> 
# number of images will be determined from <num_replicas>/<num_of_copies>
# currently only supported for 1D BEUS.

set num_of_columns 1
# (default: 1)
# if greater than 1, 2d BEUS will be activated
# number of images used must be a multiple of num_of_columns

# colvars config file (must have a harmonic block; the centers and force constant of this block can be overriden by the info in centers_tcl)
set colvars_conf colvars.conf
set centers_tcl centers.tcl
# centers.tcl is required

set num_of_neighbors 1
# (default: 1)
# for 1D BEUS (i.e. <num_of_columns> == 1): exchange will be attempted with <num_of_neighbors> neighbors in each side
# and exchange between each unique pair will be attempted every 2 * <num_of_neighbors> * <steps_per_run> steps
# for 2D BEUS (i.e. <num_of_columns> > 1): exchange will be attempted with <num_of_neighbors> neighbors in each side in both horizontal and vertical directions (forming a square)
# and exchange between each unique pair will be attempted every 4 * <num_of_neighbors> * ( <num_of_neighbors> + 1 ) * <steps_per_run> steps

#set periodic 0
# (default: 0)
# if set to 1, the first and last images in each dimension will be neighbors.

#set gridmap gridmap.tcl
# if provided, will activate a 2d BEUS with a user-defined grid
# note: it overrides num_of_neghbors and num_of_columns, if specified

#set networkmap networkmap.tcl
# if provided, will activate a BEUS with a userdefined network
# note: it overrides num_of_neghbors, num_of_columns, and gridmap, if specified

#set validate 0
# if specified 1, it will check he network consistency
# it is not recommended except for a test run
# (default: 0)

######################################################
# set the output directories here (required):
set output_root "output/%s/glpt"
# if **/%s/** is used, each image/replica will be put in a separate directory (the directories should be already made)
# otherwise, all output files will be put in the same directory.

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# the following is only relevant when job_id = 0;
set input_root "input/init.%s" ; # initial conformations; required for job_id=0 (%s represents replica_id)
set usevel 0 ; #do you have *.vel files? (0 or 1); default: 0
set temperature 310; #specify the temperature if usevel is set to 0
set usexsc 1 ; #do you have *.xsc files? (0 or 1); default: 0
#set cellinfo { {130 0 0} {0 130 0} {0 0 200} {0 0 0} } ; cellBasicVectors 1 to 3 and cellOrigin (not needed if usexsc is set to 1)

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set system_conf ../../system/glpt.inp
# this is your usual namd config file without the following commands:
# outputname, bincoordinates, binvelocities, extendedsystem, firsttimestep, and run as well as colvars related commands

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# generic configuration file for bias-exchange umbrella sampling:
source ../../codes/beus.namd