Input file
Configurational sampling with JKCS starts by making input.txt
, which can be generated by JKCS0_copy (see next chapter).
This file contains the most import definitions for sampling the desired clusters in the current directory. Example:
######################################################
## SUPERCOMPUTER PARAMETERS ##
## Number of Combinations - NoC ##
######################################################
## MAXTASKS CPU NODES REQ.TIME PARTITION MEMPERCPU ##
======================================================
ABC NoC 1 1 72:00:00 small 4000mb
XTB NoC 1 1 72:00:00 small 4000mb
G16 100 8 1 72:00:00 small 4000mb
ORCA 100 8 1 72:00:00 small 4000mb
CC 100 8 1 330:00:00 longrun 4000mb
-loc 1 1 1 - - 4000mb
======================================================
#####################################
## SYSTEM CHARGE AND MULTIPLICITY ##
#####################################
TotalCharge 0
TotalMultiplicity 1
###################################################################
## COMPOSITION: ##
## e.g.: 1_1_2 1_2_1 1_3 ##
## e.g.: 1_3-6 = 1_3 1_4 1_5 1_6 ##
## e.g.: (1,3,5)_1 = 1_1 3_5 5_1 ##
## e.g.: (2,4)_1-3_1 = 2_1_1 4_1_1 2_2_1 4_2_1 2_3_1 4_3_1 ##
## e.g.: 1_1_F2 = 1_1_0-2 #protons# to fulfill charge ##
###################################################################
Composition 1_1 2_2
######################################
## STRUCTURES OF BUILDING MONOMERS: ##
######################################
# name | q | path
sa 0 /projappl/hvehkama/kubeckaj/Apps/JKCS2.1/JKCSx/../TOOLS/STRUCTURES/JACOB/sa.xyz
sa 0 /projappl/hvehkama/kubeckaj/Apps/JKCS2.1/JKCSx/../TOOLS/STRUCTURES/JACOB/h2so4_cis.xyz
sa -1 /projappl/hvehkama/kubeckaj/Apps/JKCS2.1/JKCSx/../TOOLS/STRUCTURES/ABC/hso4.xyz
sa -2 /projappl/hvehkama/kubeckaj/Apps/JKCS2.1/JKCSx/../TOOLS/STRUCTURES/ABC/so4.xyz
am 0 /projappl/hvehkama/kubeckaj/Apps/JKCS2.1/JKCSx/../TOOLS/STRUCTURES/ABC/nh3.xyz
am 1 /projappl/hvehkama/kubeckaj/Apps/JKCS2.1/JKCSx/../TOOLS/STRUCTURES/ABC/nh4.xyz
Note
When configurational sampling needs to be done on a cluster that contains monomers not included within JKCS, then input.txt
can be created from scratch. It is of course also possible to let JKCS0_copy create an input.txt file for a random system and subsequently change the necessary parameters to fit the desired system.
Important
When creating input.txt
file through JKCS0_copy, it is likely that some parameters, like the composition, still need to be altered.
input.txt
is divided into four parts:
Contents
SUPERCOMPUTER PARAMETERS
This section defines parameters for submitting JKCS to (super)computer cluster. JKCS communicates with 3rd-party programs that are further abbreviated as: ABC = ABCluster, XTB, G16 = Gaussian16, and ORCA. For each program, the following parameters need to be specified:
- MAXTASKS
maximum number of tasks that can run in parallel. Beginners should not adjust this.
- CPU
number of CPUs.
- NODES
number of nodes. Beginners should leave 1.
- REQ.TIME
the requested/required walltime (expected length of calculations)
- PARTITION
the name of cluster partition (e.g. small, large, hugemem)
- MEMPERCPU
the amount of memory per CPU
Note
For almost all of them, you can use variables “NoC” and “M” to define the parameter as a function of “Number Of (monomer) Combinations” or “(total) number of Molecules”.
Hint
When calling one of the next JKCS scripts (e.g., JKCS3_run), the submission parameters for running that script can also be specified as additional arguments to the script. We could, for instance, call
JKCS3_run XTB -par small -mem 8gb
to change the partition name and memory per CPU from what is written in the input.txt
file (or actually in parameters.txt
formed later for each cluster type).
These commands are further explained in the ‘Cluster submission’ section of this manual.
Hint
The default table for supercomputer parameters can be changed in ~/.JKCSusersetup.txt.
SYSTEM CHARGE AND MULTIPLICITY
This section consists of two parameters that need to be set: total charge and total multiplicity of the cluster(s).
Note
The multiplicity is equal to the number of unpaired electrons plus one (TotalMultiplicity = 2S+1).
Hint
If you want to study clusters of different charges, use different folders.
COMPOSITION
The composition defines the number of each monomer in the desired cluster. For each cluster, the
composition is written as n[1]_n[2]_n[3]…_n[M], where n[i] is the number of monomers of type i in the
desired cluster. The order in which the monomers appear in this format should be the same as the
order in which the monomers are listed in the “structure of building monomers” part of input.txt
(see below).
If there are listed molecules “sa” and “am”, the composition “1_2” equals to cluster (sa)1(am)2.
When configurational sampling of multiple clusters with different compositions needs to be done, each composition can be written on one line with a space between two separate compositions. For multiple clusters, some symbols can also be used to quickly define the clusters. Writing “1-3_(4,5)” would for instance be equivalent to “1_4 2_4 3_4 1_5 2_5 3_5”.
STRUCTURE OF BUILDING MONOMERS
This section should list the name, path and charge of all available conformers and conjugate acids/bases for all the monomers in the desired cluster. All conformers and conjugate species of the same molecule should have the same name (e.g. “sa” for cis- and trans-sulfuric acid as well as for the bisulfate and sulfate ion). The order of the list should be the same as the order in which the composition was written.
EXAMPLE: Consider as an example that we would like to perform configurational sampling on a negative cluster containing two sulfuric acid molecules and one ammonia molecule. For this, we would change the total charge of the cluster to -1. The multiplicity would be left at 1. The composition would be given as “2_1”. Lastly, we fill in the “structure of building monomers” part. As we have filled in “2_1” in the composition, we first list all sulfuric acid conformers and conjugate bases and then we list the ammonia structure and conjugate acid. There are two sulfuric acid conformers to take into account: cis- and trans-sulfuric acid. Ammonia has only one conformation. We take multiple conformers of monomers into account because it is not certain that the lowest energy monomer conformer is also the preferred conformation inside the cluster. Sulfuric acid has two conjugate bases: bisulfate and sulfate. Ammonia has one conjugate acid: ammonium. We consider the conjugate acids and bases because internal acid-base reactions could occur between monomers in the cluster. The paths to all the different structures related to one monomer should be listed together.