JKCS0_copy

JKCS0_copy automatically creates input.txt based on the monomers given as arguments. JKCS contains optimized structures for the different conformers and conjugated acids/bases of some of the most prominent monomers in atmospheric clusters (such as sa = sulfuric acid, am = ammonia, na = nitric acid or w = water). Calling JKCS0_copy creates input.txt containing the paths to the optimized structures of the conformers and conjugated acids/bases of all the requested monomers in the “structure of building monomers” part of the file.

It is once again important to note that even when creating input.txt through JKCS0_copy, it is likely that some parameters, like the composition, still need to be altered. JKCS0_copy will write two example compositions for the chosen monomers. These of course do not necessarily have to coincide with the desired cluster composition. Therefore, always check input.txt before proceeding.

Hint

For help use:

JKCS0_copy -help

Here are few examples:

JKCS0_copy sa am       #creates input.txt with links to sulfuric acid and ammonia
JKCS0_copy msa am dma  #creates input.txt with links to methansulfonic acid, ammonia, and dimethylamine
JKCS0_copy -all        #created input.txt with links to all available structures

Note

If your structure is not available in JKCS database, you have to create the ABCluster input by yourself. See ABCluster manual for more details.

w ............ water (H2O,OH-,H+)         cd .......... carbon dioxide (CO2)
aq ........... water (H20)                m ........... methane (CH4)
                                          ar .......... argon (Ar)
nta .......... nitric acid (HNO3)         ne .......... neon (Ne)
sa ........... sulfuric acid (H2SO4)      he ........... helium
msa .......... methanesulfonic acid
                                          h ............ proton (H+)
am ........... ammonia (NH3)              na ........... sodium (Na+)
gd ........... guanidine (CN3H5)          cl ........... chloride (Cl-)
dma .......... dimethylamine (C2H7N)
tma .......... trimethylamine (C3H9N)     ica ......... iodic acid (HIO3)
urea ......... urea (CH4N2O)              isa ......... iodous acid (HIO2)
buoh ......... butanol (C2H5OH)           ip .......... iodine pentoxide (I2O5)

EXAMPLE: Consider an example of a negatively charged cluster containing 1 ammonia and 2 sulfuric acid molecules. Type “JKCS0_copy sa am” to creat input.txt. input.txt will already contain the information of cis- and trans-sulfuric acid, bisulfate, sulfate, ammonia and ammonium in the “structure of building monomers” section. The total charge and composition will however not be the same as our desired cluster. We will thus have to change the total charge to -1 and the composition to “2_1”.

If we would have called “JKCS0_copy A SA”, ammonia and ammonium would first be mentioned in the “structure of building monomers” section followed by the sulfuric acid monomers and conjugated bases. In this case, we should write the composition as “1_2” to obtain our desired cluster.