Input and Output Files for Molpak on Xenon

Initial Input

bondlengths

Maximum distance between atoms to be considered bonded
Also known as "cutoff"

cadpac.charges

Describes the DMA of the molecule
Also known as the punch file

dmarel.axis

Describes the axis of the molecule

pote.dat

Describes the potential model
Replaces "pots" file

minspec

Instructions to DMAREL for the minimisation
The contents are written to the end of the dmain file

molpak.xyz

Describes the rigid molecular probe used in the MOLPAK search

MOLPAK.NAME

Standard file (same for every search)

make_files.pl

Used to set up all the files for the MOLPAK search and subsequent lattice minimisation

Intermediate Files

I Output by make_files.pl then used as input for the next step

Runjobs

Calls each of the chosen packing types in turn for search and lattice energy minimisation

????????_XX_master.com

"????????" = 8 character refcode for structure
"XX" = Packing type eg AA
Calls MOLPAK, Neighbours and DMAREL to perform the grid search and lattice energy minimisation.

molpak_??.input

Input for Molpak search

search_??.data

Input for Molpak search

II Output by MOLPAK, input for Neighbours

x.fdat

"x" = structure number (within specific packing type)
Describes structure found in MOLPAK search, to be optimised in DMAREL

III Output by Neighbours, input for DMAREL

fort.20

See x.sym below

x-2.dmain(.gz)

File read in by DMAREL containing necessary information for the lattice energy minimisation

Final Output

x.sum

Summary of the lattice energy minimisation
Use grep command on these to find negative eigenvalues and curvature
Use with volmin2.x and awk to produce spreadsheet of final structures
Replaces old fort.12

x.nbs

Use grep "CELL 2" (N.B. 2 spaces between "CELL" and "2") to get reduced final cells.

x.dat

Fdat file describing the minimised structure
Can be viewed in Pluto ("Pluto -s x.dat")
Replaces the old fort.15

x.res

Shelx file describing the minimised structure
Can be viewed in Pluto ("Pluto -s x.dat")
Replaces old fort.16

x.p1res

Describes the final structure in a P1 cell
Replaces old fort.13

x.sym

Contains the fort.20 information as used by DMAREL
Replaces the fort.20

x.fort21

fort.21 file from Neighbours

x.dmarel-out(.gz)

Output from DMAREL