The control file¶
This page briefly describes the features of DL_ANALYSER control file. It is the master control file where you can decide how analysis can be carried out.
The control file is the main interaction point for users to specify what and how to analyse the configuration files specified in the input file.
By default, the control file is named as dl_analyser.control located in the workspace/ folder.
| TIP: | You can change the control filename or even create different control files for different needs. Make sure the dl_a_path is appropriately set to ensure correct control file is used. |
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Below shows the content summary of a typical control file
--- Trajectory production section
1 * Produce trajectory? (1=yes 0=no)
test.xyz * Filename for trajectory output. (.xyz or .pdb)
newpore_1x10_DLF.pdb * PDB template (needed if to produce .pdb trajectory output)
H * Atom label to be excluded for trajectory output. Put 'none' if not require.
0 * Number of every configuration to skip
off * 1 = Static window size, 2= dynamic window size, 3= off
…
…
--- Atom range definition for analysis
1 15365 * Range of atom index (Group A)
0 0 * Range of atom index (Group B)
all * Range of MD time (ps) samples are analysed (put 'all' if all samples to be included).
0 * Exclude any atoms for analysis? 0=no, any number = Number of EXCLUDE statements shown below.
EXCLUDE 4381 to 4382
…
…
--- Structural analysis
0 * Activate analysis (1=yes 0=no)
test.out * Output file
0 * Number of every configuration to skip
0 0 * Molecular matching (1=yes, 0=no) and output option (1=yes and 0=no).
I113T_holo_DLF.pdb * Template file for matching (if 'none', first config in input file will be used).
0 * Center of gravity (1=yes, 0=no)
1 * Radius of gyration (1=yes, 0=no)
1 * Asphericity (1=yes, 0=no)
0 * distance between Group A and Group B (1=yes, 0=no)
0 * Locate maximum and minimum coordinates (1=yes, 0=no)
0 * Identify closest distance pair (1=yes, 0=no)
…
…
--- Dynamical analysis
0 * Activate analysis (1=yes, 0=no)
temp.out * Output file
0 * Number of every configuration to skip
bulk * Surface or bulk?
-1.425y 62.1y * Surface definition (top and bottom threshold)
0 * kinetic energy
0 * Center of mass velocity (1=yes, 0 = no)
…
…
--- Defect analysis
0 * Activate analysis (1=yes, 0=no)
r.out * Output file
10 * Number of every configuration to skip
surface * surface or bulk?
-1.425y 62.1y * surface definition (top and bottom).
1.425 * cutoff radius around an original site.
1 * Defect distribution profile scan.(1=yes, 0=no)
…
…
--- Sputter analysis
0 * Sputter analysis (1=yes, 0=no)
s.out * Output file
1 * Number of every configuration to skip
1 * Detailed output (1=yes, 0=no)
…
…
--- Extract STATIS data
1 * Activate STATIS extraction? (1=yes, 0=no)
statis.out * Output file
…
…
All available analysis options are listed in the file and relevant analysis types are grouped into different Sections. For example, the Dynamic Analysis Section, Structural Analysis Section, Trajectory Production Section, etc.
Analysis Options
All analysis options take some forms of input parameters. The general characteristics of analysis options are as follows:
- Each analysis option is provided with a brief descriptions including the available choices of parameters.
- All analysis options include a switch which can be either off (0) or on (1). Some options require additional parameters to carry out the analysis, which can straddle across two lines.
- All analysis will be carried out according to the conditions set in the Atom Range Definition Section.
Analysis Sections
General characteristics of Sections:
- Each Section comes with a master switch. If this swtich is turned off (0), then the whole Section will be deactivated.
- Each Section comes with its own output file to which the analysis results are written out.
- The Trajectory Production Section is a stand-alone Section that do not interact with the rest of the Sections.
- All analysis Sections carry out analysis according to the conditions set in the Atom Range Definition Section.
Warning
No check will be made if more than two Sections use the same output file. Be sure to use different output filenames for each Section.
Warning
Please do not just turn on every analysis options. Depending on the systems, DL_ANALYSER can produce an error or non-sensical results. Think what you want to get out and switch on (and off) the options accordingly.