CamCASP/Notes/4
CamCASP => Notes => Odds and Ends
Converting units
The energy file produced by the ENERGY-SCAN module will probably use the units: Bohr, Degree, cm-1. These may not be appropriate and may need changing. It is easy enough to do this using a script, but there is a more convenient and probably more reliable way of converting the units in this file. That is to use the PROCESS program.
Here's the PROCESS command file to convert the energies in file energy_file.dat to kJ/mol.
Global Units kJ/mol CamCASP /home/am592/CamCASP/current End Energy Read energy_file.dat Write energy_file_kJ.dat End Finish
NOTES:
- The advantage of this over any script is first of all speed --- the code's already written for you so why bother writing your own.
- PROCESS can read in multiple files --- say, from multiple energy-scan runs --- each with its own set of units (encoded in the files), and it (should) all work correctly. PROCESS will write out one energy file containing all the data.
- Third, PROCESS will convert from any of the recognised energy units to kJ/mol and it knows what units the energies are in as this information is in the energy file. Here's an example of the header of an energy file:
TITLE Energy scan of MOL-A by MOL-B TITLE pyridine1 and pyridine2 TITLE Basis sadlej and type MC TITLE Midbonds NONE and type weighted MOL-A pyridine1 MOL-B pyridine2 POINTS 500 ENERGY-UNITS KJ/MOL LENGTH-UNITS BOHR ANGLE-UNITS DEGREE
Concatenating Energy files
Multiple energy files (for the same pair of molecules) can be concatenated into one file using PROCESS. These files may have energies in different units. No problem.
Global Units kJ/mol CamCASP /home/am592/CamCASP/current End Energy Read energy_file_1.dat Read energy_file_2.dat Read energy_file_3.dat Write energy_file_kJ.dat End Finish
NOTES:
- The advantage of this over any script is first of all speed --- the code's already written for you so why bother writing your own.
- PROCESS can read in multiple files --- say, from multiple energy-scan runs --- each with its own set of units (encoded in the files), and it (should) all work correctly. PROCESS will write out one energy file containing all the data.
- Third, PROCESS will convert from any of the recognised energy units to kJ/mol and it knows what units the energies are in as this information is in the energy file. Here's an example of the header of an energy file:
TITLE Energy scan of MOL-A by MOL-B TITLE pyridine1 and pyridine2 TITLE Basis sadlej and type MC TITLE Midbonds NONE and type weighted MOL-A pyridine1 MOL-B pyridine2 POINTS 500 ENERGY-UNITS KJ/MOL LENGTH-UNITS BOHR ANGLE-UNITS DEGREE
VIM tricks
- Inserting the Type field in the *.mom files
:map t ^vllly$a Type ^[p^[
The first '^' is the usual '^' character, but the '^[' at the end are obtained using <CRTL>-v-<ESC>. So cut-and-paste will not work. You've got to type in this sequence.
Then search for Rank and type t.
Creating an energy file
You will need an energy file (and overlap file) when creating an overlap model. The energy file should be in a the format (for example):
TITLE Energy scan of MOL-A by MOL-B
TITLE pyridine1 and pyridine2
TITLE Basis sadlej and type MC
TITLE Midbonds NONE and type weighted
MOL-A pyridine1
MOL-B pyridine2
POINTS 500
ENERGY-UNITS KJ/MOL
LENGTH-UNITS BOHR
ANGLE-UNITS DEGREE
LABELS INDEX Rx Ry Rz alphaNx Ny Nz
E(1)elst E(2)ind E(2)disp E(1)exch E(2)exind E(2)exdisp
TotOverlap Elst-Asymp Ind2-Asymp Disp-Asymp Delta
1 -5.870040E-01 3.957260E+00 9.016280E+00 1.227930E+02 -9.097780E-01 -1.008600E-01 4.026560E-01
1.087500E-01 -2.364920E+00 -9.875980E+00 4.871440E+00 0.0E+00 0.0E+00 0.0E+00
0.0E+00 0.0E+00 0.0E+00 0.0E+00
...
...
END
END-FILE
If you have performed the energy scan using the ENERGY-SCAN module in CamCASP, then this file will be in such a format. But if you have performed a number of single-point (dimer geometry) calculations at specific dimer geometries using the batch_SAPT.pl script, you will not have such a file.
So, how do you construct it?
Use the batch_search.pl script as follows.
- Create a file called keys containing just saptdft-camcasp. This keyword will tell the search.pl script to search for SAPT(DFT) energies in the format used by CamCASP.
- Run the batch_search.pl script using a command like:
batch_search.pl pyridine2 -geom random-scan2.dat -d 6 -camcasp > energy_saptdft.dat
The file energy_saptdft.dat should look something like:
TITLE
MOL-A
MOL-B
POINTS 500
ENERGY-UNITS KJ/MOL
LENGTH-UNITS
ANGLE-UNITS
LABELS INDEX Rx Ry Rz alpha Nx Ny Nz
E(1)elst E(2)ind E(2)disp E(1)exch E(2)exind E(2)exdisp TotOverlap
Elst-Asymp Ind2-Asymp Disp-Asymp Delta
1 -5.870040E-01 3.957260E+00 9.016280E+00 1.227930E+02 -9.097780E-01 -1.008600E-01 4.026560E-01
1.087500E-01 -2.364920E+00 -9.875980E+00 4.871440E+00 0.0E+00 0.0E+00 0.0E+00
0.0E+00 0.0E+00 0.0E+00 0.0E+00
...
So it is in almost the correct format. You need to fill up the preamble. For example, the complete pre-amble might look like:
TITLE Energy scan of MOL-A by MOL-B TITLE pyridine1 and pyridine2 TITLE Basis sadlej and type MC TITLE Midbonds NONE and type weighted MOL-A pyridine1 MOL-B pyridine2 POINTS 500 ENERGY-UNITS KJ/MOL LENGTH-UNITS BOHR ANGLE-UNITS DEGREE
Yes, you can have multiple TITLE fields. The first few will be used by CamCASP, the rest will be ignored. The other fields are more important, so make sure they are correct. In particular, get your units correct!
That is all you need do, unless you want to fill up the Elst-Asymp, Ind2-Asymp, Disp-Asymp and Delta fields. For the first three you will need to use ORIENT and the batch_ORIENT.pl script. The last one, Delta, is any energy correction you would like to include. See Overlap Models for more details.