Calculating Magnetic Susceptibility - Tensor Addition Method

These notes were written in 2019 on xenon, and while the scripts are available on both xenon and cposs in the same location, they have not been tested recently.

Using this method should reference Guo, R.; Uddin, M. N.; Price, L. S.; Price, S. L., Calculation of Diamagnetic Susceptibility Tensors of Organic Crystals: From Coronene to Pharmaceutical Polymorphs. The Journal of Physical Chemistry A 2020, 124 (7), 1409-1420.

This can be carried out either directly after a search, or many years after a search, and the method for each is slightly different.

Files are in /home/cposs/MagneticSusceptibility/ on both cposs and xenon. If there are any problems running things, please let Louise know and the scripts can be updated.

DIRECTLY AFTER A SEARCH.

1. Your search will be in a unique_pool, with a subdirectory for each crystal structure.
2. You will have a file called Sp_Dmacrys_unique.str with all the unique structures listed.
3. Copy setup_tensor, mag_headoffile, mag_manag, num_cor and extract_tensor to your top level directory.
4. Edit lines 4 and 12 of setup_tensor to say how many atoms are in one molecule and how many atoms of one type are in one molecule.
5. Run setup_tensor

   ./setup_tensor

   to generate all the GAUSSIAN input files and a list of them (there will be one per molecule for Z'>1 structures)
6. Run mag_manag

   nohup ./mag_manag x &

   where x is the number of lines in mag_list generated in the previous step. This will submit jobs to the nodes so a maximum of y are running, where y is the number in num_cor.
7. Run extract_tensor

   ./extract_tensor

   to extract the molecular magnetic susceptibilities of each molecule and derive the crystal tensor for each crystal structure.

SOME TIME AFTER A SEARCH

1. You will have three directories containing required files for database upload
1. REFCODE_res, with each structure named REFCODE_CONF_STRUCT.res
2. REFCODE_sum, with the fort.12 for each structure
3. REFCODE_dmaout, with the .dmaout for each structure
2. You will have a list of the structures (probably copied from REFCODE_overview) called list1
3. You will have a directory called master with a bondlengths file and a dmacrys.mols files for each possible value of Z'
4. Into your top level directory (i.e. the one that currently contains four directories and list1), copy setup_tensor_dir, mag_headoffile, mag_manag, num_cor and extract_tensor

# Change this next line

5. Edit lines 4 and XXXXXXX of setup_tensor_dir to say how many atoms are in one molecule and how many atoms of one type are in one molecule.
6. Run setup_tensor_dir

   ./setup_tensor_dir

   to reorganize all structures into the standard unique_pool structure. This gives the filenames that come from a single step DMACRYS run (important for choosing the database upload script).
7. Run mag_manag

   nohup ./mag_manag x &

   where x is the number of lines in mag_list generated in the previous step. This will submit jobs to the nodes so a maximum of y are running, where y is the number in num_cor.
8. Run extract_tensor

   ./extract_tensor

   to extract the molecular magnetic susceptibilities of each molecule and derive the crystal tensor for each crystal structure.

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