This fork of Gromacs modifies it to enable output of two-dimensional flow fields, collected during a simulation.
Follow the regular Gromacs installations instructions.
While not required, it is recommended to set the cmake option
-DGMX_VERSION_STRING_OF_FORK=flow-field.
The flow field collection uses the following MDP options:
; How often to sample the velocity field
userint1 = 40
; How often to save the velocity field to disk
userint2 = 5000
; Number of bins along the x axis
userint3 = 200
; Number of bins along the z axis
userint4 = 100
; List of groups to collect data for
user1-grps = SOL ; water
Additionally, mdrun needs to know where to save the output, for which the -flow option has been added:
$ gmx mdrun -flow maps/flow # Saves to `maps/flow_00001.dat`,
# `maps/flow_00002.dat`,
# `maps/flow_00003.dat`,
# etc.- Can currently only sample data in the x-z plane.
- Temperature calculation is only correct for water
- Currently only works for static box size
Tools used to read and manipulate the created data is available in a Python 3 module. It is available in this repository:
https://github.com/pjohansson/gmx_flow_utils
These changes are distributed under the same terms as Gromacs. See COPYING for more information.