mirror of https://github.com/lammps/lammps.git
104 lines
3.3 KiB
Plaintext
104 lines
3.3 KiB
Plaintext
These Python scripts were written originally by Keir Novik, but he can
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no longer support them. See some documentation at the top of the
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files - they are supposed to be fairly self-explanatory.
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amber2lammps.py converts AMBER files into LAMMPS input format
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dump2trj.py converts LAMMPS dump files into AMBER format
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dump2try99.py same as dump2trj for LAMMPS 99 format
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Modifications in file amber2lammps.py, by Vikas Varshney
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Dated Nov 4, 2013
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Email address: vv0210@gmail.com
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added support for flags used in current version of AMBER
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-------------------------
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Modifications in file amber2lammps.py, by Vikas Varshney
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Dated July 5, 2005
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Email address : vv5@uakron.edu
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Lines 222-226: Undid the shifting of the atoms in the periodic
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box. LAMMPS is going to take care of it by image atoms. Make sure that
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when you dump the coordinates by LAMMPS to view in VMD, print them in
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the format mentioned in the dump2ptraj.py section later.
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Lines 378-391: Added an if statement to see whether .crd or .top file
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is being read. This if statement helps in assigning the title if the
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title is not present in the files.
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Line 394: Added an if statement, not to read lines which start with
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% in the topology file.
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Lines 430-432: Changed if statement condition to read the current
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simulation time from .crd file. I put the remainder condition
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instead of equal to condition. The simulation time adds one value to
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the length of the Item_list, so remainder condition can be applied
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easily to see if simulation time data is present in the .crd file or
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not.
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In general, the initial .crd files dont have simulation time
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information while restart files do have them.
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Some other minor additions:
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I added few lines to print the names which are being read
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currently. This helps in seeing current state of the programs which
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are listed below
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Lines 382, 389, 420, 428, 436, 490, 498, 550, 555, 560, 565, 570, 575,
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580, 595, 600, 610, 615, 620, 631, 636, 648, 657, 666, 677, 688, 701,
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720, 725, 730, 735, 740, 745, 750, 755, 767, 769, 771, 778, 785, 806,
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821, 897.
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---------------------------
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Modifications in file dump2trj.py, by Vikas Varshney
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Dated July 5, 2005
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Email address: vv5@uakron.edu
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First, the atoms should be dumped in the following format.
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dump group-ID custom N tag type xs ys zs ix iy iz
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Modifications:
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Lines 117-119: I modified the lines to get the actual co-ordinates
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instead of box coordinates. If we dont do that and try to see the
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file in vmd, we observe long bond lengths of the molecules whose one
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part is on one side of periodic box and the other part is on other
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side of periodic box.
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Lines 239 & 244: Changed x to mdcrd.
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Once you do that. Open the original topology file in VMD (with parm7)
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and then mdcrd file (crdbox) to see the time evaluation of the
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problem.
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----------------------------
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Example input script, by Paul Crozier
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1 Sept 2005
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Here is an example of a typical LAMMPS input script for use with
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a data file built by amber2lammps.py:
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units real
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neigh_modify delay 5 every 1
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atom_style full
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bond_style harmonic
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angle_style harmonic
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dihedral_style harmonic
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pair_style lj/cut/coul/long 10.0
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pair_modify mix arithmetic
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kspace_style pppm 1e-4
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read_data data.yourdata
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fix 1 all nve
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special_bonds amber
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thermo 1
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thermo_style multi
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timestep 0.5
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run 2
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