0e9c3fb768
Updated test script
2024-05-15 15:26:58 +01:00
775a73b67c
cgDNA 'real' units and potential file reading for non-modifiable potential parameters ( #15 )
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* oxDNA potential file reading and real units
This allows for pair and bond coefficients to be read from an appropriately formatted potential file, and also allows for the use of 'real' units within oxDNA1. The correct backend coefficients for pair and bonded interactions are set when the atom vector is initialised through the "ConstantsOxdna" class, based on the units specified within the input file.
* Extract seqav/seqdep and temp from potential files
Also includes miscellaneous string consistency changes and removes unnecessary parameter from reader.next_line instances.
* oxDNA2 potential file reading and real units
This extends previous changes to oxDNA2 specific potentials, being FENE, excluded volume, coaxial stacking and Debye-Hückel. Units now default to LJ values rather than 0.
* oxDNA potential files
* LJ <-> real units conversion tool
Converts standard oxDNA data and input file to real units, with inverse flag available for real -> LJ.
* oxRNA2 potential file reading and real units
For RNA, d_cs_x is treated as d_cs within ConstantsOxdna in order to reduce code duplication and complexity.
* Reparameterise real units
* Generalise PotentialFileReader logs
* Extract stk xi and kappa from potential files
This allows users to edit these values from the input script, as is documented, rather than them being within the potential files.
* Real unit and potential file documentation
This adds examples for real unit parameters and specific potential file documentation for each bond and pair style.
2024-05-03 15:00:29 +01:00
ca675b557f
Minor edits for python2/3 support, improved comments
2024-05-03 11:23:42 +01:00
52ab29798a
Merge branch 'lammps:develop' into cg-dna
2024-04-19 22:07:32 +01:00
27266e72c4
Merge pull request #3984 from lammps/general-triclinic
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Add suppport for general triclinic simulation boxes and systems
2024-04-16 21:04:59 -04:00
01917cd117
add example for Ca-O with Pedone
2024-04-09 22:08:30 -04:00
a3e4788221
Minor edits
2024-03-20 16:23:17 +00:00
add5fc07fd
Changed user permissions
2024-03-20 16:23:17 +00:00
c5fc65433a
Updated and added utility scripts
2024-03-20 16:23:17 +00:00
e8606a51da
Changed permissions to non-executable
2024-03-20 16:23:17 +00:00
7fa0e7b730
Added script for 2-particle visualisation
2024-03-20 16:23:17 +00:00
01d412bdbf
Merge branch 'develop' into general-triclinic
2024-03-08 21:32:01 -05:00
3f91ee142b
Merge branch 'develop' into electrode
2024-03-04 09:31:07 -05:00
8e6ce1d0b9
Remove nonneut examples
2024-03-04 08:52:05 +01:00
835b65b644
Merge branch 'develop' into general-triclinic
2024-02-21 14:53:32 -07:00
1edec590bb
Logs for eta mix example
2024-02-19 15:01:51 +01:00
9921338ee1
update log files for MGPT package
2024-02-07 03:57:12 -05:00
35215606e8
Merge remote-tracking branch 'lammps/develop' into merge-develop
2024-01-31 14:41:36 +01:00
8cf2705d68
Merge branch 'develop' into general-triclinic
2024-01-18 15:01:09 -05:00
14abc184f8
Merge pull request #4040 from alphataubio/cgdna
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[CG-DNA examples/util] fixed indentations and ported python 2 code to python 3
2024-01-18 14:55:41 -05:00
a3682e1bd5
retain compatibility with python 2.x
2024-01-13 04:56:16 -05:00
5b05112aab
fixed indentations and ported python 2 code to python 3
2024-01-12 18:19:50 -05:00
c60217123a
Merge branch 'lammps:develop' into bond_react_fixes_aug23
2024-01-10 18:45:29 -05:00
c6d1cbef5a
Merge branch 'develop' into general-triclinic
2024-01-04 21:10:50 -05:00
13b6d40062
tiny_epoxy example correction
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not sure why this issue showed up in recent LAMMPS versions
2024-01-03 20:38:10 -05:00
d9ea10ca24
Merge branch 'lammps:develop' into bond_react_fixes_aug23
2024-01-03 14:59:26 -05:00
4ea40ed2fd
Merge branch 'ilp-tmd-update' of github.com:oywg11/lammps into collected-small-fixes
2023-12-22 14:45:43 -05:00
de066bcde0
Merge remote-tracking branch 'lammps/develop' into electrode
2023-12-21 14:13:16 +01:00
aa221e2f2b
add new potential file for aip/water/2dm
2023-12-21 10:28:53 +08:00
e98df7018b
update the example files
2023-12-19 08:17:43 +08:00
e6a510ddc5
Merge branch 'lammps:develop' into bond_react_fixes_aug23
2023-12-17 17:02:18 -05:00
89c5ee7079
Merge pull request #3996 from lafourcadep/snann_slcsa
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Compute sna/atom on fixed number of neighbors and compute slcsa/atom (Supervised Learning Crystal Structure Analysis tool)
2023-12-13 14:36:49 -05:00
0c4a1cb21d
Merge pull request #4009 from ndtrung81/gpu-updates-Dec23
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GPU package updates Dec 2023
2023-12-13 11:59:10 -05:00
754041ee36
minor fix
2023-12-13 11:57:03 -05:00
e1be6c09f7
merge with GHub version
2023-12-13 09:05:27 -07:00
665785f41e
adjust 2d box bounds
2023-12-13 09:04:23 -07:00
29cf012061
re-use existing potential file, fix screen/log output, plug memory leaks
2023-12-12 23:28:09 -05:00
e7c330db9d
Merge branch 'develop' into snann_slcsa
2023-12-12 22:30:20 -05:00
26d0671337
update compute slcsa example to better align with LAMMPS conventions and move to more appropriate folder
2023-12-12 22:30:15 -05:00
8eaaae1e99
recenter 2d boxes around 0.0
2023-12-06 08:31:41 -05:00
e53b3c76f5
Updated doc pages for the added pair styles, added a cmake preset for gpu-cuda, added "comm_modify vel yes" to in.mdpd
2023-12-05 15:32:57 -06:00
e5ae46a01a
update compute pace example to follow usual conventions
2023-12-05 06:15:40 -05:00
7d8de8301f
Merge branch 'develop' into compute-pace-update
2023-12-05 06:05:34 -05:00
82868cd583
Simplify Madelung examples with mixed eta
2023-12-04 13:59:07 +01:00
4035291a48
Merge branch 'develop' into collected-small-changes
2023-12-02 08:17:11 -05:00
ef2a420aeb
modernize
2023-12-01 17:16:25 -05:00
00be75e084
update example inputs and logs for change in ReaxFF required name
2023-11-30 10:31:08 -05:00
7f2a6b1a85
update h2 fix pimd/langevin example
2023-11-16 12:00:29 -05:00
a651697d2e
Mix eta in Electrode package
2023-11-13 14:41:13 +01:00
db4f55b76f
compatibility with new lammps-user-pace library and cleanup
2023-09-19 17:24:15 -06:00
