0e9c3fb768
Updated test script
2024-05-15 15:26:58 +01:00
59ce8c966c
Corrected energy for capped force potential
2024-05-15 15:24:36 +01:00
99b3233564
Added names of new source code files
2024-05-03 16:20:57 +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
3906eb8148
Merge branch 'lammps:develop' into cg-dna
2024-04-26 14:49:49 +01:00
628531dadb
Merge pull request #4144 from Bibobu/ave_histo_vector_bug
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Fix for fix_ave_histo bug with vector style variables
2024-04-22 09:42:24 -06:00
baaea8271b
Merge branch 'develop' of github.com:lammps/lammps into ave_histo_vector_bug
2024-04-20 17:38:38 +02:00
38c7d7aa1c
Added a vectorstyle variable check for fix_ave_histo.cpp
2024-04-20 17:31:34 +02:00
52ab29798a
Merge branch 'lammps:develop' into cg-dna
2024-04-19 22:07:32 +01:00
6836bca5f8
Merge pull request #4139 from akohlmey/eam-warning-bugfix
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Later than last minute bugfix in EAM density warning for OPENMP package
2024-04-17 15:43:23 -04:00
1b88adf73e
move communication for eam/omp warning outside the threaded region. undo for INTEL
2024-04-17 14:37:51 -04:00
cf0dc2ac21
Merge pull request #4138 from akohlmey/next_release
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Update version tags and strings for the next feature release
2024-04-17 10:37:35 -04:00
09680a3857
use MPI_SUM instead of MPI_MAX to work around OpenMPI bug on macOS with Apple CPU
2024-04-17 01:03:39 -04:00
db9e8aa43c
last minute fix for https://matsci.org/t/errors-encountered-in-the-pyrolysis-of-organic-polymers-under-reaxff-force-field/54818
2024-04-17 00:57:07 -04:00
d45a00031b
update a couple more pending version strings
2024-04-17 00:41:45 -04:00
e80954a288
Merge branch 'develop' into next_release
2024-04-17 00:38:48 -04:00
3a555c81b6
Merge pull request #4134 from akohlmey/collected-small-changes
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Collected small changes and bugfixes
2024-04-17 00:35:57 -04:00
101a937870
rephrase warning about EAM deansity exceeding tabulated embedding term
2024-04-16 23:02:29 -04:00
7f269c461e
Merge branch 'collected-small-changes' of github.com:akohlmey/lammps into collected-small-changes
2024-04-16 22:49:26 -04:00
94a95b56e6
Merge remote-tracking branch 'github/develop' into collected-small-changes
2024-04-16 22:42:48 -04:00
329d546eea
Merge pull request #4078 from jmgoff/pace-mliap
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Update ML-IAP for ACE support
2024-04-16 22:42:17 -04:00
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
98eb345615
small tweak
2024-04-16 20:07:30 -04:00
95e4364400
breathe is currently not compatible with sphinx 7.3
2024-04-16 19:59:30 -04:00
fe57f880f0
breathe is currently not compatible with sphinx 7.3
2024-04-16 19:53:49 -04:00
124516097c
breathe is currently not compatible with sphinx 7.3
2024-04-16 19:53:00 -04:00
9aceecdfa4
breathe is currently not compatible with sphinx 7.3
2024-04-16 19:51:01 -04:00
88f2ca643b
update version tags for feature release
2024-04-16 19:47:12 -04:00
89d98786ec
small doc formatting and spelling fixes
2024-04-16 19:33:14 -04:00
c855e44d0e
small doc fixes
2024-04-16 19:26:51 -04:00
49b5361088
Update labelmap.rst
2024-04-16 00:24:25 -04:00
a810f1eca8
Update Howto_type_labels.rst
2024-04-16 00:20:18 -04:00
28620a6631
propagate changes to other EAM implementations
2024-04-15 21:04:57 -04:00
8dd1d12a73
apply clang-format and whitespace cleanup
2024-04-15 21:04:22 -04:00
16e5fce31e
adjust error messaging for rho[i] > rhomax in EAM
2024-04-15 17:24:47 -06:00
1924a06466
Merge branch 'develop' into collected-small-changes
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# Conflicts:
# python/lammps/pylammps.py
2024-04-15 17:21:38 -04:00
de8b1b49a6
Merge pull request #4135 from yuhldr/develop
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pylammps small changes and bugfixes
2024-04-15 14:13:20 -04:00
d34a9bd33e
Merge pull request #4113 from evoyiatzis/restricted-angle
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Restricted squared cosine angle and dihedral potentials
2024-04-15 13:13:11 -04:00
b2fded3933
restore missing line
2024-04-15 11:24:54 -04:00
3a94e4df2d
print single warning when some rho[i] exceeded rhomax of the current EAM potential
2024-04-15 02:50:16 -04:00
a9b9f7f2c7
correct fix ttm/mod example input
2024-04-15 01:45:05 -04:00
e4a7b193aa
whitespace
2024-04-14 21:11:03 -04:00
f6992c0d34
doc: 3 py:meth:PyLammps.append_cmd_history()
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Co-authored-by: Axel Kohlmeyer <akohlmey@gmail.com >
2024-04-15 09:00:24 +08:00
bad5fcc9c4
doc: 2 py:meth:PyLammps.append_cmd_history()
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Co-authored-by: Axel Kohlmeyer <akohlmey@gmail.com >
2024-04-15 09:00:05 +08:00
90c8c3c551
doc: py:meth:PyLammps.append_cmd_history()
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Co-authored-by: Axel Kohlmeyer <akohlmey@gmail.com >
2024-04-15 08:59:02 +08:00
962219a446
make PyLammps mass property compatible with per-atom masses.
2024-04-14 18:27:17 -04:00
18d45d1ff0
pylammps: fix get atom.mass by atom.type
2024-04-14 18:17:36 -04:00
cc721816df
pylammps: append_cmd_history
2024-04-14 17:17:36 +08:00
db1598fb08
pylammps: fix get atom.mass by atom.type
2024-04-14 17:02:23 +08:00
