775a73b67c
* 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.
11 lines
1.1 KiB
Plaintext
11 lines
1.1 KiB
Plaintext
# DATE: 2024-04-26 UNITS: real CONTRIBUTOR: Oliver Henrich, oliver.henrich@strath.ac.uk
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#
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* fene 11.92337812042065 2.1295 6.409795
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* * excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576
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* * stk 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65
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* * hbond 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
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1 4 hbond 6.42073911784652 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
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2 3 hbond 6.42073911784652 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
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* * xstk 3.902852174 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0.0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
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* * coaxstk 3.77965257404268 3.4072 5.1108 1.87396 4.94044 2.0 2.541592654 0.65 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 -0.65 2.0 -0.65
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