Unverified Commit ceb2ce58 authored by Axel Kohlmeyer's avatar Axel Kohlmeyer
Browse files

Merge branch 'master' into improve-include-consistency 

# Conflicts:
#	src/USER-CGDNA/pair_oxdna2_stk.cpp
parents 2b5a6d3b 67b74aea

doc/src/PDF/USER-CGDNA.pdf

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doc/src/pair_oxdna.txt

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@@ -23,9 +23,11 @@ style1 = {hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxs 
style2 = {oxdna/excv} or {oxdna/stk} or {oxdna/hbond} or {oxdna/xstk} or {oxdna/coaxstk}

args = list of arguments for these particular styles :ul



  {oxdna/stk} args = seq T 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65

  {oxdna/stk} args = seq T xi kappa 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65

    seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)

    T = temperature (oxDNA units, 0.1 = 300 K)

    xi = temperature-independent coefficient in stacking strength

    kappa = coefficient of linear temperature dependence in stacking strength

  {oxdna/hbond} args = seq eps 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45

    seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength)

    eps = 1.077 (between base pairs A-T and C-G) or 0 (all other pairs) :pre
@@ -34,7 +36,7 @@ args = list of arguments for these particular styles :ul 


pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk

pair_coeff * * oxdna/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32

pair_coeff * * oxdna/stk     seqdep 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65

pair_coeff * * oxdna/stk     seqdep 0.1 1.3448 2.6568 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65

pair_coeff * * oxdna/hbond   seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45

pair_coeff 1 4 oxdna/hbond   seqdep 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45

pair_coeff 2 3 oxdna/hbond   seqdep 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
@@ -62,7 +64,7 @@ NOTE: These pair styles have to be used together with the related oxDNA bond sty 
{oxdna/fene} for the connectivity of the phosphate backbone (see also documentation of

"bond_style oxdna/fene"_bond_oxdna.html). Most of the coefficients

in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model.

Exceptions are the first and second coefficient after {oxdna/stk} (seq=seqdep and T=0.1 in the above example)

Exceptions are the first four coefficients after {oxdna/stk} (seq=seqdep, T=0.1, xi=1.3448 and kappa=2.6568 in the above example)

and the first coefficient after {oxdna/hbond} (seq=seqdep in the above example).

When using a Langevin thermostat, e.g. through "fix langevin"_fix_langevin.html

or "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html

doc/src/pair_oxdna2.txt

+7 −5
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@@ -24,10 +24,12 @@ style1 = {hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/ 
style2 = {oxdna2/excv} or {oxdna2/stk} or {oxdna2/hbond} or {oxdna2/xstk} or {oxdna2/coaxstk} or {oxdna2/dh}

args = list of arguments for these particular styles :ul



  {oxdna2/stk} args = seq T 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65

  {oxdna2/stk} args = seq T xi kappa 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65

    seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)

    T = temperature (oxDNA units, 0.1 = 300 K)

  {oxdna/hbond} args = seq eps 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45

    xi = temperature-independent coefficient in stacking strength 

    kappa = coefficient of linear temperature dependence in stacking strength 

  {oxdna2/hbond} args = seq eps 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45

    seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength)

    eps = 1.0678 (between base pairs A-T and C-G) or 0 (all other pairs)

  {oxdna2/dh} args = T rhos qeff
@@ -39,7 +41,7 @@ args = list of arguments for these particular styles :ul 


pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh

pair_coeff * * oxdna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32

pair_coeff * * oxdna2/stk     seqdep 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65

pair_coeff * * oxdna2/stk     seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65

pair_coeff * * oxdna2/hbond   seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45

pair_coeff 1 4 oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45

pair_coeff 2 3 oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
@@ -68,8 +70,8 @@ NOTE: These pair styles have to be used together with the related oxDNA2 bond st 
{oxdna2/fene} for the connectivity of the phosphate backbone (see also documentation of

"bond_style oxdna2/fene"_bond_oxdna.html). Most of the coefficients

in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model.

Exceptions are the first and the second coefficient after {oxdna2/stk} (seq=seqdep and T=0.1 in the above example),

the first coefficient after {oxdna/hbond} (seq=seqdep in the above example) and the three coefficients

Exceptions are the first four coefficients after {oxdna2/stk} (seq=seqdep, T=0.1, xi=1.3523 and kappa=2.6717 in the above example),

the first coefficient after {oxdna2/hbond} (seq=seqdep in the above example) and the three coefficients

after {oxdna2/dh} (T=0.1, rhos=1.0, qeff=0.815 in the above example). When using a Langevin thermostat

e.g. through "fix langevin"_fix_langevin.html or "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html

the temperature coefficients have to be matched to the one used in the fix.

doc/src/read_data.txt

+3 −0
Original line number Diff line number Diff line
@@ -565,6 +565,7 @@ molecular: atom-ID molecule-ID atom-type x y z 
peri: atom-ID atom-type volume density x y z

smd: atom-ID atom-type molecule volume mass kernel-radius contact-radius x y z

sphere: atom-ID atom-type diameter density x y z

spin: atom-ID atom-type sp x y z spx spy spz

template: atom-ID molecule-ID template-index template-atom atom-type x y z

tri: atom-ID molecule-ID atom-type triangleflag density x y z

wavepacket: atom-ID atom-type charge spin eradius etag cs_re cs_im x y z
@@ -595,6 +596,8 @@ mux,muy,muz = components of dipole moment of atom (dipole units) 
q = charge on atom (charge units)

rho = density (need units) for SPH particles

spin = electron spin (+1/-1), 0 = nuclei, 2 = fixed-core, 3 = pseudo-cores (i.e. ECP)

sp = norm of magnetic spin of atom (in number of Bohr magnetons)

spx,spy,spz = components of magnetic spin of atom (adim normalized vector)

template-atom = which atom within a template molecule the atom is

template-index = which molecule within the molecule template the atom is part of

theta = internal temperature of a DPD particle

doc/utils/sphinx-config/false_positives.txt

+1 −0
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@@ -1521,6 +1521,7 @@ Magdeburg 
magelec

Maginn

magneton

magnetons

mainboard

mainboards

makefile

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