diff --git a/doc/src/bond_oxdna.rst b/doc/src/bond_oxdna.rst index 217b3c85f4..03863eb5cf 100644 --- a/doc/src/bond_oxdna.rst +++ b/doc/src/bond_oxdna.rst @@ -6,6 +6,9 @@ bond_style oxdna/fene command bond_style oxdna2/fene command ============================== +bond_style oxrna2/fene command +============================== + Syntax """""" @@ -16,6 +19,8 @@ Syntax bond_style oxdna2/fene + bond_style oxrna2/fene + Examples """""""" @@ -28,10 +33,13 @@ Examples bond_style oxdna2/fene bond_coeff * 2.0 0.25 0.7564 + bond_style oxrna2/fene + bond_coeff \* 2.0 0.25 0.76107 + Description """"""""""" -The *oxdna/fene* and *oxdna2/fene* bond styles use the potential +The *oxdna/fene* , *oxdna2/fene* and *oxrna2/fene* bond styles use the potential .. math:: @@ -39,9 +47,9 @@ The *oxdna/fene* and *oxdna2/fene* bond styles use the potential to define a modified finite extensible nonlinear elastic (FENE) -potential :ref:`(Ouldridge) ` to model the connectivity of the -phosphate backbone in the oxDNA force field for coarse-grained -modelling of DNA. +potential :ref:`(Ouldridge) ` to model the connectivity of the +phosphate backbone in the oxDNA/oxRNA force field for coarse-grained +modelling of DNA/RNA. The following coefficients must be defined for the bond type via the :doc:`bond\_coeff ` command as given in the above example, or @@ -57,27 +65,36 @@ commands: The oxDNA bond style has to be used together with the corresponding oxDNA pair styles for excluded volume interaction - *oxdna/excv*\ , stacking *oxdna/stk*\ , cross-stacking *oxdna/xstk* and + *oxdna/excv* , stacking *oxdna/stk* , cross-stacking *oxdna/xstk* and coaxial stacking interaction *oxdna/coaxstk* as well as hydrogen-bonding interaction *oxdna/hbond* (see also documentation of :doc:`pair\_style oxdna/excv `). For the oxDNA2 - :ref:`(Snodin) ` bond style the analogous pair styles and an - additional Debye-Hueckel pair style *oxdna2/dh* have to be defined. + :ref:`(Snodin) ` bond style the analogous pair styles + *oxdna2/excv* , *oxdna2/stk* , *oxdna2/xstk* , *oxdna2/coaxstk* , + *oxdna2/hbond* and an additional Debye-Hueckel pair style + *oxdna2/dh* have to be defined. The same applies to the oxRNA2 + :ref:`(Sulc1) ` styles. The coefficients in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model. -Example input and data files for DNA duplexes can be found in -examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/. A simple python -setup tool which creates single straight or helical DNA strands, DNA -duplexes or arrays of DNA duplexes can be found in +Example input and data files for DNA and RNA duplexes can be found in +examples/USER/cgdna/examples/oxDNA/ , /oxDNA2/ and /oxRNA2/. A simple python +setup tool which creates single straight or helical DNA strands, DNA/RNA +duplexes or arrays of DNA/RNA duplexes can be found in examples/USER/cgdna/util/. -Please cite :ref:`(Henrich) ` and the relevant oxDNA articles in -any publication that uses this implementation. The article contains -more information on the model, the structure of the input file, the -setup tool and the performance of the LAMMPS-implementation of oxDNA. -The preprint version of the article can be found +Please cite :ref:`(Henrich) ` in any publication that uses +this implementation. The article contains general information +on the model, its implementation and performance as well as the structure of +the data and input file. The preprint version of the article can be found `here `_. +Please cite also the relevant oxDNA/oxRNA publications. These are +:ref:`(Ouldridge) ` and +:ref:`(Ouldridge-DPhil) ` for oxDNA, +:ref:`(Snodin) ` for oxDNA2, +:ref:`(Sulc1) ` for oxRNA2 +and for sequence-specific hydrogen-bonding and stacking interactions +:ref:`(Sulc2) `. ---------- @@ -94,32 +111,36 @@ USER-CGDNA package and the MOLECULE and ASPHERE package. See the Related commands """""""""""""""" -:doc:`pair\_style oxdna/excv `, :doc:`pair\_style oxdna2/excv `, :doc:`fix nve/dotc/langevin `, -:doc:`bond\_coeff ` +:doc:`pair\_style oxdna/excv `, :doc:`pair\_style oxdna2/excv `, :doc:`pair\_style oxrna2/excv `, +:doc:`bond\_coeff `, :doc:`fix nve/dotc/langevin ` -**Default:** none +**Default:** + +none ---------- +.. _Henrich0: -.. _Henrich2: +**(Henrich)** O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018). +.. _Ouldridge-DPhil0: +**(Ouldridge-DPhil)** T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011). -**(Henrich)** O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, -T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018). +.. _Ouldridge0: -.. _oxdna\_fene: +**(Ouldridge)** T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011). +.. _Snodin0: +**(Snodin)** B.E. Snodin, F. Randisi, M. Mosayebi, et al., J. Chem. Phys. 142, 234901 (2015). -**(Ouldridge)** T.E. Ouldridge, A.A. Louis, J.P.K. Doye, -J. Chem. Phys. 134, 085101 (2011). +.. _Sulc01: -.. _oxdna2: +**(Sulc1)** P. Sulc, F. Romano, T. E. Ouldridge, et al., J. Chem. Phys. 140, 235102 (2014). +.. _Sulc02: - -**(Snodin)** B.E. Snodin, F. Randisi, M. Mosayebi, et al., -J. Chem. Phys. 142, 234901 (2015). +**(Sulc2)** P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012). diff --git a/doc/src/fix_nve_dot.rst b/doc/src/fix_nve_dot.rst index 33d9f61b49..5fc6a46ab5 100644 --- a/doc/src/fix_nve_dot.rst +++ b/doc/src/fix_nve_dot.rst @@ -26,11 +26,11 @@ Examples Description """"""""""" -Apply a rigid-body integrator as described in :ref:`(Davidchack) ` +Apply a rigid-body integrator as described in :ref:`(Davidchack) ` to a group of atoms, but without Langevin dynamics. This command performs Molecular dynamics (MD) via a velocity-Verlet algorithm and an evolution operator that rotates -the quaternion degrees of freedom, similar to the scheme outlined in :ref:`(Miller) `. +the quaternion degrees of freedom, similar to the scheme outlined in :ref:`(Miller) `. This command is the equivalent of the :doc:`fix nve/dotc/langevin ` without damping and noise and can be used to determine the stability range @@ -40,7 +40,7 @@ The command is equivalent to the :doc:`fix nve `. The particles are always considered to have a finite size. An example input file can be found in /examples/USER/cgdna/examples/duplex1/. -Further details of the implementation and stability of the integrator are contained in :ref:`(Henrich) `. +Further details of the implementation and stability of the integrator are contained in :ref:`(Henrich) `. The preprint version of the article can be found `here `_. @@ -66,19 +66,15 @@ Related commands ---------- -.. _Davidchack1: - - - -.. _Miller1: +.. _Davidchack4: **(Davidchack)** R.L Davidchack, T.E. Ouldridge, and M.V. Tretyakov. J. Chem. Phys. 142, 144114 (2015). - -.. _Henrich3: +.. _Miller4: **(Miller)** T. F. Miller III, M. Eleftheriou, P. Pattnaik, A. Ndirango, G. J. Martyna, J. Chem. Phys., 116, 8649-8659 (2002). +.. _Henrich4: **(Henrich)** O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018). diff --git a/doc/src/fix_nve_dotc_langevin.rst b/doc/src/fix_nve_dotc_langevin.rst index 408aaf919e..3143db968f 100644 --- a/doc/src/fix_nve_dotc_langevin.rst +++ b/doc/src/fix_nve_dotc_langevin.rst @@ -38,14 +38,14 @@ Description """"""""""" Apply a rigid-body Langevin-type integrator of the kind "Langevin C" -as described in :ref:`(Davidchack) ` +as described in :ref:`(Davidchack) ` to a group of atoms, which models an interaction with an implicit background solvent. This command performs Brownian dynamics (BD) via a technique that splits the integration into a deterministic Hamiltonian part and the Ornstein-Uhlenbeck process for noise and damping. The quaternion degrees of freedom are updated though an evolution operator which performs a rotation in quaternion space, preserves -the quaternion norm and is akin to :ref:`(Miller) `. +the quaternion norm and is akin to :ref:`(Miller) `. In terms of syntax this command has been closely modelled on the :doc:`fix langevin ` and its *angmom* option. But it combines @@ -86,7 +86,7 @@ dt damp), where Kb is the Boltzmann constant, T is the desired temperature, m is the mass of the particle, dt is the timestep size, and damp is the damping factor. Random numbers are used to randomize the direction and magnitude of this force as described in -:ref:`(Dunweg) `, where a uniform random number is used (instead of +:ref:`(Dunweg) `, where a uniform random number is used (instead of a Gaussian random number) for speed. @@ -128,7 +128,7 @@ The scale factor after the *angmom* keyword gives the ratio of the rotational to the translational friction coefficient. An example input file can be found in /examples/USER/cgdna/examples/duplex2/. -Further details of the implementation and stability of the integrators are contained in :ref:`(Henrich) `. +Further details of the implementation and stability of the integrators are contained in :ref:`(Henrich) `. The preprint version of the article can be found `here `_. @@ -154,24 +154,19 @@ Related commands ---------- -.. _Davidchack2: - - - -.. _Miller2: +.. _Davidchack5: **(Davidchack)** R.L Davidchack, T.E. Ouldridge, M.V. Tretyakov. J. Chem. Phys. 142, 144114 (2015). - -.. _Dunweg3: +.. _Miller5: **(Miller)** T. F. Miller III, M. Eleftheriou, P. Pattnaik, A. Ndirango, G. J. Martyna, J. Chem. Phys., 116, 8649-8659 (2002). - -.. _Henrich4: +.. _Dunweg5: **(Dunweg)** B. Dunweg, W. Paul, Int. J. Mod. Phys. C, 2, 817-27 (1991). +.. _Henrich5: **(Henrich)** O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018). diff --git a/doc/src/pair_oxdna.rst b/doc/src/pair_oxdna.rst index b40cf1f6cc..727f19c327 100644 --- a/doc/src/pair_oxdna.rst +++ b/doc/src/pair_oxdna.rst @@ -36,8 +36,8 @@ Syntax *oxdna/stk* args = seq T xi kappa 6.0 0.4 0.9 0.32 0.75 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 + xi = 1.3448 (temperature-independent coefficient in stacking strength) + kappa = 2.6568 (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) @@ -94,11 +94,15 @@ Example input and data files for DNA duplexes can be found in examples/USER/cgdn A simple python setup tool which creates single straight or helical DNA strands, DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/. -Please cite :ref:`(Henrich) ` and the relevant oxDNA articles in any publication that uses this implementation. -The article contains more information on the model, the structure of the input file, the setup tool -and the performance of the LAMMPS-implementation of oxDNA. -The preprint version of the article can be found `here `_. - +Please cite :ref:`(Henrich) ` in any publication that uses +this implementation. The article contains general information +on the model, its implementation and performance as well as the structure of +the data and input file. The preprint version of the article can be found +`here `_. +Please cite also the relevant oxDNA publications +:ref:`(Ouldridge) `, +:ref:`(Ouldridge-DPhil) ` +and :ref:`(Sulc) `. ---------- @@ -114,39 +118,32 @@ USER-CGDNA package and the MOLECULE and ASPHERE package. See the Related commands """""""""""""""" -:doc:`bond\_style oxdna/fene `, :doc:`fix nve/dotc/langevin `, :doc:`pair\_coeff `, -:doc:`bond\_style oxdna2/fene `, :doc:`pair\_style oxdna2/excv ` - +:doc:`bond\_style oxdna/fene `, :doc:`pair\_coeff `, +:doc:`bond\_style oxdna2/fene `, :doc:`pair\_style oxdna2/excv `, +:doc:`bond\_style oxrna2/fene `, :doc:`pair\_style oxrna2/excv `, +:doc:`fix nve/dotc/langevin ` + **Default:** none ---------- - .. _Henrich1: - - **(Henrich)** O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018). -.. _Sulc1: - - - -**(Sulc)** P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012). - .. _Ouldridge-DPhil1: - - -**(Ouldrigde-DPhil)** T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011). +**(Ouldridge-DPhil)** T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011). .. _Ouldridge1: - - **(Ouldridge)** T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011). +.. _Sulc1: + +**(Sulc)** P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012). + .. _lws: http://lammps.sandia.gov .. _ld: Manual.html diff --git a/doc/src/pair_oxdna2.rst b/doc/src/pair_oxdna2.rst index 4f64197f44..77052da666 100644 --- a/doc/src/pair_oxdna2.rst +++ b/doc/src/pair_oxdna2.rst @@ -39,15 +39,15 @@ Syntax *oxdna2/stk* args = seq T xi kappa 6.0 0.4 0.9 0.32 0.75 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 + xi = 1.3523 (temperature-independent coefficient in stacking strength) + kappa = 2.6717 (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 T = temperature (oxDNA units, 0.1 = 300 K) rhos = salt concentration (mole per litre) - qeff = effective charge (elementary charges) + qeff = 0.815 (effective charge in elementary charges) Examples """""""" @@ -63,7 +63,7 @@ Examples 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 pair_coeff \* \* oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 pair_coeff \* \* oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 - pair_coeff \* \* oxdna2/dh 0.1 1.0 0.815 + pair_coeff \* \* oxdna2/dh 0.1 0.5 0.815 Description """"""""""" @@ -83,7 +83,7 @@ The exact functional form of the pair styles is rather complex. The individual potentials consist of products of modulation factors, which themselves are constructed from a number of more basic potentials (Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms. -We refer to :ref:`(Snodin) ` and the original oxDNA publications :ref:`(Ouldridge-DPhil) ` +We refer to :ref:`(Snodin) ` and the original oxDNA publications :ref:`(Ouldridge-DPhil) ` and :ref:`(Ouldridge) ` for a detailed description of the oxDNA2 force field. .. note:: @@ -94,7 +94,7 @@ and :ref:`(Ouldridge) ` for a detailed description of the oxDNA2 fo in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model. 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 + after *oxdna2/dh* (T=0.1, rhos=0.5, qeff=0.815 in the above example). When using a Langevin thermostat e.g. through :doc:`fix langevin ` or :doc:`fix nve/dotc/langevin ` the temperature coefficients have to be matched to the one used in the fix. @@ -102,11 +102,13 @@ Example input and data files for DNA duplexes can be found in examples/USER/cgdn A simple python setup tool which creates single straight or helical DNA strands, DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/. -Please cite :ref:`(Henrich) ` and the relevant oxDNA articles in any publication that uses this implementation. -The article contains more information on the model, the structure of the input file, the setup tool -and the performance of the LAMMPS-implementation of oxDNA. -The preprint version of the article can be found `here `_. - +Please cite :ref:`(Henrich) ` in any publication that uses +this implementation. The article contains general information +on the model, its implementation and performance as well as the structure of +the data and input file. The preprint version of the article can be found +`here `_. +Please cite also the relevant oxDNA2 publications +:ref:`(Snodin) ` and :ref:`(Sulc) `. ---------- @@ -122,43 +124,34 @@ USER-CGDNA package and the MOLECULE and ASPHERE package. See the Related commands """""""""""""""" -:doc:`bond\_style oxdna2/fene `, :doc:`fix nve/dotc/langevin `, :doc:`pair\_coeff `, -:doc:`bond\_style oxdna/fene `, :doc:`pair\_style oxdna/excv ` +:doc:`bond\_style oxdna2/fene `, :doc:`pair\_coeff `, +:doc:`bond\_style oxdna/fene `, :doc:`pair\_style oxdna/excv `, +:doc:`bond\_style oxrna2/fene `, :doc:`pair\_style oxrna2/excv `, +:doc:`fix nve/dotc/langevin ` **Default:** none ---------- - -.. _Henrich: - - +.. _Henrich2: **(Henrich)** O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018). -.. _Sulc2: - - - -**(Sulc)** P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012). - -.. _Snodin: - - +.. _Snodin2: **(Snodin)** B.E. Snodin, F. Randisi, M. Mosayebi, et al., J. Chem. Phys. 142, 234901 (2015). +.. _Sulc2: + +**(Sulc)** P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012). + .. _Ouldridge-DPhil2: - - -**(Ouldrigde-DPhil)** T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011). +**(Ouldridge-DPhil)** T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011). .. _Ouldridge2: - - **(Ouldridge)** T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011). diff --git a/doc/src/pair_oxrna2.rst b/doc/src/pair_oxrna2.rst new file mode 100644 index 0000000000..3cc6e7f4a6 --- /dev/null +++ b/doc/src/pair_oxrna2.rst @@ -0,0 +1,158 @@ +.. index:: pair_style oxrna2/excv + +pair_style oxrna2/excv command +============================== + +pair_style oxrna2/stk command +============================= + +pair_style oxrna2/hbond command +=============================== + +pair_style oxrna2/xstk command +============================== + +pair_style oxrna2/coaxstk command +================================= + +pair_style oxrna2/dh command +============================ + +Syntax +"""""" + + +.. code-block:: LAMMPS + + pair_style style1 + + pair_coeff * * style2 args + +* style1 = *hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh* + +* style2 = *oxrna2/excv* or *oxrna2/stk* or *oxrna2/hbond* or *oxrna2/xstk* or *oxrna2/coaxstk* or *oxrna2/dh* +* args = list of arguments for these particular styles + + +.. parsed-literal:: + + *oxrna2/stk* args = seq T xi kappa 6.0 0.43 0.93 0.35 0.78 0.9 0 0.95 0.9 0 0.95 1.3 0 0.8 1.3 0 0.8 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 = 1.40206 (temperature-independent coefficient in stacking strength) + kappa = 2.77 (coefficient of linear temperature dependence in stacking strength) + *oxrna2/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 = 0.870439 (between base pairs A-T, C-G and G-T) or 0 (all other pairs) + *oxrna2/dh* args = T rhos qeff + T = temperature (oxDNA units, 0.1 = 300 K) + rhos = salt concentration (mole per litre) + qeff = 1.02455 (effective charge in elementary charges) + +Examples +"""""""" + + +.. code-block:: LAMMPS + + pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh + pair_coeff * * oxrna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 + pair_coeff * * oxrna2/stk seqdep 0.1 1.40206 2.77 6.0 0.43 0.93 0.35 0.78 0.9 0 0.95 0.9 0 0.95 1.3 0 0.8 1.3 0 0.8 2.0 0.65 2.0 0.65 + pair_coeff * * oxrna2/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 oxrna2/hbond seqdep 0.870439 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 oxrna2/hbond seqdep 0.870439 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 3 4 oxrna2/hbond seqdep 0.870439 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 * * oxrna2/xstk 59.9626 0.5 0.6 0.42 0.58 2.25 0.505 0.58 1.7 1.266 0.68 1.7 1.266 0.68 1.7 0.309 0.68 1.7 0.309 0.68 + pair_coeff * * oxrna2/coaxstk 80 0.5 0.6 0.42 0.58 2.0 2.592 0.65 1.3 0.151 0.8 0.9 0.685 0.95 0.9 0.685 0.95 2.0 -0.65 2.0 -0.65 + pair_coeff * * oxrna2/dh 0.1 0.5 1.02455 + +Description +""""""""""" + +The *oxrna2* pair styles compute the pairwise-additive parts of the oxDNA force field +for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the +excluded volume interaction *oxrna2/excv*\ , the stacking *oxrna2/stk*\ , cross-stacking *oxrna2/xstk* +and coaxial stacking interaction *oxrna2/coaxstk*\ , electrostatic Debye-Hueckel interaction *oxrna2/dh* +as well as the hydrogen-bonding interaction *oxrna2/hbond* between complementary pairs of nucleotides on +opposite strands. Average sequence or sequence-dependent stacking and base-pairing strengths +are supported :ref:`(Sulc2) `. Quasi-unique base-pairing between nucleotides can be achieved by using +more complementary pairs of atom types like 5-8 and 6-7, 9-12 and 10-11, 13-16 and 14-15, etc. +This prevents the hybridization of in principle complementary bases within Ntypes/4 bases +up and down along the backbone. + +The exact functional form of the pair styles is rather complex. +The individual potentials consist of products of modulation factors, +which themselves are constructed from a number of more basic potentials +(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms. +We refer to :ref:`(Sulc1) ` and the original oxDNA publications :ref:`(Ouldridge-DPhil) ` +and :ref:`(Ouldridge) ` for a detailed description of the oxRNA2 force field. + +.. note:: + + These pair styles have to be used together with the related oxDNA2 bond style + *oxrna2/fene* for the connectivity of the phosphate backbone (see also documentation of + :doc:`bond\_style oxrna2/fene `). 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 four coefficients after *oxrna2/stk* (seq=seqdep, T=0.1, xi=1.40206 and kappa=2.77 in the above example), + the first coefficient after *oxrna2/hbond* (seq=seqdep in the above example) and the three coefficients + after *oxrna2/dh* (T=0.1, rhos=0.5, qeff=1.02455 in the above example). When using a Langevin thermostat + e.g. through :doc:`fix langevin ` or :doc:`fix nve/dotc/langevin ` + the temperature coefficients have to be matched to the one used in the fix. + +Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/. +A simple python setup tool which creates single straight or helical DNA strands, +DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/. + +Please cite :ref:`(Henrich) ` in any publication that uses +this implementation. The article contains general information +on the model, its implementation and performance as well as the structure of +the data and input file. The preprint version of the article can be found +`here `_. +Please cite also the relevant oxRNA2 publications +:ref:`(Sulc1) ` and :ref:`(Sulc2) `. + +---------- + + +Restrictions +"""""""""""" + + +These pair styles can only be used if LAMMPS was built with the +USER-CGDNA package and the MOLECULE and ASPHERE package. See the +:doc:`Build package ` doc page for more info. + +Related commands +"""""""""""""""" + +:doc:`bond\_style oxrna2/fene `, :doc:`pair\_coeff `, +:doc:`bond\_style oxdna/fene `, :doc:`pair\_style oxdna/excv `, +:doc:`bond\_style oxdna2/fene `, :doc:`pair\_style oxdna2/excv `, +:doc:`fix nve/dotc/langevin ` + +**Default:** + +none + + +---------- + +.. _Henrich3: + +**(Henrich)** O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018). + +.. _Sulc31: + +**(Sulc1)** P. Sulc, F. Romano, T. E. Ouldridge, et al., J. Chem. Phys. 140, 235102 (2014). + +.. _Sulc32: + +**(Sulc2)** P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012). + +.. _Ouldridge-DPhil3: + +**(Ouldridge-DPhil)** T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011). + +.. _Ouldridge3: + +**(Ouldridge)** T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011). diff --git a/examples/USER/cgdna/README b/examples/USER/cgdna/README index 8a9dc44359..49b7cd1f84 100644 --- a/examples/USER/cgdna/README +++ b/examples/USER/cgdna/README @@ -1,8 +1,12 @@ This directory contains example data and input files -and utility scripts for the oxDNA coarse-grained model -for DNA. +as well as utility scripts for the oxDNA/oxDNA2/oxRNA2 +coarse-grained model of DNA and RNA. + +/******************************************************************************/ + +/examples/oxDNA/duplex1: +/examples/oxDNA2/duplex1: -/examples/duplex1: Input, data and log files for a DNA duplex (double-stranded DNA) consisiting of 5 base pairs. The duplex contains two strands with complementary base pairs. The topology is @@ -11,7 +15,14 @@ A - C - G - T - A | | | | | T - G - C - A - T -/examples/duplex2: +Note that in this example the stacking and hydrogen-bonding interactions +are sequence-averaged (cf. keyword 'seqav' in according pair styles). + +/******************************************************************************/ + +/examples/oxDNA/duplex2: +/examples/oxDNA2/duplex2: + Input, data and log files for a nicked DNA duplex (double-stranded DNA) consisiting of 8 base pairs. The duplex contains strands with complementary base pairs, but the backbone on one side is not continuous: @@ -22,16 +33,52 @@ A - C - G - T - A - C - G - T | | | | | | | | T - G - C - A T - G - C - A -/examples/duplex3: -This is basically the duplex1 run with sequence-dependent stacking -and hydrogen-bonding strengths enabled and both nucleotide mass and -moment of inertia set to the value of the standalone implementation -of oxDNA (M = I = 1). To achieve this, the masses can be set directly -in the input and data file, whereas the moment of inertia is set via -the diameter of the ellipsoid in the data file and has a value of 3.16227766. +Note that in this example the stacking and hydrogen-bonding interactions +are sequence-averaged (cf. keyword 'seqav' in according pair styles). + +/******************************************************************************/ + +/examples/oxDNA2/duplex3: + +This example uses the duplex1 with sequence-dependent stacking and +hydrogen-bonding interactions and both nucleotide mass and +moment of inertia set to the value used in the standalone implementation +of oxDNA (M = I = 1). The masses can be set directly in the input and +data file, whereas the moment of inertia is set via the diameter of the +ellipsoid in the data file and has a value of 3.16227766. The change of mass and moment of inertia allows direct comparision of -e.g. trajectory data, energies or time-dependent observables on a per-timestep -basis until numerical noise causes deviations at later simulation times. +trajectory data or time-dependent observables on a per-timestep basis. + +As mentioned above, the stacking and hydrogen-bonding interactions +are sequence-dependent (cf. keyword 'seqdep' in according pair styles). + +/******************************************************************************/ + +/examples/oxDNA2/unique_bp: + +This example uses atom types 1-8 to model a 13 base pair duplex. +The nucleotide types are assigned as follows: +A = 1,5; C = 2,6; G = 3,7; T = 4,8 + +The topology is +A C G T A C G T A C G T A +1 - 2 - 3 - 4 - 5 - 6 - 7 - 8 - 1 - 2 - 7 - 8 - 1 +| | | | | | | | | | | | | +4 - 3 - 2 - 1 - 8 - 7 - 6 - 5 - 4 - 3 - 6 - 5 - 4 +T G C A T G C A T G C A T + +With a large (32 or 64) number of atom types quasi-unique base pairing +between two individual nucleotides can be established. + +/******************************************************************************/ + +/examples/oxRNA2/duplex4 + +This example uses the duplex2 with the oxRNA2 force field instead of oxDNA or +oxDNA2 force field. Sequence-dependent stacking and hydrogen-bonding +strengths enabled (cf. keyword 'seqdep' in according pair styles). + +/******************************************************************************/ /util: This directory contains a simple python setup tool which creates diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex3/in.duplex3 b/examples/USER/cgdna/examples/oxDNA2/duplex3/in.duplex3 index fd75a6fc3f..033783dc15 100644 --- a/examples/USER/cgdna/examples/oxDNA2/duplex3/in.duplex3 +++ b/examples/USER/cgdna/examples/oxDNA2/duplex3/in.duplex3 @@ -1,4 +1,4 @@ -variable number equal 1 +variable number equal 3 variable ofreq equal 1000 variable efreq equal 1000 variable T equal 0.1 diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex3/log.07Aug19.duplex3.g++.1 b/examples/USER/cgdna/examples/oxDNA2/duplex3/log.07Aug19.duplex3.g++.1 index 8f70e9ec96..9172c99492 100644 --- a/examples/USER/cgdna/examples/oxDNA2/duplex3/log.07Aug19.duplex3.g++.1 +++ b/examples/USER/cgdna/examples/oxDNA2/duplex3/log.07Aug19.duplex3.g++.1 @@ -1,5 +1,5 @@ LAMMPS (7 Aug 2019) -variable number equal 1 +variable number equal 3 variable ofreq equal 1000 variable efreq equal 1000 variable T equal 0.1 diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex3/log.07Aug19.duplex3.g++.4 b/examples/USER/cgdna/examples/oxDNA2/duplex3/log.07Aug19.duplex3.g++.4 index f110e20906..491f91e671 100644 --- a/examples/USER/cgdna/examples/oxDNA2/duplex3/log.07Aug19.duplex3.g++.4 +++ b/examples/USER/cgdna/examples/oxDNA2/duplex3/log.07Aug19.duplex3.g++.4 @@ -1,5 +1,5 @@ LAMMPS (7 Aug 2019) -variable number equal 1 +variable number equal 3 variable ofreq equal 1000 variable efreq equal 1000 variable T equal 0.1 diff --git a/examples/USER/cgdna/examples/oxDNA2/unique_bp/data.duplex4.4type b/examples/USER/cgdna/examples/oxDNA2/unique_bp/data.duplex4.4type new file mode 100644 index 0000000000..a8412eef07 --- /dev/null +++ b/examples/USER/cgdna/examples/oxDNA2/unique_bp/data.duplex4.4type @@ -0,0 +1,130 @@ +# LAMMPS data file +26 atoms +26 ellipsoids +24 bonds + +4 atom types +1 bond types + +# System size +-20.000000 20.000000 xlo xhi +-20.000000 20.000000 ylo yhi +-20.000000 20.000000 zlo zhi + +# Atom-ID, type, position, molecule-ID, ellipsoid flag, density +Atoms + +1 1 -6.000000000000001e-01 0.000000000000000e+00 0.000000000000000e+00 1 1 1 +2 2 -4.957432645895970e-01 -3.379920348381733e-01 3.897628551303122e-01 1 1 1 +3 3 -2.192046146198370e-01 -5.585242491865227e-01 7.795257102606244e-01 1 1 1 +4 4 1.335125603737887e-01 -5.849567473090943e-01 1.169288565390937e+00 1 1 1 +5 1 4.398311230978960e-01 -4.081036426625517e-01 1.559051420521249e+00 1 1 1 +6 2 5.932984957350773e-01 -8.942535970570469e-02 1.948814275651561e+00 1 1 1 +7 3 5.405813207414517e-01 2.603302434705350e-01 2.338577130781873e+00 1 1 1 +8 4 3.000000000000002e-01 5.196152422706634e-01 2.728339985912185e+00 1 1 1 +9 1 -4.483805615185452e-02 5.983222783087083e-01 3.118102841042497e+00 1 1 1 +10 2 -3.740938811152403e-01 4.690988894808181e-01 3.507865696172809e+00 1 1 1 +11 3 -5.733436834716847e-01 1.768531046465427e-01 3.897628551303121e+00 1 1 1 +12 4 -5.733436834716849e-01 -1.768531046465427e-01 4.287391406433434e+00 1 1 1 +13 1 -3.740938811152403e-01 -4.690988894808182e-01 4.677154261563746e+00 1 1 1 +14 4 3.740938811152403e-01 4.690988894808182e-01 4.677154261563746e+00 2 1 1 +15 1 5.733436834716849e-01 1.768531046465427e-01 4.287391406433434e+00 2 1 1 +16 2 5.733436834716849e-01 -1.768531046465426e-01 3.897628551303122e+00 2 1 1 +17 3 3.740938811152403e-01 -4.690988894808181e-01 3.507865696172810e+00 2 1 1 +18 4 4.483805615185462e-02 -5.983222783087085e-01 3.118102841042498e+00 2 1 1 +19 1 -3.000000000000003e-01 -5.196152422706636e-01 2.728339985912186e+00 2 1 1 +20 2 -5.405813207414519e-01 -2.603302434705351e-01 2.338577130781874e+00 2 1 1 +21 3 -5.932984957350776e-01 8.942535970570474e-02 1.948814275651561e+00 2 1 1 +22 4 -4.398311230978962e-01 4.081036426625520e-01 1.559051420521249e+00 2 1 1 +23 1 -1.335125603737888e-01 5.849567473090947e-01 1.169288565390937e+00 2 1 1 +24 2 2.192046146198373e-01 5.585242491865231e-01 7.795257102606246e-01 2 1 1 +25 3 4.957432645895974e-01 3.379920348381736e-01 3.897628551303123e-01 2 1 1 +26 4 6.000000000000006e-01 0.000000000000000e+00 1.110223024625157e-16 2 1 1 + +# Atom-ID, translational, rotational velocity +Velocities + +1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +2 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +3 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +4 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +5 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +6 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +7 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +8 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +9 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +10 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +11 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +12 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +13 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +14 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +15 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +16 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +17 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +18 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +19 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +20 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +21 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +22 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +23 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +24 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +25 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +26 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 + +# Atom-ID, shape, quaternion +Ellipsoids + +1 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +2 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.555728057861408e-01 0.000000000000000e+00 0.000000000000000e+00 2.947551744109042e-01 +3 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 8.262387743159949e-01 0.000000000000000e+00 0.000000000000000e+00 5.633200580636221e-01 +4 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 6.234898018587335e-01 0.000000000000000e+00 0.000000000000000e+00 7.818314824680299e-01 +5 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 3.653410243663950e-01 0.000000000000000e+00 0.000000000000000e+00 9.308737486442042e-01 +6 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 7.473009358642424e-02 0.000000000000000e+00 0.000000000000000e+00 9.972037971811802e-01 +7 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -2.225209339563144e-01 0.000000000000000e+00 0.000000000000000e+00 9.749279121818237e-01 +8 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -5.000000000000001e-01 0.000000000000000e+00 0.000000000000000e+00 8.660254037844387e-01 +9 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 7.330518718298263e-01 -0.000000000000000e+00 0.000000000000000e+00 -6.801727377709196e-01 +10 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.009688679024190e-01 -0.000000000000000e+00 0.000000000000000e+00 -4.338837391175581e-01 +11 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.888308262251286e-01 -0.000000000000000e+00 0.000000000000000e+00 -1.490422661761745e-01 +12 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.888308262251286e-01 0.000000000000000e+00 0.000000000000000e+00 1.490422661761745e-01 +13 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.009688679024190e-01 0.000000000000000e+00 0.000000000000000e+00 4.338837391175582e-01 +14 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 -4.338837391175582e-01 9.009688679024190e-01 0.000000000000000e+00 +15 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 -1.490422661761746e-01 9.888308262251286e-01 0.000000000000000e+00 +16 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 1.490422661761745e-01 9.888308262251286e-01 -0.000000000000000e+00 +17 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 4.338837391175581e-01 9.009688679024190e-01 -0.000000000000000e+00 +18 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 6.801727377709192e-01 7.330518718298267e-01 0.000000000000000e+00 +19 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 8.660254037844386e-01 5.000000000000001e-01 0.000000000000000e+00 +20 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.749279121818235e-01 2.225209339563145e-01 0.000000000000000e+00 +21 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.972037971811801e-01 -7.473009358642428e-02 0.000000000000000e+00 +22 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.308737486442041e-01 -3.653410243663952e-01 0.000000000000000e+00 +23 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 7.818314824680296e-01 -6.234898018587339e-01 0.000000000000000e+00 +24 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 5.633200580636215e-01 -8.262387743159952e-01 0.000000000000000e+00 +25 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 -2.947551744109044e-01 9.555728057861407e-01 0.000000000000000e+00 +26 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 -0.000000000000000e+00 + +# Bond topology +Bonds + +1 1 1 2 +2 1 2 3 +3 1 3 4 +4 1 4 5 +5 1 5 6 +6 1 6 7 +7 1 7 8 +8 1 8 9 +9 1 9 10 +10 1 10 11 +11 1 11 12 +12 1 12 13 +13 1 14 15 +14 1 15 16 +15 1 16 17 +16 1 17 18 +17 1 18 19 +18 1 19 20 +19 1 20 21 +20 1 21 22 +21 1 22 23 +22 1 23 24 +23 1 24 25 +24 1 25 26 diff --git a/examples/USER/cgdna/examples/oxDNA2/unique_bp/data.duplex4.8type b/examples/USER/cgdna/examples/oxDNA2/unique_bp/data.duplex4.8type new file mode 100644 index 0000000000..b4d622ac46 --- /dev/null +++ b/examples/USER/cgdna/examples/oxDNA2/unique_bp/data.duplex4.8type @@ -0,0 +1,130 @@ +# LAMMPS data file +26 atoms +26 ellipsoids +24 bonds + +8 atom types +1 bond types + +# System size +-20.000000 20.000000 xlo xhi +-20.000000 20.000000 ylo yhi +-20.000000 20.000000 zlo zhi + +# Atom-ID, type, position, molecule-ID, ellipsoid flag, density +Atoms + +1 1 -6.000000000000001e-01 0.000000000000000e+00 0.000000000000000e+00 1 1 1 +2 2 -4.957432645895970e-01 -3.379920348381733e-01 3.897628551303122e-01 1 1 1 +3 3 -2.192046146198370e-01 -5.585242491865227e-01 7.795257102606244e-01 1 1 1 +4 4 1.335125603737887e-01 -5.849567473090943e-01 1.169288565390937e+00 1 1 1 +5 5 4.398311230978960e-01 -4.081036426625517e-01 1.559051420521249e+00 1 1 1 +6 6 5.932984957350773e-01 -8.942535970570469e-02 1.948814275651561e+00 1 1 1 +7 7 5.405813207414517e-01 2.603302434705350e-01 2.338577130781873e+00 1 1 1 +8 8 3.000000000000002e-01 5.196152422706634e-01 2.728339985912185e+00 1 1 1 +9 1 -4.483805615185452e-02 5.983222783087083e-01 3.118102841042497e+00 1 1 1 +10 2 -3.740938811152403e-01 4.690988894808181e-01 3.507865696172809e+00 1 1 1 +11 7 -5.733436834716847e-01 1.768531046465427e-01 3.897628551303121e+00 1 1 1 +12 8 -5.733436834716849e-01 -1.768531046465427e-01 4.287391406433434e+00 1 1 1 +13 1 -3.740938811152403e-01 -4.690988894808182e-01 4.677154261563746e+00 1 1 1 +14 4 3.740938811152403e-01 4.690988894808182e-01 4.677154261563746e+00 2 1 1 +15 5 5.733436834716849e-01 1.768531046465427e-01 4.287391406433434e+00 2 1 1 +16 6 5.733436834716849e-01 -1.768531046465426e-01 3.897628551303122e+00 2 1 1 +17 3 3.740938811152403e-01 -4.690988894808181e-01 3.507865696172810e+00 2 1 1 +18 4 4.483805615185462e-02 -5.983222783087085e-01 3.118102841042498e+00 2 1 1 +19 5 -3.000000000000003e-01 -5.196152422706636e-01 2.728339985912186e+00 2 1 1 +20 6 -5.405813207414519e-01 -2.603302434705351e-01 2.338577130781874e+00 2 1 1 +21 7 -5.932984957350776e-01 8.942535970570474e-02 1.948814275651561e+00 2 1 1 +22 8 -4.398311230978962e-01 4.081036426625520e-01 1.559051420521249e+00 2 1 1 +23 1 -1.335125603737888e-01 5.849567473090947e-01 1.169288565390937e+00 2 1 1 +24 2 2.192046146198373e-01 5.585242491865231e-01 7.795257102606246e-01 2 1 1 +25 3 4.957432645895974e-01 3.379920348381736e-01 3.897628551303123e-01 2 1 1 +26 4 6.000000000000006e-01 0.000000000000000e+00 1.110223024625157e-16 2 1 1 + +# Atom-ID, translational, rotational velocity +Velocities + +1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +2 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +3 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +4 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +5 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +6 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +7 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +8 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +9 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +10 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +11 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +12 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +13 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +14 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +15 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +16 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +17 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +18 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +19 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +20 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +21 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +22 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +23 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +24 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +25 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +26 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 + +# Atom-ID, shape, quaternion +Ellipsoids + +1 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +2 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.555728057861408e-01 0.000000000000000e+00 0.000000000000000e+00 2.947551744109042e-01 +3 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 8.262387743159949e-01 0.000000000000000e+00 0.000000000000000e+00 5.633200580636221e-01 +4 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 6.234898018587335e-01 0.000000000000000e+00 0.000000000000000e+00 7.818314824680299e-01 +5 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 3.653410243663950e-01 0.000000000000000e+00 0.000000000000000e+00 9.308737486442042e-01 +6 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 7.473009358642424e-02 0.000000000000000e+00 0.000000000000000e+00 9.972037971811802e-01 +7 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -2.225209339563144e-01 0.000000000000000e+00 0.000000000000000e+00 9.749279121818237e-01 +8 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -5.000000000000001e-01 0.000000000000000e+00 0.000000000000000e+00 8.660254037844387e-01 +9 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 7.330518718298263e-01 -0.000000000000000e+00 0.000000000000000e+00 -6.801727377709196e-01 +10 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.009688679024190e-01 -0.000000000000000e+00 0.000000000000000e+00 -4.338837391175581e-01 +11 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.888308262251286e-01 -0.000000000000000e+00 0.000000000000000e+00 -1.490422661761745e-01 +12 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.888308262251286e-01 0.000000000000000e+00 0.000000000000000e+00 1.490422661761745e-01 +13 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.009688679024190e-01 0.000000000000000e+00 0.000000000000000e+00 4.338837391175582e-01 +14 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 -4.338837391175582e-01 9.009688679024190e-01 0.000000000000000e+00 +15 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 -1.490422661761746e-01 9.888308262251286e-01 0.000000000000000e+00 +16 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 1.490422661761745e-01 9.888308262251286e-01 -0.000000000000000e+00 +17 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 4.338837391175581e-01 9.009688679024190e-01 -0.000000000000000e+00 +18 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 6.801727377709192e-01 7.330518718298267e-01 0.000000000000000e+00 +19 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 8.660254037844386e-01 5.000000000000001e-01 0.000000000000000e+00 +20 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.749279121818235e-01 2.225209339563145e-01 0.000000000000000e+00 +21 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.972037971811801e-01 -7.473009358642428e-02 0.000000000000000e+00 +22 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.308737486442041e-01 -3.653410243663952e-01 0.000000000000000e+00 +23 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 7.818314824680296e-01 -6.234898018587339e-01 0.000000000000000e+00 +24 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 5.633200580636215e-01 -8.262387743159952e-01 0.000000000000000e+00 +25 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 -2.947551744109044e-01 9.555728057861407e-01 0.000000000000000e+00 +26 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 -0.000000000000000e+00 + +# Bond topology +Bonds + +1 1 1 2 +2 1 2 3 +3 1 3 4 +4 1 4 5 +5 1 5 6 +6 1 6 7 +7 1 7 8 +8 1 8 9 +9 1 9 10 +10 1 10 11 +11 1 11 12 +12 1 12 13 +13 1 14 15 +14 1 15 16 +15 1 16 17 +16 1 17 18 +17 1 18 19 +18 1 19 20 +19 1 20 21 +20 1 21 22 +21 1 22 23 +22 1 23 24 +23 1 24 25 +24 1 25 26 diff --git a/examples/USER/cgdna/examples/oxDNA2/unique_bp/generate_unique.py b/examples/USER/cgdna/examples/oxDNA2/unique_bp/generate_unique.py new file mode 100644 index 0000000000..e5141bc47a --- /dev/null +++ b/examples/USER/cgdna/examples/oxDNA2/unique_bp/generate_unique.py @@ -0,0 +1,828 @@ +#!/usr/bin/env python +""" +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) +------------------------------------------------------------------------- */ +""" +""" +Creates unique base-pairings to avoid asymmetrical H-bonds. + +Modified to create the bead wall setup. +N_BEADS is the number of beads along one direction, the final system will have N_BEADS^2 beads in the wall. N_BEADS should be set to be odd number. +""" + + +#Define number of base-pairs per turn for B-form DNA +N = 10.5 +#Define distance between the big bead and the centre of mass of the last base-pair +BEAD_OFFSET = 2.0 +WALL_PARTICLE_SIZE = 2.0 +N_BEADS = 11 + +#Number of unique base type groups (1-4) ACGT counts as one group +N_BASE_TYPES = 20 + + +""" +Import basic modules +""" +import sys, os, timeit + +from timeit import default_timer as timer +start_time = timer() +""" +Try to import numpy; if failed, import a local version mynumpy +which needs to be provided +""" +try: + import numpy as np +except: + print("numpy not found. Exiting.", file=sys.stderr) + sys.exit(1) + +""" +Check that the required arguments (box offset and size in simulation units +and the sequence file were provided +""" +try: + box_offset = float(sys.argv[1]) + box_length = float(sys.argv[2]) + infile = sys.argv[3] + if len(sys.argv) == 4: + topo = 'strand' + lk = 0 + elif len(sys.argv) == 5: + topo = 'strand' + lk = int(sys.argv[4]) + +except: + print("Usage: %s <%s> <%s> <%s> <%s> " % (sys.argv[0], \ + "box offset", "box length", "file with sequences", "[Lk]"), file=sys.stderr) + sys.exit(1) +box = np.array ([box_length, box_length, box_length]) + +""" +Try to open the file and fail gracefully if file cannot be opened +""" +try: + inp = open (infile, 'r') + inp.close() +except: + print("Could not open file '%s' for reading. \ + Aborting." % infile, file=sys.stderr) + sys.exit(2) + +# return parts of a string +def partition(s, d): + if d in s: + sp = s.split(d, 1) + return sp[0], d, sp[1] + else: + return s, "", "" + +""" +Define the model constants +""" +# set model constants +PI = np.pi +POS_BASE = 0.4 +POS_BACK = -0.4 +EXCL_RC1 = 0.711879214356 +EXCL_RC2 = 0.335388426126 +EXCL_RC3 = 0.52329943261 + +""" +Define auxillary variables for the construction of a helix +""" +# center of the double strand +COM_CENTRE_DS = POS_BASE + 0.2 + +# ideal rise between two consecutive nucleotides on the +# same strand which are to be base paired in a duplex +BASE_BASE = 0.3897628551303122 + +# cutoff distance for overlap check +RC2 = 16 + +# squares of the excluded volume distances for overlap check +RC2_BACK = EXCL_RC1**2 +RC2_BASE = EXCL_RC2**2 +RC2_BACK_BASE = EXCL_RC3**2 + +# enumeration to translate from letters to numbers and vice versa +number_to_base = {1 : 'A', 2 : 'C', 3 : 'G', 4 : 'T'} +base_to_number = {'A' : 1, 'a' : 1, 'C' : 2, 'c' : 2, + 'G' : 3, 'g' : 3, 'T' : 4, 't' : 4} + +# auxillary arrays +positions = [] +a1s = [] +a3s = [] +quaternions = [] + +newpositions = [] +newa1s = [] +newa3s = [] + +basetype = [] +strandnum = [] + +bonds = [] + +""" +Convert local body frame to quaternion DOF +""" +def exyz_to_quat (mya1, mya3): + + mya2 = np.cross(mya3, mya1) + myquat = [1,0,0,0] + + q0sq = 0.25 * (mya1[0] + mya2[1] + mya3[2] + 1.0) + q1sq = q0sq - 0.5 * (mya2[1] + mya3[2]) + q2sq = q0sq - 0.5 * (mya1[0] + mya3[2]) + q3sq = q0sq - 0.5 * (mya1[0] + mya2[1]) + + # some component must be greater than 1/4 since they sum to 1 + # compute other components from it + + if q0sq >= 0.25: + myquat[0] = np.sqrt(q0sq) + myquat[1] = (mya2[2] - mya3[1]) / (4.0*myquat[0]) + myquat[2] = (mya3[0] - mya1[2]) / (4.0*myquat[0]) + myquat[3] = (mya1[1] - mya2[0]) / (4.0*myquat[0]) + elif q1sq >= 0.25: + myquat[1] = np.sqrt(q1sq) + myquat[0] = (mya2[2] - mya3[1]) / (4.0*myquat[1]) + myquat[2] = (mya2[0] + mya1[1]) / (4.0*myquat[1]) + myquat[3] = (mya1[2] + mya3[0]) / (4.0*myquat[1]) + elif q2sq >= 0.25: + myquat[2] = np.sqrt(q2sq) + myquat[0] = (mya3[0] - mya1[2]) / (4.0*myquat[2]) + myquat[1] = (mya2[0] + mya1[1]) / (4.0*myquat[2]) + myquat[3] = (mya3[1] + mya2[2]) / (4.0*myquat[2]) + elif q3sq >= 0.25: + myquat[3] = np.sqrt(q3sq) + myquat[0] = (mya1[1] - mya2[0]) / (4.0*myquat[3]) + myquat[1] = (mya3[0] + mya1[2]) / (4.0*myquat[3]) + myquat[2] = (mya3[1] + mya2[2]) / (4.0*myquat[3]) + + norm = 1.0/np.sqrt(myquat[0]*myquat[0] + myquat[1]*myquat[1] + \ + myquat[2]*myquat[2] + myquat[3]*myquat[3]) + myquat[0] *= norm + myquat[1] *= norm + myquat[2] *= norm + myquat[3] *= norm + + return np.array([myquat[0],myquat[1],myquat[2],myquat[3]]) + +""" +Adds a strand to the system by appending it to the array of previous strands +""" +def add_strands (mynewpositions, mynewa1s, mynewa3s): + overlap = False + + # This is a simple check for each of the particles where for previously + # placed particles i we check whether it overlaps with any of the + # newly created particles j + + print("## Checking for overlaps", file=sys.stdout) + + for i in range(len(positions)): + + p = positions[i] + pa1 = a1s[i] + + for j in range (len(mynewpositions)): + + q = mynewpositions[j] + qa1 = mynewa1s[j] + + # skip particles that are anyway too far away + dr = p - q + dr -= box * np.rint (dr / box) + if np.dot(dr, dr) > RC2: + continue + + # base site and backbone site of the two particles + p_pos_back = p + pa1 * POS_BACK + p_pos_base = p + pa1 * POS_BASE + q_pos_back = q + qa1 * POS_BACK + q_pos_base = q + qa1 * POS_BASE + + # check for no overlap between the two backbone sites + dr = p_pos_back - q_pos_back + dr -= box * np.rint (dr / box) + if np.dot(dr, dr) < RC2_BACK: + overlap = True + + # check for no overlap between the two base sites + dr = p_pos_base - q_pos_base + dr -= box * np.rint (dr / box) + if np.dot(dr, dr) < RC2_BASE: + overlap = True + + # check for no overlap between backbone site of particle p + # with base site of particle q + dr = p_pos_back - q_pos_base + dr -= box * np.rint (dr / box) + if np.dot(dr, dr) < RC2_BACK_BASE: + overlap = True + + # check for no overlap between base site of particle p and + # backbone site of particle q + dr = p_pos_base - q_pos_back + dr -= box * np.rint (dr / box) + if np.dot(dr, dr) < RC2_BACK_BASE: + overlap = True + + # exit if there is an overlap + if overlap: + return False + + # append to the existing list if no overlap is found + if not overlap: + + for p in mynewpositions: + positions.append(p) + for p in mynewa1s: + a1s.append (p) + for p in mynewa3s: + a3s.append (p) + # calculate quaternion from local body frame and append + for ia in range(len(mynewpositions)): + mynewquaternions = exyz_to_quat(mynewa1s[ia],mynewa3s[ia]) + quaternions.append(mynewquaternions) + + return True + +""" +Calculate angle of rotation site to site +""" +def get_angle(bp): + #n, minimal number of bases per turn + n = 10.5 + found = False + while found == False: + turns = bp/n + diff = abs( turns - round(turns)) + if diff < 0.03: + found = True + turns = round(turns)+lk + angle = (360*turns)/bp + angle = round (angle,2) + #angle =round( 360/n,2) + elif n > 11.5: + angle = 35.9 + found = True + else: + n += 0.02 + return angle + + +def get_angle2(bp): + turns = bp/N + lk + angle = (360*turns)/bp + + return angle + + + +""" +Returns the rotation matrix defined by an axis and angle +""" +def get_rotation_matrix(axis, anglest, nbp=0): + # The argument anglest can be either an angle in radiants + # (accepted types are float, int or np.float64 or np.float64) + # or a tuple [angle, units] where angle is a number and + # units is a string. It tells the routine whether to use degrees, + # radiants (the default) or base pairs turns. + if not isinstance (anglest, (np.float64, np.float32, float, int)): + if len(anglest) > 1: + if anglest[1] in ["degrees", "deg", "o"]: + angle = (np.pi / 180.) * (anglest[0]) + elif anglest[1] in ["bp"]: + if nbp == 0: + angle = int(anglest[0]) * (np.pi / 180.) * (35.9) + else: + ang = get_angle2(nbp) + angle = int(anglest[0]) * (np.pi / 180.) * (ang) + else: + angle = float(anglest[0]) + else: + angle = float(anglest[0]) + else: + angle = float(anglest) # in degrees (?) + + axis = np.array(axis) + axis /= np.sqrt(np.dot(axis, axis)) + + ct = np.cos(angle) + st = np.sin(angle) + olc = 1. - ct + x, y, z = axis + + return np.array([[olc*x*x+ct, olc*x*y-st*z, olc*x*z+st*y], + [olc*x*y+st*z, olc*y*y+ct, olc*y*z-st*x], + [olc*x*z-st*y, olc*y*z+st*x, olc*z*z+ct]]) + +""" +Generates the position and orientation vectors of a +(single or double) strand from a sequence string +""" +def generate_strand(bp, sequence=None, start_pos=np.array([0, 0, 0]), \ + dir=np.array([0, 0, 1]), perp=False, double=True, rot=0.): + # generate empty arrays + mynewpositions, mynewa1s, mynewa3s = [], [], [] + + # cast the provided start_pos array into a numpy array + start_pos = np.array(start_pos, dtype=float) + + # overall direction of the helix + dir = np.array(dir, dtype=float) + #if sequence == None: + # sequence = np.random.randint(1, 5, bp) + + # the elseif here is most likely redundant + #elif len(sequence) != bp: + # n = bp - len(sequence) + # sequence += np.random.randint(1, 5, n) + # print("sequence is too short, adding %d random bases" % n, file=sys.stderr) + + # normalize direction + dir_norm = np.sqrt(np.dot(dir,dir)) + if dir_norm < 1e-10: + print("direction must be a valid vector,\ + defaulting to (0, 0, 1)", file=sys.stderr) + dir = np.array([0, 0, 1]) + else: dir /= dir_norm + + # find a vector orthogonal to dir to act as helix direction, + # if not provided switch off random orientation + if perp is None or perp is False: + v1 = np.random.random_sample(3) + # comment in to suppress randomised base vector + v1 = [1,0,0] + v1 -= dir * (np.dot(dir, v1)) + v1 /= np.sqrt(sum(v1*v1)) + else: + v1 = perp; + + # generate rotational matrix representing the overall rotation of the helix + R0 = get_rotation_matrix(dir, rot) + + # rotation matrix corresponding to one step along the helix + R = get_rotation_matrix(dir, [1, "bp"],bp) + + # set the vector a1 (backbone to base) to v1 + a1 = v1 + + # apply the global rotation to a1 + a1 = np.dot(R0, a1) + + # set the position of the fist backbone site to start_pos + rb = np.array(start_pos) + + # set a3 to the direction of the helix + a3 = dir + + for i in range(bp): + # work out the position of the centre of mass of the nucleotide + rcom = rb - COM_CENTRE_DS * a1 + + # append to newpositions + mynewpositions.append(rcom) + mynewa1s.append(a1) + mynewa3s.append(a3) + + # if we are not at the end of the helix, we work out a1 and rb for the + # next nucleotide along the helix + if i != bp - 1: + a1 = np.dot(R, a1) + rb += a3 * BASE_BASE + + # if we are working on a double strand, we do a cycle similar + # to the previous one but backwards + if double == True: + a1 = -a1 + a3 = -dir + R = R.transpose() + for i in range(bp): + rcom = rb - COM_CENTRE_DS * a1 + mynewpositions.append (rcom) + mynewa1s.append (a1) + mynewa3s.append (a3) + a1 = np.dot(R, a1) + rb += a3 * BASE_BASE + + + #Calculate the positions of the bead wall + + last_base1 = mynewpositions[int( len(mynewpositions)/2 - 1) ] + last_base2 = mynewpositions[int( len(mynewpositions)/2) ] + mid_point = (last_base1 + last_base2) / 2 + + NN = N_BEADS**2 + p1 = [mid_point[0] - (N_BEADS-1)*WALL_PARTICLE_SIZE, mid_point[1] - (N_BEADS-1)*WALL_PARTICLE_SIZE, mid_point[2] + BEAD_OFFSET ] + for i in range(N_BEADS): + for j in range(N_BEADS): + position = [ p1[0] + 2*i*WALL_PARTICLE_SIZE, p1[1] + 2*j*WALL_PARTICLE_SIZE, p1[2]] + mynewa1s.append([1,0,0]) + mynewa3s.append([1,0,0]) + mynewpositions.append(position) + + assert (len (mynewpositions) > 0) + + return [mynewpositions, mynewa1s, mynewa3s] + + + +""" +Main function for this script. +Reads a text file with the following format: +- Each line contains the sequence for a single strand (A,C,G,T) +- Lines beginning with the keyword 'DOUBLE' produce double-stranded DNA + +Ex: Two ssDNA (single stranded DNA) +ATATATA +GCGCGCG + +Ex: Two strands, one double stranded, the other single stranded. +DOUBLE AGGGCT +CCTGTA + +""" + +def read_strands(filename): + try: + infile = open (filename) + except: + print("Could not open file '%s'. Aborting." % filename, file=sys.stderr) + sys.exit(2) + + # This block works out the number of nucleotides and strands by reading + # the number of non-empty lines in the input file and the number of letters, + # taking the possible DOUBLE keyword into account. + nstrands, nnucl, nbonds = 0, 0, 0 + lines = infile.readlines() + for line in lines: + line = line.upper().strip() + if len(line) == 0: + continue + if line[:6] == 'DOUBLE': + line = line.split()[1] + length = len(line) + print("## Found duplex of %i base pairs" % length, file=sys.stdout) + nnucl += 2*length + nstrands += 2 + nbonds+= 2*length + + else: + line = line.split()[0] + length = len(line) + print("## Found single strand of %i bases" % length, file=sys.stdout) + nnucl += length + nstrands += 1 + if topo == 'ring': + nbonds =+ length + else: + nbonds += length+1 + # rewind the sequence input file + infile.seek(0) + + print("## nstrands, nnucl = ", nstrands, nnucl, file=sys.stdout) + + # generate the data file in LAMMPS format + try: + out = open ("data.oxdna", "w") + except: + print("Could not open data file for writing. Aborting.", file=sys.stderr) + sys.exit(2) + + lines = infile.readlines() + nlines = len(lines) + i = 1 + myns = 0 + noffset = 1 + + for line in lines: + line = line.upper().strip() + + # skip empty lines + if len(line) == 0: + i += 1 + continue + + # block for duplexes: last argument of the generate function + # is set to 'True' + if line[:6] == 'DOUBLE': + line = line.split()[1] + length = len(line) + seq = [(base_to_number[x]) for x in line] + seq = np.array(seq,dtype=int) + n_a, n_c, n_g, n_t = 0, 0, 0, 0 + for s in range(seq.size): + if seq[s] == 1: + n_a += 1 + elif seq[s] == 2: + n_c += 1 + elif seq[s] ==3: + n_g += 1 + elif seq[s] == 4: + n_t += 1 + smallest_n_bases = n_c + if n_a < n_c: + smallest_n_bases = n_a + if smallest_n_bases > n_t: + smallest_n_bases = n_t + if smallest_n_bases > n_g: + smallest_n_bases = n_g + + if smallest_n_bases < N_BASE_TYPES: + print('## Not enough occurances of base types in the sequence for ' + str(N_BASE_TYPES)) + print('## unique base types, switching to ' + str(smallest_n_bases) + ' unique types') + else: + smallest_n_bases = N_BASE_TYPES + + a, c, g, t = -3, -2, -1, 0 + for s in range(seq.size): + if seq[s] == 1: + if a < (smallest_n_bases*4-3): + a += 4 + else: + a = 1 + seq[s] = a + + elif seq[s] == 2: + if c < (smallest_n_bases*4-2): + c += 4 + else: + c = 2 + seq[s] = c + + elif seq[s] == 3: + if g < (smallest_n_bases*4-1): + g += 4 + else: + g = 3 + seq[s] = g + elif seq[s] == 4: + if t < (smallest_n_bases*4): + t += 4 + else: + t = 4 + seq[s] = t + + + + myns += 1 + + for b in range(length): + basetype.append(seq[b]) + strandnum.append(myns) + + for b in range(length-1): + bondpair = [noffset + b, noffset + b + 1] + bonds.append(bondpair) + + + noffset += length + + # create the sequence of the second strand as made of + # complementary bases + #seq2 = [5-s for s in seq] + seq2 = seq + for s in range(seq2.size): + if seq2[s]%4 == 1: + seq2[s] += 3 + elif seq2[s]%4 == 2: + seq2[s] += 1 + elif seq2[s]%4 == 3: + seq2[s] -= 1 + elif seq2[s]%4 == 0: + seq2[s] -= 3 + + #seq2.reverse() + + myns += 1 + + for b in range(length): + basetype.append(seq2[b]) + strandnum.append(myns) + + for b in range(length-1): + bondpair = [noffset + b, noffset + b + 1] + bonds.append(bondpair) + + + #create wall bead types + bead_type = 4*smallest_n_bases + 1 + for i in range(N_BEADS**2): + + basetype.append(bead_type) + basetype.append(bead_type) + strandnum.append(bead_type) + strandnum.append(bead_type) + #bonds.append([length, noffset + length]) + #bonds.append([length+1, noffset + length]) + + noffset += length + + print("## Created duplex of %i bases" % (2*length), file=sys.stdout) + + # generate random position of the first nucleotide + com = box_offset + np.random.random_sample(3) * box + # comment out to randomise + com = [0,0,0] + + # generate the random direction of the helix + axis = np.random.random_sample(3) + # comment out to randomise + axis = [0,0,1] + axis /= np.sqrt(np.dot(axis, axis)) + + # use the generate function defined above to create + # the position and orientation vector of the strand + if topo == 'ring': + newpositions, newa1s, newa3s = generate_ring(len(line), \ + sequence=seq, dir=axis, start_pos=com, double=True) + else: + newpositions, newa1s, newa3s = generate_strand(len(line), \ + sequence=seq, dir=axis, start_pos=com, double=True) + + # generate a new position for the strand until it does not overlap + # with anything already present + start = timer() + while not add_strands(newpositions, newa1s, newa3s): + com = box_offset + np.random.random_sample(3) * box + axis = np.random.random_sample(3) + axis /= np.sqrt(np.dot(axis, axis)) + if topo == 'ring': + newpositions, newa1s, newa3s = generate_ring(len(line), \ + sequence=seq, dir=axis, start_pos=com, double=True) + else: + newpositions, newa1s, newa3s = generate_strand(len(line), \ + sequence=seq, dir=axis, start_pos=com, double=True) + print("## Trying %i" % i, file=sys.stdout) + end = timer() + print("## Added duplex of %i bases (line %i/%i) in %.2fs, now at %i/%i" % \ + (2*length, i, nlines, end-start, len(positions), nnucl), file=sys.stdout) + + # block for single strands: last argument of the generate function + # is set to 'False' + else: + length = len(line) + seq = [(base_to_number[x]) for x in line] + + myns += 1 + for b in range(length): + basetype.append(seq[b]) + strandnum.append(myns) + + for b in range(length-1): + bondpair = [noffset + b, noffset + b + 1] + bonds.append(bondpair) + if topo == 'ring': + bondpair = [noffset, noffset + length-1] + bonds.append(bondpair) + noffset += length + + + # generate random position of the first nucleotide + com = box_offset + np.random.random_sample(3) * box + # comment out to randomise + com = [-30,0,0] + + # generate the random direction of the helix + axis = np.random.random_sample(3) + # comment out to randomise + axis = [0,0,1] + axis /= np.sqrt(np.dot(axis, axis)) + + print("## Created single strand of %i bases" % length, file=sys.stdout) + if topo == 'ring': + newpositions, newa1s, newa3s = generate_ring(length, \ + sequence=seq, dir=axis, start_pos=com, double=False) + else: + newpositions, newa1s, newa3s = generate_strand(length, \ + sequence=seq, dir=axis, start_pos=com, double=False) + start = timer() + while not add_strands(newpositions, newa1s, newa3s): + com = box_offset + np.random.random_sample(3) * box + axis = np.random.random_sample(3) + axis /= np.sqrt(np.dot(axis, axis)) + if topo == 'ring': + newpositions, newa1s, newa3s = generate_ring(length, \ + sequence=seq, dir=axis, start_pos=com, double=False) + + else: + newpositions, newa1s, newa3s = generate_strand(length, \ + sequence=seq, dir=axis, start_pos=com, double=False) + print("## Trying %i" % (i), file=sys.stdout) + end = timer() + print("## Added single strand of %i bases (line %i/%i) in %.2fs, now at %i/%i" % \ + (length, i, nlines, end-start,len(positions), nnucl), file=sys.stdout) + + i += 1 + + # sanity check + #if not len(positions) == nnucl: + # print(len(positions), nnucl) + # raise AssertionError + nnucl = nnucl + (N_BEADS**2) + nbonds -= 4 + + out.write('# LAMMPS data file\n') + out.write('%d atoms\n' % nnucl) + out.write('%d ellipsoids\n' % nnucl) + out.write('%d bonds\n' % nbonds) + out.write('\n') + out.write('%d atom types\n' %bead_type ) + out.write('1 bond types\n') + out.write('\n') + out.write('# System size\n') + out.write('%f %f xlo xhi\n' % (box_offset,box_offset+box_length)) + out.write('%f %f ylo yhi\n' % (box_offset,box_offset+box_length)) + out.write('%f %f zlo zhi\n' % (0,box_length)) + + #out.write('\n') + #out.write('Masses\n') + #out.write('\n') + #out.write('1 3.1575\n') + #out.write('2 3.1575\n') + #out.write('3 3.1575\n') + #out.write('4 3.1575\n') + #out.write('5 3.1575\n') + + # for each nucleotide print a line under the headers + # Atoms, Velocities, Ellipsoids and Bonds + out.write('\n') + out.write(\ + '# Atom-ID, type, position, molecule-ID, ellipsoid flag, density\n') + out.write('Atoms\n') + out.write('\n') + + for i in range(nnucl): + out.write('%d %d %22.15le %22.15le %22.15le %d 1 1\n' \ + % (i+1, basetype[i], \ + positions[i][0], positions[i][1], positions[i][2], \ + strandnum[i])) + + out.write('\n') + out.write('# Atom-ID, translational, rotational velocity\n') + out.write('Velocities\n') + out.write('\n') + + for i in range(nnucl): + out.write("%d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le\n" \ + % (i+1,0.0,0.0,0.0,0.0,0.0,0.0)) + + out.write('\n') + out.write('# Atom-ID, shape, quaternion\n') + out.write('Ellipsoids\n') + out.write('\n') + + for i in range(nnucl): + out.write(\ + "%d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le\n" \ + % (i+1,1.1739845031423408,1.1739845031423408,1.1739845031423408, \ + quaternions[i][0],quaternions[i][1], quaternions[i][2],quaternions[i][3])) + + out.write('\n') + out.write('# Bond topology\n') + out.write('Bonds\n') + out.write('\n') + + for i in range(nbonds): + if i < nbonds-2: + out.write("%d %d %d %d\n" % (i+1,1,bonds[i][0],bonds[i][1])) + #else: + + #out.write("%d %d %d %d\n" % (i+1,2,bonds[i][0],bonds[i][1])) + + out.close() + + print("## Wrote data to 'data.oxdna'", file=sys.stdout) + print("## DONE", file=sys.stdout) + +# call the above main() function, which executes the program +read_strands (infile) + +end_time=timer() +runtime = end_time-start_time +hours = runtime/3600 +minutes = (runtime-np.rint(hours)*3600)/60 +seconds = (runtime-np.rint(hours)*3600-np.rint(minutes)*60)%60 +print("## Total runtime %ih:%im:%.2fs" % (hours,minutes,seconds), file=sys.stdout) diff --git a/examples/USER/cgdna/examples/oxDNA2/unique_bp/in.duplex4.4type b/examples/USER/cgdna/examples/oxDNA2/unique_bp/in.duplex4.4type new file mode 100644 index 0000000000..0570cf042d --- /dev/null +++ b/examples/USER/cgdna/examples/oxDNA2/unique_bp/in.duplex4.4type @@ -0,0 +1,94 @@ +variable number equal 1 +variable ofreq equal 10000 +variable efreq equal 10000 + +variable ntype equal 4 + +variable T equal 0.1 + +units lj + +dimension 3 + +newton off + +boundary p p p + +atom_style hybrid bond ellipsoid +atom_modify sort 0 1.0 + +# Pair interactions require lists of neighbours to be calculated +neighbor 2.0 bin +neigh_modify every 10 delay 0 check yes + +read_data data.duplex4.4type +mass * 3.1575 + +group all type 1 4 + +# oxDNA bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 2.0 0.25 0.7564 + +# oxDNA pair interactions +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 ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 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 + +label loop +variable base loop ${ntype} + variable basemod equal ${base}%4 + if "${basemod} == 1" then & + "variable comp equal ${base}+3" & + "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" + if "${basemod} == 2" then & + "variable comp equal ${base}+1" & + "pair_coeff ${base} ${comp} 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" +next base +jump in.duplex4.4type loop + +pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 +pair_coeff * * oxdna2/dh ${T} 0.2 0.815 + +# Langevin dynamics +fix 1 all nve/asphere +fix 2 all langevin ${T} ${T} 25.0 457145 angmom 10 + +timestep 1e-4 + +#comm_style tiled +#fix 3 all balance 10000 1.1 rcb + +#compute mol all chunk/atom molecule +#compute mychunk all vcm/chunk mol +#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector + +#dump pos all xyz ${ofreq} traj.${number}.xyz + +compute quat all property/atom quatw quati quatj quatk +#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] +#dump_modify quat sort id +#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz +dump_modify out sort id +dump_modify out format line "%d %d %d %13.6le %13.6le %13.6le %d %d %d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le " + +#restart 10000 config0_restart config1_restart + +run 100000 + +#write_restart config.${number}.* + + diff --git a/examples/USER/cgdna/examples/oxDNA2/unique_bp/in.duplex4.8type b/examples/USER/cgdna/examples/oxDNA2/unique_bp/in.duplex4.8type new file mode 100644 index 0000000000..dae853a113 --- /dev/null +++ b/examples/USER/cgdna/examples/oxDNA2/unique_bp/in.duplex4.8type @@ -0,0 +1,94 @@ +variable number equal 1 +variable ofreq equal 10000 +variable efreq equal 10000 + +variable ntype equal 8 + +variable T equal 0.1 + +units lj + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid +atom_modify sort 0 1.0 + +# Pair interactions require lists of neighbours to be calculated +neighbor 1.0 bin +neigh_modify every 10 delay 0 check yes + +read_data data.duplex4.8type +mass * 3.1575 + +group all type 1 8 + +# oxDNA bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 2.0 0.25 0.7564 + +# oxDNA pair interactions +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 ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 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 + +label loop +variable base loop ${ntype} + variable basemod equal ${base}%4 + if "${basemod} == 1" then & + "variable comp equal ${base}+3" & + "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" + if "${basemod} == 2" then & + "variable comp equal ${base}+1" & + "pair_coeff ${base} ${comp} 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" +next base +jump in.duplex4.8type loop + +pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 +pair_coeff * * oxdna2/dh ${T} 0.2 0.815 + +# Langevin dynamics +fix 1 all nve/asphere +fix 2 all langevin ${T} ${T} 25.0 457145 angmom 10 + +timestep 1e-4 + +#comm_style tiled +#fix 3 all balance 10000 1.1 rcb + +#compute mol all chunk/atom molecule +#compute mychunk all vcm/chunk mol +#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector + +#dump pos all xyz ${ofreq} traj.${number}.xyz + +compute quat all property/atom quatw quati quatj quatk +#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] +#dump_modify quat sort id +#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz +dump_modify out sort id +dump_modify out format line "%d %d %d %13.6le %13.6le %13.6le %d %d %d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le " + +#restart 10000 config0_restart config1_restart + +run 100000 + +#write_restart config.${number}.* + + diff --git a/examples/USER/cgdna/examples/oxDNA2/unique_bp/log.07Aug19.duplex4.4type.g++1 b/examples/USER/cgdna/examples/oxDNA2/unique_bp/log.07Aug19.duplex4.4type.g++1 new file mode 100644 index 0000000000..d0195dd8e8 --- /dev/null +++ b/examples/USER/cgdna/examples/oxDNA2/unique_bp/log.07Aug19.duplex4.4type.g++1 @@ -0,0 +1,232 @@ +LAMMPS (7 Aug 2019) +variable number equal 1 +variable ofreq equal 10000 +variable efreq equal 10000 + +variable ntype equal 4 + +variable T equal 0.1 + +units lj + +dimension 3 + +newton off + +boundary p p p + +atom_style hybrid bond ellipsoid +atom_modify sort 0 1.0 + +# Pair interactions require lists of neighbours to be calculated +neighbor 2.0 bin +neigh_modify every 10 delay 0 check yes + +read_data data.duplex4.4type + orthogonal box = (-20 -20 -20) to (20 20 20) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 26 atoms + reading velocities ... + 26 velocities + 26 ellipsoids + scanning bonds ... + 2 = max bonds/atom + reading bonds ... + 24 bonds + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 6.2e-05 secs + read_data CPU = 0.001124 secs +mass * 3.1575 + +group all type 1 4 +26 atoms in group all + +# oxDNA bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 2.0 0.25 0.7564 + +# oxDNA pair interactions +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 ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 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 0.75 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 + +label loop +variable base loop ${ntype} +variable base loop 4 + variable basemod equal ${base}%4 + variable basemod equal 1%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} 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" +variable comp equal ${base}+3 +variable comp equal 1+3 +pair_coeff ${base} ${comp} 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 1 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} 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" +next base +jump in.duplex4.4type loop +variable base loop ${ntype} +variable base loop 4 + variable basemod equal ${base}%4 + variable basemod equal 2%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} 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" +variable comp equal ${base}+1 +variable comp equal 2+1 +pair_coeff ${base} ${comp} 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 ${comp} 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 +next base +jump in.duplex4.4type loop +variable base loop ${ntype} +variable base loop 4 + variable basemod equal ${base}%4 + variable basemod equal 3%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} 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" +next base +jump in.duplex4.4type loop +variable base loop ${ntype} +variable base loop 4 + variable basemod equal ${base}%4 + variable basemod equal 4%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} 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" +next base +jump in.duplex4.4type loop + +pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 +pair_coeff * * oxdna2/dh ${T} 0.2 0.815 +pair_coeff * * oxdna2/dh 0.1 0.2 0.815 + +# Langevin dynamics +fix 1 all nve/asphere +fix 2 all langevin ${T} ${T} 25.0 457145 angmom 10 +fix 2 all langevin 0.1 ${T} 25.0 457145 angmom 10 +fix 2 all langevin 0.1 0.1 25.0 457145 angmom 10 + +timestep 1e-4 + +#comm_style tiled +#fix 3 all balance 10000 1.1 rcb + +#compute mol all chunk/atom molecule +#compute mychunk all vcm/chunk mol +#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector + +#dump pos all xyz ${ofreq} traj.${number}.xyz + +compute quat all property/atom quatw quati quatj quatk +#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] +#dump_modify quat sort id +#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 10000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz +dump out all custom 10000 out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz +dump out all custom 10000 out.1.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz +dump_modify out sort id +dump_modify out format line "%d %d %d %13.6le %13.6le %13.6le %d %d %d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le " + +#restart 10000 config0_restart config1_restart + +run 100000 +Neighbor list info ... + update every 10 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.63899 + ghost atom cutoff = 5.63899 + binsize = 2.81949, bins = 15 15 15 + 6 neighbor lists, perpetual/occasional/extra = 6 0 0 + (1) pair oxdna2/excv, perpetual + attributes: half, newton off + pair build: half/bin/newtoff + stencil: half/bin/3d/newtoff + bin: standard + (2) pair oxdna2/stk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (3) pair oxdna2/hbond, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (4) pair oxdna2/xstk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (5) pair oxdna2/coaxstk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (6) pair oxdna2/dh, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 3.89 | 3.89 | 3.89 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -1.6384018 0.037304147 -1.6010976 6.7769766e-05 +10000 ekin = 1.01296379553452 | erot = 1.38476360245491 | epot = -41.9785360036035 | etot = -39.5808086056141 +20000 ekin = 1.75607695499755 | erot = 1.86620102096623 | epot = -41.9558496477913 | etot = -38.3335716718275 +30000 ekin = 2.25878673688255 | erot = 2.60035907744906 | epot = -41.2869827431736 | etot = -36.427836928842 +40000 ekin = 2.11105717434601 | erot = 3.16611217122795 | epot = -40.2762731426449 | etot = -34.999103797071 +50000 ekin = 3.05379083545185 | erot = 2.45050275456902 | epot = -40.3032957287999 | etot = -34.799002138779 +60000 ekin = 3.05154113920288 | erot = 2.52539576708931 | epot = -39.6800099891302 | etot = -34.103073082838 +70000 ekin = 3.23212209366503 | erot = 3.28914763888578 | epot = -40.1240667487288 | etot = -33.602797016178 +80000 ekin = 2.82623224207568 | erot = 2.91292948677805 | epot = -39.0983962904507 | etot = -33.3592345615969 +90000 ekin = 3.05995314905566 | erot = 3.5429982411034 | epot = -39.1646070343971 | etot = -32.561655644238 +100000 ekin = 3.46139546969836 | erot = 4.11704803295073 | epot = -38.5124679837256 | etot = -30.9340244810765 + 100000 0.092303879 -1.5243833 0.043134544 -1.3481182 6.862374e-06 +Loop time of 7.99505 on 1 procs for 100000 steps with 26 atoms + +Performance: 108066.893 tau/day, 12507.742 timesteps/s +99.8% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 7.2072 | 7.2072 | 7.2072 | 0.0 | 90.15 +Bond | 0.14292 | 0.14292 | 0.14292 | 0.0 | 1.79 +Neigh | 1.9e-05 | 1.9e-05 | 1.9e-05 | 0.0 | 0.00 +Comm | 0.015676 | 0.015676 | 0.015676 | 0.0 | 0.20 +Output | 0.001372 | 0.001372 | 0.001372 | 0.0 | 0.02 +Modify | 0.61071 | 0.61071 | 0.61071 | 0.0 | 7.64 +Other | | 0.01714 | | | 0.21 + +Nlocal: 26 ave 26 max 26 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 325 ave 325 max 325 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 325 +Ave neighs/atom = 12.5 +Ave special neighs/atom = 5.07692 +Neighbor list builds = 1 +Dangerous builds = 0 + +#write_restart config.${number}.* + + +Total wall time: 0:00:07 diff --git a/examples/USER/cgdna/examples/oxDNA2/unique_bp/log.07Aug19.duplex4.4type.g++4 b/examples/USER/cgdna/examples/oxDNA2/unique_bp/log.07Aug19.duplex4.4type.g++4 new file mode 100644 index 0000000000..a5647ccd77 --- /dev/null +++ b/examples/USER/cgdna/examples/oxDNA2/unique_bp/log.07Aug19.duplex4.4type.g++4 @@ -0,0 +1,232 @@ +LAMMPS (7 Aug 2019) +variable number equal 1 +variable ofreq equal 10000 +variable efreq equal 10000 + +variable ntype equal 4 + +variable T equal 0.1 + +units lj + +dimension 3 + +newton off + +boundary p p p + +atom_style hybrid bond ellipsoid +atom_modify sort 0 1.0 + +# Pair interactions require lists of neighbours to be calculated +neighbor 2.0 bin +neigh_modify every 10 delay 0 check yes + +read_data data.duplex4.4type + orthogonal box = (-20 -20 -20) to (20 20 20) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 26 atoms + reading velocities ... + 26 velocities + 26 ellipsoids + scanning bonds ... + 2 = max bonds/atom + reading bonds ... + 24 bonds + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000173 secs + read_data CPU = 0.00242 secs +mass * 3.1575 + +group all type 1 4 +26 atoms in group all + +# oxDNA bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 2.0 0.25 0.7564 + +# oxDNA pair interactions +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 ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 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 0.75 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 + +label loop +variable base loop ${ntype} +variable base loop 4 + variable basemod equal ${base}%4 + variable basemod equal 1%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} 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" +variable comp equal ${base}+3 +variable comp equal 1+3 +pair_coeff ${base} ${comp} 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 1 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} 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" +next base +jump in.duplex4.4type loop +variable base loop ${ntype} +variable base loop 4 + variable basemod equal ${base}%4 + variable basemod equal 2%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} 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" +variable comp equal ${base}+1 +variable comp equal 2+1 +pair_coeff ${base} ${comp} 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 ${comp} 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 +next base +jump in.duplex4.4type loop +variable base loop ${ntype} +variable base loop 4 + variable basemod equal ${base}%4 + variable basemod equal 3%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} 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" +next base +jump in.duplex4.4type loop +variable base loop ${ntype} +variable base loop 4 + variable basemod equal ${base}%4 + variable basemod equal 4%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} 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" +next base +jump in.duplex4.4type loop + +pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 +pair_coeff * * oxdna2/dh ${T} 0.2 0.815 +pair_coeff * * oxdna2/dh 0.1 0.2 0.815 + +# Langevin dynamics +fix 1 all nve/asphere +fix 2 all langevin ${T} ${T} 25.0 457145 angmom 10 +fix 2 all langevin 0.1 ${T} 25.0 457145 angmom 10 +fix 2 all langevin 0.1 0.1 25.0 457145 angmom 10 + +timestep 1e-4 + +#comm_style tiled +#fix 3 all balance 10000 1.1 rcb + +#compute mol all chunk/atom molecule +#compute mychunk all vcm/chunk mol +#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector + +#dump pos all xyz ${ofreq} traj.${number}.xyz + +compute quat all property/atom quatw quati quatj quatk +#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] +#dump_modify quat sort id +#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 10000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz +dump out all custom 10000 out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz +dump out all custom 10000 out.1.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz +dump_modify out sort id +dump_modify out format line "%d %d %d %13.6le %13.6le %13.6le %d %d %d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le " + +#restart 10000 config0_restart config1_restart + +run 100000 +Neighbor list info ... + update every 10 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.63899 + ghost atom cutoff = 5.63899 + binsize = 2.81949, bins = 15 15 15 + 6 neighbor lists, perpetual/occasional/extra = 6 0 0 + (1) pair oxdna2/excv, perpetual + attributes: half, newton off + pair build: half/bin/newtoff + stencil: half/bin/3d/newtoff + bin: standard + (2) pair oxdna2/stk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (3) pair oxdna2/hbond, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (4) pair oxdna2/xstk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (5) pair oxdna2/coaxstk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (6) pair oxdna2/dh, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 9.499 | 9.682 | 9.864 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -1.6384018 0.037304147 -1.6010976 6.7769766e-05 +10000 ekin = 1.20524984175817 | erot = 1.2679122962101 | epot = -41.9183873815797 | etot = -39.4452252436114 +20000 ekin = 1.60856540355485 | erot = 2.64140880508964 | epot = -41.0106168994545 | etot = -36.76064269081 +30000 ekin = 2.821101638199 | erot = 3.06373823252434 | epot = -40.9348041675027 | etot = -35.0499642967793 +40000 ekin = 2.36296917392486 | erot = 3.53353555114673 | epot = -39.5591676362755 | etot = -33.6626629112039 +50000 ekin = 2.93383938780818 | erot = 3.39920211088179 | epot = -40.3602175538497 | etot = -34.0271760551597 +60000 ekin = 2.42811021532829 | erot = 2.75130045540831 | epot = -39.3178531324554 | etot = -34.1384424617188 +70000 ekin = 2.7282200818863 | erot = 3.76502037022117 | epot = -40.5673105068195 | etot = -34.074070054712 +80000 ekin = 2.90877851656705 | erot = 2.43617899356904 | epot = -38.4099618426175 | etot = -33.0650043324814 +90000 ekin = 3.89203816080263 | erot = 2.67194811393274 | epot = -39.1880466354802 | etot = -32.6240603607448 +100000 ekin = 3.98445325397832 | erot = 2.77079124049636 | epot = -39.2805505658488 | etot = -32.5253060713741 + 100000 0.10625209 -1.5603519 0.049561514 -1.3575422 -1.7755557e-05 +Loop time of 7.14827 on 4 procs for 100000 steps with 26 atoms + +Performance: 120868.376 tau/day, 13989.395 timesteps/s +99.7% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.047776 | 3.0726 | 6.3143 | 172.8 | 42.98 +Bond | 0.00736 | 0.056846 | 0.10864 | 20.7 | 0.80 +Neigh | 1.9e-05 | 1.9e-05 | 1.9e-05 | 0.0 | 0.00 +Comm | 0.30925 | 3.451 | 6.3739 | 157.5 | 48.28 +Output | 0.000896 | 0.0010197 | 0.001301 | 0.5 | 0.01 +Modify | 0.015512 | 0.18417 | 0.37845 | 39.4 | 2.58 +Other | | 0.3826 | | | 5.35 + +Nlocal: 6.5 ave 13 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 19.5 ave 26 max 13 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 123.5 ave 247 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 494 +Ave neighs/atom = 19 +Ave special neighs/atom = 5.07692 +Neighbor list builds = 1 +Dangerous builds = 0 + +#write_restart config.${number}.* + + +Total wall time: 0:00:07 diff --git a/examples/USER/cgdna/examples/oxDNA2/unique_bp/log.07Aug19.duplex4.8type.g++1 b/examples/USER/cgdna/examples/oxDNA2/unique_bp/log.07Aug19.duplex4.8type.g++1 new file mode 100644 index 0000000000..c93943a4c7 --- /dev/null +++ b/examples/USER/cgdna/examples/oxDNA2/unique_bp/log.07Aug19.duplex4.8type.g++1 @@ -0,0 +1,274 @@ +LAMMPS (7 Aug 2019) +variable number equal 1 +variable ofreq equal 10000 +variable efreq equal 10000 + +variable ntype equal 8 + +variable T equal 0.1 + +units lj + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid +atom_modify sort 0 1.0 + +# Pair interactions require lists of neighbours to be calculated +neighbor 1.0 bin +neigh_modify every 10 delay 0 check yes + +read_data data.duplex4.8type + orthogonal box = (-20 -20 -20) to (20 20 20) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 26 atoms + reading velocities ... + 26 velocities + 26 ellipsoids + scanning bonds ... + 1 = max bonds/atom + reading bonds ... + 24 bonds + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 6.5e-05 secs + read_data CPU = 0.001139 secs +mass * 3.1575 + +group all type 1 8 +26 atoms in group all + +# oxDNA bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 2.0 0.25 0.7564 + +# oxDNA pair interactions +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 ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 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 0.75 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 + +label loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 1%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} 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" +variable comp equal ${base}+3 +variable comp equal 1+3 +pair_coeff ${base} ${comp} 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 1 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} 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" +next base +jump in.duplex4.8type loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 2%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} 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" +variable comp equal ${base}+1 +variable comp equal 2+1 +pair_coeff ${base} ${comp} 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 ${comp} 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 +next base +jump in.duplex4.8type loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 3%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} 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" +next base +jump in.duplex4.8type loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 4%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} 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" +next base +jump in.duplex4.8type loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 5%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} 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" +variable comp equal ${base}+3 +variable comp equal 5+3 +pair_coeff ${base} ${comp} 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 5 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 5 8 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} 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" +next base +jump in.duplex4.8type loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 6%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} 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" +variable comp equal ${base}+1 +variable comp equal 6+1 +pair_coeff ${base} ${comp} 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 6 ${comp} 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 6 7 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 +next base +jump in.duplex4.8type loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 7%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} 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" +next base +jump in.duplex4.8type loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 8%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} 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" +next base +jump in.duplex4.8type loop + +pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 +pair_coeff * * oxdna2/dh ${T} 0.2 0.815 +pair_coeff * * oxdna2/dh 0.1 0.2 0.815 + +# Langevin dynamics +fix 1 all nve/asphere +fix 2 all langevin ${T} ${T} 25.0 457145 angmom 10 +fix 2 all langevin 0.1 ${T} 25.0 457145 angmom 10 +fix 2 all langevin 0.1 0.1 25.0 457145 angmom 10 + +timestep 1e-4 + +#comm_style tiled +#fix 3 all balance 10000 1.1 rcb + +#compute mol all chunk/atom molecule +#compute mychunk all vcm/chunk mol +#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector + +#dump pos all xyz ${ofreq} traj.${number}.xyz + +compute quat all property/atom quatw quati quatj quatk +#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] +#dump_modify quat sort id +#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 10000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz +dump out all custom 10000 out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz +dump out all custom 10000 out.1.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz +dump_modify out sort id +dump_modify out format line "%d %d %d %13.6le %13.6le %13.6le %d %d %d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le " + +#restart 10000 config0_restart config1_restart + +run 100000 +Neighbor list info ... + update every 10 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4.63899 + ghost atom cutoff = 4.63899 + binsize = 2.31949, bins = 18 18 18 + 6 neighbor lists, perpetual/occasional/extra = 6 0 0 + (1) pair oxdna2/excv, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) pair oxdna2/stk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (3) pair oxdna2/hbond, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (4) pair oxdna2/xstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (5) pair oxdna2/coaxstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (6) pair oxdna2/dh, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 3.905 | 3.905 | 3.905 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -1.6384018 0.037304147 -1.6010976 6.7769766e-05 +10000 ekin = 1.0129637955345 | erot = 1.38476360245492 | epot = -41.9785360036034 | etot = -39.580808605614 +20000 ekin = 1.75607695499755 | erot = 1.86620102096618 | epot = -41.9558496477911 | etot = -38.3335716718274 +30000 ekin = 2.25878673688259 | erot = 2.60035907744898 | epot = -41.2869827431736 | etot = -36.427836928842 +40000 ekin = 2.11105717434584 | erot = 3.16611217122799 | epot = -40.2762731426449 | etot = -34.9991037970711 +50000 ekin = 3.05379083545187 | erot = 2.45050275456888 | epot = -40.3032957287998 | etot = -34.7990021387791 +60000 ekin = 3.05154113920291 | erot = 2.5253957670889 | epot = -39.6800099891299 | etot = -34.1030730828381 +70000 ekin = 3.23212209366464 | erot = 3.28914763888543 | epot = -40.1240667487278 | etot = -33.6027970161777 +80000 ekin = 2.82623224207591 | erot = 2.91292948677732 | epot = -39.0983962904496 | etot = -33.3592345615963 +90000 ekin = 3.05995314905694 | erot = 3.54299824110274 | epot = -39.164607034397 | etot = -32.5616556442373 +100000 ekin = 3.46139546969892 | erot = 4.11704803295143 | epot = -38.512467983727 | etot = -30.9340244810767 + 100000 0.092303879 -1.5243833 0.043134544 -1.3481182 6.862374e-06 +Loop time of 7.94086 on 1 procs for 100000 steps with 26 atoms + +Performance: 108804.336 tau/day, 12593.094 timesteps/s +99.8% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 7.1507 | 7.1507 | 7.1507 | 0.0 | 90.05 +Bond | 0.14487 | 0.14487 | 0.14487 | 0.0 | 1.82 +Neigh | 6.4e-05 | 6.4e-05 | 6.4e-05 | 0.0 | 0.00 +Comm | 0.032259 | 0.032259 | 0.032259 | 0.0 | 0.41 +Output | 0.003484 | 0.003484 | 0.003484 | 0.0 | 0.04 +Modify | 0.59013 | 0.59013 | 0.59013 | 0.0 | 7.43 +Other | | 0.01934 | | | 0.24 + +Nlocal: 26 ave 26 max 26 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 323 ave 323 max 323 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 323 +Ave neighs/atom = 12.4231 +Ave special neighs/atom = 5.07692 +Neighbor list builds = 4 +Dangerous builds = 0 + +#write_restart config.${number}.* + + +Total wall time: 0:00:07 diff --git a/examples/USER/cgdna/examples/oxDNA2/unique_bp/log.07Aug19.duplex4.8type.g++4 b/examples/USER/cgdna/examples/oxDNA2/unique_bp/log.07Aug19.duplex4.8type.g++4 new file mode 100644 index 0000000000..5cda079e9c --- /dev/null +++ b/examples/USER/cgdna/examples/oxDNA2/unique_bp/log.07Aug19.duplex4.8type.g++4 @@ -0,0 +1,274 @@ +LAMMPS (7 Aug 2019) +variable number equal 1 +variable ofreq equal 10000 +variable efreq equal 10000 + +variable ntype equal 8 + +variable T equal 0.1 + +units lj + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid +atom_modify sort 0 1.0 + +# Pair interactions require lists of neighbours to be calculated +neighbor 1.0 bin +neigh_modify every 10 delay 0 check yes + +read_data data.duplex4.8type + orthogonal box = (-20 -20 -20) to (20 20 20) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 26 atoms + reading velocities ... + 26 velocities + 26 ellipsoids + scanning bonds ... + 1 = max bonds/atom + reading bonds ... + 24 bonds + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000232 secs + read_data CPU = 0.002447 secs +mass * 3.1575 + +group all type 1 8 +26 atoms in group all + +# oxDNA bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 2.0 0.25 0.7564 + +# oxDNA pair interactions +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 ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 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 0.75 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 + +label loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 1%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} 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" +variable comp equal ${base}+3 +variable comp equal 1+3 +pair_coeff ${base} ${comp} 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 1 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} 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" +next base +jump in.duplex4.8type loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 2%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} 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" +variable comp equal ${base}+1 +variable comp equal 2+1 +pair_coeff ${base} ${comp} 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 ${comp} 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 +next base +jump in.duplex4.8type loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 3%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} 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" +next base +jump in.duplex4.8type loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 4%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} 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" +next base +jump in.duplex4.8type loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 5%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} 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" +variable comp equal ${base}+3 +variable comp equal 5+3 +pair_coeff ${base} ${comp} 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 5 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 5 8 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} 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" +next base +jump in.duplex4.8type loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 6%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} 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" +variable comp equal ${base}+1 +variable comp equal 6+1 +pair_coeff ${base} ${comp} 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 6 ${comp} 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 6 7 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 +next base +jump in.duplex4.8type loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 7%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} 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" +next base +jump in.duplex4.8type loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 8%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} 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" +next base +jump in.duplex4.8type loop + +pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 +pair_coeff * * oxdna2/dh ${T} 0.2 0.815 +pair_coeff * * oxdna2/dh 0.1 0.2 0.815 + +# Langevin dynamics +fix 1 all nve/asphere +fix 2 all langevin ${T} ${T} 25.0 457145 angmom 10 +fix 2 all langevin 0.1 ${T} 25.0 457145 angmom 10 +fix 2 all langevin 0.1 0.1 25.0 457145 angmom 10 + +timestep 1e-4 + +#comm_style tiled +#fix 3 all balance 10000 1.1 rcb + +#compute mol all chunk/atom molecule +#compute mychunk all vcm/chunk mol +#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector + +#dump pos all xyz ${ofreq} traj.${number}.xyz + +compute quat all property/atom quatw quati quatj quatk +#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] +#dump_modify quat sort id +#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 10000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +dump out all custom ${ofreq} out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz +dump out all custom 10000 out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz +dump out all custom 10000 out.1.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz +dump_modify out sort id +dump_modify out format line "%d %d %d %13.6le %13.6le %13.6le %d %d %d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le " + +#restart 10000 config0_restart config1_restart + +run 100000 +Neighbor list info ... + update every 10 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4.63899 + ghost atom cutoff = 4.63899 + binsize = 2.31949, bins = 18 18 18 + 6 neighbor lists, perpetual/occasional/extra = 6 0 0 + (1) pair oxdna2/excv, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) pair oxdna2/stk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (3) pair oxdna2/hbond, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (4) pair oxdna2/xstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (5) pair oxdna2/coaxstk, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (6) pair oxdna2/dh, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 9.381 | 9.563 | 9.746 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -1.6384018 0.037304147 -1.6010976 6.7769766e-05 +10000 ekin = 1.20524984175816 | erot = 1.26791229621008 | epot = -41.9183873815797 | etot = -39.4452252436115 +20000 ekin = 1.6085654035548 | erot = 2.6414088050897 | epot = -41.0106168994546 | etot = -36.7606426908101 +30000 ekin = 2.82110163819891 | erot = 3.06373823252419 | epot = -40.9348041675026 | etot = -35.0499642967795 +40000 ekin = 2.35553603700794 | erot = 3.60405945883761 | epot = -39.5418687902286 | etot = -33.5822732943831 +50000 ekin = 3.06061403125833 | erot = 3.35548669087246 | epot = -40.3236585928169 | etot = -33.9075578706861 +60000 ekin = 2.7347216991605 | erot = 4.23926242244084 | epot = -39.5379959923263 | etot = -32.564011870725 +70000 ekin = 3.46562604991873 | erot = 2.8521307045909 | epot = -38.7237000550356 | etot = -32.4059433005259 +80000 ekin = 3.17815543267806 | erot = 3.11078099027451 | epot = -39.7525036398366 | etot = -33.463567216884 +90000 ekin = 3.51635117668857 | erot = 2.58384069017333 | epot = -39.4762533092413 | etot = -33.3760614423795 +100000 ekin = 3.64218174280962 | erot = 2.88607181210736 | epot = -37.6002449519119 | etot = -31.0719913969949 + 100000 0.097124846 -1.5164679 0.070304678 -1.3060794 -2.9111933e-05 +Loop time of 5.64462 on 4 procs for 100000 steps with 26 atoms + +Performance: 153066.031 tau/day, 17715.976 timesteps/s +99.0% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.069668 | 2.1601 | 4.2189 | 138.7 | 38.27 +Bond | 0.008542 | 0.052544 | 0.095929 | 18.7 | 0.93 +Neigh | 4.8e-05 | 5.6e-05 | 6.4e-05 | 0.0 | 0.00 +Comm | 0.90402 | 3.1443 | 5.4155 | 124.9 | 55.70 +Output | 0.001003 | 0.0011317 | 0.001468 | 0.6 | 0.02 +Modify | 0.021098 | 0.20024 | 0.38154 | 39.2 | 3.55 +Other | | 0.0863 | | | 1.53 + +Nlocal: 6.5 ave 13 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 17.5 ave 22 max 13 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 80.25 ave 167 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 321 +Ave neighs/atom = 12.3462 +Ave special neighs/atom = 5.07692 +Neighbor list builds = 3 +Dangerous builds = 0 + +#write_restart config.${number}.* + + +Total wall time: 0:00:05 diff --git a/examples/USER/cgdna/examples/oxRNA2/duplex4/data.duplex4 b/examples/USER/cgdna/examples/oxRNA2/duplex4/data.duplex4 new file mode 100644 index 0000000000..72872d431a --- /dev/null +++ b/examples/USER/cgdna/examples/oxRNA2/duplex4/data.duplex4 @@ -0,0 +1,96 @@ +# LAMMPS data file +16 atoms +16 ellipsoids +13 bonds + +4 atom types +1 bond types + +# System size +-20.000000 20.000000 xlo xhi +-20.000000 20.000000 ylo yhi +-20.000000 20.000000 zlo zhi + +Masses + +1 3.1575 +2 3.1575 +3 3.1575 +4 3.1575 + +# Atom-ID, type, position, molecule-ID, ellipsoid flag, density +Atoms + +1 1 -6.000000000000001e-01 0.000000000000000e+00 0.000000000000000e+00 1 1 1 +2 2 -4.860249842674776e-01 -3.518234140414736e-01 3.897628551303122e-01 1 1 1 +3 3 -1.874009511073395e-01 -5.699832309147915e-01 7.795257102606244e-01 1 1 1 +4 4 1.824198365552941e-01 -5.715968887521518e-01 1.169288565390937e+00 1 1 1 +5 1 4.829362784135484e-01 -3.560513319622209e-01 1.559051420521249e+00 1 1 1 +6 2 5.999771538385027e-01 -5.235921299024461e-03 1.948814275651561e+00 1 1 1 +7 3 4.890766774371325e-01 3.475687034056071e-01 2.338577130781873e+00 1 1 1 +8 4 1.923677943514057e-01 5.683261666476170e-01 2.728339985912185e+00 1 1 1 +9 1 -1.923677943514057e-01 -5.683261666476170e-01 2.728339985912185e+00 2 1 1 +10 2 -4.890766774371324e-01 -3.475687034056071e-01 2.338577130781873e+00 2 1 1 +11 3 -5.999771538385025e-01 5.235921299024461e-03 1.948814275651561e+00 2 1 1 +12 4 -4.829362784135481e-01 3.560513319622207e-01 1.559051420521249e+00 2 1 1 +13 1 -1.824198365552940e-01 5.715968887521514e-01 1.169288565390936e+00 2 1 1 +14 2 1.874009511073395e-01 5.699832309147912e-01 7.795257102606241e-01 2 1 1 +15 3 4.860249842674773e-01 3.518234140414733e-01 3.897628551303119e-01 2 1 1 +16 4 5.999999999999995e-01 -3.330669073875470e-17 -3.330669073875470e-16 2 1 1 + +# Atom-ID, translational velocity, angular momentum +Velocities + +1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +2 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +3 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +4 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +5 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +6 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +7 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +8 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +9 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +10 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +11 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +12 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +13 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +14 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +15 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +16 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 + +# Atom-ID, shape, quaternion +Ellipsoids + +1 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +2 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.513258223252946e-01 0.000000000000000e+00 0.000000000000000e+00 3.081869234362515e-01 +3 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 8.100416404457962e-01 0.000000000000000e+00 0.000000000000000e+00 5.863723567357894e-01 +4 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 5.899012371043606e-01 0.000000000000000e+00 0.000000000000000e+00 8.074754054847398e-01 +5 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 3.123349185122326e-01 0.000000000000000e+00 0.000000000000000e+00 9.499720515246527e-01 +6 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 4.363309284746654e-03 0.000000000000000e+00 0.000000000000000e+00 9.999904807207346e-01 +7 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -3.040330609254902e-01 0.000000000000000e+00 0.000000000000000e+00 9.526614812535865e-01 +8 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 5.828323126827837e-01 0.000000000000000e+00 0.000000000000000e+00 -8.125924533816677e-01 +9 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 8.125924533816681e-01 5.828323126827832e-01 -0.000000000000000e+00 +10 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.526614812535864e-01 3.040330609254902e-01 0.000000000000000e+00 +11 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.999904807207346e-01 -4.363309284746654e-03 0.000000000000000e+00 +12 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.499720515246526e-01 -3.123349185122325e-01 0.000000000000000e+00 +13 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 8.074754054847402e-01 -5.899012371043603e-01 0.000000000000000e+00 +14 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 5.863723567357898e-01 -8.100416404457959e-01 0.000000000000000e+00 +15 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 -3.081869234362514e-01 9.513258223252948e-01 0.000000000000000e+00 +16 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 2.775557561562893e-17 1.000000000000000e+00 -0.000000000000000e+00 + +# Bond topology +Bonds + +1 1 1 2 +2 1 2 3 +3 1 3 4 +4 1 4 5 +5 1 5 6 +6 1 6 7 +7 1 7 8 +8 1 9 10 +9 1 10 11 +10 1 11 12 +11 1 13 14 +12 1 14 15 +13 1 15 16 diff --git a/examples/USER/cgdna/examples/oxRNA2/duplex4/in.duplex4 b/examples/USER/cgdna/examples/oxRNA2/duplex4/in.duplex4 new file mode 100644 index 0000000000..ed2fafbe8b --- /dev/null +++ b/examples/USER/cgdna/examples/oxRNA2/duplex4/in.duplex4 @@ -0,0 +1,80 @@ +variable number equal 4 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 0.1 + +units lj + +dimension 3 + +newton off + +boundary p p p + +atom_style hybrid bond ellipsoid +atom_modify sort 0 1.0 + +# Pair interactions require lists of neighbours to be calculated +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex4 + +set atom * mass 3.1575 + +group all type 1 4 + +# oxRNA2 bond interactions - FENE backbone +bond_style oxrna2/fene +bond_coeff * 2.0 0.25 0.761070781051 + +# oxRNA2 pair interactions +pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh + +pair_coeff * * oxrna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 +pair_coeff * * oxrna2/stk seqdep ${T} 1.40206 2.77 6.0 0.43 0.93 0.35 0.78 0.9 0 0.95 0.9 0 0.95 1.3 0 0.8 1.3 0 0.8 2.0 0.65 2.0 0.65 +pair_coeff * * oxrna2/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 oxrna2/hbond seqdep 0.870439 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 oxrna2/hbond seqdep 0.870439 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 3 4 oxrna2/hbond seqdep 0.870439 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 * * oxrna2/xstk 59.9626 0.5 0.6 0.42 0.58 2.25 0.505 0.58 1.7 1.266 0.68 1.7 1.266 0.68 1.7 0.309 0.68 1.7 0.309 0.68 +pair_coeff * * oxrna2/coaxstk 80 0.5 0.6 0.42 0.58 2.0 2.592 0.65 1.3 0.151 0.8 0.9 0.685 0.95 0.9 0.685 0.95 2.0 -0.65 2.0 -0.65 +pair_coeff * * oxrna2/dh ${T} 0.5 1.02455 + +# NVE ensemble +#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10 +#fix 1 all nve/dot +fix 1 all nve/asphere + +timestep 1e-5 + +#comm_style tiled +#fix 3 all balance 10000 1.1 rcb + +#compute mol all chunk/atom molecule +#compute mychunk all vcm/chunk mol +#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector + +#dump pos all xyz ${ofreq} traj.${number}.xyz + +#compute quat all property/atom quatw quati quatj quatk +#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] +#dump_modify quat sort id +#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz +#dump_modify out sort id +#dump_modify out format line "%d %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f" + +run 1000000 + +#write_restart config.${number}.* diff --git a/examples/USER/cgdna/examples/oxRNA2/duplex4/log.30Oct19.duplex4.g++.1 b/examples/USER/cgdna/examples/oxRNA2/duplex4/log.30Oct19.duplex4.g++.1 new file mode 100644 index 0000000000..d4c9fa3fcc --- /dev/null +++ b/examples/USER/cgdna/examples/oxRNA2/duplex4/log.30Oct19.duplex4.g++.1 @@ -0,0 +1,1174 @@ +LAMMPS (30 Oct 2019) +variable number equal 4 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 0.1 + +units lj + +dimension 3 + +newton off + +boundary p p p + +atom_style hybrid bond ellipsoid +atom_modify sort 0 1.0 + +# Pair interactions require lists of neighbours to be calculated +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex4 + orthogonal box = (-20 -20 -20) to (20 20 20) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 16 atoms + reading velocities ... + 16 velocities + 16 ellipsoids + scanning bonds ... + 2 = max bonds/atom + reading bonds ... + 13 bonds + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 5.9e-05 secs + read_data CPU = 0.038375 secs + +set atom * mass 3.1575 + 16 settings made for mass + +group all type 1 4 +16 atoms in group all + +# oxRNA2 bond interactions - FENE backbone +bond_style oxrna2/fene +bond_coeff * 2.0 0.25 0.761070781051 + +# oxRNA2 pair interactions +pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh + +pair_coeff * * oxrna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 +pair_coeff * * oxrna2/stk seqdep ${T} 1.40206 2.77 6.0 0.43 0.93 0.35 0.78 0.9 0 0.95 0.9 0 0.95 1.3 0 0.8 1.3 0 0.8 2.0 0.65 2.0 0.65 +pair_coeff * * oxrna2/stk seqdep 0.1 1.40206 2.77 6.0 0.43 0.93 0.35 0.78 0.9 0 0.95 0.9 0 0.95 1.3 0 0.8 1.3 0 0.8 2.0 0.65 2.0 0.65 +pair_coeff * * oxrna2/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 oxrna2/hbond seqdep 0.870439 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 oxrna2/hbond seqdep 0.870439 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 3 4 oxrna2/hbond seqdep 0.870439 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 * * oxrna2/xstk 59.9626 0.5 0.6 0.42 0.58 2.25 0.505 0.58 1.7 1.266 0.68 1.7 1.266 0.68 1.7 0.309 0.68 1.7 0.309 0.68 +pair_coeff * * oxrna2/coaxstk 80 0.5 0.6 0.42 0.58 2.0 2.592 0.65 1.3 0.151 0.8 0.9 0.685 0.95 0.9 0.685 0.95 2.0 -0.65 2.0 -0.65 +pair_coeff * * oxrna2/dh ${T} 0.5 1.02455 +pair_coeff * * oxrna2/dh 0.1 0.5 1.02455 + +# NVE ensemble +#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10 +#fix 1 all nve/dot +fix 1 all nve/asphere + +timestep 1e-5 + +#comm_style tiled +#fix 3 all balance 10000 1.1 rcb + +#compute mol all chunk/atom molecule +#compute mychunk all vcm/chunk mol +#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector + +#dump pos all xyz ${ofreq} traj.${number}.xyz + +#compute quat all property/atom quatw quati quatj quatk +#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] +#dump_modify quat sort id +#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz +#dump_modify out sort id +#dump_modify out format line "%d %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f" + +run 1000000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 3.3015 + ghost atom cutoff = 3.3015 + binsize = 1.65075, bins = 25 25 25 + 6 neighbor lists, perpetual/occasional/extra = 6 0 0 + (1) pair oxrna2/excv, perpetual + attributes: half, newton off + pair build: half/bin/newtoff + stencil: half/bin/3d/newtoff + bin: standard + (2) pair oxrna2/stk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (3) pair oxrna2/hbond, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (4) pair oxrna2/xstk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (5) pair oxrna2/coaxstk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (6) pair oxrna2/dh, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none +0 ekin = 0 | erot = 0 | epot = -13.282537590974 | etot = -13.282537590974 +Per MPI rank memory allocation (min/avg/max) = 2.951 | 2.951 | 2.951 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -0.84341458 0.013255977 -0.8301586 -2.0169485e-05 +1000 ekin = 0.00448503054656468 | erot = 0.00825381229611384 | epot = -13.2952764343122 | etot = -13.2825375914695 +2000 ekin = 0.0179027901180511 | erot = 0.0327684151335467 | epot = -13.3332087967732 | etot = -13.2825375915216 +3000 ekin = 0.0401478317723584 | erot = 0.0728240143066062 | epot = -13.3955094376815 | etot = -13.2825375916026 +4000 ekin = 0.0710654348932282 | erot = 0.127292706283096 | epot = -13.4808957328808 | etot = -13.2825375917044 +5000 ekin = 0.110480309743662 | erot = 0.194739074279834 | epot = -13.5877569758405 | etot = -13.282537591817 +6000 ekin = 0.158231230694432 | erot = 0.273546913858903 | epot = -13.7143157364827 | etot = -13.2825375919294 +7000 ekin = 0.214206450831754 | erot = 0.362058396901232 | epot = -13.8588024397642 | etot = -13.2825375920312 +8000 ekin = 0.278374111850069 | erot = 0.458709556672181 | epot = -14.0196212606361 | etot = -13.2825375921138 +9000 ekin = 0.35080209403022 | erot = 0.562145629088178 | epot = -14.1954853152903 | etot = -13.2825375921719 +10000 ekin = 0.431663021447766 | erot = 0.671302139462136 | epot = -14.385502753114 | etot = -13.2825375922041 +11000 ekin = 0.521222365620265 | erot = 0.78544264622411 | epot = -14.5892026040572 | etot = -13.2825375922128 +12000 ekin = 0.61981039873542 | erot = 0.904150888366026 | epot = -14.8064988793055 | etot = -13.2825375922041 +13000 ekin = 0.72778153179885 | erot = 1.02728222251243 | epot = -15.0376013464974 | etot = -13.2825375921861 +14000 ekin = 0.845466747659446 | erot = 1.154885201864 | epot = -15.2828895416915 | etot = -13.2825375921681 +15000 ekin = 0.973515286429446 | erot = 1.28640002432487 | epot = -15.5424529041413 | etot = -13.2825375933869 +16000 ekin = 1.12323013751098 | erot = 1.40387495398598 | epot = -15.8096426839256 | etot = -13.2825375924286 +17000 ekin = 1.2976927283263 | erot = 1.51347784068661 | epot = -16.0937081607397 | etot = -13.2825375917268 +18000 ekin = 1.48565191084531 | erot = 1.63592970999661 | epot = -16.4041192134347 | etot = -13.2825375925928 +19000 ekin = 1.66750911163348 | erot = 1.77940241938721 | epot = -16.7294491246368 | etot = -13.2825375936161 +20000 ekin = 1.84148924290423 | erot = 1.93695511183687 | epot = -17.0609819484057 | etot = -13.2825375936646 +21000 ekin = 2.02307741366163 | erot = 2.09844265792961 | epot = -17.4040576653939 | etot = -13.2825375938027 +22000 ekin = 2.21183606977224 | erot = 2.26260708947302 | epot = -17.7569807531587 | etot = -13.2825375939134 +23000 ekin = 2.40735468792977 | erot = 2.42817202047308 | epot = -18.1180643024997 | etot = -13.2825375940968 +24000 ekin = 2.60896890448861 | erot = 2.59357882573853 | epot = -18.485085324508 | etot = -13.2825375942809 +25000 ekin = 2.81580135477345 | erot = 2.75706655667055 | epot = -18.855405505957 | etot = -13.282537594513 +26000 ekin = 3.02680083558485 | erot = 2.91667946897257 | epot = -19.2260178993271 | etot = -13.2825375947697 +27000 ekin = 3.24067707260308 | erot = 3.07027299756498 | epot = -19.5934876652175 | etot = -13.2825375950495 +28000 ekin = 3.45601412953572 | erot = 3.21560615188039 | epot = -19.9541578767293 | etot = -13.2825375953132 +29000 ekin = 3.6713683081319 | erot = 3.35037905822946 | epot = -20.304284961999 | etot = -13.2825375956376 +30000 ekin = 3.88476027224393 | erot = 3.47208481891837 | epot = -20.639382687185 | etot = -13.2825375960227 +31000 ekin = 4.09387957878895 | erot = 3.57821385032035 | epot = -20.9546310254509 | etot = -13.2825375963416 +32000 ekin = 4.29662185345806 | erot = 3.66648606531138 | epot = -21.2456455154186 | etot = -13.2825375966492 +33000 ekin = 4.49089153394062 | erot = 3.73482555362569 | epot = -21.5082546845018 | etot = -13.2825375969355 +34000 ekin = 4.67464118182276 | erot = 3.78142516888995 | epot = -21.738603947901 | etot = -13.2825375971883 +35000 ekin = 4.84586411782047 | erot = 3.80480460777895 | epot = -21.9332063229962 | etot = -13.2825375973967 +36000 ekin = 5.00270940487365 | erot = 3.8039453503275 | epot = -22.0891923527593 | etot = -13.2825375975582 +37000 ekin = 5.14355281474259 | erot = 3.7783370953036 | epot = -22.204427507712 | etot = -13.2825375976658 +38000 ekin = 5.26699752588855 | erot = 3.72801268545693 | epot = -22.2775478090594 | etot = -13.2825375977139 +39000 ekin = 5.37191151713863 | erot = 3.65359747923659 | epot = -22.3080465940736 | etot = -13.2825375976984 +40000 ekin = 5.45746010972423 | erot = 3.55633701588595 | epot = -22.2963347232305 | etot = -13.2825375976203 +41000 ekin = 5.52312188621308 | erot = 3.43809872369854 | epot = -22.2437582073842 | etot = -13.2825375974726 +42000 ekin = 5.56872044211992 | erot = 3.30135279333163 | epot = -22.1526108327155 | etot = -13.2825375972639 +43000 ekin = 5.59443660082917 | erot = 3.14910305123731 | epot = -22.0260772490691 | etot = -13.2825375970026 +44000 ekin = 5.60078634437692 | erot = 2.98477133565124 | epot = -21.8680952767294 | etot = -13.2825375967012 +45000 ekin = 5.58859564323333 | erot = 2.81204277265316 | epot = -21.6831760122617 | etot = -13.2825375963752 +46000 ekin = 5.55896198288794 | erot = 2.63469562167501 | epot = -21.4761952006007 | etot = -13.2825375960378 +47000 ekin = 5.51320424221946 | erot = 2.45646420183046 | epot = -21.2522060397483 | etot = -13.2825375956984 +48000 ekin = 5.45280176988517 | erot = 2.28095947573118 | epot = -21.0162988409769 | etot = -13.2825375953605 +49000 ekin = 5.37933239946638 | erot = 2.11161440403257 | epot = -20.7734843985446 | etot = -13.2825375950457 +50000 ekin = 5.29440598595185 | erot = 1.95156309993188 | epot = -20.5285066806346 | etot = -13.2825375947508 +51000 ekin = 5.19960275040233 | erot = 1.8036634398305 | epot = -20.2858037847152 | etot = -13.2825375944824 +52000 ekin = 5.09244091535756 | erot = 1.66034071449473 | epot = -20.0353192196127 | etot = -13.2825375897604 +53000 ekin = 5.00219098599272 | erot = 1.54003539006211 | epot = -19.8247639698981 | etot = -13.2825375938433 +54000 ekin = 4.90058329526777 | erot = 1.45132465506075 | epot = -19.6344455614683 | etot = -13.2825376111398 +55000 ekin = 4.70838087935139 | erot = 1.38368494594893 | epot = -19.3746034336678 | etot = -13.2825376083675 +56000 ekin = 4.44064498303545 | erot = 1.42525549496303 | epot = -19.1484380668508 | etot = -13.2825375888523 +57000 ekin = 4.28012764787285 | erot = 1.59067222265512 | epot = -19.1533374833604 | etot = -13.2825376128325 +58000 ekin = 4.17606446205098 | erot = 1.6926959141941 | epot = -19.1512979674148 | etot = -13.2825375911697 +59000 ekin = 4.0674801293444 | erot = 1.75788112721294 | epot = -19.1078988477137 | etot = -13.2825375911564 +60000 ekin = 3.9544882347638 | erot = 1.84391663061768 | epot = -19.0809424565336 | etot = -13.2825375911521 +61000 ekin = 3.83840387031284 | erot = 1.95003019237208 | epot = -19.0709716537088 | etot = -13.2825375910239 +62000 ekin = 3.72130809963045 | erot = 2.07501703895377 | epot = -19.0788627296237 | etot = -13.2825375910394 +63000 ekin = 3.60440089032981 | erot = 2.21773397929798 | epot = -19.1046724606768 | etot = -13.282537591049 +64000 ekin = 3.48898621429844 | erot = 2.37695650761985 | epot = -19.1484803129713 | etot = -13.282537591053 +65000 ekin = 3.37647880025293 | erot = 2.55140907448467 | epot = -19.2104254657961 | etot = -13.2825375910585 +66000 ekin = 3.26833067403372 | erot = 2.73974236805088 | epot = -19.2906106331593 | etot = -13.2825375910747 +67000 ekin = 3.16594788215578 | erot = 2.94047174698236 | epot = -19.3889572202528 | etot = -13.2825375911146 +68000 ekin = 3.07060531612276 | erot = 3.15188029478627 | epot = -19.5050232021015 | etot = -13.2825375911924 +69000 ekin = 2.98334905059819 | erot = 3.37190853325577 | epot = -19.6377951751758 | etot = -13.2825375913219 +70000 ekin = 2.90492955397884 | erot = 3.59802295152975 | epot = -19.7854900970223 | etot = -13.2825375915137 +71000 ekin = 2.83572376329218 | erot = 3.8271560839742 | epot = -19.9454174390314 | etot = -13.282537591765 +72000 ekin = 2.77568510798997 | erot = 4.05569348668259 | epot = -20.1139161867768 | etot = -13.2825375921043 +73000 ekin = 2.72437405649527 | erot = 4.27929863267978 | epot = -20.2862102816556 | etot = -13.2825375924805 +74000 ekin = 2.6809894320095 | erot = 4.4934031024691 | epot = -20.4569301273605 | etot = -13.2825375928819 +75000 ekin = 2.6444530940616 | erot = 4.69339307186043 | epot = -20.6203837591939 | etot = -13.2825375932719 +76000 ekin = 2.61355415206022 | erot = 4.87501053156087 | epot = -20.7711022772329 | etot = -13.2825375936118 +77000 ekin = 2.58710084062323 | erot = 5.03478939172066 | epot = -20.9044278262183 | etot = -13.2825375938744 +78000 ekin = 2.56403853914049 | erot = 5.17029283961051 | epot = -21.0168689727798 | etot = -13.2825375940288 +79000 ekin = 2.54361120788211 | erot = 5.28037161018751 | epot = -21.1065204121487 | etot = -13.2825375940791 +80000 ekin = 2.52540527324247 | erot = 5.36512720853065 | epot = -21.173070075803 | etot = -13.2825375940298 +81000 ekin = 2.50929384303298 | erot = 5.42576598242971 | epot = -21.2175974194025 | etot = -13.2825375939398 +82000 ekin = 2.49524917644589 | erot = 5.46414530531067 | epot = -21.2419320755728 | etot = -13.2825375938163 +83000 ekin = 2.4833426959312 | erot = 5.48242032921998 | epot = -21.248300618845 | etot = -13.2825375936939 +84000 ekin = 2.47365997802594 | erot = 5.48271691205541 | epot = -21.2389144836696 | etot = -13.2825375935882 +85000 ekin = 2.46626808184772 | erot = 5.46691083838924 | epot = -21.2157165137399 | etot = -13.2825375935029 +86000 ekin = 2.46123154184243 | erot = 5.43653398177485 | epot = -21.1803031170841 | etot = -13.2825375934668 +87000 ekin = 2.45852093879055 | erot = 5.39265692383446 | epot = -21.1337154560121 | etot = -13.2825375933871 +88000 ekin = 2.45840646060175 | erot = 5.33627030736198 | epot = -21.0772143612561 | etot = -13.2825375932924 +89000 ekin = 2.46146480126887 | erot = 5.26838646846783 | epot = -21.0123888631742 | etot = -13.2825375934375 +90000 ekin = 2.4677317783594 | erot = 5.18930366181446 | epot = -20.9395730335193 | etot = -13.2825375933455 +91000 ekin = 2.47726011905719 | erot = 5.09951749277777 | epot = -20.8593152050595 | etot = -13.2825375932246 +92000 ekin = 2.49074261962909 | erot = 5.00022791911595 | epot = -20.7735081318254 | etot = -13.2825375930803 +93000 ekin = 2.50902833057362 | erot = 4.89281259013106 | epot = -20.6843785136292 | etot = -13.2825375929245 +94000 ekin = 2.53301288183075 | erot = 4.77876912035546 | epot = -20.5943195949544 | etot = -13.2825375927682 +95000 ekin = 2.56354598704907 | erot = 4.6596420581626 | epot = -20.5057256378352 | etot = -13.2825375926235 +96000 ekin = 2.60133194738611 | erot = 4.53693642149354 | epot = -20.4208059613806 | etot = -13.2825375925009 +97000 ekin = 2.64684712537105 | erot = 4.41204173729005 | epot = -20.3414264550665 | etot = -13.2825375924053 +98000 ekin = 2.70029551800324 | erot = 4.28619503995162 | epot = -20.2690281502928 | etot = -13.2825375923379 +99000 ekin = 2.76159183076381 | erot = 4.16048163754163 | epot = -20.2046110606006 | etot = -13.2825375922951 +100000 ekin = 2.83036874776579 | erot = 4.03587523010376 | epot = -20.1487815701408 | etot = -13.2825375922712 +101000 ekin = 2.90599845693996 | erot = 3.91330077540588 | epot = -20.1018368246064 | etot = -13.2825375922606 +102000 ekin = 2.98761606367604 | erot = 3.79369343963812 | epot = -20.0638470955752 | etot = -13.2825375922611 +103000 ekin = 3.07413620026802 | erot = 3.67802597580043 | epot = -20.0346997683418 | etot = -13.2825375922734 +104000 ekin = 3.16426099663645 | erot = 3.56728973636564 | epot = -20.0140883253047 | etot = -13.2825375923026 +105000 ekin = 3.25648344622793 | erot = 3.46242766269272 | epot = -20.0014487012763 | etot = -13.2825375923557 +106000 ekin = 3.34909407537355 | erot = 3.36423261094161 | epot = -19.9958642787542 | etot = -13.282537592439 +107000 ekin = 3.4401993069765 | erot = 3.27323316283015 | epot = -19.9959700623645 | etot = -13.2825375925578 +108000 ekin = 3.52775814523602 | erot = 3.18959025645786 | epot = -19.999885994407 | etot = -13.2825375927131 +109000 ekin = 3.60964009104214 | erot = 3.11302339299888 | epot = -20.0052010769433 | etot = -13.2825375929023 +110000 ekin = 3.68370388524509 | erot = 3.04277828887564 | epot = -20.0090197672386 | etot = -13.2825375931179 +111000 ekin = 3.74789440567183 | erot = 2.97764201100029 | epot = -20.0080740100205 | etot = -13.2825375933484 +112000 ekin = 3.80035415830428 | erot = 2.91600823448521 | epot = -19.9988999863676 | etot = -13.2825375935781 +113000 ekin = 3.839544891464 | erot = 2.8559933088984 | epot = -19.9780757941506 | etot = -13.2825375937882 +114000 ekin = 3.86437452036816 | erot = 2.79560177874327 | epot = -19.9425138930678 | etot = -13.2825375939563 +115000 ekin = 3.87432139555448 | erot = 2.7329343736024 | epot = -19.8897933632161 | etot = -13.2825375940592 +116000 ekin = 3.86954570193439 | erot = 2.66642221950682 | epot = -19.8185055155168 | etot = -13.2825375940755 +117000 ekin = 3.85097050791378 | erot = 2.59505981730843 | epot = -19.7285679191997 | etot = -13.2825375939775 +118000 ekin = 3.82031843896371 | erot = 2.51866416069826 | epot = -19.6215201934448 | etot = -13.2825375937828 +119000 ekin = 3.78008379969918 | erot = 2.43788144963878 | epot = -19.5005028428254 | etot = -13.2825375934874 +120000 ekin = 3.73339325084433 | erot = 2.35417060362233 | epot = -19.3701014475786 | etot = -13.282537593112 +121000 ekin = 3.68379362023519 | erot = 2.26974086129527 | epot = -19.23607207422 | etot = -13.2825375926895 +122000 ekin = 3.63497633455468 | erot = 2.18733107351197 | epot = -19.1048450003258 | etot = -13.2825375922591 +123000 ekin = 3.59047168903067 | erot = 2.10992442969337 | epot = -18.9829337105841 | etot = -13.2825375918601 +124000 ekin = 3.55336069064742 | erot = 2.040449477976 | epot = -18.8763477601487 | etot = -13.2825375915253 +125000 ekin = 3.526052756485 | erot = 1.98151529341996 | epot = -18.7901056411805 | etot = -13.2825375912756 +126000 ekin = 3.51088386083626 | erot = 1.93492307727824 | epot = -18.728344529054 | etot = -13.2825375909395 +127000 ekin = 3.51016542665131 | erot = 1.90135594382336 | epot = -18.6940589614221 | etot = -13.2825375909474 +128000 ekin = 3.52366007691459 | erot = 1.88146923500262 | epot = -18.6876669021183 | etot = -13.2825375902011 +129000 ekin = 3.52804447871109 | erot = 1.87939379818812 | epot = -18.6899759099344 | etot = -13.2825376330352 +130000 ekin = 3.39121727536937 | erot = 1.95375354402963 | epot = -18.6275084102343 | etot = -13.2825375908353 +131000 ekin = 3.51597185423296 | erot = 2.06600773707502 | epot = -18.8645172230933 | etot = -13.2825376317853 +132000 ekin = 3.65680948155273 | erot = 2.09675964820427 | epot = -19.0361067214651 | etot = -13.2825375917081 +133000 ekin = 3.78260898444153 | erot = 2.11778864665409 | epot = -19.1829352240667 | etot = -13.2825375929711 +134000 ekin = 3.90291219401782 | erot = 2.13993246768634 | epot = -19.3253822549312 | etot = -13.282537593227 +135000 ekin = 4.0130725329214 | erot = 2.16317596346888 | epot = -19.4587860898102 | etot = -13.2825375934199 +136000 ekin = 4.10942813981085 | erot = 2.18779054238602 | epot = -19.579756275755 | etot = -13.2825375935581 +137000 ekin = 4.18918244084739 | erot = 2.21413018926373 | epot = -19.6858502237401 | etot = -13.282537593629 +138000 ekin = 4.25055180725538 | erot = 2.24252417705096 | epot = -19.7756135779486 | etot = -13.2825375936422 +139000 ekin = 4.29264193993076 | erot = 2.27334414892611 | epot = -19.8485236824514 | etot = -13.2825375935945 +140000 ekin = 4.31542981069473 | erot = 2.30704736065647 | epot = -19.9050147648392 | etot = -13.282537593488 +141000 ekin = 4.31969657449582 | erot = 2.34420108979785 | epot = -19.9464352576258 | etot = -13.2825375933322 +142000 ekin = 4.30689625825181 | erot = 2.38546661972145 | epot = -19.9749004711164 | etot = -13.2825375931432 +143000 ekin = 4.27897643633865 | erot = 2.43154322469962 | epot = -19.9930572539778 | etot = -13.2825375929395 +144000 ekin = 4.23817759048809 | erot = 2.4830525431645 | epot = -20.0037677263996 | etot = -13.282537592747 +145000 ekin = 4.18683687366757 | erot = 2.54040585524226 | epot = -20.0097803214924 | etot = -13.2825375925826 +146000 ekin = 4.1272243777605 | erot = 2.60369949546902 | epot = -20.0134614656897 | etot = -13.2825375924601 +147000 ekin = 4.06142641942193 | erot = 2.67262771534946 | epot = -20.0165917271588 | etot = -13.2825375923874 +148000 ekin = 3.9912803569092 | erot = 2.74643868481959 | epot = -20.0202566340943 | etot = -13.2825375923655 +149000 ekin = 3.91835859675027 | erot = 2.82393987441759 | epot = -20.0248360635575 | etot = -13.2825375923896 +150000 ekin = 3.84399502540854 | erot = 2.90355368904202 | epot = -20.0300863068999 | etot = -13.2825375924493 +151000 ekin = 3.76934462696646 | erot = 2.98342057410476 | epot = -20.0353027936018 | etot = -13.2825375925305 +152000 ekin = 3.69546503896298 | erot = 3.06154297168136 | epot = -20.0395456032602 | etot = -13.2825375926159 +153000 ekin = 3.62340677772839 | erot = 3.13595781467703 | epot = -20.0419021850935 | etot = -13.2825375926881 +154000 ekin = 3.55429442921676 | erot = 3.20491770297265 | epot = -20.0417497249216 | etot = -13.2825375927321 +155000 ekin = 3.48935808553585 | erot = 3.26703376494699 | epot = -20.0389294432276 | etot = -13.2825375927448 +156000 ekin = 3.42995719397496 | erot = 3.32146386703849 | epot = -20.0339586537003 | etot = -13.2825375926868 +157000 ekin = 3.37758377439356 | erot = 3.36807693572793 | epot = -20.0281983027502 | etot = -13.2825375926288 +158000 ekin = 3.32977839475207 | erot = 3.40502394976504 | epot = -20.0173399361875 | etot = -13.2825375916704 +159000 ekin = 3.28790229188226 | erot = 3.43232801110884 | epot = -20.0027678906268 | etot = -13.2825375876357 +160000 ekin = 3.2827995172835 | erot = 3.46457454882488 | epot = -20.0299116571487 | etot = -13.2825375910404 +161000 ekin = 3.29006841785848 | erot = 3.48756894666501 | epot = -20.0601749524886 | etot = -13.2825375879651 +162000 ekin = 3.30320279765029 | erot = 3.50064541816097 | epot = -20.0863858038423 | etot = -13.282537588031 +163000 ekin = 3.32680445360257 | erot = 3.50703979240478 | epot = -20.1163818341648 | etot = -13.2825375881575 +164000 ekin = 3.35978204864574 | erot = 3.50639799900046 | epot = -20.1487176359768 | etot = -13.2825375883306 +165000 ekin = 3.40052448161995 | erot = 3.49807859199014 | epot = -20.1811406621343 | etot = -13.2825375885243 +166000 ekin = 3.44710440323596 | erot = 3.48135096319306 | epot = -20.2109929551315 | etot = -13.2825375887025 +167000 ekin = 3.4975648313672 | erot = 3.45565303648312 | epot = -20.2357554566791 | etot = -13.2825375888288 +168000 ekin = 3.55023572858497 | erot = 3.42084325030349 | epot = -20.2536165677605 | etot = -13.282537588872 +169000 ekin = 3.60406985696843 | erot = 3.37750569995077 | epot = -20.2641131456975 | etot = -13.2825375887783 +170000 ekin = 3.41798406778448 | erot = 3.07782048145476 | epot = -19.7783420668553 | etot = -13.282537517616 +171000 ekin = 3.24552871157827 | erot = 2.73637390316214 | epot = -19.2644400103087 | etot = -13.2825373955683 +172000 ekin = 3.78367855051371 | erot = 3.0727453748938 | epot = -20.1389614956922 | etot = -13.2825375702847 +173000 ekin = 4.03457273059443 | erot = 3.1833646910841 | epot = -20.5004749222031 | etot = -13.2825375005245 +174000 ekin = 4.14002439986023 | erot = 3.16763893899922 | epot = -20.5902008391762 | etot = -13.2825375003167 +175000 ekin = 4.24061478727573 | erot = 3.15086312051219 | epot = -20.6740154078953 | etot = -13.2825375001074 +176000 ekin = 4.33750550891641 | erot = 3.1355261006119 | epot = -20.7555691095056 | etot = -13.2825374999773 +177000 ekin = 4.43118634626255 | erot = 3.12342668205083 | epot = -20.8371505282964 | etot = -13.282537499983 +178000 ekin = 4.52112038535911 | erot = 3.11516996838714 | epot = -20.9188278538863 | etot = -13.28253750014 +179000 ekin = 4.60569122910559 | erot = 3.10997891303161 | epot = -20.9982076425525 | etot = -13.2825375004153 +180000 ekin = 4.68248742105205 | erot = 3.10587534040976 | epot = -21.0709002621995 | etot = -13.2825375007377 +181000 ekin = 4.74885008880769 | erot = 3.10016969122633 | epot = -21.1315572810546 | etot = -13.2825375010206 +182000 ekin = 4.80252004240904 | erot = 3.09010778323153 | epot = -21.1751653268271 | etot = -13.2825375011865 +183000 ekin = 4.84185836209392 | erot = 3.07355401450656 | epot = -21.1979498780501 | etot = -13.2825375014496 +184000 ekin = 4.86305938218274 | erot = 3.04972947015758 | epot = -21.1953263537857 | etot = -13.2825375014454 +185000 ekin = 4.86484048379853 | erot = 3.01830532387125 | epot = -21.165683308955 | etot = -13.2825375012852 +186000 ekin = 4.84781115921877 | erot = 2.97987576045986 | epot = -21.1102244206817 | etot = -13.2825375010031 +187000 ekin = 4.8135776433552 | erot = 2.93597501879465 | epot = -21.032090162799 | etot = -13.2825375006491 +188000 ekin = 4.76439584097176 | erot = 2.8887503176203 | epot = -20.9356836588659 | etot = -13.2825375002739 +189000 ekin = 4.7028202134345 | erot = 2.84056846871295 | epot = -20.8259261820664 | etot = -13.282537499919 +190000 ekin = 4.63141632940872 | erot = 2.79367442377689 | epot = -20.7076282527969 | etot = -13.2825374996113 +191000 ekin = 4.55257205219687 | erot = 2.74995133907398 | epot = -20.5850608906317 | etot = -13.2825374993609 +192000 ekin = 4.46841445137449 | erot = 2.7108083514329 | epot = -20.4617603019722 | etot = -13.2825374991648 +193000 ekin = 4.38080987485702 | erot = 2.67717312167301 | epot = -20.3405204955445 | etot = -13.2825374990145 +194000 ekin = 4.29140314493158 | erot = 2.64952891334607 | epot = -20.2234695571822 | etot = -13.2825374989045 +195000 ekin = 4.20164846020147 | erot = 2.62793199519283 | epot = -20.1121179542319 | etot = -13.2825374988376 +196000 ekin = 4.112799736886 | erot = 2.6119729730638 | epot = -20.0073102087726 | etot = -13.2825374988228 +197000 ekin = 4.0258589719236 | erot = 2.60069607327732 | epot = -19.9090925440707 | etot = -13.2825374988698 +198000 ekin = 3.94151021740635 | erot = 2.59254113732139 | epot = -19.8165888537063 | etot = -13.2825374989786 +199000 ekin = 3.86008920571504 | erot = 2.58539978552083 | epot = -19.728026490366 | etot = -13.2825374991301 +200000 ekin = 3.78163650515412 | erot = 2.57685633277384 | epot = -19.6410303372136 | etot = -13.2825374992857 +201000 ekin = 3.70604145366868 | erot = 2.56461316993842 | epot = -19.5531921230031 | etot = -13.282537499396 +202000 ekin = 3.63323784111708 | erot = 2.54700321074533 | epot = -19.4627785512819 | etot = -13.2825374994195 +203000 ekin = 3.56337600429933 | erot = 2.52342549129417 | epot = -19.3693389949301 | etot = -13.2825374993366 +204000 ekin = 3.49690618989364 | erot = 2.49455276327499 | epot = -19.2739964523245 | etot = -13.2825374991559 +205000 ekin = 3.43455338767261 | erot = 2.46224574346265 | epot = -19.1793366300441 | etot = -13.2825374989088 +206000 ekin = 3.37721205721374 | erot = 2.42921548153353 | epot = -19.0889650373857 | etot = -13.2825374986384 +207000 ekin = 3.32580575275754 | erot = 2.39854397251178 | epot = -19.0068872236571 | etot = -13.2825374983878 +208000 ekin = 3.28114891016496 | erot = 2.37318814654829 | epot = -18.9368745549054 | etot = -13.2825374981921 +209000 ekin = 3.24383236356932 | erot = 2.35556506548921 | epot = -18.8819349271337 | etot = -13.2825374980752 +210000 ekin = 3.21413821976281 | erot = 2.34727297364745 | epot = -18.8439486914582 | etot = -13.282537498048 +211000 ekin = 3.19199204395966 | erot = 2.34895966766644 | epot = -18.823489209736 | etot = -13.2825374981099 +212000 ekin = 3.17695628121177 | erot = 2.360321472034 | epot = -18.819815251497 | etot = -13.2825374982512 +213000 ekin = 3.16826455951518 | erot = 2.38020171954861 | epot = -18.8310037775187 | etot = -13.2825374984549 +214000 ekin = 3.16489343854634 | erot = 2.4067605217501 | epot = -18.8541914589957 | etot = -13.2825374986993 +215000 ekin = 3.16566474352153 | erot = 2.4376973804056 | epot = -18.8858996228856 | etot = -13.2825374989585 +216000 ekin = 3.16936807503256 | erot = 2.47051711068081 | epot = -18.9224226849174 | etot = -13.282537499204 +217000 ekin = 3.16266988026838 | erot = 2.47868467134127 | epot = -18.9238920507831 | etot = -13.2825374991734 +218000 ekin = 3.17835235865319 | erot = 2.45704329444878 | epot = -18.9179331413792 | etot = -13.2825374882772 +219000 ekin = 3.26524817202019 | erot = 2.48120766962855 | epot = -19.0289933444494 | etot = -13.2825375028007 +220000 ekin = 3.31083663795614 | erot = 2.50602061547625 | epot = -19.0993947418608 | etot = -13.2825374884285 +221000 ekin = 3.33748530919716 | erot = 2.52276996124467 | epot = -19.1427927588607 | etot = -13.2825374884189 +222000 ekin = 3.36243211589499 | erot = 2.53668587910066 | epot = -19.181655483376 | etot = -13.2825374883803 +223000 ekin = 3.38541896904217 | erot = 2.54888617169842 | epot = -19.2168426290796 | etot = -13.282537488339 +224000 ekin = 3.40625812507986 | erot = 2.56049920868626 | epot = -19.2492948220809 | etot = -13.2825374883148 +225000 ekin = 3.42484722909618 | erot = 2.57234499865719 | epot = -19.2797297160695 | etot = -13.2825374883162 +226000 ekin = 3.44121067431411 | erot = 2.58472036633686 | epot = -19.3084685289968 | etot = -13.2825374883458 +227000 ekin = 3.45552721377379 | erot = 2.59730386680743 | epot = -19.3353685689834 | etot = -13.2825374884022 +228000 ekin = 3.46810974282139 | erot = 2.6091693120744 | epot = -19.3598165433777 | etot = -13.2825374884819 +229000 ekin = 3.4793267631311 | erot = 2.61888809507087 | epot = -19.3807523467836 | etot = -13.2825374885816 +230000 ekin = 3.48948003513645 | erot = 2.62469570471749 | epot = -19.3967132285507 | etot = -13.2825374886968 +231000 ekin = 3.49867242979377 | erot = 2.62469374220078 | epot = -19.4059036608153 | etot = -13.2825374888207 +232000 ekin = 3.50671171842654 | erot = 2.6170613032781 | epot = -19.4063105106474 | etot = -13.2825374889427 +233000 ekin = 3.51309701132125 | erot = 2.60026316425572 | epot = -19.395897664621 | etot = -13.2825374890441 +234000 ekin = 3.51712117494327 | erot = 2.5732608561 | epot = -19.3729195201406 | etot = -13.2825374890973 +235000 ekin = 3.51809173982137 | erot = 2.53573892922866 | epot = -19.3363681581185 | etot = -13.2825374890685 +236000 ekin = 3.51562949139304 | erot = 2.48833922691111 | epot = -19.2865062072295 | etot = -13.2825374889254 +237000 ekin = 3.50996386129235 | erot = 2.43285732073676 | epot = -19.2253586706787 | etot = -13.2825374886496 +238000 ekin = 3.50212794781253 | erot = 2.37232394343562 | epot = -19.1569893794952 | etot = -13.2825374882471 +239000 ekin = 3.49397580570111 | erot = 2.31089750062538 | epot = -19.0874107940787 | etot = -13.2825374877522 +240000 ekin = 3.48799489984455 | erot = 2.2535377170645 | epot = -19.0240701041318 | etot = -13.2825374872227 +241000 ekin = 3.4869474415209 | erot = 2.2054938684223 | epot = -18.9749787966723 | etot = -13.2825374867291 +242000 ekin = 3.49341769740518 | erot = 2.1716922310321 | epot = -18.9476474147781 | etot = -13.2825374863409 +243000 ekin = 3.50935803683834 | erot = 2.15612557817114 | epot = -18.9480211011257 | etot = -13.2825374861162 +244000 ekin = 3.53571412218956 | erot = 2.16133426987289 | epot = -18.979585878157 | etot = -13.2825374860946 +245000 ekin = 3.57218201231806 | erot = 2.18803987534361 | epot = -19.0427593739549 | etot = -13.2825374862933 +246000 ekin = 3.61712090977309 | erot = 2.23496626996945 | epot = -19.134624666449 | etot = -13.2825374867064 +247000 ekin = 3.66762313707197 | erot = 2.29886938892499 | epot = -19.2490300133012 | etot = -13.2825374873042 +248000 ekin = 3.7197330409766 | erot = 2.3747925366233 | epot = -19.377063065633 | etot = -13.2825374880331 +249000 ekin = 3.7687988475912 | erot = 2.45655776432188 | epot = -19.5078941007305 | etot = -13.2825374888175 +250000 ekin = 3.80993596354031 | erot = 2.53748030029899 | epot = -19.6299537534039 | etot = -13.2825374895646 +251000 ekin = 3.83856187827056 | erot = 2.61124537605178 | epot = -19.7323447445001 | etot = -13.2825374901778 +252000 ekin = 3.85094160348732 | erot = 2.67282602420842 | epot = -19.8063051182675 | etot = -13.2825374905717 +253000 ekin = 3.84466267221376 | erot = 2.71927370140095 | epot = -19.8464738643054 | etot = -13.2825374906907 +254000 ekin = 3.81895334833665 | erot = 2.75020964906229 | epot = -19.8517004879202 | etot = -13.2825374905212 +255000 ekin = 3.77477712370614 | erot = 2.76789565653814 | epot = -19.8252102703408 | etot = -13.2825374900966 +256000 ekin = 3.71467746908406 | erot = 2.77685421459328 | epot = -19.7740691731677 | etot = -13.2825374894904 +257000 ekin = 3.64239785971379 | erot = 2.78310854270386 | epot = -19.7080438912194 | etot = -13.2825374888018 +258000 ekin = 3.56234912666851 | erot = 2.79319020432263 | epot = -19.6380768191282 | etot = -13.2825374881371 +259000 ekin = 3.47902170398396 | erot = 2.81309489223268 | epot = -19.5746540838083 | etot = -13.2825374875917 +260000 ekin = 3.39644765746004 | erot = 2.84735592157315 | epot = -19.5263410662695 | etot = -13.2825374872363 +261000 ekin = 3.31779785755485 | erot = 2.89836390677654 | epot = -19.4986992514401 | etot = -13.2825374871087 +262000 ekin = 3.24516405277549 | erot = 2.96601202360082 | epot = -19.493713563585 | etot = -13.2825374872087 +263000 ekin = 3.17954694530476 | erot = 3.04771661067519 | epot = -19.509801043485 | etot = -13.2825374875051 +264000 ekin = 3.12100159498054 | erot = 3.13875568824872 | epot = -19.5422947711677 | etot = -13.2825374879384 +265000 ekin = 3.068909969511 | erot = 3.23291804297596 | epot = -19.5843655009193 | etot = -13.2825374884324 +266000 ekin = 3.02230555156861 | erot = 3.32335252530508 | epot = -19.6281955657834 | etot = -13.2825374889098 +267000 ekin = 2.98016989218859 | erot = 3.40345614747457 | epot = -19.6661635289715 | etot = -13.2825374893083 +268000 ekin = 2.94163501488609 | erot = 3.46763177350625 | epot = -19.6918042779853 | etot = -13.282537489593 +269000 ekin = 2.90604069318514 | erot = 3.51175626238839 | epot = -19.7003344453578 | etot = -13.2825374897842 +270000 ekin = 2.87284037255906 | erot = 3.53329819601916 | epot = -19.6886760584274 | etot = -13.2825374898492 +271000 ekin = 2.84156688817829 | erot = 3.53141495904851 | epot = -19.6555193370576 | etot = -13.2825374898308 +272000 ekin = 2.81169493920539 | erot = 3.50673144119823 | epot = -19.6009638701441 | etot = -13.2825374897405 +273000 ekin = 2.78262532285011 | erot = 3.46115906465197 | epot = -19.5263218770821 | etot = -13.28253748958 +274000 ekin = 2.7538098130557 | erot = 3.39781487150794 | epot = -19.4341621738894 | etot = -13.2825374893258 +275000 ekin = 2.72497357924299 | erot = 3.32097131772016 | epot = -19.3284823859418 | etot = -13.2825374889787 +276000 ekin = 2.69631002934824 | erot = 3.23585259467473 | epot = -19.2147001125792 | etot = -13.2825374885562 +277000 ekin = 2.66855210196767 | erot = 3.14826501869249 | epot = -19.0993546087625 | etot = -13.2825374881024 +278000 ekin = 2.64286719085242 | erot = 3.06403640806158 | epot = -18.9894410865919 | etot = -13.2825374876779 +279000 ekin = 2.6206102822317 | erot = 2.98836162249344 | epot = -18.8915093920683 | etot = -13.2825374873432 +280000 ekin = 2.60303022005365 | erot = 2.92520891289703 | epot = -18.810776620091 | etot = -13.2825374871403 +281000 ekin = 2.59103448458094 | erot = 2.87693253510625 | epot = -18.7505045067693 | etot = -13.2825374870821 +282000 ekin = 2.58508390620569 | erot = 2.84417540765416 | epot = -18.7117968010114 | etot = -13.2825374871516 +283000 ekin = 2.58523135936705 | erot = 2.82606103956356 | epot = -18.6938298862415 | etot = -13.2825374873109 +284000 ekin = 2.59126091870015 | erot = 2.82059473157549 | epot = -18.6943931377914 | etot = -13.2825374875157 +285000 ekin = 2.6028463107778 | erot = 2.82514472713204 | epot = -18.7105285256397 | etot = -13.2825374877299 +286000 ekin = 2.61964775973889 | erot = 2.83687342635821 | epot = -18.7390586740322 | etot = -13.2825374879351 +287000 ekin = 2.64167894317198 | erot = 2.8528506609398 | epot = -18.777067092287 | etot = -13.2825374881753 +288000 ekin = 2.6687167813722 | erot = 2.87022930110005 | epot = -18.8214835708729 | etot = -13.2825374884007 +289000 ekin = 2.69931643718217 | erot = 2.88698660758031 | epot = -18.8688405333603 | etot = -13.2825374885979 +290000 ekin = 2.73194963658564 | erot = 2.90163654912848 | epot = -18.91612367448 | etot = -13.2825374887658 +291000 ekin = 2.76502957907501 | erot = 2.91324911168725 | epot = -18.9608161796579 | etot = -13.2825374888956 +292000 ekin = 2.79700561900648 | erot = 2.92149576190988 | epot = -19.0010388698883 | etot = -13.282537488972 +293000 ekin = 2.82654239554718 | erot = 2.92669002283955 | epot = -19.0357699073658 | etot = -13.2825374889791 +294000 ekin = 2.85272969462388 | erot = 2.92951972788893 | epot = -19.0647869114596 | etot = -13.2825374889468 +295000 ekin = 2.87508597590098 | erot = 2.9311082644765 | epot = -19.0887317291891 | etot = -13.2825374888116 +296000 ekin = 2.89378047526675 | erot = 2.93349300132876 | epot = -19.1098109651873 | etot = -13.2825374885917 +297000 ekin = 2.90976516784938 | erot = 2.93912517174385 | epot = -19.1314278279134 | etot = -13.2825374883201 +298000 ekin = 2.92469477926692 | erot = 2.95047845944716 | epot = -19.1577107267524 | etot = -13.2825374880383 +299000 ekin = 2.94065805823336 | erot = 2.96967690612592 | epot = -19.1928724521541 | etot = -13.2825374877948 +300000 ekin = 2.95980003469262 | erot = 2.99812642992008 | epot = -19.2404639522493 | etot = -13.2825374876367 +301000 ekin = 2.98391272977048 | erot = 3.03621252497702 | epot = -19.302662742346 | etot = -13.2825374875985 +302000 ekin = 3.01408971368422 | erot = 3.08312901018064 | epot = -19.3797562115572 | etot = -13.2825374876923 +303000 ekin = 3.05053302665408 | erot = 3.13689255668996 | epot = -19.4699630712472 | etot = -13.2825374879032 +304000 ekin = 3.08584972584671 | erot = 3.19556015974062 | epot = -19.5639473752475 | etot = -13.2825374896602 +305000 ekin = 3.11890909070302 | erot = 3.26281224727061 | epot = -19.6642588266132 | etot = -13.2825374886396 +306000 ekin = 3.16699270587545 | erot = 3.33070506272287 | epot = -19.7802352601681 | etot = -13.2825374915697 +307000 ekin = 3.22023032257278 | erot = 3.3799777181515 | epot = -19.8827455298064 | etot = -13.2825374890821 +308000 ekin = 3.27268739663165 | erot = 3.41969099128438 | epot = -19.9749158771467 | etot = -13.2825374892307 +309000 ekin = 3.32280425481028 | erot = 3.44976402097079 | epot = -20.0551057651176 | etot = -13.2825374893365 +310000 ekin = 3.36903652740728 | erot = 3.46970323071463 | epot = -20.1212772475588 | etot = -13.2825374894369 +311000 ekin = 3.40972253534196 | erot = 3.47940229944893 | epot = -20.1716623243582 | etot = -13.2825374895673 +312000 ekin = 3.44308129108907 | erot = 3.47898447382754 | epot = -20.204603254423 | etot = -13.2825374895064 +313000 ekin = 3.46879202758663 | erot = 3.47087869840748 | epot = -20.2222082156487 | etot = -13.2825374896546 +314000 ekin = 3.48565385463278 | erot = 3.45582059749242 | epot = -20.2240119419355 | etot = -13.2825374898103 +315000 ekin = 3.4921631329082 | erot = 3.43373104094955 | epot = -20.2084316637809 | etot = -13.2825374899231 +316000 ekin = 3.48736213303232 | erot = 3.40482567255629 | epot = -20.1747252955269 | etot = -13.2825374899383 +317000 ekin = 3.46994132507374 | erot = 3.36841330847356 | epot = -20.1208921250387 | etot = -13.2825374914914 +318000 ekin = 3.43614022048189 | erot = 3.32066657788102 | epot = -20.0393442896713 | etot = -13.2825374913084 +319000 ekin = 3.38694293952315 | erot = 3.2636491069797 | epot = -19.9331295374394 | etot = -13.2825374909366 +320000 ekin = 3.32506744212965 | erot = 3.20113650606275 | epot = -19.8087414386365 | etot = -13.2825374904441 +321000 ekin = 3.25415482891539 | erot = 3.13766117542953 | epot = -19.6743534942655 | etot = -13.2825374899206 +322000 ekin = 3.17813669787398 | erot = 3.07780020747378 | epot = -19.5384743947986 | etot = -13.2825374894508 +323000 ekin = 3.10066688252112 | erot = 3.02549088180775 | epot = -19.4086952534164 | etot = -13.2825374890875 +324000 ekin = 3.02479637479555 | erot = 2.9835512249436 | epot = -19.2908850885836 | etot = -13.2825374888444 +325000 ekin = 2.95294332411579 | erot = 2.95347420684863 | epot = -19.1889550196703 | etot = -13.2825374887059 +326000 ekin = 2.88706743998012 | erot = 2.93544936652532 | epot = -19.1050542951527 | etot = -13.2825374886473 +327000 ekin = 2.82887581625042 | erot = 2.92851219862423 | epot = -19.0399255035249 | etot = -13.2825374886502 +328000 ekin = 2.7799083006856 | erot = 2.93074772300673 | epot = -18.9931935123989 | etot = -13.2825374887065 +329000 ekin = 2.74145002280429 | erot = 2.93954016638564 | epot = -18.9635276780016 | etot = -13.2825374888116 +330000 ekin = 2.71432845550724 | erot = 2.95189909643594 | epot = -18.9487650408976 | etot = -13.2825374889545 +331000 ekin = 2.69870867088015 | erot = 2.96486608415783 | epot = -18.9461122441539 | etot = -13.2825374891159 +332000 ekin = 2.69398517733071 | erot = 2.9759351218084 | epot = -18.9524577884139 | etot = -13.2825374892748 +333000 ekin = 2.69881348537833 | erot = 2.98337443171614 | epot = -18.9647254065077 | etot = -13.2825374894133 +334000 ekin = 2.71127609678656 | erot = 2.98637176000363 | epot = -18.9801853463082 | etot = -13.282537489518 +335000 ekin = 2.72916096430101 | erot = 2.98501165510017 | epot = -18.9967101089767 | etot = -13.2825374895756 +336000 ekin = 2.75032164400955 | erot = 2.98016551096549 | epot = -19.0130246445444 | etot = -13.2825374895694 +337000 ekin = 2.77304615866171 | erot = 2.97336445321275 | epot = -19.0289481013653 | etot = -13.2825374894909 +338000 ekin = 2.79631213711555 | erot = 2.96664518651948 | epot = -19.0454948129873 | etot = -13.2825374893522 +339000 ekin = 2.8198251309544 | erot = 2.96230352229863 | epot = -19.0646661424453 | etot = -13.2825374891923 +340000 ekin = 2.84381599358249 | erot = 2.96250923740561 | epot = -19.0888627200583 | etot = -13.2825374890702 +341000 ekin = 2.86861716322249 | erot = 2.96879944354184 | epot = -19.1199540958278 | etot = -13.2825374890635 +342000 ekin = 2.8942330530754 | erot = 2.98159830919509 | epot = -19.1583688514537 | etot = -13.2825374891832 +343000 ekin = 2.92230469127443 | erot = 3.00151195978065 | epot = -19.2063541396099 | etot = -13.2825374885548 +344000 ekin = 2.95328542678957 | erot = 3.02739469587516 | epot = -19.2632176118817 | etot = -13.282537489217 +345000 ekin = 2.98288076792584 | erot = 3.05397730230856 | epot = -19.3193955601209 | etot = -13.2825374898865 +346000 ekin = 3.0068362280629 | erot = 3.07579634903275 | epot = -19.3651700675335 | etot = -13.2825374904379 +347000 ekin = 3.021682039197 | erot = 3.0883226978178 | epot = -19.3925422277954 | etot = -13.2825374907806 +348000 ekin = 3.02528371459214 | erot = 3.08873432783574 | epot = -19.3965555333152 | etot = -13.2825374908873 +349000 ekin = 3.01708434471769 | erot = 3.07610751269362 | epot = -19.3757293482008 | etot = -13.2825374907895 +350000 ekin = 2.99803087494402 | erot = 3.05108999688533 | epot = -19.3316583623752 | etot = -13.2825374905459 +351000 ekin = 2.97033325354314 | erot = 3.01539362128504 | epot = -19.268264365027 | etot = -13.2825374901988 +352000 ekin = 2.93755453890544 | erot = 2.97175102427381 | epot = -19.1918430529999 | etot = -13.2825374898207 +353000 ekin = 2.90330530001813 | erot = 2.92291261114237 | epot = -19.1087554005693 | etot = -13.2825374894088 +354000 ekin = 2.87126755833568 | erot = 2.87170321125813 | epot = -19.0255082585641 | etot = -13.2825374889703 +355000 ekin = 2.84520639660643 | erot = 2.82119115452776 | epot = -18.948935039652 | etot = -13.2825374885178 +356000 ekin = 2.8287863971603 | erot = 2.7746321329023 | epot = -18.8859560181437 | etot = -13.2825374880811 +357000 ekin = 2.82589501110754 | erot = 2.73507904234615 | epot = -18.8435115424282 | etot = -13.2825374889745 +358000 ekin = 2.83567543256197 | erot = 2.6999034357179 | epot = -18.8181163574566 | etot = -13.2825374891768 +359000 ekin = 2.85413863003174 | erot = 2.66477535390921 | epot = -18.8014514734662 | etot = -13.2825374895252 +360000 ekin = 2.87797108635824 | erot = 2.62716069413401 | epot = -18.7876692705271 | etot = -13.2825374900349 +361000 ekin = 2.90295419334403 | erot = 2.58324525246715 | epot = -18.7687369364404 | etot = -13.2825374906292 +362000 ekin = 2.92446718933308 | erot = 2.52862237257544 | epot = -18.7356270530351 | etot = -13.2825374911266 +363000 ekin = 2.93848759933348 | erot = 2.45989164640849 | epot = -18.680916737042 | etot = -13.2825374913 +364000 ekin = 2.94271150164586 | erot = 2.37661313123214 | epot = -18.6018621239955 | etot = -13.2825374911175 +365000 ekin = 2.93600170081438 | erot = 2.28250131433965 | epot = -18.5010405056253 | etot = -13.2825374904713 +366000 ekin = 2.91934189957478 | erot = 2.18525996401368 | epot = -18.3871393531652 | etot = -13.2825374895768 +367000 ekin = 2.89548895825519 | erot = 2.0946888564492 | epot = -18.2727153033882 | etot = -13.2825374886839 +368000 ekin = 2.86763306547926 | erot = 2.02026878405327 | epot = -18.1704393375192 | etot = -13.2825374879867 +369000 ekin = 2.83845106986046 | erot = 1.96931673436804 | epot = -18.0903052917965 | etot = -13.282537487568 +370000 ekin = 2.80963551309284 | erot = 1.94618455936313 | epot = -18.0383575598705 | etot = -13.2825374874145 +371000 ekin = 2.78188668089849 | erot = 1.95235490032645 | epot = -18.0167790686888 | etot = -13.2825374874639 +372000 ekin = 2.75518266190993 | erot = 1.98699478725745 | epot = -18.0247149368147 | etot = -13.2825374876473 +373000 ekin = 2.7291288052834 | erot = 2.04757125854604 | epot = -18.0592375517431 | etot = -13.2825374879136 +374000 ekin = 2.7032481730965 | erot = 2.13030562163268 | epot = -18.1160912829679 | etot = -13.2825374882387 +375000 ekin = 2.67714701016873 | erot = 2.23039820126271 | epot = -18.1900827000525 | etot = -13.282537488621 +376000 ekin = 2.65054772278943 | erot = 2.34206662745006 | epot = -18.2751518393106 | etot = -13.2825374890711 +377000 ekin = 2.62322866602789 | erot = 2.45852983339147 | epot = -18.3642959890092 | etot = -13.2825374895898 +378000 ekin = 2.59495135704074 | erot = 2.57214449993232 | epot = -18.4496333471184 | etot = -13.2825374901453 +379000 ekin = 2.56546707826881 | erot = 2.67491697597423 | epot = -18.522921544903 | etot = -13.2825374906599 +380000 ekin = 2.53466143096452 | erot = 2.75950320018323 | epot = -18.5767021221686 | etot = -13.2825374910209 +381000 ekin = 2.50280930121905 | erot = 2.82054519918234 | epot = -18.605891991525 | etot = -13.2825374911236 +382000 ekin = 2.47081272773286 | erot = 2.85587907290837 | epot = -18.6092292915673 | etot = -13.2825374909261 +383000 ekin = 2.44026108011578 | erot = 2.86702983653801 | epot = -18.5898284071325 | etot = -13.2825374904788 +384000 ekin = 2.41324034479873 | erot = 2.85867137365971 | epot = -18.5544492083626 | etot = -13.2825374899041 +385000 ekin = 2.3919736779495 | erot = 2.83724859058569 | epot = -18.5117597578745 | etot = -13.2825374893393 +386000 ekin = 2.37848037079693 | erot = 2.80936838549168 | epot = -18.4703862451677 | etot = -13.2825374888791 +387000 ekin = 2.37440773877138 | erot = 2.78057799551461 | epot = -18.4375232228406 | etot = -13.2825374885547 +388000 ekin = 2.38106033998944 | erot = 2.75482980994152 | epot = -18.4184276382777 | etot = -13.2825374883468 +389000 ekin = 2.3995269472836 | erot = 2.73455852133737 | epot = -18.4166229568386 | etot = -13.2825374882176 +390000 ekin = 2.43075796801538 | erot = 2.72108399953604 | epot = -18.4343794556925 | etot = -13.2825374881411 +391000 ekin = 2.47547758104125 | erot = 2.71503282252802 | epot = -18.4730478916894 | etot = -13.2825374881201 +392000 ekin = 2.53389941336301 | erot = 2.71657607916961 | epot = -18.5330129807166 | etot = -13.282537488184 +393000 ekin = 2.60531467139514 | erot = 2.72543162367145 | epot = -18.6132837834377 | etot = -13.2825374883712 +394000 ekin = 2.68770614221053 | erot = 2.74072420161599 | epot = -18.710967832529 | etot = -13.2825374887024 +395000 ekin = 2.77757589910946 | erot = 2.76089277951269 | epot = -18.821006167779 | etot = -13.2825374891568 +396000 ekin = 2.87012638573289 | erot = 2.78383015196004 | epot = -18.9364940273591 | etot = -13.2825374896661 +397000 ekin = 2.95979968456986 | erot = 2.80730760068458 | epot = -19.0496447753932 | etot = -13.2825374901387 +398000 ekin = 3.04101675292502 | erot = 2.82953067572591 | epot = -19.1530849191498 | etot = -13.2825374904989 +399000 ekin = 3.10335323687934 | erot = 2.84223393462917 | epot = -19.2281247208206 | etot = -13.2825375493121 +400000 ekin = 3.10435999781796 | erot = 2.68059016642954 | epot = -19.0674876235022 | etot = -13.2825374592547 +401000 ekin = 3.39309095570315 | erot = 2.63997900103007 | epot = -19.3156074940371 | etot = -13.2825375373039 +402000 ekin = 3.44106634979645 | erot = 2.659790716706 | epot = -19.3833945765517 | etot = -13.2825375100493 +403000 ekin = 3.43207406397009 | erot = 2.67998452069831 | epot = -19.394596094653 | etot = -13.2825375099846 +404000 ekin = 3.40426891789311 | erot = 2.70237957195789 | epot = -19.3891859997632 | etot = -13.2825375099122 +405000 ekin = 3.3593347341666 | erot = 2.72607645467142 | epot = -19.367948698657 | etot = -13.282537509819 +406000 ekin = 3.29966540905146 | erot = 2.74995079993995 | epot = -19.3321537186901 | etot = -13.2825375096987 +407000 ekin = 3.2282311798008 | erot = 2.77286165525633 | epot = -19.2836303446157 | etot = -13.2825375095586 +408000 ekin = 3.1483591073718 | erot = 2.79373949027867 | epot = -19.2246361070933 | etot = -13.2825375094428 +409000 ekin = 3.06351542881959 | erot = 2.81131469884056 | epot = -19.1573676369638 | etot = -13.2825375093037 +410000 ekin = 2.97699949579686 | erot = 2.82462679197841 | epot = -19.0841637969767 | etot = -13.2825375092014 +411000 ekin = 2.89165449989684 | erot = 2.83289882075493 | epot = -19.0070908297837 | etot = -13.2825375091319 +412000 ekin = 2.80978906687504 | erot = 2.83549592230531 | epot = -18.9278224982521 | etot = -13.2825375090718 +413000 ekin = 2.73325536965585 | erot = 2.83215388787228 | epot = -18.8479467665131 | etot = -13.282537508985 +414000 ekin = 2.66364879696115 | erot = 2.82325639291671 | epot = -18.7694426987162 | etot = -13.2825375088383 +415000 ekin = 2.60253860597198 | erot = 2.81004531899789 | epot = -18.6951214335864 | etot = -13.2825375086165 +416000 ekin = 2.55161661471215 | erot = 2.7946463118532 | epot = -18.6288004349012 | etot = -13.2825375083358 +417000 ekin = 2.51265407611577 | erot = 2.77984605489432 | epot = -18.5750376413434 | etot = -13.2825375103333 +418000 ekin = 2.47334604007925 | erot = 2.77799997552572 | epot = -18.5338835235875 | etot = -13.2825375079825 +419000 ekin = 2.44559608969893 | erot = 2.79655231012718 | epot = -18.5246859081463 | etot = -13.2825375083202 +420000 ekin = 2.44884495813904 | erot = 2.81276776866598 | epot = -18.5441502345702 | etot = -13.2825375077651 +421000 ekin = 2.47134322854002 | erot = 2.82756585669941 | epot = -18.5814465933144 | etot = -13.2825375080749 +422000 ekin = 2.50522487694504 | erot = 2.84806830842347 | epot = -18.6358306938984 | etot = -13.2825375085299 +423000 ekin = 2.54673540365736 | erot = 2.87162843047175 | epot = -18.7009013431671 | etot = -13.282537509038 +424000 ekin = 2.5915545267989 | erot = 2.89540834353031 | epot = -18.7695003798181 | etot = -13.2825375094888 +425000 ekin = 2.63549518712503 | erot = 2.9172494646209 | epot = -18.8352821615391 | etot = -13.2825375097932 +426000 ekin = 2.67515430284032 | erot = 2.93632167691171 | epot = -18.8940134896611 | etot = -13.2825375099091 +427000 ekin = 2.70835356711895 | erot = 2.95332774897864 | epot = -18.9442188259411 | etot = -13.2825375098435 +428000 ekin = 2.73429370857904 | erot = 2.97029523905205 | epot = -18.9871264572657 | etot = -13.2825375096346 +429000 ekin = 2.75344687778548 | erot = 2.99015713231241 | epot = -19.026141519429 | etot = -13.2825375093311 +430000 ekin = 2.76726512076715 | erot = 3.01631311484004 | epot = -19.0661157445923 | etot = -13.2825375089851 +431000 ekin = 2.77776520584482 | erot = 3.05220345439827 | epot = -19.1125061689064 | etot = -13.2825375086633 +432000 ekin = 2.78700254672782 | erot = 3.10077153004471 | epot = -19.1703115852294 | etot = -13.2825375084569 +433000 ekin = 2.79644099946406 | erot = 3.16368547122764 | epot = -19.2426639791689 | etot = -13.2825375084772 +434000 ekin = 2.8062952810192 | erot = 3.24036053939458 | epot = -19.3291933292362 | etot = -13.2825375088224 +435000 ekin = 2.81503854863169 | erot = 3.32707633256549 | epot = -19.4246523907207 | etot = -13.2825375095236 +436000 ekin = 2.81936003428183 | erot = 3.41666372807462 | epot = -19.5185612728498 | etot = -13.2825375104934 +437000 ekin = 2.81480689571151 | erot = 3.49920681099962 | epot = -19.5965512182294 | etot = -13.2825375115182 +438000 ekin = 2.79709037800121 | erot = 3.56380823492809 | epot = -19.643436125261 | etot = -13.2825375123317 +439000 ekin = 2.76357573484572 | erot = 3.60097663047473 | epot = -19.6470898780363 | etot = -13.2825375127159 +440000 ekin = 2.71419714341371 | erot = 3.6047593537822 | epot = -19.6014940098261 | etot = -13.2825375126302 +441000 ekin = 2.65147586146338 | erot = 3.57350682801194 | epot = -19.5075202016436 | etot = -13.2825375121683 +442000 ekin = 2.57978868207942 | erot = 3.50949061111828 | epot = -19.3718168046656 | etot = -13.2825375114679 +443000 ekin = 2.50456558754104 | erot = 3.4178674196423 | epot = -19.2049705178168 | etot = -13.2825375106335 +444000 ekin = 2.43185299049922 | erot = 3.30558723792078 | epot = -19.0199777381447 | etot = -13.2825375097247 +445000 ekin = 2.36817510309063 | erot = 3.18052048207573 | epot = -18.8312330939526 | etot = -13.2825375087862 +446000 ekin = 2.32036350430527 | erot = 3.05081891044131 | epot = -18.6537199226123 | etot = -13.2825375078657 +447000 ekin = 2.29507009387958 | erot = 2.92434156859069 | epot = -18.5019491695481 | etot = -13.2825375070778 +448000 ekin = 2.29792306265903 | erot = 2.80795199471116 | epot = -18.3884125638822 | etot = -13.282537506512 +449000 ekin = 2.33256968728525 | erot = 2.7069587718453 | epot = -18.3220659653954 | etot = -13.2825375062648 +450000 ekin = 2.39980570006764 | erot = 2.6245346844449 | epot = -18.3068778909135 | etot = -13.282537506401 +451000 ekin = 2.49706752601175 | erot = 2.56128240620743 | epot = -18.3408874391531 | etot = -13.2825375069339 +452000 ekin = 2.61842576959501 | erot = 2.51510244034445 | epot = -18.4160657177213 | etot = -13.2825375077819 +453000 ekin = 2.75505822099958 | erot = 2.48156991528656 | epot = -18.5191656452411 | etot = -13.2825375089549 +454000 ekin = 2.89583245290297 | erot = 2.45420794646339 | epot = -18.6325779096657 | etot = -13.2825375102994 +455000 ekin = 3.02803920576056 | erot = 2.42568753016163 | epot = -18.736264247583 | etot = -13.2825375116608 +456000 ekin = 3.13847091959985 | erot = 2.38932191986942 | epot = -18.8103303522404 | etot = -13.2825375127711 +457000 ekin = 3.21547363215232 | erot = 2.34093725374963 | epot = -18.83894839917 | etot = -13.2825375132681 +458000 ekin = 3.2519255085167 | erot = 2.28077893487382 | epot = -18.8152419562951 | etot = -13.2825375129046 +459000 ekin = 3.24761130320326 | erot = 2.21429904484092 | epot = -18.744447859815 | etot = -13.2825375117708 +460000 ekin = 3.20922400634736 | erot = 2.15086461860742 | epot = -18.6426261352081 | etot = -13.2825375102533 +461000 ekin = 3.14796311215653 | erot = 2.10092694607039 | epot = -18.5314275670048 | etot = -13.2825375087779 +462000 ekin = 3.07634336775073 | erot = 2.07329933806439 | epot = -18.4321802134279 | etot = -13.2825375076128 +463000 ekin = 3.00570913413418 | erot = 2.07367404520667 | epot = -18.3619206861977 | etot = -13.2825375068568 +464000 ekin = 2.9448582997097 | erot = 2.10431183996111 | epot = -18.331707646191 | etot = -13.2825375065202 +465000 ekin = 2.89946798284609 | erot = 2.16425406354561 | epot = -18.3462595529816 | etot = -13.2825375065899 +466000 ekin = 2.87195252749972 | erot = 2.24955307487499 | epot = -18.4040431094255 | etot = -13.2825375070508 +467000 ekin = 2.86158324930207 | erot = 2.3533892427293 | epot = -18.4975099999046 | etot = -13.2825375078732 +468000 ekin = 2.86493243611993 | erot = 2.46640127706619 | epot = -18.6138712219846 | etot = -13.2825375087985 +469000 ekin = 2.87700241085747 | erot = 2.57824581694139 | epot = -18.7377857379035 | etot = -13.2825375101046 +470000 ekin = 2.89115454215414 | erot = 2.67606199010798 | epot = -18.8497540435902 | etot = -13.2825375113281 +471000 ekin = 2.90087699699085 | erot = 2.74765202467846 | epot = -18.9310665338721 | etot = -13.2825375122028 +472000 ekin = 2.90129360656583 | erot = 2.7844228810356 | epot = -18.9682540001117 | etot = -13.2825375125102 +473000 ekin = 2.89014262487726 | erot = 2.78350866545128 | epot = -18.9561888025163 | etot = -13.2825375121877 +474000 ekin = 2.8679845551896 | erot = 2.74843722225596 | epot = -18.8989592888163 | etot = -13.2825375113708 +475000 ekin = 2.83751222123126 | erot = 2.68789202057427 | epot = -18.8079417521389 | etot = -13.2825375103333 +476000 ekin = 2.80225697256743 | erot = 2.61311305367502 | epot = -18.6979075356038 | etot = -13.2825375093613 +477000 ekin = 2.76525060538535 | erot = 2.53510543119006 | epot = -18.5828935452222 | etot = -13.2825375086468 +478000 ekin = 2.72814283271883 | erot = 2.46266477167839 | epot = -18.4733451126463 | etot = -13.282537508249 +479000 ekin = 2.69099471858041 | erot = 2.40160392945098 | epot = -18.375136156148 | etot = -13.2825375081166 +480000 ekin = 2.6526681049776 | erot = 2.35496214915731 | epot = -18.2901677623243 | etot = -13.2825375081894 +481000 ekin = 2.611442355162 | erot = 2.32364519373677 | epot = -18.2176250571627 | etot = -13.282537508264 +482000 ekin = 2.565776730153 | erot = 2.30767778316155 | epot = -18.1559920216392 | etot = -13.2825375083247 +483000 ekin = 2.51481850308162 | erot = 2.30660853349362 | epot = -18.1039645449013 | etot = -13.2825375083261 +484000 ekin = 2.45838132863017 | erot = 2.3198450068296 | epot = -18.0607638434524 | etot = -13.2825375079926 +485000 ekin = 2.37536403481855 | erot = 2.30798475223331 | epot = -17.9658863029946 | etot = -13.2825375159427 +486000 ekin = 2.31029787369058 | erot = 2.27486987654653 | epot = -17.8677052455649 | etot = -13.2825374953278 +487000 ekin = 2.35903895728042 | erot = 2.35840823831765 | epot = -17.9999847156837 | etot = -13.2825375200856 +488000 ekin = 2.35207405535098 | erot = 2.45495770508831 | epot = -18.0895692764695 | etot = -13.2825375160302 +489000 ekin = 2.32025825397052 | erot = 2.54616767539779 | epot = -18.1489634454364 | etot = -13.2825375160681 +490000 ekin = 2.29515153869984 | erot = 2.64227715696153 | epot = -18.2199662119964 | etot = -13.282537516335 +491000 ekin = 2.27724499850078 | erot = 2.73950547060331 | epot = -18.2992879857125 | etot = -13.2825375166084 +492000 ekin = 2.26670396937252 | erot = 2.83351832936053 | epot = -18.3827598156682 | etot = -13.2825375169351 +493000 ekin = 2.26314468317306 | erot = 2.91977614251813 | epot = -18.4654583429642 | etot = -13.282537517273 +494000 ekin = 2.26577113863215 | erot = 2.99399214332928 | epot = -18.5423007995401 | etot = -13.2825375175787 +495000 ekin = 2.27355094493377 | erot = 3.05259857144223 | epot = -18.6086870341908 | etot = -13.2825375178148 +496000 ekin = 2.28538641733465 | erot = 3.09313022185941 | epot = -18.661054157153 | etot = -13.282537517959 +497000 ekin = 2.3002347482521 | erot = 3.11444072103781 | epot = -18.6972129872905 | etot = -13.2825375180006 +498000 ekin = 2.31719365941364 | erot = 3.11678508297333 | epot = -18.7165162603266 | etot = -13.2825375179397 +499000 ekin = 2.33554254163157 | erot = 3.10178716717433 | epot = -18.7198672265901 | etot = -13.2825375177842 +500000 ekin = 2.31317350075609 | erot = 3.05449093052383 | epot = -18.6502019679387 | etot = -13.2825375366588 +501000 ekin = 2.31231722963358 | erot = 3.00810318070389 | epot = -18.6029579370661 | etot = -13.2825375267286 +502000 ekin = 2.38999638954889 | erot = 2.98467042895374 | epot = -18.657204342138 | etot = -13.2825375236353 +503000 ekin = 2.41312387634462 | erot = 2.93091691360098 | epot = -18.6265783132937 | etot = -13.2825375233481 +504000 ekin = 2.43600229238282 | erot = 2.88130858484448 | epot = -18.5998484003617 | etot = -13.2825375231344 +505000 ekin = 2.45757791197103 | erot = 2.84011866669662 | epot = -18.5802341017161 | etot = -13.2825375230484 +506000 ekin = 2.47627134224707 | erot = 2.81025901810999 | epot = -18.5690678834978 | etot = -13.2825375231408 +507000 ekin = 2.48985246050729 | erot = 2.79268587937519 | epot = -18.5650758633262 | etot = -13.2825375234437 +508000 ekin = 2.49542483825231 | erot = 2.78597986942009 | epot = -18.5639422316207 | etot = -13.2825375239483 +509000 ekin = 2.48963204749862 | erot = 2.78630577999958 | epot = -18.5584753520799 | etot = -13.2825375245818 +510000 ekin = 2.46917438876006 | erot = 2.78796571286371 | epot = -18.5396776268285 | etot = -13.2825375252047 +511000 ekin = 2.43159454916956 | erot = 2.78459744700141 | epot = -18.4987295218192 | etot = -13.2825375256482 +512000 ekin = 2.37609227914812 | erot = 2.7707369794783 | epot = -18.4293667844085 | etot = -13.2825375257821 +513000 ekin = 2.30402039320529 | erot = 2.74317280239451 | epot = -18.3297307211707 | etot = -13.2825375255709 +514000 ekin = 2.21884081240883 | erot = 2.70155414867794 | epot = -18.2029324861636 | etot = -13.2825375250768 +515000 ekin = 2.12561338169144 | erot = 2.64810551844221 | epot = -18.0562564245494 | etot = -13.2825375244158 +516000 ekin = 2.0302995856451 | erot = 2.5867398599196 | epot = -17.8995769692659 | etot = -13.2825375237012 +517000 ekin = 1.93914577194817 | erot = 2.52206054313542 | epot = -17.7437438380945 | etot = -13.2825375230109 +518000 ekin = 1.85826662411615 | erot = 2.45858700715108 | epot = -17.5993911536592 | etot = -13.2825375223919 +519000 ekin = 1.79333215324367 | erot = 2.40035341708211 | epot = -17.4762230921876 | etot = -13.2825375218619 +520000 ekin = 1.74929005168975 | erot = 2.35078235676691 | epot = -17.3826099298929 | etot = -13.2825375214363 +521000 ekin = 1.73007209345073 | erot = 2.31266171840817 | epot = -17.3252713329969 | etot = -13.282537521138 +522000 ekin = 1.73822781682595 | erot = 2.2881155718937 | epot = -17.3088809097143 | etot = -13.2825375209947 +523000 ekin = 1.77456624772603 | erot = 2.2785083458307 | epot = -17.3356121145903 | etot = -13.2825375210336 +524000 ekin = 1.83790458514344 | erot = 2.28429322274723 | epot = -17.4047353291616 | etot = -13.2825375212709 +525000 ekin = 1.92500868748296 | erot = 2.30484700359195 | epot = -17.5123932127819 | etot = -13.282537521707 +526000 ekin = 2.0307578025818 | erot = 2.33833465322601 | epot = -17.651629978134 | etot = -13.2825375223262 +527000 ekin = 2.14850843905356 | erot = 2.38164040104833 | epot = -17.8126863631983 | etot = -13.2825375230964 +528000 ekin = 2.27060096649051 | erot = 2.43041424715665 | epot = -17.9835527376135 | etot = -13.2825375239663 +529000 ekin = 2.38896012863249 | erot = 2.4793138751117 | epot = -18.1508115286032 | etot = -13.282537524859 +530000 ekin = 2.49576940535655 | erot = 2.52254117021849 | epot = -18.3008481012414 | etot = -13.2825375256663 +531000 ekin = 2.58420744220974 | erot = 2.55472238426385 | epot = -18.4214673527334 | etot = -13.2825375262598 +532000 ekin = 2.64918587017627 | erot = 2.57201883162556 | epot = -18.5037422283274 | etot = -13.2825375265255 +533000 ekin = 2.68793333155572 | erot = 2.57313230810709 | epot = -18.5436031660763 | etot = -13.2825375264134 +534000 ekin = 2.70021208216117 | erot = 2.55975253147949 | epot = -18.542502139612 | etot = -13.2825375259714 +535000 ekin = 2.68802701634936 | erot = 2.53615014862128 | epot = -18.5067146903044 | etot = -13.2825375253337 +536000 ekin = 2.65489019113449 | erot = 2.50801671125187 | epot = -18.445444427055 | etot = -13.2825375246686 +537000 ekin = 2.60490332065097 | erot = 2.48102333788784 | epot = -18.3684641826523 | etot = -13.2825375241135 +538000 ekin = 2.54198784537002 | erot = 2.45965628961172 | epot = -18.2841816579271 | etot = -13.2825375229454 +539000 ekin = 2.47150013366557 | erot = 2.44756195583901 | epot = -18.2015996124771 | etot = -13.2825375229725 +540000 ekin = 2.39647534126896 | erot = 2.4452543590462 | epot = -18.1242672233716 | etot = -13.2825375230564 +541000 ekin = 2.31786635168338 | erot = 2.45130088253407 | epot = -18.0517047573377 | etot = -13.2825375231202 +542000 ekin = 2.23702678132889 | erot = 2.4642388816219 | epot = -17.983803186044 | etot = -13.2825375230932 +543000 ekin = 2.15612181951174 | erot = 2.483136674149 | epot = -17.9217960165952 | etot = -13.2825375229345 +544000 ekin = 2.07836492819822 | erot = 2.50789688708103 | epot = -17.8687993379301 | etot = -13.2825375226508 +545000 ekin = 2.00794258372951 | erot = 2.53918840886296 | epot = -17.8296685148941 | etot = -13.2825375223016 +546000 ekin = 1.94957099412975 | erot = 2.578008196098 | epot = -17.8101167122069 | etot = -13.2825375219791 +547000 ekin = 1.9077624243153 | erot = 2.62501532097517 | epot = -17.8153152670783 | etot = -13.2825375217878 +548000 ekin = 1.88600984710573 | erot = 2.67988146408135 | epot = -17.8484288329841 | etot = -13.282537521797 +549000 ekin = 1.88615242689691 | erot = 2.74090375620349 | epot = -17.909593705124 | etot = -13.2825375220236 +550000 ekin = 1.90811801080135 | erot = 2.80501593005898 | epot = -17.9956714632894 | etot = -13.282537522429 +551000 ekin = 1.95008337623402 | erot = 2.86816804419082 | epot = -18.1007889433658 | etot = -13.2825375229409 +552000 ekin = 2.00893649351174 | erot = 2.92590890426342 | epot = -18.2173829212562 | etot = -13.282537523481 +553000 ekin = 2.08084803911103 | erot = 2.97396311008449 | epot = -18.3373486731828 | etot = -13.2825375239872 +554000 ekin = 2.16178844742615 | erot = 3.00865361313796 | epot = -18.4529795849852 | etot = -13.2825375244211 +555000 ekin = 2.24792031030894 | erot = 3.02713377648476 | epot = -18.5575916115531 | etot = -13.2825375247594 +556000 ekin = 2.3358895304738 | erot = 3.02749801445229 | epot = -18.6459250699077 | etot = -13.2825375249816 +557000 ekin = 2.42273135018697 | erot = 3.00799378133903 | epot = -18.7132626568713 | etot = -13.2825375253453 +558000 ekin = 2.50467530619079 | erot = 2.96457109807151 | epot = -18.7517839296409 | etot = -13.2825375253786 +559000 ekin = 2.57989829547792 | erot = 2.89795083547094 | epot = -18.7603866561117 | etot = -13.2825375251628 +560000 ekin = 2.64819333040997 | erot = 2.8115011418383 | epot = -18.7422319969952 | etot = -13.282537524747 +561000 ekin = 2.71041014716014 | erot = 2.71050571090859 | epot = -18.7034533823107 | etot = -13.282537524242 +562000 ekin = 2.76764108184349 | erot = 2.60142670481719 | epot = -18.6516053104339 | etot = -13.2825375237732 +563000 ekin = 2.82041332178183 | erot = 2.49094539995269 | epot = -18.5938962451522 | etot = -13.2825375234177 +564000 ekin = 2.86835957176528 | erot = 2.38512022706598 | epot = -18.5360173220094 | etot = -13.2825375231781 +565000 ekin = 2.9105055625117 | erot = 2.2888699309895 | epot = -18.4819130165188 | etot = -13.2825375230176 +566000 ekin = 2.9458361953691 | erot = 2.20572382108587 | epot = -18.4340975393717 | etot = -13.2825375229167 +567000 ekin = 2.97364576057443 | erot = 2.13764971279795 | epot = -18.3938329962642 | etot = -13.2825375228919 +568000 ekin = 2.99348659092395 | erot = 2.08490808290625 | epot = -18.3609321968044 | etot = -13.2825375229742 +569000 ekin = 3.00487691648673 | erot = 2.04604350391468 | epot = -18.3334579435673 | etot = -13.2825375231659 +570000 ekin = 3.00710556183365 | erot = 2.01819764938775 | epot = -18.3078407346463 | etot = -13.2825375234249 +571000 ekin = 2.99930468668979 | erot = 1.99774357915448 | epot = -18.2795857895248 | etot = -13.2825375236806 +572000 ekin = 2.98076231240025 | erot = 1.98107714031761 | epot = -18.2443769765725 | etot = -13.2825375238547 +573000 ekin = 2.95134611356941 | erot = 1.96535938854021 | epot = -18.1992430259928 | etot = -13.2825375238832 +574000 ekin = 2.91190615159568 | erot = 1.94906161388935 | epot = -18.1435052892122 | etot = -13.2825375237272 +575000 ekin = 2.86455063786228 | erot = 1.93223482555562 | epot = -18.0793229868005 | etot = -13.2825375233826 +576000 ekin = 2.81270724058511 | erot = 1.91646454101314 | epot = -18.0117093044836 | etot = -13.2825375228853 +577000 ekin = 2.76090536133269 | erot = 1.90450382048591 | epot = -17.9479467041287 | etot = -13.2825375223101 +578000 ekin = 2.71428886863997 | erot = 1.89991544414445 | epot = -17.8967418344493 | etot = -13.2825375216648 +579000 ekin = 2.67747364116322 | erot = 1.90598531717311 | epot = -17.8659964796474 | etot = -13.2825375213111 +580000 ekin = 2.65399321105106 | erot = 1.92422800253716 | epot = -17.8607587347071 | etot = -13.2825375211188 +581000 ekin = 2.64614770794032 | erot = 1.95489680825185 | epot = -17.8835820373323 | etot = -13.2825375211401 +582000 ekin = 2.65445309241879 | erot = 1.99685469221747 | epot = -17.9338453060313 | etot = -13.2825375213951 +583000 ekin = 2.67733631615637 | erot = 2.04763712314961 | epot = -18.0075109611623 | etot = -13.2825375218563 +584000 ekin = 2.71054840612045 | erot = 2.10372916962355 | epot = -18.096815098413 | etot = -13.282537522669 +585000 ekin = 2.7473776369314 | erot = 2.16073411837509 | epot = -18.1906492786902 | etot = -13.2825375233837 +586000 ekin = 2.78137869995175 | erot = 2.21419390101714 | epot = -18.2781101249393 | etot = -13.2825375239704 +587000 ekin = 2.80697388616102 | erot = 2.26053952383221 | epot = -18.3500509343302 | etot = -13.282537524337 +588000 ekin = 2.82026432882546 | erot = 2.29760845660692 | epot = -18.4004103098989 | etot = -13.2825375244665 +589000 ekin = 2.81926713949848 | erot = 2.32471340247678 | epot = -18.4265180663829 | etot = -13.2825375244076 +590000 ekin = 2.80363912226355 | erot = 2.34232144628702 | epot = -18.4284980927864 | etot = -13.2825375242358 +591000 ekin = 2.77414618261205 | erot = 2.35158565793045 | epot = -18.4082693645578 | etot = -13.2825375240153 +592000 ekin = 2.7321416208566 | erot = 2.3539767270547 | epot = -18.3686558716927 | etot = -13.2825375237814 +593000 ekin = 2.67919893320834 | erot = 2.35111989743036 | epot = -18.3128563541844 | etot = -13.2825375235457 +594000 ekin = 2.61691997595324 | erot = 2.34478637080631 | epot = -18.2442438700672 | etot = -13.2825375233077 +595000 ekin = 2.54687226720393 | erot = 2.33692048101831 | epot = -18.1663302712882 | etot = -13.282537523066 +596000 ekin = 2.47060065869688 | erot = 2.32961421032747 | epot = -18.0827523918473 | etot = -13.2825375228229 +597000 ekin = 2.38967001339545 | erot = 2.32500896596326 | epot = -17.9972165019425 | etot = -13.2825375225838 +598000 ekin = 2.30571268105541 | erot = 2.32515834060355 | epot = -17.913408544013 | etot = -13.2825375223541 +599000 ekin = 2.22046028573514 | erot = 2.33189649117281 | epot = -17.8348942990478 | etot = -13.2825375221398 +600000 ekin = 2.13574370513921 | erot = 2.34673734055139 | epot = -17.7650185676378 | etot = -13.2825375219472 +601000 ekin = 2.05345123960456 | erot = 2.37080533027377 | epot = -17.7067940916633 | etot = -13.282537521785 +602000 ekin = 1.97544542075628 | erot = 2.40478648027266 | epot = -17.6627694226918 | etot = -13.2825375216629 +603000 ekin = 1.90345105222632 | erot = 2.44889273151597 | epot = -17.6348813053331 | etot = -13.2825375215908 +604000 ekin = 1.83893895965995 | erot = 2.50284547564257 | epot = -17.6243219568744 | etot = -13.2825375215719 +605000 ekin = 1.78304137675034 | erot = 2.56590806862715 | epot = -17.6314869669817 | etot = -13.2825375216042 +606000 ekin = 1.73651700581096 | erot = 2.63697396076247 | epot = -17.6560284882492 | etot = -13.2825375216757 +607000 ekin = 1.69978182244358 | erot = 2.71471645477294 | epot = -17.6970357989852 | etot = -13.2825375217686 +608000 ekin = 1.67299629761026 | erot = 2.79777529949349 | epot = -17.7533091189676 | etot = -13.2825375218638 +609000 ekin = 1.65617951207475 | erot = 2.88492902620219 | epot = -17.8236460602245 | etot = -13.2825375219476 +610000 ekin = 1.64931072757095 | erot = 2.97519911997342 | epot = -17.9070473695603 | etot = -13.282537522016 +611000 ekin = 1.65238727041245 | erot = 3.06785620888426 | epot = -18.0027810013707 | etot = -13.282537522074 +612000 ekin = 1.66542824850629 | erot = 3.16233835683711 | epot = -18.1103041274766 | etot = -13.2825375221332 +613000 ekin = 1.68843555876185 | erot = 3.25812385015835 | epot = -18.229096931125 | etot = -13.2825375222048 +614000 ekin = 1.72133601897789 | erot = 3.35460405549752 | epot = -18.3584775967737 | etot = -13.2825375222983 +615000 ekin = 1.7639238606995 | erot = 3.45098117154084 | epot = -18.4974425546615 | etot = -13.2825375224212 +616000 ekin = 1.81580855367603 | erot = 3.54618284196742 | epot = -18.6445289182257 | etot = -13.2825375225823 +617000 ekin = 1.87635766459386 | erot = 3.63876572276478 | epot = -18.7976609101535 | etot = -13.2825375227949 +618000 ekin = 1.94461656677602 | erot = 3.72678561689433 | epot = -18.9539397067471 | etot = -13.2825375230768 +619000 ekin = 2.01919440960516 | erot = 3.80764382999315 | epot = -19.1093757630453 | etot = -13.282537523447 +620000 ekin = 2.09812821746402 | erot = 3.87796751070656 | epot = -19.2586332520846 | etot = -13.282537523914 +621000 ekin = 2.17876896466308 | erot = 3.93362434682925 | epot = -19.3949308359561 | etot = -13.2825375244638 +622000 ekin = 2.25776112958401 | erot = 3.96997899351304 | epot = -19.5102776481477 | etot = -13.2825375250507 +623000 ekin = 2.33118920334088 | erot = 3.98244070292824 | epot = -19.5961674318684 | etot = -13.2825375255993 +624000 ekin = 2.39492361725441 | erot = 3.96722578250777 | epot = -19.6446869257843 | etot = -13.2825375260221 +625000 ekin = 2.44512221108716 | erot = 3.9221202536408 | epot = -19.6497799909757 | etot = -13.2825375262478 +626000 ekin = 2.47876984854015 | erot = 3.84697362699248 | epot = -19.6082810017757 | etot = -13.282537526243 +627000 ekin = 2.49411681806274 | erot = 3.74375083232696 | epot = -19.5204051764073 | etot = -13.2825375260176 +628000 ekin = 2.49092177732992 | erot = 3.61617309028914 | epot = -19.3896323932286 | etot = -13.2825375256095 +629000 ekin = 2.47048208798929 | erot = 3.46915451618023 | epot = -19.2221741292344 | etot = -13.2825375250648 +630000 ekin = 2.43548970076025 | erot = 3.30827690339842 | epot = -19.0263041285834 | etot = -13.2825375244248 +631000 ekin = 2.38975949010187 | erot = 3.13944249310663 | epot = -18.8117395069329 | etot = -13.2825375237244 +632000 ekin = 2.33785618710456 | erot = 2.96869689900809 | epot = -18.5890906091134 | etot = -13.2825375230008 +633000 ekin = 2.28462964554081 | erot = 2.80211551079199 | epot = -18.3692826786328 | etot = -13.2825375223 +634000 ekin = 2.2346774623099 | erot = 2.64563252181923 | epot = -18.1628475058086 | etot = -13.2825375216794 +635000 ekin = 2.15322765553028 | erot = 2.4783509433522 | epot = -17.9141161496004 | etot = -13.2825375507179 +636000 ekin = 2.045499081381 | erot = 2.31412508402215 | epot = -17.6421616868316 | etot = -13.2825375214284 +637000 ekin = 2.11104805172142 | erot = 2.29419960724925 | epot = -17.6877852051452 | etot = -13.2825375461745 +638000 ekin = 2.16990019918255 | erot = 2.26795673930499 | epot = -17.720394476478 | etot = -13.2825375379904 +639000 ekin = 2.15825321743049 | erot = 2.17815663921299 | epot = -17.618947382429 | etot = -13.2825375257855 +640000 ekin = 2.18911467639275 | erot = 2.15600946820072 | epot = -17.627661668601 | etot = -13.2825375240076 +641000 ekin = 2.26653815117271 | erot = 2.22106973659358 | epot = -17.7701454239566 | etot = -13.2825375361904 +642000 ekin = 2.31444694707114 | erot = 2.28426426133692 | epot = -17.881248736019 | etot = -13.282537527611 +643000 ekin = 2.32966846048322 | erot = 2.3262511385741 | epot = -17.9384571271816 | etot = -13.2825375281243 +644000 ekin = 2.33971908597949 | erot = 2.36941556707019 | epot = -17.9916721815437 | etot = -13.2825375284941 +645000 ekin = 2.34497836829283 | erot = 2.40804261243074 | epot = -18.0355585093822 | etot = -13.2825375286587 +646000 ekin = 2.34716147904814 | erot = 2.43809135035135 | epot = -18.0677903580053 | etot = -13.2825375286058 +647000 ekin = 2.3490135196742 | erot = 2.45765540462488 | epot = -18.0892064526769 | etot = -13.2825375283778 +648000 ekin = 2.35429037946817 | erot = 2.46814608860667 | epot = -18.1049739961949 | etot = -13.28253752812 +649000 ekin = 2.36637490458858 | erot = 2.47306901786727 | epot = -18.1219814504981 | etot = -13.2825375280423 +650000 ekin = 2.38594651005796 | erot = 2.47280388226564 | epot = -18.1412879203047 | etot = -13.2825375279811 +651000 ekin = 2.4129073237406 | erot = 2.4679750054794 | epot = -18.163419857161 | etot = -13.282537527941 +652000 ekin = 2.44657292389676 | erot = 2.45942209560756 | epot = -18.1885325474125 | etot = -13.2825375279081 +653000 ekin = 2.48591189111066 | erot = 2.44818643115487 | epot = -18.2166358501265 | etot = -13.282537527861 +654000 ekin = 2.52980786333011 | erot = 2.43558904341108 | epot = -18.2479344345246 | etot = -13.2825375277834 +655000 ekin = 2.57725720727345 | erot = 2.42329690324718 | epot = -18.2830916381947 | etot = -13.2825375276741 +656000 ekin = 2.62745567851939 | erot = 2.41329334478414 | epot = -18.3232865508506 | etot = -13.2825375275471 +657000 ekin = 2.67977157718863 | erot = 2.40771681171411 | epot = -18.3700259163334 | etot = -13.2825375274306 +658000 ekin = 2.73363379212944 | erot = 2.40858022047282 | epot = -18.4247515399622 | etot = -13.2825375273599 +659000 ekin = 2.78837854445156 | erot = 2.41741767313059 | epot = -18.4883337449508 | etot = -13.2825375273687 +660000 ekin = 2.8431453631021 | erot = 2.43497153575953 | epot = -18.5606544262937 | etot = -13.282537527432 +661000 ekin = 2.89550751705154 | erot = 2.46002725134826 | epot = -18.6380722964866 | etot = -13.2825375280868 +662000 ekin = 2.93874528639294 | erot = 2.48685588449209 | epot = -18.708138699583 | etot = -13.282537528698 +663000 ekin = 2.96871719420213 | erot = 2.51022783061785 | epot = -18.7614825540622 | etot = -13.2825375292422 +664000 ekin = 2.98246138426592 | erot = 2.52516926728115 | epot = -18.7901681811315 | etot = -13.2825375295844 +665000 ekin = 2.97884445496409 | erot = 2.52787955702933 | epot = -18.7892615416111 | etot = -13.2825375296177 +666000 ekin = 2.95920183358837 | erot = 2.5166150843606 | epot = -18.7583544472577 | etot = -13.2825375293087 +667000 ekin = 2.92742550364064 | erot = 2.49210329863614 | epot = -18.7020663309941 | etot = -13.2825375287173 +668000 ekin = 2.88934250727334 | erot = 2.45736670758744 | epot = -18.6292467428357 | etot = -13.2825375279749 +669000 ekin = 2.85155010055246 | erot = 2.41708074188009 | epot = -18.5511683696627 | etot = -13.2825375272301 +670000 ekin = 2.82014314483841 | erot = 2.37673699564913 | epot = -18.4794176670842 | etot = -13.2825375265966 +671000 ekin = 2.79977472973266 | erot = 2.34183940288387 | epot = -18.4241516588856 | etot = -13.2825375262691 +672000 ekin = 2.7929325264564 | erot = 2.3169522602719 | epot = -18.3924223127253 | etot = -13.282537525997 +673000 ekin = 2.80034442418812 | erot = 2.30554472221923 | epot = -18.3884266723436 | etot = -13.2825375259362 +674000 ekin = 2.82129825266147 | erot = 2.30955451996833 | epot = -18.4133902987243 | etot = -13.2825375260945 +675000 ekin = 2.85361934154458 | erot = 2.32878748983352 | epot = -18.4649443578395 | etot = -13.2825375264614 +676000 ekin = 2.89394925003076 | erot = 2.36084337721496 | epot = -18.5373301542345 | etot = -13.2825375269888 +677000 ekin = 2.93819888444081 | erot = 2.40146056818827 | epot = -18.6221969802158 | etot = -13.2825375275867 +678000 ekin = 2.98219881053812 | erot = 2.44527797803552 | epot = -18.7100143167158 | etot = -13.2825375281422 +679000 ekin = 3.02242735526952 | erot = 2.48684948039664 | epot = -18.7918143642177 | etot = -13.2825375285515 +680000 ekin = 3.05660821688331 | erot = 2.52163649392475 | epot = -18.860782239561 | etot = -13.282537528753 +681000 ekin = 3.08399348193173 | erot = 2.54671087872184 | epot = -18.913241889389 | etot = -13.2825375287354 +682000 ekin = 3.10527370313695 | erot = 2.56103519422108 | epot = -18.9488464258989 | etot = -13.2825375285409 +683000 ekin = 3.12217420792303 | erot = 2.5653012869435 | epot = -18.9700130231063 | etot = -13.2825375282397 +684000 ekin = 3.13689854385765 | erot = 2.56147023269689 | epot = -18.9809063044635 | etot = -13.282537527909 +685000 ekin = 3.15161752084921 | erot = 2.55220833209368 | epot = -18.9863633805374 | etot = -13.2825375275945 +686000 ekin = 3.16825656296352 | erot = 2.54047141966045 | epot = -18.9912655100342 | etot = -13.2825375274102 +687000 ekin = 3.18756268905896 | erot = 2.5286150857463 | epot = -18.9987153021306 | etot = -13.2825375273253 +688000 ekin = 3.20935294731744 | erot = 2.51834078650268 | epot = -19.010231261173 | etot = -13.2825375273529 +689000 ekin = 3.23260385768977 | erot = 2.51058529366538 | epot = -19.0257266788501 | etot = -13.2825375274949 +690000 ekin = 3.25550449418191 | erot = 2.50541094761942 | epot = -19.0434529695448 | etot = -13.2825375277435 +691000 ekin = 3.27559454465419 | erot = 2.50196131508042 | epot = -19.0600933878108 | etot = -13.2825375280762 +692000 ekin = 3.29000453531072 | erot = 2.49851988080605 | epot = -19.0710619445671 | etot = -13.2825375284504 +693000 ekin = 3.29579865375948 | erot = 2.4927397485969 | epot = -19.0710759311631 | etot = -13.2825375288067 +694000 ekin = 3.290367420064 | erot = 2.48207188558618 | epot = -19.0549768347317 | etot = -13.2825375290815 +695000 ekin = 3.27176421099226 | erot = 2.46431581834491 | epot = -19.0186175585658 | etot = -13.2825375292286 +696000 ekin = 3.23887890264527 | erot = 2.43812365839389 | epot = -18.9595400902738 | etot = -13.2825375292346 +697000 ekin = 3.19141377365438 | erot = 2.40329594557291 | epot = -18.8772472483422 | etot = -13.2825375291149 +698000 ekin = 3.12971664160265 | erot = 2.3607993405226 | epot = -18.7730535110309 | etot = -13.2825375289056 +699000 ekin = 3.05458980607575 | erot = 2.31258576051436 | epot = -18.6497130952223 | etot = -13.2825375286322 +700000 ekin = 2.96718102277338 | erot = 2.26139197222678 | epot = -18.5111105233092 | etot = -13.282537528309 +701000 ekin = 2.86896613270987 | erot = 2.21057215475942 | epot = -18.3620758154114 | etot = -13.2825375279421 +702000 ekin = 2.76178671310755 | erot = 2.16397434370647 | epot = -18.2082985843512 | etot = -13.2825375275372 +703000 ekin = 2.64787120281757 | erot = 2.12574771765488 | epot = -18.0561564514672 | etot = -13.2825375309947 +704000 ekin = 2.52933762816201 | erot = 2.08674637167894 | epot = -17.8986215285157 | etot = -13.2825375286748 +705000 ekin = 2.41679696488455 | erot = 2.0566401236899 | epot = -17.7559746148443 | etot = -13.2825375262699 +706000 ekin = 2.30501007301267 | erot = 2.06115876579317 | epot = -17.6487063632602 | etot = -13.2825375244543 +707000 ekin = 2.19269241312063 | erot = 2.11375046401179 | epot = -17.5889804017709 | etot = -13.2825375246385 +708000 ekin = 2.09960598295589 | erot = 2.19681319913428 | epot = -17.5789567090833 | etot = -13.2825375269932 +709000 ekin = 2.01320280572636 | erot = 2.28016876669421 | epot = -17.5759090978068 | etot = -13.2825375253862 +710000 ekin = 1.93302644378252 | erot = 2.3747322880584 | epot = -17.5902962577935 | etot = -13.2825375259526 +711000 ekin = 1.85957279021245 | erot = 2.47358324949964 | epot = -17.6156935663468 | etot = -13.2825375266347 +712000 ekin = 1.79282630225992 | erot = 2.56690430163368 | epot = -17.6422681311821 | etot = -13.2825375272885 +713000 ekin = 1.73341814837551 | erot = 2.64462400363359 | epot = -17.660579679756 | etot = -13.2825375277469 +714000 ekin = 1.68328438218602 | erot = 2.6981736471422 | epot = -17.6639955572078 | etot = -13.2825375278795 +715000 ekin = 1.64594117620278 | erot = 2.72207244137003 | epot = -17.6505511452259 | etot = -13.2825375276531 +716000 ekin = 1.62610172677928 | erot = 2.71479815184846 | epot = -17.6234374057783 | etot = -13.2825375271506 +717000 ekin = 1.62864489608611 | erot = 2.67867233654835 | epot = -17.5898547591674 | etot = -13.2825375265329 +718000 ekin = 1.65730138294327 | erot = 2.6189183930066 | epot = -17.5587573019149 | etot = -13.282537525965 +719000 ekin = 1.71360335043978 | erot = 2.54235654261391 | epot = -17.5384974186061 | etot = -13.2825375255524 +720000 ekin = 1.79650653895858 | erot = 2.45621436721656 | epot = -17.5352584314959 | etot = -13.2825375253208 +721000 ekin = 1.90273489837533 | erot = 2.36731439674759 | epot = -17.5525868203611 | etot = -13.2825375252382 +722000 ekin = 2.02756635859999 | erot = 2.28163864623686 | epot = -17.5917425300939 | etot = -13.2825375252571 +723000 ekin = 2.16566245404416 | erot = 2.20411346317412 | epot = -17.6523134425647 | etot = -13.2825375253464 +724000 ekin = 2.31164907954197 | erot = 2.13844446421075 | epot = -17.7326310692571 | etot = -13.2825375255043 +725000 ekin = 2.46036017261476 | erot = 2.0869120442021 | epot = -17.8298097425667 | etot = -13.2825375257498 +726000 ekin = 2.6068349632846 | erot = 2.05013619410202 | epot = -17.9395086834918 | etot = -13.2825375261052 +727000 ekin = 2.74622028370769 | erot = 2.02690424048558 | epot = -18.0556620507673 | etot = -13.2825375265741 +728000 ekin = 2.87374866232265 | erot = 2.01419303060157 | epot = -18.1704792200511 | etot = -13.2825375271269 +729000 ekin = 2.98490085153144 | erot = 2.00751009684072 | epot = -18.2749484760646 | etot = -13.2825375276924 +730000 ekin = 3.07576690645469 | erot = 2.00160558057494 | epot = -18.3599100152017 | etot = -13.2825375281721 +731000 ekin = 3.14351022556136 | erot = 1.99146923005515 | epot = -18.4175169840844 | etot = -13.2825375284679 +732000 ekin = 3.18676307270908 | erot = 1.9733775068131 | epot = -18.4426781080378 | etot = -13.2825375285156 +733000 ekin = 3.20579220143817 | erot = 1.94568706577985 | epot = -18.4340167955229 | etot = -13.2825375283049 +734000 ekin = 3.20238921808403 | erot = 1.9091725140226 | epot = -18.3940992599778 | etot = -13.2825375278711 +735000 ekin = 3.17951096478395 | erot = 1.86680153214189 | epot = -18.3288500242332 | etot = -13.2825375273073 +736000 ekin = 3.1407386539016 | erot = 1.82300587571906 | epot = -18.2462820563141 | etot = -13.2825375266935 +737000 ekin = 3.08984658439833 | erot = 1.78292392999538 | epot = -18.1553080405002 | etot = -13.2825375261065 +738000 ekin = 3.03043228105068 | erot = 1.7516193492114 | epot = -18.0645891558627 | etot = -13.2825375256006 +739000 ekin = 2.96566842761532 | erot = 1.73346651074128 | epot = -17.9816724635652 | etot = -13.2825375252086 +740000 ekin = 2.89817088990248 | erot = 1.73175552827542 | epot = -17.9124639431193 | etot = -13.2825375249414 +741000 ekin = 2.82995232215527 | erot = 1.74850528578322 | epot = -17.8609951327411 | etot = -13.2825375248026 +742000 ekin = 2.76247533975977 | erot = 1.78434362324901 | epot = -17.8293564878077 | etot = -13.2825375247989 +743000 ekin = 2.69668176522496 | erot = 1.83847103615502 | epot = -17.8176903262763 | etot = -13.2825375248963 +744000 ekin = 2.63311444617166 | erot = 1.90875045497562 | epot = -17.8244024262527 | etot = -13.2825375251054 +745000 ekin = 2.57196493518836 | erot = 1.99171779916653 | epot = -17.8462202597747 | etot = -13.2825375254198 +746000 ekin = 2.5131159615418 | erot = 2.08264215541026 | epot = -17.8782956427778 | etot = -13.2825375258257 +747000 ekin = 2.4562102402775 | erot = 2.17571767167211 | epot = -17.9144654382424 | etot = -13.2825375262928 +748000 ekin = 2.4007641204688 | erot = 2.2644524277425 | epot = -17.9477540749797 | etot = -13.2825375267684 +749000 ekin = 2.34635697391007 | erot = 2.34231237519854 | epot = -17.9712068762851 | etot = -13.2825375271765 +750000 ekin = 2.29290375451717 | erot = 2.40359513791455 | epot = -17.979036419863 | etot = -13.2825375274312 +751000 ekin = 2.24097207238015 | erot = 2.44437862762129 | epot = -17.9678882274625 | etot = -13.2825375274611 +752000 ekin = 2.19206377657606 | erot = 2.46328788077229 | epot = -17.937889184575 | etot = -13.2825375272267 +753000 ekin = 2.0191073671841 | erot = 2.37844688220293 | epot = -17.6800917192494 | etot = -13.2825374698623 +754000 ekin = 2.03397419691681 | erot = 2.38379927449377 | epot = -17.7003109683856 | etot = -13.282537496975 +755000 ekin = 2.10287082567493 | erot = 2.42269050483285 | epot = -17.8080987746467 | etot = -13.2825374441389 +756000 ekin = 2.09556625439565 | erot = 2.405750962181 | epot = -17.7838546600866 | etot = -13.2825374435099 +757000 ekin = 2.11013463581362 | erot = 2.39174642164209 | epot = -17.7844185004694 | etot = -13.2825374430137 +758000 ekin = 2.14991880579705 | erot = 2.38537981437436 | epot = -17.8178360628955 | etot = -13.2825374427241 +759000 ekin = 2.21691275063063 | erot = 2.38948785825167 | epot = -17.8889380515667 | etot = -13.2825374426844 +760000 ekin = 2.31141054860375 | erot = 2.40468264900161 | epot = -17.9986306405271 | etot = -13.2825374429218 +761000 ekin = 2.4317547235321 | erot = 2.42917556854271 | epot = -18.14346773552 | etot = -13.2825374434452 +762000 ekin = 2.57423243233675 | erot = 2.45878794777349 | epot = -18.3155578243444 | etot = -13.2825374442342 +763000 ekin = 2.73317609318437 | erot = 2.48721280711223 | epot = -18.5029263455259 | etot = -13.2825374452293 +764000 ekin = 2.90131643265847 | erot = 2.50663479921391 | epot = -18.6904886781953 | etot = -13.2825374463229 +765000 ekin = 3.07040159501002 | erot = 2.50879317398454 | epot = -18.8617322163581 | etot = -13.2825374473636 +766000 ekin = 3.23203070978082 | erot = 2.48644536574614 | epot = -19.0010135237083 | etot = -13.2825374481813 +767000 ekin = 3.37856609433327 | erot = 2.43498274045147 | epot = -19.096086283418 | etot = -13.2825374486333 +768000 ekin = 3.50392633253189 | erot = 2.35374465438907 | epot = -19.14020843557 | etot = -13.282537448649 +769000 ekin = 3.60408079934929 | erot = 2.2465665844398 | epot = -19.1331848320412 | etot = -13.2825374482521 +770000 ekin = 3.67731902040089 | erot = 2.12129310034524 | epot = -19.0811495682864 | etot = -13.2825374475402 +771000 ekin = 3.7250046645363 | erot = 1.98803923032005 | epot = -18.9955813415612 | etot = -13.2825374467049 +772000 ekin = 3.73784328843035 | erot = 1.84847100678562 | epot = -18.8688517433746 | etot = -13.2825374481586 +773000 ekin = 3.73518377757204 | erot = 1.74399251359463 | epot = -18.7617137365844 | etot = -13.2825374454177 +774000 ekin = 3.73326270308357 | erot = 1.69319142531066 | epot = -18.7089915825401 | etot = -13.2825374541459 +775000 ekin = 3.70600760956875 | erot = 1.65662399761182 | epot = -18.6451690552018 | etot = -13.2825374480212 +776000 ekin = 3.66620955944038 | erot = 1.65229490513874 | epot = -18.6010419124108 | etot = -13.2825374478317 +777000 ekin = 3.6164959066655 | erot = 1.68124406400525 | epot = -18.5802774185067 | etot = -13.2825374478359 +778000 ekin = 3.5589217195722 | erot = 1.74156460645431 | epot = -18.5830237740648 | etot = -13.2825374480383 +779000 ekin = 3.49505249793887 | erot = 1.82861083484593 | epot = -18.6062007816394 | etot = -13.2825374488546 +780000 ekin = 3.4260605289351 | erot = 1.93200454544541 | epot = -18.6406025240164 | etot = -13.2825374496359 +781000 ekin = 3.35141348649702 | erot = 2.04005284529073 | epot = -18.6740037822594 | etot = -13.2825374504716 +782000 ekin = 3.27002343600189 | erot = 2.14152553689654 | epot = -18.6940864240875 | etot = -13.2825374511891 +783000 ekin = 3.18141085606315 | erot = 2.22636120778713 | epot = -18.6903095154617 | etot = -13.2825374516114 +784000 ekin = 3.08656488448361 | erot = 2.28735807323151 | epot = -18.6564604093344 | etot = -13.2825374516193 +785000 ekin = 2.98843913984933 | erot = 2.32136711553602 | epot = -18.592343706592 | etot = -13.2825374512067 +786000 ekin = 2.89178850735618 | erot = 2.32954149828313 | epot = -18.5038674561269 | etot = -13.2825374504876 +787000 ekin = 2.80233070714568 | erot = 2.31656731743012 | epot = -18.4014354742217 | etot = -13.2825374496459 +788000 ekin = 2.72556137455006 | erot = 2.28924565768276 | epot = -18.2973444810906 | etot = -13.2825374488578 +789000 ekin = 2.66569850120894 | erot = 2.25498711353627 | epot = -18.2032230629877 | etot = -13.2825374482425 +790000 ekin = 2.62507547495403 | erot = 2.22062577794997 | epot = -18.1282387007584 | etot = -13.2825374478544 +791000 ekin = 2.60400664845757 | erot = 2.19166523695208 | epot = -18.0782093331145 | etot = -13.2825374477048 +792000 ekin = 2.60095165826993 | erot = 2.17186849883267 | epot = -18.0553576048892 | etot = -13.2825374477866 +793000 ekin = 2.61278727136947 | erot = 2.1630579475058 | epot = -18.0583826669628 | etot = -13.2825374480875 +794000 ekin = 2.63509078750899 | erot = 2.16503786010594 | epot = -18.0826660962031 | etot = -13.2825374485882 +795000 ekin = 2.66245645496094 | erot = 2.17562900151097 | epot = -18.1206229057215 | etot = -13.2825374492496 +796000 ekin = 2.68895951797515 | erot = 2.19088748039119 | epot = -18.1623844483558 | etot = -13.2825374499895 +797000 ekin = 2.70892452636473 | erot = 2.20564060882902 | epot = -18.197102585859 | etot = -13.2825374506652 +798000 ekin = 2.7187387406754 | erot = 2.21455364300775 | epot = -18.2158298332747 | etot = -13.2825374495916 +799000 ekin = 2.70000300099405 | erot = 2.21050545408876 | epot = -18.193045904985 | etot = -13.2825374499022 +800000 ekin = 2.65392049001821 | erot = 2.17300546938151 | epot = -18.109463378289 | etot = -13.2825374188892 +801000 ekin = 2.82505345096871 | erot = 2.13616134701489 | epot = -18.2437522525054 | etot = -13.2825374545218 +802000 ekin = 2.90470228802172 | erot = 2.10953657449614 | epot = -18.2967762799053 | etot = -13.2825374173874 +803000 ekin = 2.9677525986453 | erot = 2.08137573444383 | epot = -18.3316657512964 | etot = -13.2825374182072 +804000 ekin = 3.01419864036155 | erot = 2.05336319939514 | epot = -18.3500992581057 | etot = -13.282537418349 +805000 ekin = 3.03950260682403 | erot = 2.02738087474037 | epot = -18.3494208999164 | etot = -13.282537418352 +806000 ekin = 3.04147612212525 | erot = 2.00524180108709 | epot = -18.3292553414124 | etot = -13.2825374182001 +807000 ekin = 3.02009152418646 | erot = 1.98876425940777 | epot = -18.2913932015099 | etot = -13.2825374179157 +808000 ekin = 2.97716861905469 | erot = 1.9797928070483 | epot = -18.2394988436566 | etot = -13.2825374175536 +809000 ekin = 2.91576405317411 | erot = 1.98007542202132 | epot = -18.1783768923745 | etot = -13.282537417179 +810000 ekin = 2.83951999241211 | erot = 1.9910201414007 | epot = -18.1130775506578 | etot = -13.282537416845 +811000 ekin = 2.75216924413256 | erot = 2.01344070631007 | epot = -18.0481473670229 | etot = -13.2825374165802 +812000 ekin = 2.65727213949033 | erot = 2.04739495870437 | epot = -17.9872045145838 | etot = -13.2825374163891 +813000 ekin = 2.55815480063288 | erot = 2.0921579466292 | epot = -17.9328501635216 | etot = -13.2825374162596 +814000 ekin = 2.45796623947603 | erot = 2.14630993528002 | epot = -17.8868135909302 | etot = -13.2825374161741 +815000 ekin = 2.35976627429823 | erot = 2.20788718833984 | epot = -17.8501908787554 | etot = -13.2825374161174 +816000 ekin = 2.26657575180629 | erot = 2.27454135561794 | epot = -17.8236545235058 | etot = -13.2825374160815 +817000 ekin = 2.18134946662811 | erot = 2.34367133400565 | epot = -17.807558216702 | etot = -13.2825374160682 +818000 ekin = 2.10686415591836 | erot = 2.41251844102779 | epot = -17.8019200130316 | etot = -13.2825374160855 +819000 ekin = 2.04554497258418 | erot = 2.47824070162555 | epot = -17.806323090351 | etot = -13.2825374161413 +820000 ekin = 1.99927680295696 | erot = 2.53799486378974 | epot = -17.8198090829855 | etot = -13.2825374162388 +821000 ekin = 1.9692530805303 | erot = 2.58905270210877 | epot = -17.8408431990125 | etot = -13.2825374163734 +822000 ekin = 1.95590272174924 | erot = 2.62895986938386 | epot = -17.8674000076635 | etot = -13.2825374165304 +823000 ekin = 1.95890926788755 | erot = 2.6557286058008 | epot = -17.8971752903778 | etot = -13.2825374166894 +824000 ekin = 1.97731046162633 | erot = 2.66804286128345 | epot = -17.9278907397372 | etot = -13.2825374168275 +825000 ekin = 2.00964945342457 | erot = 2.66544750451175 | epot = -17.9576343748594 | etot = -13.2825374169231 +826000 ekin = 2.05414423139186 | erot = 2.64849047550104 | epot = -17.985172123854 | etot = -13.2825374169611 +827000 ekin = 2.10884212199665 | erot = 2.61877894485958 | epot = -18.0101584837945 | etot = -13.2825374169382 +828000 ekin = 2.1717293569375 | erot = 2.57890618314315 | epot = -18.0331729569469 | etot = -13.2825374168662 +829000 ekin = 2.24077304847179 | erot = 2.53221651091816 | epot = -18.0555269761626 | etot = -13.2825374167726 +830000 ekin = 2.31389012743404 | erot = 2.4824115756111 | epot = -18.0788391197418 | etot = -13.2825374166967 +831000 ekin = 2.38886546542343 | erot = 2.43305573494131 | epot = -18.1044586170416 | etot = -13.2825374166768 +832000 ekin = 2.4632691578231 | erot = 2.3870870487244 | epot = -18.1328936232866 | etot = -13.2825374167391 +833000 ekin = 2.5344365632194 | erot = 2.34645691813147 | epot = -18.1634308982373 | etot = -13.2825374168864 +834000 ekin = 2.59956439019907 | erot = 2.31199374777391 | epot = -18.1940955550686 | etot = -13.2825374170956 +835000 ekin = 2.65594315943653 | erot = 2.28352232821168 | epot = -18.2220029049695 | etot = -13.2825374173213 +836000 ekin = 2.70130042683167 | erot = 2.26019210697788 | epot = -18.244029951319 | etot = -13.2825374175095 +837000 ekin = 2.73418787962871 | erot = 2.24090836893314 | epot = -18.2576336661722 | etot = -13.2825374176104 +838000 ekin = 2.75431729342696 | erot = 2.22474076288568 | epot = -18.2615954739057 | etot = -13.2825374175931 +839000 ekin = 2.76274241629131 | erot = 2.21121141093012 | epot = -18.256491244675 | etot = -13.2825374174536 +840000 ekin = 2.76179432989972 | erot = 2.20041723303662 | epot = -18.2447489801545 | etot = -13.2825374172182 +841000 ekin = 2.75470877518085 | erot = 2.19297958495076 | epot = -18.2302257770756 | etot = -13.2825374169439 +842000 ekin = 2.74495192528053 | erot = 2.18982916449433 | epot = -18.2173185064846 | etot = -13.2825374167098 +843000 ekin = 2.73536701846579 | erot = 2.19185320024881 | epot = -18.2097576353086 | etot = -13.282537416594 +844000 ekin = 2.72739699349177 | erot = 2.1994851694244 | epot = -18.2094195795621 | etot = -13.2825374166459 +845000 ekin = 2.7206968024524 | erot = 2.21238342751528 | epot = -18.2156176468218 | etot = -13.2825374168541 +846000 ekin = 2.71335246036253 | erot = 2.22935500856137 | epot = -18.2252448860709 | etot = -13.282537417147 +847000 ekin = 2.70267547916117 | erot = 2.24859000373239 | epot = -18.2338029003123 | etot = -13.2825374174188 +848000 ekin = 2.68627675195779 | erot = 2.26812231144288 | epot = -18.236936480973 | etot = -13.2825374175723 +849000 ekin = 2.66300406671244 | erot = 2.2863229263121 | epot = -18.2318644105805 | etot = -13.282537417556 +850000 ekin = 2.63341305523148 | erot = 2.30223029747857 | epot = -18.2181807700874 | etot = -13.2825374173774 +851000 ekin = 2.59966043365591 | erot = 2.3156167587262 | epot = -18.1978146094748 | etot = -13.2825374170927 +852000 ekin = 2.56493307993571 | erot = 2.32681510713484 | epot = -18.1742856038479 | etot = -13.2825374167774 +853000 ekin = 2.53268459155754 | erot = 2.33642702138572 | epot = -18.1516490294471 | etot = -13.2825374165038 +854000 ekin = 2.50591352797944 | erot = 2.34503055123976 | epot = -18.1334814955374 | etot = -13.2825374163182 +855000 ekin = 2.4866740476675 | erot = 2.35297873120409 | epot = -18.1221901951049 | etot = -13.2825374162333 +856000 ekin = 2.47592780860343 | erot = 2.36034202539965 | epot = -18.1188072502362 | etot = -13.2825374162331 +857000 ekin = 2.47367803510516 | erot = 2.36697109794411 | epot = -18.1231865493438 | etot = -13.2825374162946 +858000 ekin = 2.47922391681366 | erot = 2.37260088210265 | epot = -18.1343622152926 | etot = -13.2825374163763 +859000 ekin = 2.49150776870147 | erot = 2.37701215984104 | epot = -18.1510573449986 | etot = -13.282537416456 +860000 ekin = 2.50937686784747 | erot = 2.38013993594023 | epot = -18.1720542203101 | etot = -13.2825374165224 +861000 ekin = 2.53170635996116 | erot = 2.38211817150425 | epot = -18.1963619480387 | etot = -13.2825374165732 +862000 ekin = 2.55742566626407 | erot = 2.38328933264109 | epot = -18.2232524155165 | etot = -13.2825374166114 +863000 ekin = 2.58549483187838 | erot = 2.38419488482973 | epot = -18.252227133347 | etot = -13.2825374166389 +864000 ekin = 2.61488041066499 | erot = 2.38555368834993 | epot = -18.2829715156728 | etot = -13.2825374166579 +865000 ekin = 2.64455846347095 | erot = 2.38821849192421 | epot = -18.3153143720654 | etot = -13.2825374166702 +866000 ekin = 2.67354800424437 | erot = 2.39309523344314 | epot = -18.3491806543665 | etot = -13.282537416679 +867000 ekin = 2.70096216988177 | erot = 2.40101926554071 | epot = -18.3845188521138 | etot = -13.2825374166913 +868000 ekin = 2.72584498338572 | erot = 2.41260829074957 | epot = -18.420990690944 | etot = -13.2825374168087 +869000 ekin = 2.74685098606623 | erot = 2.42808376653873 | epot = -18.4574721694777 | etot = -13.2825374168728 +870000 ekin = 2.76334516398283 | erot = 2.44707202879413 | epot = -18.4929546097441 | etot = -13.2825374169672 +871000 ekin = 2.77488977710316 | erot = 2.46856883163597 | epot = -18.5259960258323 | etot = -13.2825374170932 +872000 ekin = 2.7811573123189 | erot = 2.49101078851438 | epot = -18.5547055180778 | etot = -13.2825374172445 +873000 ekin = 2.78190152502928 | erot = 2.51241399879738 | epot = -18.5768529412309 | etot = -13.2825374174043 +874000 ekin = 2.77696693725528 | erot = 2.53063897161364 | epot = -18.5901433264131 | etot = -13.2825374175441 +875000 ekin = 2.76636320213146 | erot = 2.54374754436265 | epot = -18.5926481641224 | etot = -13.2825374176283 +876000 ekin = 2.7504069828229 | erot = 2.55039472310231 | epot = -18.5833391235459 | etot = -13.2825374176207 +877000 ekin = 2.72989722810813 | erot = 2.55017286557422 | epot = -18.5626075111784 | etot = -13.2825374174961 +878000 ekin = 2.70625700294355 | erot = 2.54382115071376 | epot = -18.5326155709077 | etot = -13.2825374172503 +879000 ekin = 2.68156506653427 | erot = 2.5332421351554 | epot = -18.4973446185932 | etot = -13.2825374169036 +880000 ekin = 2.65843100554442 | erot = 2.52132216836891 | epot = -18.4622905904093 | etot = -13.282537416496 +881000 ekin = 2.63972432922979 | erot = 2.51160592366972 | epot = -18.4338676689779 | etot = -13.2825374160784 +882000 ekin = 2.62822235403347 | erot = 2.50790034454678 | epot = -18.4186601142802 | etot = -13.2825374157 +883000 ekin = 2.62626662137136 | erot = 2.51387422299541 | epot = -18.4226782597687 | etot = -13.2825374154019 +884000 ekin = 2.63550251772652 | erot = 2.53269090787765 | epot = -18.4507308408175 | etot = -13.2825374152133 +885000 ekin = 2.65673814855014 | erot = 2.56668643457077 | epot = -18.5059619982733 | etot = -13.2825374151524 +886000 ekin = 2.68991717237218 | erot = 2.61709354768266 | epot = -18.5895481352837 | etot = -13.2825374152289 +887000 ekin = 2.734175532827 | erot = 2.68381522130244 | epot = -18.700528169575 | etot = -13.2825374154455 +888000 ekin = 2.78795008719356 | erot = 2.76526591136903 | epot = -18.8357534143588 | etot = -13.2825374157962 +889000 ekin = 2.8491201813508 | erot = 2.85831710930318 | epot = -18.989974706918 | etot = -13.282537416264 +890000 ekin = 2.91517691868807 | erot = 2.95839462643955 | epot = -19.1561089619448 | etot = -13.2825374168172 +891000 ekin = 2.98341767192295 | erot = 3.0597676506775 | epot = -19.3257227400102 | etot = -13.2825374174098 +892000 ekin = 3.05115351644501 | erot = 3.15603968258129 | epot = -19.4897306170114 | etot = -13.2825374179851 +893000 ekin = 3.11590367361418 | erot = 3.24080526805507 | epot = -19.6392463601538 | etot = -13.2825374184846 +894000 ekin = 3.17554453075818 | erot = 3.30838805788589 | epot = -19.7664700075009 | etot = -13.2825374188568 +895000 ekin = 3.22839008561766 | erot = 3.35454380060236 | epot = -19.8654713052867 | etot = -13.2825374190666 +896000 ekin = 3.27319975165836 | erot = 3.37700709394957 | epot = -19.9327442647079 | etot = -13.2825374191 +897000 ekin = 3.30912548499472 | erot = 3.37578332995761 | epot = -19.9674462339186 | etot = -13.2825374189663 +898000 ekin = 3.33561719415195 | erot = 3.35313099566656 | epot = -19.9712856085154 | etot = -13.2825374186968 +899000 ekin = 3.3523031028265 | erot = 3.31323476596136 | epot = -19.9480752871285 | etot = -13.2825374183407 +900000 ekin = 3.35886034531518 | erot = 3.26162723064569 | epot = -19.9030249939161 | etot = -13.2825374179552 +901000 ekin = 3.35489762759567 | erot = 3.2044644832284 | epot = -19.8418995284194 | etot = -13.2825374175953 +902000 ekin = 3.33988398839342 | erot = 3.14778460407791 | epot = -19.7702060097741 | etot = -13.2825374173028 +903000 ekin = 3.31316641909532 | erot = 3.09687096103035 | epot = -19.6925747972223 | etot = -13.2825374170966 +904000 ekin = 3.27411465419852 | erot = 3.05580881217869 | epot = -19.6124608833472 | etot = -13.2825374169699 +905000 ekin = 3.22240761869358 | erot = 3.02727711490202 | epot = -19.5322221504879 | etot = -13.2825374168923 +906000 ekin = 3.15843123363071 | erot = 3.01257047164431 | epot = -19.4535391220934 | etot = -13.2825374168184 +907000 ekin = 3.08369713046712 | erot = 3.01180553644323 | epot = -19.3780400836148 | etot = -13.2825374167044 +908000 ekin = 3.00113487352882 | erot = 3.02423547646297 | epot = -19.3079077665171 | etot = -13.2825374165253 +909000 ekin = 2.91509126964 | erot = 3.04858097597399 | epot = -19.246209661904 | etot = -13.28253741629 +910000 ekin = 2.83091809249006 | erot = 3.08328866196603 | epot = -19.1967441705011 | etot = -13.282537416045 +911000 ekin = 2.75416042802549 | erot = 3.12665661766781 | epot = -19.1633544615573 | etot = -13.282537415864 +912000 ekin = 2.68982240197673 | erot = 3.17670303509253 | epot = -19.1490628528293 | etot = -13.2825374157601 +913000 ekin = 2.64026279480142 | erot = 3.23106967171228 | epot = -19.1538698824696 | etot = -13.2825374159559 +914000 ekin = 2.60494541586834 | erot = 3.28757760350067 | epot = -19.1750604355173 | etot = -13.2825374161483 +915000 ekin = 2.58331294380949 | erot = 3.34356245576663 | epot = -19.2094128163232 | etot = -13.282537416747 +916000 ekin = 2.572225278094 | erot = 3.39542630003117 | epot = -19.250188995406 | etot = -13.2825374172809 +917000 ekin = 2.56717380000648 | erot = 3.43991413165374 | epot = -19.2896253494389 | etot = -13.2825374177786 +918000 ekin = 2.56366862414259 | erot = 3.47431911369141 | epot = -19.3205251559853 | etot = -13.2825374181513 +919000 ekin = 2.55808580528835 | erot = 3.4968825160616 | epot = -19.337505739687 | etot = -13.2825374183371 +920000 ekin = 2.54828083604877 | erot = 3.50706786620944 | epot = -19.3378861205732 | etot = -13.2825374183149 +921000 ekin = 2.5338583783986 | erot = 3.5055796155901 | epot = -19.3219754120972 | etot = -13.2825374181085 +922000 ekin = 2.516060534879 | erot = 3.49409623125511 | epot = -19.2926941839177 | etot = -13.2825374177836 +923000 ekin = 2.49728909023619 | erot = 3.47476611514256 | epot = -19.2545926228132 | etot = -13.2825374174344 +924000 ekin = 2.48035717414061 | erot = 3.44958564359935 | epot = -19.2124802348989 | etot = -13.282537417159 +925000 ekin = 2.46765713433988 | erot = 3.41982437245358 | epot = -19.1700189238237 | etot = -13.2825374170303 +926000 ekin = 2.46048446299621 | erot = 3.38566546870185 | epot = -19.1286873487718 | etot = -13.2825374170737 +927000 ekin = 2.45872404418899 | erot = 3.34617863044022 | epot = -19.0874400918875 | etot = -13.2825374172583 +928000 ekin = 2.46097855235184 | erot = 3.29964380866974 | epot = -19.043159778532 | etot = -13.2825374175104 +929000 ekin = 2.46505358100394 | erot = 3.24413140303551 | epot = -18.99172240178 | etot = -13.2825374177406 +930000 ekin = 2.46859437790869 | erot = 3.17816487222183 | epot = -18.9292966680023 | etot = -13.2825374178718 +931000 ekin = 2.46965047248253 | erot = 3.10127887163483 | epot = -18.8534667619775 | etot = -13.2825374178601 +932000 ekin = 2.46701732520898 | erot = 3.01434779059203 | epot = -18.7639025334928 | etot = -13.2825374176918 +933000 ekin = 2.46031519086868 | erot = 2.91973998893973 | epot = -18.662592597222 | etot = -13.2825374174136 +934000 ekin = 2.44985996507097 | erot = 2.82081794907183 | epot = -18.5532153312021 | etot = -13.2825374170593 +935000 ekin = 2.43642057973712 | erot = 2.72162862891861 | epot = -18.4405866253331 | etot = -13.2825374166773 +936000 ekin = 2.42095423648383 | erot = 2.62651830339036 | epot = -18.3300099561839 | etot = -13.2825374163097 +937000 ekin = 2.40438434874151 | erot = 2.53973621394318 | epot = -18.2266579786711 | etot = -13.2825374159864 +938000 ekin = 2.38744919883856 | erot = 2.46512923461683 | epot = -18.1351158491807 | etot = -13.2825374157253 +939000 ekin = 2.37062067030574 | erot = 2.40593643917341 | epot = -18.0590945250148 | etot = -13.2825374155357 +940000 ekin = 2.35407564413747 | erot = 2.36465978775718 | epot = -18.0012728473171 | etot = -13.2825374154225 +941000 ekin = 2.33770002379755 | erot = 2.34297759096208 | epot = -17.9632150301481 | etot = -13.2825374153884 +942000 ekin = 2.32111004775224 | erot = 2.34167204163274 | epot = -17.9453195048215 | etot = -13.2825374154365 +943000 ekin = 2.30368578996793 | erot = 2.36056240830405 | epot = -17.9467856138391 | etot = -13.2825374155671 +944000 ekin = 2.28462216232314 | erot = 2.39846175787113 | epot = -17.9656213359689 | etot = -13.2825374157746 +945000 ekin = 2.26300913007938 | erot = 2.45319770726134 | epot = -17.9987442533843 | etot = -13.2825374160436 +946000 ekin = 2.23795189170117 | erot = 2.52174524353285 | epot = -18.0422345515794 | etot = -13.2825374163454 +947000 ekin = 2.20873145116087 | erot = 2.60050188059525 | epot = -18.091770748396 | etot = -13.2825374166398 +948000 ekin = 2.17498954714479 | erot = 2.685690959925 | epot = -18.1432179239527 | etot = -13.2825374168829 +949000 ekin = 2.13690579554511 | erot = 2.77382147697832 | epot = -18.1932646895605 | etot = -13.2825374170371 +950000 ekin = 2.09532426593736 | erot = 2.86208909954954 | epot = -18.23995078257 | etot = -13.2825374170831 +951000 ekin = 2.05179335117992 | erot = 2.94860198603871 | epot = -18.2829327542442 | etot = -13.2825374170256 +952000 ekin = 2.00850116862718 | erot = 3.03236285097458 | epot = -18.3234014364934 | etot = -13.2825374168917 +953000 ekin = 1.96811370669122 | erot = 3.11301524857533 | epot = -18.3636663719922 | etot = -13.2825374167257 +954000 ekin = 1.93354422355624 | erot = 3.19043207917699 | epot = -18.4065137193093 | etot = -13.2825374165761 +955000 ekin = 1.907692996046 | erot = 3.26426019428037 | epot = -18.4544906068132 | etot = -13.2825374164868 +956000 ekin = 1.89319483896647 | erot = 3.33353105128001 | epot = -18.5092633067365 | etot = -13.28253741649 +957000 ekin = 1.89220136882553 | erot = 3.39641763089531 | epot = -18.5711564163223 | etot = -13.2825374166015 +958000 ekin = 1.90621184477869 | erot = 3.45018116396587 | epot = -18.6389304255644 | etot = -13.2825374168199 +959000 ekin = 1.93595602669004 | erot = 3.49131884076761 | epot = -18.7098122845856 | etot = -13.2825374171279 +960000 ekin = 1.98132739841468 | erot = 3.51589596637559 | epot = -18.7797607822856 | etot = -13.2825374174953 +961000 ekin = 2.04135467368814 | erot = 3.5202262282781 | epot = -18.8441183198727 | etot = -13.2825374179065 +962000 ekin = 2.11395441204344 | erot = 3.50134462359753 | epot = -18.8978364539492 | etot = -13.2825374183082 +963000 ekin = 2.19624676723989 | erot = 3.45688460115197 | epot = -18.9356687870206 | etot = -13.2825374186287 +964000 ekin = 2.28502253674575 | erot = 3.38607259828084 | epot = -18.9536325538576 | etot = -13.282537418831 +965000 ekin = 2.37703902148585 | erot = 3.29004867798671 | epot = -18.9496251180009 | etot = -13.2825374185283 +966000 ekin = 2.47063968385215 | erot = 3.17235139654337 | epot = -18.9255284988459 | etot = -13.2825374184504 +967000 ekin = 2.56372995555254 | erot = 3.03797961239301 | epot = -18.8842469861485 | etot = -13.2825374182029 +968000 ekin = 2.65424152965125 | erot = 2.89333165879526 | epot = -18.83011060625 | etot = -13.2825374178035 +969000 ekin = 2.74102205813625 | erot = 2.74597895036798 | epot = -18.769538425812 | etot = -13.2825374173078 +970000 ekin = 2.82317857011101 | erot = 2.60419008501349 | epot = -18.7099060720296 | etot = -13.2825374169051 +971000 ekin = 2.89946896083441 | erot = 2.47604958426315 | epot = -18.658055961612 | etot = -13.2825374165144 +972000 ekin = 2.96927883277251 | erot = 2.36783972346085 | epot = -18.6196559725141 | etot = -13.2825374162807 +973000 ekin = 3.03160430380023 | erot = 2.28373901071249 | epot = -18.5978807307479 | etot = -13.2825374162352 +974000 ekin = 3.08487810119919 | erot = 2.22552920056088 | epot = -18.5929447181232 | etot = -13.2825374163631 +975000 ekin = 3.12708218363217 | erot = 2.1927093869337 | epot = -18.6023289871792 | etot = -13.2825374166133 +976000 ekin = 3.15606698430949 | erot = 2.18294126831253 | epot = -18.6215456695412 | etot = -13.2825374169192 +977000 ekin = 3.16994500357178 | erot = 2.19267118206454 | epot = -18.6451536028545 | etot = -13.2825374172182 +978000 ekin = 3.16742946522118 | erot = 2.21776877494467 | epot = -18.6677356576302 | etot = -13.2825374174643 +979000 ekin = 3.14804045998247 | erot = 2.25406876588806 | epot = -18.6846466435015 | etot = -13.282537417631 +980000 ekin = 3.11216367723466 | erot = 2.29776911466814 | epot = -18.6924702096109 | etot = -13.2825374177081 +981000 ekin = 3.06099215360332 | erot = 2.34569300138965 | epot = -18.6892225726894 | etot = -13.2825374176964 +982000 ekin = 2.99639965214887 | erot = 2.39544433518914 | epot = -18.6743814049394 | etot = -13.2825374176014 +983000 ekin = 2.92078844513084 | erot = 2.44547840887849 | epot = -18.6488042714436 | etot = -13.2825374174343 +984000 ekin = 2.83693459670618 | erot = 2.4950891273926 | epot = -18.6145611413098 | etot = -13.282537417211 +985000 ekin = 2.74783420133486 | erot = 2.54430433679905 | epot = -18.5746759550876 | etot = -13.2825374169537 +986000 ekin = 2.65654532109889 | erot = 2.59369131660279 | epot = -18.5327740543913 | etot = -13.2825374166896 +987000 ekin = 2.56602544086508 | erot = 2.64409904101799 | epot = -18.4926618983298 | etot = -13.2825374164468 +988000 ekin = 2.47897321649663 | erot = 2.69638105882724 | epot = -18.4578916915741 | etot = -13.2825374162503 +989000 ekin = 2.39763961716918 | erot = 2.75059396137744 | epot = -18.4307709947858 | etot = -13.2825374162392 +990000 ekin = 2.32368779821633 | erot = 2.80603342998527 | epot = -18.4122586443938 | etot = -13.2825374161922 +991000 ekin = 2.2582530149192 | erot = 2.86226671787586 | epot = -18.4030571490211 | etot = -13.282537416226 +992000 ekin = 2.20187988997662 | erot = 2.91825634939035 | epot = -18.4026736557096 | etot = -13.2825374163427 +993000 ekin = 2.15452775947043 | erot = 2.97231721293149 | epot = -18.4093823889398 | etot = -13.2825374165378 +994000 ekin = 2.11561176914432 | erot = 3.02214023523714 | epot = -18.4202894211813 | etot = -13.2825374167998 +995000 ekin = 2.08408161375424 | erot = 3.06489403643897 | epot = -18.4315130673008 | etot = -13.2825374171076 +996000 ekin = 2.05854312749319 | erot = 3.09743221500535 | epot = -18.4385127599264 | etot = -13.2825374174279 +997000 ekin = 2.03742523569505 | erot = 3.11662356420229 | epot = -18.4365862176148 | etot = -13.2825374177175 +998000 ekin = 2.01918449064732 | erot = 3.11978989603429 | epot = -18.42151180461 | etot = -13.2825374179284 +999000 ekin = 2.00252382621622 | erot = 3.10518925481745 | epot = -18.390250499052 | etot = -13.2825374180184 +1000000 ekin = 1.98658902577819 | erot = 3.07244217845672 | epot = -18.3415686221954 | etot = -13.2825374179605 + 1000000 0.088292846 -1.1874188 0.041070751 -1.0221862 -7.1515284e-05 +Loop time of 31.7925 on 1 procs for 1000000 steps with 16 atoms + +Performance: 27176.198 tau/day, 31453.933 timesteps/s +99.5% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 28.401 | 28.401 | 28.401 | 0.0 | 89.33 +Bond | 0.86019 | 0.86019 | 0.86019 | 0.0 | 2.71 +Neigh | 0.00018 | 0.00018 | 0.00018 | 0.0 | 0.00 +Comm | 0.16311 | 0.16311 | 0.16311 | 0.0 | 0.51 +Output | 7e-06 | 7e-06 | 7e-06 | 0.0 | 0.00 +Modify | 2.1003 | 2.1003 | 2.1003 | 0.0 | 6.61 +Other | | 0.2673 | | | 0.84 + +Nlocal: 16 ave 16 max 16 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 93 ave 93 max 93 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 93 +Ave neighs/atom = 5.8125 +Ave special neighs/atom = 3.75 +Neighbor list builds = 6 +Dangerous builds = 0 + +#write_restart config.${number}.* +Total wall time: 0:00:31 diff --git a/examples/USER/cgdna/examples/oxRNA2/duplex4/log.30Oct19.duplex4.g++.4 b/examples/USER/cgdna/examples/oxRNA2/duplex4/log.30Oct19.duplex4.g++.4 new file mode 100644 index 0000000000..8a3a723a1e --- /dev/null +++ b/examples/USER/cgdna/examples/oxRNA2/duplex4/log.30Oct19.duplex4.g++.4 @@ -0,0 +1,1174 @@ +LAMMPS (30 Oct 2019) +variable number equal 4 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 0.1 + +units lj + +dimension 3 + +newton off + +boundary p p p + +atom_style hybrid bond ellipsoid +atom_modify sort 0 1.0 + +# Pair interactions require lists of neighbours to be calculated +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex4 + orthogonal box = (-20 -20 -20) to (20 20 20) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 16 atoms + reading velocities ... + 16 velocities + 16 ellipsoids + scanning bonds ... + 2 = max bonds/atom + reading bonds ... + 13 bonds + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000281 secs + read_data CPU = 0.003043 secs + +set atom * mass 3.1575 + 16 settings made for mass + +group all type 1 4 +16 atoms in group all + +# oxRNA2 bond interactions - FENE backbone +bond_style oxrna2/fene +bond_coeff * 2.0 0.25 0.761070781051 + +# oxRNA2 pair interactions +pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh + +pair_coeff * * oxrna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 +pair_coeff * * oxrna2/stk seqdep ${T} 1.40206 2.77 6.0 0.43 0.93 0.35 0.78 0.9 0 0.95 0.9 0 0.95 1.3 0 0.8 1.3 0 0.8 2.0 0.65 2.0 0.65 +pair_coeff * * oxrna2/stk seqdep 0.1 1.40206 2.77 6.0 0.43 0.93 0.35 0.78 0.9 0 0.95 0.9 0 0.95 1.3 0 0.8 1.3 0 0.8 2.0 0.65 2.0 0.65 +pair_coeff * * oxrna2/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 oxrna2/hbond seqdep 0.870439 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 oxrna2/hbond seqdep 0.870439 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 3 4 oxrna2/hbond seqdep 0.870439 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 * * oxrna2/xstk 59.9626 0.5 0.6 0.42 0.58 2.25 0.505 0.58 1.7 1.266 0.68 1.7 1.266 0.68 1.7 0.309 0.68 1.7 0.309 0.68 +pair_coeff * * oxrna2/coaxstk 80 0.5 0.6 0.42 0.58 2.0 2.592 0.65 1.3 0.151 0.8 0.9 0.685 0.95 0.9 0.685 0.95 2.0 -0.65 2.0 -0.65 +pair_coeff * * oxrna2/dh ${T} 0.5 1.02455 +pair_coeff * * oxrna2/dh 0.1 0.5 1.02455 + +# NVE ensemble +#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10 +#fix 1 all nve/dot +fix 1 all nve/asphere + +timestep 1e-5 + +#comm_style tiled +#fix 3 all balance 10000 1.1 rcb + +#compute mol all chunk/atom molecule +#compute mychunk all vcm/chunk mol +#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector + +#dump pos all xyz ${ofreq} traj.${number}.xyz + +#compute quat all property/atom quatw quati quatj quatk +#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] +#dump_modify quat sort id +#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz +#dump_modify out sort id +#dump_modify out format line "%d %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f" + +run 1000000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 3.3015 + ghost atom cutoff = 3.3015 + binsize = 1.65075, bins = 25 25 25 + 6 neighbor lists, perpetual/occasional/extra = 6 0 0 + (1) pair oxrna2/excv, perpetual + attributes: half, newton off + pair build: half/bin/newtoff + stencil: half/bin/3d/newtoff + bin: standard + (2) pair oxrna2/stk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (3) pair oxrna2/hbond, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (4) pair oxrna2/xstk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (5) pair oxrna2/coaxstk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (6) pair oxrna2/dh, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none +0 ekin = 0 | erot = 0 | epot = -13.282537590974 | etot = -13.282537590974 +Per MPI rank memory allocation (min/avg/max) = 7.755 | 7.937 | 8.119 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -0.84341458 0.013255977 -0.8301586 -2.0169485e-05 +1000 ekin = 0.00448503054655829 | erot = 0.00825381229599554 | epot = -13.2952764343121 | etot = -13.2825375914696 +2000 ekin = 0.0179027901180383 | erot = 0.0327684151333158 | epot = -13.333208796773 | etot = -13.2825375915216 +3000 ekin = 0.0401478317723388 | erot = 0.0728240143062734 | epot = -13.3955094376812 | etot = -13.2825375916026 +4000 ekin = 0.0710654348932012 | erot = 0.127292706282676 | epot = -13.4808957328803 | etot = -13.2825375917044 +5000 ekin = 0.110480309743627 | erot = 0.194739074279345 | epot = -13.58775697584 | etot = -13.282537591817 +6000 ekin = 0.158231230694386 | erot = 0.273546913858364 | epot = -13.7143157364821 | etot = -13.2825375919294 +7000 ekin = 0.214206450831694 | erot = 0.362058396900661 | epot = -13.8588024397635 | etot = -13.2825375920312 +8000 ekin = 0.27837411184999 | erot = 0.458709556671591 | epot = -14.0196212606354 | etot = -13.2825375921138 +9000 ekin = 0.350802094030117 | erot = 0.562145629087582 | epot = -14.1954853152897 | etot = -13.282537592172 +10000 ekin = 0.431663021447632 | erot = 0.671302139461542 | epot = -14.3855027531133 | etot = -13.2825375922041 +11000 ekin = 0.521222365620092 | erot = 0.785442646223518 | epot = -14.5892026040564 | etot = -13.2825375922128 +12000 ekin = 0.619810398735201 | erot = 0.90415088836544 | epot = -14.8064988793047 | etot = -13.2825375922041 +13000 ekin = 0.727781531798581 | erot = 1.02728222251184 | epot = -15.0376013464965 | etot = -13.2825375921861 +14000 ekin = 0.845466747659119 | erot = 1.15488520186341 | epot = -15.2828895416906 | etot = -13.2825375921681 +15000 ekin = 0.973515286429056 | erot = 1.28640002432427 | epot = -15.5424529041403 | etot = -13.282537593387 +16000 ekin = 1.12323013751051 | erot = 1.4038749539854 | epot = -15.8096426839246 | etot = -13.2825375924286 +17000 ekin = 1.29769272832575 | erot = 1.51347784068601 | epot = -16.0937081607386 | etot = -13.2825375917268 +18000 ekin = 1.48565191084472 | erot = 1.63592970999597 | epot = -16.4041192134335 | etot = -13.2825375925929 +19000 ekin = 1.66750911163292 | erot = 1.77940241938649 | epot = -16.7294491246356 | etot = -13.2825375936162 +20000 ekin = 1.84148924290367 | erot = 1.93695511183614 | epot = -17.0609819484045 | etot = -13.2825375936647 +21000 ekin = 2.02307741366106 | erot = 2.09844265792887 | epot = -17.4040576653927 | etot = -13.2825375938028 +22000 ekin = 2.21183606977167 | erot = 2.26260708947227 | epot = -17.7569807531574 | etot = -13.2825375939135 +23000 ekin = 2.40735468792923 | erot = 2.42817202047232 | epot = -18.1180643024984 | etot = -13.2825375940969 +24000 ekin = 2.60896890448811 | erot = 2.59357882573777 | epot = -18.4850853245068 | etot = -13.2825375942809 +25000 ekin = 2.815801354773 | erot = 2.75706655666979 | epot = -18.8554055059558 | etot = -13.282537594513 +26000 ekin = 3.02680083558447 | erot = 2.91667946897181 | epot = -19.2260178993261 | etot = -13.2825375947698 +27000 ekin = 3.24067707260278 | erot = 3.07027299756425 | epot = -19.5934876652165 | etot = -13.2825375950495 +28000 ekin = 3.45601412953551 | erot = 3.21560615187967 | epot = -19.9541578767284 | etot = -13.2825375953133 +29000 ekin = 3.67136830813179 | erot = 3.35037905822876 | epot = -20.3042849619982 | etot = -13.2825375956377 +30000 ekin = 3.88476027224393 | erot = 3.47208481891771 | epot = -20.6393826871844 | etot = -13.2825375960227 +31000 ekin = 4.09387957878907 | erot = 3.57821385031972 | epot = -20.9546310254505 | etot = -13.2825375963417 +32000 ekin = 4.2966218534583 | erot = 3.6664860653108 | epot = -21.2456455154184 | etot = -13.2825375966493 +33000 ekin = 4.49089153394099 | erot = 3.73482555362516 | epot = -21.5082546845017 | etot = -13.2825375969356 +34000 ekin = 4.67464118182325 | erot = 3.78142516888949 | epot = -21.7386039479011 | etot = -13.2825375971883 +35000 ekin = 4.84586411782109 | erot = 3.80480460777856 | epot = -21.9332063229965 | etot = -13.2825375973968 +36000 ekin = 5.0027094048744 | erot = 3.80394535032719 | epot = -22.0891923527598 | etot = -13.2825375975582 +37000 ekin = 5.14355281474345 | erot = 3.77833709530338 | epot = -22.2044275077127 | etot = -13.2825375976659 +38000 ekin = 5.26699752588952 | erot = 3.72801268545681 | epot = -22.2775478090603 | etot = -13.282537597714 +39000 ekin = 5.37191151713971 | erot = 3.65359747923658 | epot = -22.3080465940747 | etot = -13.2825375976984 +40000 ekin = 5.45746010972539 | erot = 3.55633701588603 | epot = -22.2963347232318 | etot = -13.2825375976204 +41000 ekin = 5.52312188621432 | erot = 3.43809872369872 | epot = -22.2437582073857 | etot = -13.2825375974727 +42000 ekin = 5.56872044212123 | erot = 3.3013527933319 | epot = -22.1526108327172 | etot = -13.2825375972641 +43000 ekin = 5.59443660083054 | erot = 3.14910305123766 | epot = -22.0260772490709 | etot = -13.2825375970027 +44000 ekin = 5.60078634437832 | erot = 2.98477133565166 | epot = -21.8680952767313 | etot = -13.2825375967014 +45000 ekin = 5.58859564323475 | erot = 2.81204277265363 | epot = -21.6831760122637 | etot = -13.2825375963753 +46000 ekin = 5.55896198288938 | erot = 2.6346956216755 | epot = -21.4761952006028 | etot = -13.2825375960379 +47000 ekin = 5.51320424222089 | erot = 2.45646420183095 | epot = -21.2522060397504 | etot = -13.2825375956985 +48000 ekin = 5.45280176988658 | erot = 2.28095947573165 | epot = -21.0162988409789 | etot = -13.2825375953606 +49000 ekin = 5.37933239946777 | erot = 2.11161440403301 | epot = -20.7734843985466 | etot = -13.2825375950459 +50000 ekin = 5.29440598595322 | erot = 1.95156309993227 | epot = -20.5285066806364 | etot = -13.2825375947509 +51000 ekin = 5.19960275040365 | erot = 1.80366343983081 | epot = -20.2858037847169 | etot = -13.2825375944825 +52000 ekin = 5.09244091535893 | erot = 1.66034071449528 | epot = -20.0353192196147 | etot = -13.2825375897605 +53000 ekin = 5.00219098599359 | erot = 1.54003539006203 | epot = -19.8247639698989 | etot = -13.2825375938433 +54000 ekin = 4.9005832952689 | erot = 1.45132465506065 | epot = -19.6344455614694 | etot = -13.2825376111398 +55000 ekin = 4.70838087935279 | erot = 1.38368494594859 | epot = -19.374603433669 | etot = -13.2825376083676 +56000 ekin = 4.44064498303654 | erot = 1.42525549496225 | epot = -19.1484380668512 | etot = -13.2825375888524 +57000 ekin = 4.28012764787381 | erot = 1.59067222265449 | epot = -19.1533374833608 | etot = -13.2825376128325 +58000 ekin = 4.17606446205197 | erot = 1.69269591419354 | epot = -19.1512979674153 | etot = -13.2825375911698 +59000 ekin = 4.06748012934537 | erot = 1.75788112721229 | epot = -19.107898847714 | etot = -13.2825375911564 +60000 ekin = 3.95448823476477 | erot = 1.84391663061692 | epot = -19.0809424565338 | etot = -13.2825375911521 +61000 ekin = 3.83840387031379 | erot = 1.95003019237122 | epot = -19.0709716537089 | etot = -13.2825375910239 +62000 ekin = 3.72130809963139 | erot = 2.0750170389528 | epot = -19.0788627296236 | etot = -13.2825375910394 +63000 ekin = 3.60440089033071 | erot = 2.21773397929691 | epot = -19.1046724606766 | etot = -13.282537591049 +64000 ekin = 3.4889862142993 | erot = 2.37695650761868 | epot = -19.148480312971 | etot = -13.282537591053 +65000 ekin = 3.37647880025376 | erot = 2.55140907448341 | epot = -19.2104254657956 | etot = -13.2825375910584 +66000 ekin = 3.26833067403449 | erot = 2.73974236804954 | epot = -19.2906106331586 | etot = -13.2825375910746 +67000 ekin = 3.16594788215649 | erot = 2.94047174698095 | epot = -19.388957220252 | etot = -13.2825375911146 +68000 ekin = 3.0706053161234 | erot = 3.15188029478479 | epot = -19.5050232021006 | etot = -13.2825375911924 +69000 ekin = 2.98334905059876 | erot = 3.37190853325425 | epot = -19.6377951751748 | etot = -13.2825375913218 +70000 ekin = 2.90492955397934 | erot = 3.59802295152821 | epot = -19.7854900970212 | etot = -13.2825375915136 +71000 ekin = 2.8357237632926 | erot = 3.82715608397267 | epot = -19.9454174390302 | etot = -13.282537591765 +72000 ekin = 2.77568510799032 | erot = 4.05569348668108 | epot = -20.1139161867756 | etot = -13.2825375921042 +73000 ekin = 2.72437405649554 | erot = 4.27929863267833 | epot = -20.2862102816544 | etot = -13.2825375924805 +74000 ekin = 2.68098943200971 | erot = 4.49340310246777 | epot = -20.4569301273593 | etot = -13.2825375928818 +75000 ekin = 2.64445309406174 | erot = 4.69339307185924 | epot = -20.6203837591928 | etot = -13.2825375932718 +76000 ekin = 2.6135541520603 | erot = 4.87501053155987 | epot = -20.7711022772319 | etot = -13.2825375936117 +77000 ekin = 2.58710084062325 | erot = 5.03478939171986 | epot = -20.9044278262174 | etot = -13.2825375938743 +78000 ekin = 2.56403853914047 | erot = 5.17029283960992 | epot = -21.0168689727791 | etot = -13.2825375940288 +79000 ekin = 2.54361120788205 | erot = 5.28037161018718 | epot = -21.1065204121483 | etot = -13.2825375940791 +80000 ekin = 2.52540527324235 | erot = 5.36512720853055 | epot = -21.1730700758027 | etot = -13.2825375940298 +81000 ekin = 2.50929384303282 | erot = 5.42576598242984 | epot = -21.2175974194024 | etot = -13.2825375939398 +82000 ekin = 2.49524917644569 | erot = 5.46414530531101 | epot = -21.2419320755729 | etot = -13.2825375938162 +83000 ekin = 2.48334269593095 | erot = 5.4824203292205 | epot = -21.2483006188452 | etot = -13.2825375936938 +84000 ekin = 2.47365997802566 | erot = 5.48271691205612 | epot = -21.2389144836699 | etot = -13.2825375935881 +85000 ekin = 2.46626808184741 | erot = 5.46691083839012 | epot = -21.2157165137403 | etot = -13.2825375935028 +86000 ekin = 2.46123154184209 | erot = 5.43653398177587 | epot = -21.1803031170847 | etot = -13.2825375934667 +87000 ekin = 2.45852093879021 | erot = 5.39265692383558 | epot = -21.1337154560128 | etot = -13.282537593387 +88000 ekin = 2.45840646060141 | erot = 5.33627030736318 | epot = -21.0772143612568 | etot = -13.2825375932922 +89000 ekin = 2.46146480126854 | erot = 5.26838646846911 | epot = -21.012388863175 | etot = -13.2825375934373 +90000 ekin = 2.46773177835907 | erot = 5.18930366181577 | epot = -20.9395730335201 | etot = -13.2825375933453 +91000 ekin = 2.47726011905689 | erot = 5.09951749277907 | epot = -20.8593152050603 | etot = -13.2825375932243 +92000 ekin = 2.4907426196288 | erot = 5.00022791911722 | epot = -20.7735081318261 | etot = -13.2825375930801 +93000 ekin = 2.50902833057334 | erot = 4.89281259013229 | epot = -20.6843785136299 | etot = -13.2825375929243 +94000 ekin = 2.53301288183049 | erot = 4.77876912035663 | epot = -20.5943195949551 | etot = -13.282537592768 +95000 ekin = 2.56354598704884 | erot = 4.6596420581637 | epot = -20.5057256378358 | etot = -13.2825375926232 +96000 ekin = 2.60133194738592 | erot = 4.53693642149458 | epot = -20.4208059613811 | etot = -13.2825375925006 +97000 ekin = 2.6468471253709 | erot = 4.41204173729102 | epot = -20.341426455067 | etot = -13.2825375924051 +98000 ekin = 2.70029551800313 | erot = 4.28619503995253 | epot = -20.2690281502933 | etot = -13.2825375923376 +99000 ekin = 2.76159183076374 | erot = 4.1604816375425 | epot = -20.2046110606011 | etot = -13.2825375922949 +100000 ekin = 2.83036874776577 | erot = 4.0358752301046 | epot = -20.1487815701413 | etot = -13.2825375922709 +101000 ekin = 2.90599845693998 | erot = 3.9133007754067 | epot = -20.101836824607 | etot = -13.2825375922603 +102000 ekin = 2.98761606367611 | erot = 3.79369343963891 | epot = -20.0638470955759 | etot = -13.2825375922608 +103000 ekin = 3.07413620026815 | erot = 3.67802597580122 | epot = -20.0346997683425 | etot = -13.2825375922731 +104000 ekin = 3.16426099663664 | erot = 3.5672897363664 | epot = -20.0140883253055 | etot = -13.2825375923024 +105000 ekin = 3.25648344622817 | erot = 3.46242766269347 | epot = -20.0014487012771 | etot = -13.2825375923554 +106000 ekin = 3.34909407537385 | erot = 3.36423261094233 | epot = -19.995864278755 | etot = -13.2825375924388 +107000 ekin = 3.44019930697686 | erot = 3.27323316283083 | epot = -19.9959700623653 | etot = -13.2825375925576 +108000 ekin = 3.52775814523643 | erot = 3.18959025645848 | epot = -19.9998859944077 | etot = -13.2825375927128 +109000 ekin = 3.6096400910426 | erot = 3.11302339299944 | epot = -20.005201076944 | etot = -13.282537592902 +110000 ekin = 3.6837038852456 | erot = 3.04277828887611 | epot = -20.0090197672392 | etot = -13.2825375931175 +111000 ekin = 3.74789440567239 | erot = 2.97764201100065 | epot = -20.008074010021 | etot = -13.2825375933479 +112000 ekin = 3.80035415830488 | erot = 2.91600823448545 | epot = -19.998899986368 | etot = -13.2825375935777 +113000 ekin = 3.83954489146462 | erot = 2.8559933088985 | epot = -19.9780757941509 | etot = -13.2825375937878 +114000 ekin = 3.86437452036879 | erot = 2.79560177874322 | epot = -19.9425138930679 | etot = -13.2825375939559 +115000 ekin = 3.87432139555512 | erot = 2.7329343736022 | epot = -19.8897933632162 | etot = -13.2825375940589 +116000 ekin = 3.86954570193501 | erot = 2.66642221950647 | epot = -19.8185055155167 | etot = -13.2825375940752 +117000 ekin = 3.85097050791437 | erot = 2.59505981730791 | epot = -19.7285679191994 | etot = -13.2825375939772 +118000 ekin = 3.82031843896425 | erot = 2.5186641606976 | epot = -19.6215201934443 | etot = -13.2825375937824 +119000 ekin = 3.78008379969966 | erot = 2.43788144963801 | epot = -19.5005028428247 | etot = -13.282537593487 +120000 ekin = 3.73339325084474 | erot = 2.35417060362146 | epot = -19.3701014475778 | etot = -13.2825375931116 +121000 ekin = 3.68379362023552 | erot = 2.26974086129434 | epot = -19.2360720742189 | etot = -13.282537592689 +122000 ekin = 3.63497633455493 | erot = 2.187331073511 | epot = -19.1048450003246 | etot = -13.2825375922586 +123000 ekin = 3.59047168903083 | erot = 2.10992442969239 | epot = -18.9829337105828 | etot = -13.2825375918596 +124000 ekin = 3.55336069064751 | erot = 2.04044947797503 | epot = -18.8763477601473 | etot = -13.2825375915248 +125000 ekin = 3.52605275648501 | erot = 1.98151529341901 | epot = -18.7901056411792 | etot = -13.2825375912752 +126000 ekin = 3.51088386083619 | erot = 1.93492307727733 | epot = -18.7283445290526 | etot = -13.2825375909391 +127000 ekin = 3.51016542665117 | erot = 1.90135594382251 | epot = -18.6940589614207 | etot = -13.282537590947 +128000 ekin = 3.52366007691443 | erot = 1.88146923500183 | epot = -18.6876669021169 | etot = -13.2825375902006 +129000 ekin = 3.52804447870926 | erot = 1.87939379818771 | epot = -18.6899759099317 | etot = -13.2825376330347 +130000 ekin = 3.3912172753683 | erot = 1.9537535440301 | epot = -18.6275084102333 | etot = -13.2825375908349 +131000 ekin = 3.51597185423426 | erot = 2.06600773707507 | epot = -18.8645172230942 | etot = -13.2825376317848 +132000 ekin = 3.65680948155317 | erot = 2.09675964820366 | epot = -19.0361067214645 | etot = -13.2825375917077 +133000 ekin = 3.7826089844419 | erot = 2.11778864665351 | epot = -19.1829352240661 | etot = -13.2825375929707 +134000 ekin = 3.90291219401812 | erot = 2.13993246768579 | epot = -19.3253822549305 | etot = -13.2825375932266 +135000 ekin = 4.01307253292161 | erot = 2.16317596346837 | epot = -19.4587860898094 | etot = -13.2825375934194 +136000 ekin = 4.10942813981098 | erot = 2.18779054238556 | epot = -19.5797562757542 | etot = -13.2825375935576 +137000 ekin = 4.18918244084745 | erot = 2.21413018926333 | epot = -19.6858502237394 | etot = -13.2825375936286 +138000 ekin = 4.2505518072554 | erot = 2.24252417705063 | epot = -19.7756135779478 | etot = -13.2825375936417 +139000 ekin = 4.29264193993074 | erot = 2.27334414892585 | epot = -19.8485236824507 | etot = -13.2825375935941 +140000 ekin = 4.3154298106947 | erot = 2.30704736065629 | epot = -19.9050147648385 | etot = -13.2825375934876 +141000 ekin = 4.31969657449578 | erot = 2.34420108979774 | epot = -19.9464352576252 | etot = -13.2825375933317 +142000 ekin = 4.30689625825177 | erot = 2.38546661972142 | epot = -19.9749004711159 | etot = -13.2825375931427 +143000 ekin = 4.27897643633862 | erot = 2.43154322469966 | epot = -19.9930572539773 | etot = -13.282537592939 +144000 ekin = 4.23817759048806 | erot = 2.48305254316461 | epot = -20.0037677263992 | etot = -13.2825375927466 +145000 ekin = 4.18683687366753 | erot = 2.54040585524244 | epot = -20.009780321492 | etot = -13.2825375925821 +146000 ekin = 4.12722437776044 | erot = 2.60369949546926 | epot = -20.0134614656893 | etot = -13.2825375924596 +147000 ekin = 4.06142641942185 | erot = 2.67262771534978 | epot = -20.0165917271585 | etot = -13.2825375923869 +148000 ekin = 3.99128035690908 | erot = 2.74643868481997 | epot = -20.020256634094 | etot = -13.282537592365 +149000 ekin = 3.91835859675011 | erot = 2.82393987441806 | epot = -20.0248360635573 | etot = -13.2825375923891 +150000 ekin = 3.84399502540833 | erot = 2.90355368904256 | epot = -20.0300863068997 | etot = -13.2825375924488 +151000 ekin = 3.76934462696621 | erot = 2.98342057410539 | epot = -20.0353027936016 | etot = -13.28253759253 +152000 ekin = 3.69546503896268 | erot = 3.06154297168208 | epot = -20.0395456032601 | etot = -13.2825375926153 +153000 ekin = 3.62340677772804 | erot = 3.13595781467784 | epot = -20.0419021850934 | etot = -13.2825375926875 +154000 ekin = 3.55429442921638 | erot = 3.20491770297356 | epot = -20.0417497249215 | etot = -13.2825375927316 +155000 ekin = 3.48935808553542 | erot = 3.267033764948 | epot = -20.0389294432276 | etot = -13.2825375927442 +156000 ekin = 3.42995719397451 | erot = 3.32146386703958 | epot = -20.0339586537004 | etot = -13.2825375926863 +157000 ekin = 3.37758377439308 | erot = 3.3680769357291 | epot = -20.0281983027503 | etot = -13.2825375926282 +158000 ekin = 3.32977839475207 | erot = 3.40502394976649 | epot = -20.0173399361884 | etot = -13.2825375916698 +159000 ekin = 3.28790229188182 | erot = 3.43232801111001 | epot = -20.0027678906269 | etot = -13.2825375876351 +160000 ekin = 3.28279951728226 | erot = 3.4645745488256 | epot = -20.0299116571476 | etot = -13.2825375910398 +161000 ekin = 3.29006841785755 | erot = 3.48756894666592 | epot = -20.060174952488 | etot = -13.2825375879645 +162000 ekin = 3.30320279764929 | erot = 3.5006454181618 | epot = -20.0863858038415 | etot = -13.2825375880305 +163000 ekin = 3.3268044536015 | erot = 3.5070397924055 | epot = -20.1163818341639 | etot = -13.2825375881569 +164000 ekin = 3.35978204864461 | erot = 3.50639799900104 | epot = -20.1487176359757 | etot = -13.2825375883301 +165000 ekin = 3.40052448161875 | erot = 3.49807859199056 | epot = -20.181140662133 | etot = -13.2825375885237 +166000 ekin = 3.44710440323471 | erot = 3.48135096319333 | epot = -20.2109929551299 | etot = -13.2825375887019 +167000 ekin = 3.49756483136592 | erot = 3.45565303648324 | epot = -20.2357554566773 | etot = -13.2825375888282 +168000 ekin = 3.55023572858368 | erot = 3.42084325030349 | epot = -20.2536165677586 | etot = -13.2825375888714 +169000 ekin = 3.60406985696714 | erot = 3.37750569995069 | epot = -20.2641131456955 | etot = -13.2825375887777 +170000 ekin = 3.41798406778751 | erot = 3.07782048145922 | epot = -19.778342066862 | etot = -13.2825375176153 +171000 ekin = 3.24552871157498 | erot = 2.73637390316101 | epot = -19.2644400103033 | etot = -13.2825373955674 +172000 ekin = 3.78367855050775 | erot = 3.07274537488996 | epot = -20.1389614956815 | etot = -13.2825375702838 +173000 ekin = 4.03457273059295 | erot = 3.18336469108423 | epot = -20.5004749222008 | etot = -13.2825375005236 +174000 ekin = 4.14002439985893 | erot = 3.16763893899956 | epot = -20.5902008391742 | etot = -13.2825375003158 +175000 ekin = 4.24061478727453 | erot = 3.15086312051272 | epot = -20.6740154078936 | etot = -13.2825375001064 +176000 ekin = 4.33750550891526 | erot = 3.13552610061259 | epot = -20.7555691095042 | etot = -13.2825374999763 +177000 ekin = 4.43118634626137 | erot = 3.12342668205163 | epot = -20.8371505282951 | etot = -13.2825374999821 +178000 ekin = 4.52112038535783 | erot = 3.11516996838801 | epot = -20.9188278538849 | etot = -13.282537500139 +179000 ekin = 4.60569122910417 | erot = 3.10997891303252 | epot = -20.998207642551 | etot = -13.2825375004143 +180000 ekin = 4.68248742105047 | erot = 3.1058753404107 | epot = -21.0709002621979 | etot = -13.2825375007368 +181000 ekin = 4.74885008880596 | erot = 3.10016969122731 | epot = -21.1315572810529 | etot = -13.2825375010196 +182000 ekin = 4.8025200424072 | erot = 3.09010778323257 | epot = -21.1751653268254 | etot = -13.2825375011856 +183000 ekin = 4.84185836209202 | erot = 3.07355401450771 | epot = -21.1979498780484 | etot = -13.2825375014487 +184000 ekin = 4.86305938218088 | erot = 3.04972947015888 | epot = -21.1953263537842 | etot = -13.2825375014444 +185000 ekin = 4.86484048379678 | erot = 3.01830532387275 | epot = -21.1656833089538 | etot = -13.2825375012843 +186000 ekin = 4.84781115921716 | erot = 2.97987576046156 | epot = -21.1102244206809 | etot = -13.2825375010021 +187000 ekin = 4.81357764335378 | erot = 2.93597501879657 | epot = -21.0320901627985 | etot = -13.2825375006482 +188000 ekin = 4.76439584097053 | erot = 2.8887503176224 | epot = -20.9356836588659 | etot = -13.282537500273 +189000 ekin = 4.70282021343345 | erot = 2.84056846871519 | epot = -20.8259261820667 | etot = -13.282537499918 +190000 ekin = 4.63141632940784 | erot = 2.79367442377921 | epot = -20.7076282527974 | etot = -13.2825374996104 +191000 ekin = 4.55257205219614 | erot = 2.74995133907631 | epot = -20.5850608906324 | etot = -13.28253749936 +192000 ekin = 4.4684144513739 | erot = 2.71080835143519 | epot = -20.461760301973 | etot = -13.2825374991639 +193000 ekin = 4.38080987485654 | erot = 2.67717312167521 | epot = -20.3405204955454 | etot = -13.2825374990136 +194000 ekin = 4.29140314493119 | erot = 2.64952891334815 | epot = -20.223469557183 | etot = -13.2825374989037 +195000 ekin = 4.20164846020117 | erot = 2.62793199519477 | epot = -20.1121179542326 | etot = -13.2825374988367 +196000 ekin = 4.11279973688578 | erot = 2.61197297306555 | epot = -20.0073102087732 | etot = -13.2825374988219 +197000 ekin = 4.02585897192346 | erot = 2.6006960732789 | epot = -19.9090925440713 | etot = -13.2825374988689 +198000 ekin = 3.94151021740631 | erot = 2.59254113732279 | epot = -19.8165888537068 | etot = -13.2825374989777 +199000 ekin = 3.8600892057151 | erot = 2.58539978552207 | epot = -19.7280264903664 | etot = -13.2825374991292 +200000 ekin = 3.78163650515432 | erot = 2.57685633277492 | epot = -19.641030337214 | etot = -13.2825374992847 +201000 ekin = 3.70604145366902 | erot = 2.56461316993936 | epot = -19.5531921230034 | etot = -13.2825374993951 +202000 ekin = 3.63323784111755 | erot = 2.54700321074615 | epot = -19.4627785512822 | etot = -13.2825374994185 +203000 ekin = 3.56337600429993 | erot = 2.52342549129483 | epot = -19.3693389949304 | etot = -13.2825374993357 +204000 ekin = 3.49690618989434 | erot = 2.49455276327548 | epot = -19.2739964523247 | etot = -13.2825374991549 +205000 ekin = 3.4345533876734 | erot = 2.46224574346295 | epot = -19.1793366300441 | etot = -13.2825374989078 +206000 ekin = 3.37721205721461 | erot = 2.42921548153362 | epot = -19.0889650373856 | etot = -13.2825374986374 +207000 ekin = 3.32580575275846 | erot = 2.39854397251164 | epot = -19.0068872236569 | etot = -13.2825374983868 +208000 ekin = 3.28114891016592 | erot = 2.3731881465479 | epot = -18.9368745549049 | etot = -13.2825374981911 +209000 ekin = 3.24383236357031 | erot = 2.35556506548857 | epot = -18.881934927133 | etot = -13.2825374980741 +210000 ekin = 3.21413821976384 | erot = 2.34727297364657 | epot = -18.8439486914573 | etot = -13.2825374980469 +211000 ekin = 3.1919920439607 | erot = 2.34895966766535 | epot = -18.8234892097349 | etot = -13.2825374981088 +212000 ekin = 3.17695628121283 | erot = 2.36032147203272 | epot = -18.8198152514957 | etot = -13.2825374982501 +213000 ekin = 3.16826455951627 | erot = 2.3802017195472 | epot = -18.8310037775173 | etot = -13.2825374984538 +214000 ekin = 3.16489343854745 | erot = 2.40676052174862 | epot = -18.8541914589943 | etot = -13.2825374986982 +215000 ekin = 3.16566474352266 | erot = 2.43769738040411 | epot = -18.8858996228842 | etot = -13.2825374989574 +216000 ekin = 3.16936807503371 | erot = 2.47051711067938 | epot = -18.922422684916 | etot = -13.2825374992029 +217000 ekin = 3.16266988026928 | erot = 2.47868467133945 | epot = -18.9238920507811 | etot = -13.2825374991723 +218000 ekin = 3.17835235865462 | erot = 2.45704329444748 | epot = -18.9179331413782 | etot = -13.2825374882761 +219000 ekin = 3.26524817202182 | erot = 2.48120766962804 | epot = -19.0289933444494 | etot = -13.2825375027995 +220000 ekin = 3.3108366379572 | erot = 2.50602061547593 | epot = -19.0993947418604 | etot = -13.2825374884273 +221000 ekin = 3.33748530919814 | erot = 2.52276996124463 | epot = -19.1427927588605 | etot = -13.2825374884177 +222000 ekin = 3.36243211589585 | erot = 2.53668587910087 | epot = -19.1816554833759 | etot = -13.2825374883791 +223000 ekin = 3.38541896904289 | erot = 2.54888617169885 | epot = -19.2168426290795 | etot = -13.2825374883378 +224000 ekin = 3.40625812508042 | erot = 2.56049920868685 | epot = -19.2492948220808 | etot = -13.2825374883136 +225000 ekin = 3.42484722909655 | erot = 2.57234499865789 | epot = -19.2797297160694 | etot = -13.2825374883149 +226000 ekin = 3.44121067431426 | erot = 2.5847203663376 | epot = -19.3084685289965 | etot = -13.2825374883446 +227000 ekin = 3.45552721377372 | erot = 2.59730386680816 | epot = -19.3353685689828 | etot = -13.2825374884009 +228000 ekin = 3.46810974282108 | erot = 2.60916931207508 | epot = -19.3598165433769 | etot = -13.2825374884807 +229000 ekin = 3.47932676313057 | erot = 2.61888809507148 | epot = -19.3807523467825 | etot = -13.2825374885804 +230000 ekin = 3.48948003513572 | erot = 2.62469570471801 | epot = -19.3967132285493 | etot = -13.2825374886956 +231000 ekin = 3.49867242979287 | erot = 2.62469374220123 | epot = -19.4059036608136 | etot = -13.2825374888195 +232000 ekin = 3.50671171842553 | erot = 2.61706130327851 | epot = -19.4063105106456 | etot = -13.2825374889415 +233000 ekin = 3.51309701132019 | erot = 2.60026316425614 | epot = -19.3958976646192 | etot = -13.2825374890429 +234000 ekin = 3.51712117494225 | erot = 2.57326085610047 | epot = -19.3729195201389 | etot = -13.2825374890961 +235000 ekin = 3.51809173982046 | erot = 2.53573892922922 | epot = -19.336368158117 | etot = -13.2825374890673 +236000 ekin = 3.51562949139228 | erot = 2.48833922691179 | epot = -19.2865062072283 | etot = -13.2825374889242 +237000 ekin = 3.50996386129181 | erot = 2.43285732073755 | epot = -19.2253586706778 | etot = -13.2825374886484 +238000 ekin = 3.50212794781223 | erot = 2.37232394343651 | epot = -19.1569893794947 | etot = -13.2825374882459 +239000 ekin = 3.49397580570105 | erot = 2.3108975006263 | epot = -19.0874107940784 | etot = -13.282537487751 +240000 ekin = 3.48799489984471 | erot = 2.25353771706539 | epot = -19.0240701041317 | etot = -13.2825374872216 +241000 ekin = 3.48694744152127 | erot = 2.20549386842306 | epot = -18.9749787966723 | etot = -13.2825374867279 +242000 ekin = 3.4934176974057 | erot = 2.17169223103266 | epot = -18.947647414778 | etot = -13.2825374863397 +243000 ekin = 3.50935803683896 | erot = 2.15612557817141 | epot = -18.9480211011254 | etot = -13.282537486115 +244000 ekin = 3.53571412219025 | erot = 2.16133426987283 | epot = -18.9795858781565 | etot = -13.2825374860934 +245000 ekin = 3.57218201231882 | erot = 2.18803987534321 | epot = -19.0427593739541 | etot = -13.2825374862921 +246000 ekin = 3.61712090977394 | erot = 2.23496626996872 | epot = -19.1346246664479 | etot = -13.2825374867053 +247000 ekin = 3.66762313707291 | erot = 2.29886938892395 | epot = -19.2490300132999 | etot = -13.282537487303 +248000 ekin = 3.71973304097767 | erot = 2.37479253662205 | epot = -19.3770630656317 | etot = -13.282537488032 +249000 ekin = 3.76879884759244 | erot = 2.45655776432051 | epot = -19.5078941007293 | etot = -13.2825374888163 +250000 ekin = 3.80993596354176 | erot = 2.5374803002976 | epot = -19.6299537534029 | etot = -13.2825374895636 +251000 ekin = 3.83856187827227 | erot = 2.6112453760505 | epot = -19.7323447444996 | etot = -13.2825374901768 +252000 ekin = 3.85094160348931 | erot = 2.67282602420732 | epot = -19.8063051182674 | etot = -13.2825374905708 +253000 ekin = 3.84466267221602 | erot = 2.71927370140011 | epot = -19.8464738643058 | etot = -13.2825374906897 +254000 ekin = 3.81895334833917 | erot = 2.75020964906172 | epot = -19.8517004879211 | etot = -13.2825374905202 +255000 ekin = 3.77477712370886 | erot = 2.76789565653784 | epot = -19.8252102703423 | etot = -13.2825374900956 +256000 ekin = 3.71467746908689 | erot = 2.7768542145932 | epot = -19.7740691731695 | etot = -13.2825374894894 +257000 ekin = 3.64239785971663 | erot = 2.78310854270393 | epot = -19.7080438912214 | etot = -13.2825374888008 +258000 ekin = 3.56234912667125 | erot = 2.79319020432275 | epot = -19.6380768191301 | etot = -13.2825374881361 +259000 ekin = 3.47902170398649 | erot = 2.81309489223277 | epot = -19.5746540838101 | etot = -13.2825374875908 +260000 ekin = 3.39644765746229 | erot = 2.84735592157313 | epot = -19.5263410662708 | etot = -13.2825374872354 +261000 ekin = 3.31779785755677 | erot = 2.89836390677638 | epot = -19.4986992514409 | etot = -13.2825374871077 +262000 ekin = 3.24516405277705 | erot = 2.96601202360051 | epot = -19.4937135635853 | etot = -13.2825374872077 +263000 ekin = 3.179546945306 | erot = 3.04771661067476 | epot = -19.5098010434848 | etot = -13.2825374875041 +264000 ekin = 3.12100159498149 | erot = 3.13875568824824 | epot = -19.5422947711671 | etot = -13.2825374879374 +265000 ekin = 3.06890996951173 | erot = 3.23291804297549 | epot = -19.5843655009186 | etot = -13.2825374884314 +266000 ekin = 3.02230555156918 | erot = 3.3233525253047 | epot = -19.6281955657826 | etot = -13.2825374889087 +267000 ekin = 2.98016989218907 | erot = 3.40345614747432 | epot = -19.6661635289706 | etot = -13.2825374893072 +268000 ekin = 2.94163501488653 | erot = 3.46763177350614 | epot = -19.6918042779846 | etot = -13.2825374895919 +269000 ekin = 2.90604069318559 | erot = 3.5117562623884 | epot = -19.7003344453572 | etot = -13.2825374897832 +270000 ekin = 2.87284037255953 | erot = 3.53329819601925 | epot = -19.688676058427 | etot = -13.2825374898482 +271000 ekin = 2.8415668881788 | erot = 3.53141495904858 | epot = -19.6555193370572 | etot = -13.2825374898299 +272000 ekin = 2.81169493920591 | erot = 3.50673144119824 | epot = -19.6009638701438 | etot = -13.2825374897396 +273000 ekin = 2.78262532285067 | erot = 3.46115906465187 | epot = -19.5263218770816 | etot = -13.282537489579 +274000 ekin = 2.75380981305629 | erot = 3.39781487150763 | epot = -19.4341621738888 | etot = -13.2825374893249 +275000 ekin = 2.7249735792436 | erot = 3.32097131771962 | epot = -19.3284823859411 | etot = -13.2825374889778 +276000 ekin = 2.6963100293489 | erot = 3.23585259467393 | epot = -19.2147001125781 | etot = -13.2825374885553 +277000 ekin = 2.66855210196835 | erot = 3.14826501869141 | epot = -19.0993546087612 | etot = -13.2825374881014 +278000 ekin = 2.64286719085315 | erot = 3.06403640806022 | epot = -18.9894410865903 | etot = -13.282537487677 +279000 ekin = 2.62061028223249 | erot = 2.98836162249181 | epot = -18.8915093920665 | etot = -13.2825374873422 +280000 ekin = 2.60303022005452 | erot = 2.92520891289514 | epot = -18.810776620089 | etot = -13.2825374871393 +281000 ekin = 2.59103448458187 | erot = 2.87693253510413 | epot = -18.7505045067671 | etot = -13.2825374870811 +282000 ekin = 2.58508390620669 | erot = 2.84417540765184 | epot = -18.7117968010092 | etot = -13.2825374871506 +283000 ekin = 2.58523135936813 | erot = 2.82606103956109 | epot = -18.6938298862392 | etot = -13.2825374873099 +284000 ekin = 2.59126091870129 | erot = 2.82059473157291 | epot = -18.6943931377889 | etot = -13.2825374875147 +285000 ekin = 2.60284631077899 | erot = 2.82514472712939 | epot = -18.7105285256372 | etot = -13.2825374877289 +286000 ekin = 2.61964775974011 | erot = 2.83687342635554 | epot = -18.7390586740297 | etot = -13.2825374879341 +287000 ekin = 2.6416789431732 | erot = 2.85285066093716 | epot = -18.7770670922847 | etot = -13.2825374881743 +288000 ekin = 2.6687167813734 | erot = 2.8702293010975 | epot = -18.8214835708707 | etot = -13.2825374883998 +289000 ekin = 2.69931643718338 | erot = 2.88698660757789 | epot = -18.8688405333582 | etot = -13.282537488597 +290000 ekin = 2.73194963658688 | erot = 2.90163654912622 | epot = -18.9161236744781 | etot = -13.282537488765 +291000 ekin = 2.76502957907631 | erot = 2.91324911168519 | epot = -18.9608161796562 | etot = -13.2825374888947 +292000 ekin = 2.79700561900786 | erot = 2.92149576190804 | epot = -19.0010388698871 | etot = -13.2825374889712 +293000 ekin = 2.82654239554868 | erot = 2.92669002283791 | epot = -19.0357699073648 | etot = -13.2825374889783 +294000 ekin = 2.85272969462551 | erot = 2.92951972788748 | epot = -19.064786911459 | etot = -13.282537488946 +295000 ekin = 2.87508597590273 | erot = 2.9311082644752 | epot = -19.0887317291887 | etot = -13.2825374888108 +296000 ekin = 2.8937804752686 | erot = 2.93349300132756 | epot = -19.1098109651871 | etot = -13.2825374885909 +297000 ekin = 2.90976516785128 | erot = 2.93912517174271 | epot = -19.1314278279134 | etot = -13.2825374883194 +298000 ekin = 2.92469477926885 | erot = 2.95047845944604 | epot = -19.1577107267523 | etot = -13.2825374880374 +299000 ekin = 2.94065805823525 | erot = 2.96967690612477 | epot = -19.192872452154 | etot = -13.282537487794 +300000 ekin = 2.95980003469444 | erot = 2.99812642991887 | epot = -19.2404639522491 | etot = -13.2825374876358 +301000 ekin = 2.9839127297722 | erot = 3.03621252497576 | epot = -19.3026627423455 | etot = -13.2825374875976 +302000 ekin = 3.01408971368584 | erot = 3.08312901017938 | epot = -19.3797562115566 | etot = -13.2825374876914 +303000 ekin = 3.05053302665562 | erot = 3.13689255668877 | epot = -19.4699630712467 | etot = -13.2825374879023 +304000 ekin = 3.08584972584791 | erot = 3.19556015973973 | epot = -19.563947375247 | etot = -13.2825374896594 +305000 ekin = 3.11890909070429 | erot = 3.26281224727038 | epot = -19.6642588266134 | etot = -13.2825374886387 +306000 ekin = 3.16699270587699 | erot = 3.33070506272307 | epot = -19.7802352601689 | etot = -13.2825374915688 +307000 ekin = 3.22023032257454 | erot = 3.3799777181521 | epot = -19.8827455298078 | etot = -13.2825374890812 +308000 ekin = 3.2726873966337 | erot = 3.41969099128558 | epot = -19.974915877149 | etot = -13.2825374892298 +309000 ekin = 3.32280425481262 | erot = 3.44976402097258 | epot = -20.0551057651207 | etot = -13.2825374893356 +310000 ekin = 3.36903652740989 | erot = 3.46970323071698 | epot = -20.1212772475628 | etot = -13.282537489436 +311000 ekin = 3.40972253534481 | erot = 3.47940229945176 | epot = -20.1716623243629 | etot = -13.2825374895663 +312000 ekin = 3.44308129109209 | erot = 3.47898447383071 | epot = -20.2046032544282 | etot = -13.2825374895054 +313000 ekin = 3.46879202758971 | erot = 3.47087869841085 | epot = -20.2222082156542 | etot = -13.2825374896536 +314000 ekin = 3.48565385463582 | erot = 3.45582059749585 | epot = -20.2240119419411 | etot = -13.2825374898094 +315000 ekin = 3.49216313291107 | erot = 3.43373104095289 | epot = -20.2084316637861 | etot = -13.2825374899221 +316000 ekin = 3.4873621330349 | erot = 3.4048256725594 | epot = -20.1747252955317 | etot = -13.2825374899373 +317000 ekin = 3.4699413250759 | erot = 3.36841330847627 | epot = -20.1208921250426 | etot = -13.2825374914904 +318000 ekin = 3.43614022048349 | erot = 3.32066657788322 | epot = -20.0393442896741 | etot = -13.2825374913073 +319000 ekin = 3.38694293952412 | erot = 3.26364910698136 | epot = -19.933129537441 | etot = -13.2825374909355 +320000 ekin = 3.32506744212997 | erot = 3.20113650606391 | epot = -19.8087414386369 | etot = -13.282537490443 +321000 ekin = 3.25415482891508 | erot = 3.13766117543029 | epot = -19.6743534942649 | etot = -13.2825374899195 +322000 ekin = 3.17813669787313 | erot = 3.07780020747427 | epot = -19.5384743947971 | etot = -13.2825374894497 +323000 ekin = 3.10066688251982 | erot = 3.0254908818081 | epot = -19.4086952534143 | etot = -13.2825374890864 +324000 ekin = 3.02479637479388 | erot = 2.98355122494391 | epot = -19.2908850885811 | etot = -13.2825374888433 +325000 ekin = 2.95294332411383 | erot = 2.95347420684896 | epot = -19.1889550196676 | etot = -13.2825374887048 +326000 ekin = 2.88706743997792 | erot = 2.93544936652566 | epot = -19.1050542951497 | etot = -13.2825374886462 +327000 ekin = 2.82887581624799 | erot = 2.92851219862454 | epot = -19.0399255035216 | etot = -13.2825374886491 +328000 ekin = 2.77990830068301 | erot = 2.93074772300687 | epot = -18.9931935123953 | etot = -13.2825374887054 +329000 ekin = 2.74145002280153 | erot = 2.9395401663855 | epot = -18.9635276779975 | etot = -13.2825374888105 +330000 ekin = 2.71432845550434 | erot = 2.95189909643542 | epot = -18.948765040893 | etot = -13.2825374889532 +331000 ekin = 2.69870867087714 | erot = 2.96486608415688 | epot = -18.9461122441487 | etot = -13.2825374891147 +332000 ekin = 2.69398517732769 | erot = 2.97593512180702 | epot = -18.9524577884083 | etot = -13.2825374892736 +333000 ekin = 2.69881348537541 | erot = 2.98337443171444 | epot = -18.9647254065019 | etot = -13.282537489412 +334000 ekin = 2.71127609678388 | erot = 2.98637176000176 | epot = -18.9801853463025 | etot = -13.2825374895168 +335000 ekin = 2.72916096429869 | erot = 2.9850116550983 | epot = -18.9967101089713 | etot = -13.2825374895743 +336000 ekin = 2.75032164400772 | erot = 2.98016551096382 | epot = -19.0130246445397 | etot = -13.2825374895682 +337000 ekin = 2.77304615866046 | erot = 2.97336445321142 | epot = -19.0289481013616 | etot = -13.2825374894897 +338000 ekin = 2.79631213711493 | erot = 2.96664518651861 | epot = -19.0454948129846 | etot = -13.2825374893511 +339000 ekin = 2.81982513095444 | erot = 2.96230352229829 | epot = -19.0646661424439 | etot = -13.2825374891912 +340000 ekin = 2.84381599358321 | erot = 2.96250923740585 | epot = -19.0888627200581 | etot = -13.282537489069 +341000 ekin = 2.86861716322387 | erot = 2.96879944354266 | epot = -19.1199540958289 | etot = -13.2825374890623 +342000 ekin = 2.8942330530774 | erot = 2.9815983091965 | epot = -19.1583688514559 | etot = -13.282537489182 +343000 ekin = 2.92230469127694 | erot = 3.00151195978259 | epot = -19.2063541396131 | etot = -13.2825374885536 +344000 ekin = 2.95328542679254 | erot = 3.02739469587761 | epot = -19.263217611886 | etot = -13.2825374892158 +345000 ekin = 2.98288076792924 | erot = 3.0539773023115 | epot = -19.319395560126 | etot = -13.2825374898853 +346000 ekin = 3.00683622806662 | erot = 3.07579634903604 | epot = -19.3651700675394 | etot = -13.2825374904367 +347000 ekin = 3.02168203920098 | erot = 3.08832269782129 | epot = -19.3925422278017 | etot = -13.2825374907794 +348000 ekin = 3.02528371459624 | erot = 3.08873432783917 | epot = -19.3965555333216 | etot = -13.2825374908862 +349000 ekin = 3.01708434472178 | erot = 3.07610751269672 | epot = -19.3757293482069 | etot = -13.2825374907884 +350000 ekin = 2.99803087494797 | erot = 3.05108999688778 | epot = -19.3316583623806 | etot = -13.2825374905448 +351000 ekin = 2.97033325354683 | erot = 3.0153936212866 | epot = -19.2682643650312 | etot = -13.2825374901978 +352000 ekin = 2.9375545389088 | erot = 2.97175102427437 | epot = -19.1918430530028 | etot = -13.2825374898196 +353000 ekin = 2.90330530002109 | erot = 2.9229126111419 | epot = -19.1087554005707 | etot = -13.2825374894077 +354000 ekin = 2.87126755833817 | erot = 2.8717032112567 | epot = -19.0255082585642 | etot = -13.2825374889693 +355000 ekin = 2.8452063966084 | erot = 2.82119115452554 | epot = -18.9489350396508 | etot = -13.2825374885168 +356000 ekin = 2.8287863971617 | erot = 2.77463213289955 | epot = -18.8859560181414 | etot = -13.2825374880802 +357000 ekin = 2.82589501110838 | erot = 2.73507904234315 | epot = -18.8435115424251 | etot = -13.2825374889736 +358000 ekin = 2.83567543256236 | erot = 2.69990343571512 | epot = -18.8181163574533 | etot = -13.2825374891758 +359000 ekin = 2.85413863003171 | erot = 2.66477535390693 | epot = -18.8014514734629 | etot = -13.2825374895243 +360000 ekin = 2.87797108635789 | erot = 2.62716069413247 | epot = -18.7876692705243 | etot = -13.2825374900339 +361000 ekin = 2.90295419334349 | erot = 2.58324525246655 | epot = -18.7687369364383 | etot = -13.2825374906282 +362000 ekin = 2.92446718933245 | erot = 2.52862237257584 | epot = -18.7356270530339 | etot = -13.2825374911256 +363000 ekin = 2.93848759933288 | erot = 2.4598916464099 | epot = -18.6809167370418 | etot = -13.282537491299 +364000 ekin = 2.94271150164537 | erot = 2.37661313123448 | epot = -18.6018621239963 | etot = -13.2825374911165 +365000 ekin = 2.93600170081407 | erot = 2.28250131434272 | epot = -18.5010405056271 | etot = -13.2825374904703 +366000 ekin = 2.91934189957468 | erot = 2.18525996401723 | epot = -18.3871393531676 | etot = -13.2825374895757 +367000 ekin = 2.89548895825523 | erot = 2.09468885645295 | epot = -18.272715303391 | etot = -13.2825374886828 +368000 ekin = 2.86763306547941 | erot = 2.02026878405696 | epot = -18.170439337522 | etot = -13.2825374879856 +369000 ekin = 2.83845106986062 | erot = 1.96931673437145 | epot = -18.0903052917991 | etot = -13.282537487567 +370000 ekin = 2.80963551309293 | erot = 1.9461845593661 | epot = -18.0383575598726 | etot = -13.2825374874135 +371000 ekin = 2.78188668089845 | erot = 1.95235490032886 | epot = -18.0167790686903 | etot = -13.282537487463 +372000 ekin = 2.75518266190969 | erot = 1.98699478725925 | epot = -18.0247149368153 | etot = -13.2825374876464 +373000 ekin = 2.72912880528294 | erot = 2.04757125854723 | epot = -18.059237551743 | etot = -13.2825374879128 +374000 ekin = 2.7032481730958 | erot = 2.13030562163336 | epot = -18.116091282967 | etot = -13.2825374882379 +375000 ekin = 2.67714701016783 | erot = 2.230398201263 | epot = -18.190082700051 | etot = -13.2825374886202 +376000 ekin = 2.65054772278835 | erot = 2.34206662745015 | epot = -18.2751518393088 | etot = -13.2825374890703 +377000 ekin = 2.6232286660267 | erot = 2.4585298333916 | epot = -18.3642959890073 | etot = -13.282537489589 +378000 ekin = 2.59495135703951 | erot = 2.57214449993273 | epot = -18.4496333471167 | etot = -13.2825374901445 +379000 ekin = 2.56546707826761 | erot = 2.67491697597518 | epot = -18.5229215449019 | etot = -13.2825374906591 +380000 ekin = 2.5346614309634 | erot = 2.75950320018496 | epot = -18.5767021221684 | etot = -13.28253749102 +381000 ekin = 2.50280930121805 | erot = 2.820545199185 | epot = -18.6058919915259 | etot = -13.2825374911229 +382000 ekin = 2.470812727732 | erot = 2.85587907291203 | epot = -18.6092292915694 | etot = -13.2825374909253 +383000 ekin = 2.44026108011508 | erot = 2.86702983654261 | epot = -18.5898284071357 | etot = -13.282537490478 +384000 ekin = 2.41324034479816 | erot = 2.85867137366513 | epot = -18.5544492083667 | etot = -13.2825374899034 +385000 ekin = 2.39197367794907 | erot = 2.83724859059171 | epot = -18.5117597578793 | etot = -13.2825374893386 +386000 ekin = 2.37848037079664 | erot = 2.80936838549805 | epot = -18.4703862451731 | etot = -13.2825374888784 +387000 ekin = 2.37440773877127 | erot = 2.78057799552109 | epot = -18.4375232228463 | etot = -13.282537488554 +388000 ekin = 2.38106033998957 | erot = 2.75482980994791 | epot = -18.4184276382837 | etot = -13.2825374883462 +389000 ekin = 2.39952694728403 | erot = 2.73455852134344 | epot = -18.4166229568446 | etot = -13.2825374882171 +390000 ekin = 2.43075796801616 | erot = 2.72108399954165 | epot = -18.4343794556986 | etot = -13.2825374881408 +391000 ekin = 2.47547758104241 | erot = 2.71503282253302 | epot = -18.4730478916951 | etot = -13.2825374881197 +392000 ekin = 2.53389941336453 | erot = 2.7165760791739 | epot = -18.5330129807221 | etot = -13.2825374881837 +393000 ekin = 2.60531467139695 | erot = 2.72543162367493 | epot = -18.6132837834427 | etot = -13.2825374883708 +394000 ekin = 2.68770614221252 | erot = 2.74072420161865 | epot = -18.7109678325333 | etot = -13.2825374887021 +395000 ekin = 2.77757589911151 | erot = 2.76089277951452 | epot = -18.8210061677825 | etot = -13.2825374891565 +396000 ekin = 2.87012638573488 | erot = 2.78383015196109 | epot = -18.9364940273617 | etot = -13.2825374896658 +397000 ekin = 2.95979968457167 | erot = 2.80730760068494 | epot = -19.049644775395 | etot = -13.2825374901384 +398000 ekin = 3.04101675292653 | erot = 2.82953067572568 | epot = -19.1530849191508 | etot = -13.2825374904986 +399000 ekin = 3.10335323688597 | erot = 2.84223393463616 | epot = -19.228124720834 | etot = -13.2825375493118 +400000 ekin = 3.10435999780448 | erot = 2.68059016645162 | epot = -19.0674876235106 | etot = -13.2825374592545 +401000 ekin = 3.39309095567053 | erot = 2.6399790010433 | epot = -19.3156074940173 | etot = -13.2825375373034 +402000 ekin = 3.44106634978254 | erot = 2.65979071672222 | epot = -19.3833945765536 | etot = -13.2825375100489 +403000 ekin = 3.43207406395648 | erot = 2.67998452071647 | epot = -19.3945960946571 | etot = -13.2825375099842 +404000 ekin = 3.40426891788004 | erot = 2.70237957197844 | epot = -19.3891859997704 | etot = -13.2825375099119 +405000 ekin = 3.35933473415418 | erot = 2.72607645469475 | epot = -19.3679486986676 | etot = -13.2825375098187 +406000 ekin = 3.29966540903968 | erot = 2.74995079996642 | epot = -19.3321537187046 | etot = -13.2825375096985 +407000 ekin = 3.22823117978945 | erot = 2.77286165528619 | epot = -19.2836303446341 | etot = -13.2825375095584 +408000 ekin = 3.1483591073605 | erot = 2.79373949031154 | epot = -19.2246361071148 | etot = -13.2825375094427 +409000 ekin = 3.06351542880808 | erot = 2.81131469887469 | epot = -19.1573676369864 | etot = -13.2825375093037 +410000 ekin = 2.97699949578463 | erot = 2.8246267920136 | epot = -19.0841637969997 | etot = -13.2825375092014 +411000 ekin = 2.89165449988321 | erot = 2.83289882079081 | epot = -19.007090829806 | etot = -13.282537509132 +412000 ekin = 2.80978906685915 | erot = 2.83549592234132 | epot = -18.9278224982724 | etot = -13.2825375090719 +413000 ekin = 2.73325536963672 | erot = 2.83215388790773 | epot = -18.8479467665295 | etot = -13.2825375089851 +414000 ekin = 2.66364879693787 | erot = 2.82325639295092 | epot = -18.7694426987271 | etot = -13.2825375088383 +415000 ekin = 2.60253860594386 | erot = 2.81004531903034 | epot = -18.6951214335909 | etot = -13.2825375086167 +416000 ekin = 2.55161661467894 | erot = 2.79464631188373 | epot = -18.6288004348987 | etot = -13.2825375083361 +417000 ekin = 2.51265407607916 | erot = 2.77984605492258 | epot = -18.5750376413351 | etot = -13.2825375103333 +418000 ekin = 2.4733460400696 | erot = 2.77799997552928 | epot = -18.5338835235814 | etot = -13.2825375079825 +419000 ekin = 2.44559608968299 | erot = 2.79655231011318 | epot = -18.5246859081161 | etot = -13.2825375083199 +420000 ekin = 2.44884495810883 | erot = 2.8127677686639 | epot = -18.5441502345376 | etot = -13.2825375077648 +421000 ekin = 2.47134322850907 | erot = 2.8275658566971 | epot = -18.581446593281 | etot = -13.2825375080748 +422000 ekin = 2.50522487691509 | erot = 2.84806830842189 | epot = -18.6358306938666 | etot = -13.2825375085297 +423000 ekin = 2.54673540362963 | erot = 2.87162843047139 | epot = -18.7009013431387 | etot = -13.2825375090377 +424000 ekin = 2.59155452677409 | erot = 2.89540834353099 | epot = -18.7695003797936 | etot = -13.2825375094885 +425000 ekin = 2.63549518710331 | erot = 2.91724946462186 | epot = -18.8352821615182 | etot = -13.282537509793 +426000 ekin = 2.67515430282142 | erot = 2.9363216769118 | epot = -18.8940134896421 | etot = -13.2825375099089 +427000 ekin = 2.70835356710237 | erot = 2.95332774897657 | epot = -18.9442188259222 | etot = -13.2825375098433 +428000 ekin = 2.73429370856415 | erot = 2.97029523904671 | epot = -18.9871264572452 | etot = -13.2825375096344 +429000 ekin = 2.75344687777166 | erot = 2.99015713230311 | epot = -19.0261415194056 | etot = -13.2825375093308 +430000 ekin = 2.76726512075389 | erot = 3.01631311482664 | epot = -19.0661157445654 | etot = -13.2825375089849 +431000 ekin = 2.77776520583174 | erot = 3.05220345438128 | epot = -19.1125061688761 | etot = -13.282537508663 +432000 ekin = 2.78700254671475 | erot = 3.10077153002521 | epot = -19.1703115851965 | etot = -13.2825375084566 +433000 ekin = 2.79644099945107 | erot = 3.16368547120708 | epot = -19.2426639791351 | etot = -13.2825375084769 +434000 ekin = 2.80629528100655 | erot = 3.24036053937453 | epot = -19.3291933292032 | etot = -13.2825375088222 +435000 ekin = 2.81503854861979 | erot = 3.32707633254736 | epot = -19.4246523906905 | etot = -13.2825375095233 +436000 ekin = 2.81936003427121 | erot = 3.41666372805949 | epot = -19.5185612728238 | etot = -13.2825375104931 +437000 ekin = 2.81480689570261 | erot = 3.4992068109881 | epot = -19.5965512182087 | etot = -13.282537511518 +438000 ekin = 2.79709037799446 | erot = 3.56380823491998 | epot = -19.6434361252458 | etot = -13.2825375123314 +439000 ekin = 2.76357573484127 | erot = 3.60097663046949 | epot = -19.6470898780263 | etot = -13.2825375127155 +440000 ekin = 2.71419714341147 | erot = 3.60475935377896 | epot = -19.6014940098203 | etot = -13.2825375126299 +441000 ekin = 2.65147586146302 | erot = 3.5735068280095 | epot = -19.5075202016404 | etot = -13.2825375121679 +442000 ekin = 2.57978868208042 | erot = 3.50949061111538 | epot = -19.3718168046633 | etot = -13.2825375114675 +443000 ekin = 2.5045655875428 | erot = 3.41786741963772 | epot = -19.2049705178136 | etot = -13.2825375106331 +444000 ekin = 2.4318529905012 | erot = 3.30558723791353 | epot = -19.0199777381389 | etot = -13.2825375097241 +445000 ekin = 2.36817510309247 | erot = 3.18052048206526 | epot = -18.8312330939434 | etot = -13.2825375087857 +446000 ekin = 2.32036350430697 | erot = 3.05081891042797 | epot = -18.6537199226 | etot = -13.2825375078651 +447000 ekin = 2.29507009388122 | erot = 2.92434156857507 | epot = -18.5019491695335 | etot = -13.2825375070773 +448000 ekin = 2.29792306266074 | erot = 2.80795199469404 | epot = -18.3884125638663 | etot = -13.2825375065115 +449000 ekin = 2.33256968728711 | erot = 2.7069587718276 | epot = -18.3220659653791 | etot = -13.2825375062644 +450000 ekin = 2.39980570006952 | erot = 2.62453468442755 | epot = -18.3068778908976 | etot = -13.2825375064006 +451000 ekin = 2.49706752601316 | erot = 2.56128240619122 | epot = -18.340887439138 | etot = -13.2825375069336 +452000 ekin = 2.61842576959522 | erot = 2.51510244033024 | epot = -18.4160657177069 | etot = -13.2825375077814 +453000 ekin = 2.75505822099767 | erot = 2.4815699152751 | epot = -18.5191656452272 | etot = -13.2825375089544 +454000 ekin = 2.89583245289786 | erot = 2.45420794645489 | epot = -18.6325779096516 | etot = -13.2825375102988 +455000 ekin = 3.02803920575135 | erot = 2.42568753015633 | epot = -18.7362642475679 | etot = -13.2825375116602 +456000 ekin = 3.13847091958599 | erot = 2.38932191986764 | epot = -18.8103303522241 | etot = -13.2825375127704 +457000 ekin = 3.21547363213364 | erot = 2.34093725375183 | epot = -18.838948399153 | etot = -13.2825375132675 +458000 ekin = 3.2519255084935 | erot = 2.28077893488055 | epot = -18.8152419562781 | etot = -13.282537512904 +459000 ekin = 3.24761130317629 | erot = 2.2142990448528 | epot = -18.7444478597993 | etot = -13.2825375117702 +460000 ekin = 3.20922400631774 | erot = 2.15086461862506 | epot = -18.6426261351955 | etot = -13.2825375102527 +461000 ekin = 3.14796311212567 | erot = 2.10092694609436 | epot = -18.5314275669974 | etot = -13.2825375087774 +462000 ekin = 3.07634336772018 | erot = 2.07329933809505 | epot = -18.4321802134275 | etot = -13.2825375076122 +463000 ekin = 3.00570913410551 | erot = 2.0736740452441 | epot = -18.3619206862057 | etot = -13.2825375068561 +464000 ekin = 2.94485829968431 | erot = 2.104311840005 | epot = -18.3317076462087 | etot = -13.2825375065194 +465000 ekin = 2.89946798282509 | erot = 2.16425406359513 | epot = -18.3462595530094 | etot = -13.2825375065892 +466000 ekin = 2.87195252748384 | erot = 2.24955307492882 | epot = -18.4040431094629 | etot = -13.2825375070502 +467000 ekin = 2.86158324929155 | erot = 2.35338924278566 | epot = -18.4975099999498 | etot = -13.2825375078726 +468000 ekin = 2.86493243611462 | erot = 2.46640127712313 | epot = -18.6138712220354 | etot = -13.2825375087976 +469000 ekin = 2.87700241085683 | erot = 2.57824581699685 | epot = -18.7377857379574 | etot = -13.2825375101037 +470000 ekin = 2.89115454215717 | erot = 2.6760619901597 | epot = -18.8497540436439 | etot = -13.2825375113271 +471000 ekin = 2.90087699699639 | erot = 2.74765202472445 | epot = -18.9310665339225 | etot = -13.2825375122017 +472000 ekin = 2.90129360657261 | erot = 2.78442288107442 | epot = -18.968254000156 | etot = -13.282537512509 +473000 ekin = 2.89014262488401 | erot = 2.78350866548211 | epot = -18.9561888025525 | etot = -13.2825375121863 +474000 ekin = 2.86798455519513 | erot = 2.74843722227868 | epot = -18.8989592888434 | etot = -13.2825375113696 +475000 ekin = 2.83751222123448 | erot = 2.68789202058937 | epot = -18.8079417521561 | etot = -13.2825375103323 +476000 ekin = 2.80225697256735 | erot = 2.6131130536835 | epot = -18.6979075356112 | etot = -13.2825375093603 +477000 ekin = 2.76525060538104 | erot = 2.5351054311932 | epot = -18.5828935452201 | etot = -13.2825375086459 +478000 ekin = 2.72814283270942 | erot = 2.46266477167759 | epot = -18.4733451126352 | etot = -13.2825375082482 +479000 ekin = 2.69099471856512 | erot = 2.40160392944764 | epot = -18.3751361561287 | etot = -13.282537508116 +480000 ekin = 2.65266810495577 | erot = 2.35496214915267 | epot = -18.2901677622972 | etot = -13.2825375081888 +481000 ekin = 2.61144235513308 | erot = 2.32364519373199 | epot = -18.2176250571285 | etot = -13.2825375082635 +482000 ekin = 2.56577673011677 | erot = 2.30767778315765 | epot = -18.1559920215987 | etot = -13.2825375083243 +483000 ekin = 2.51481850303814 | erot = 2.3066085334913 | epot = -18.1039645448551 | etot = -13.2825375083257 +484000 ekin = 2.4583813285785 | erot = 2.31984500682984 | epot = -18.0607638434006 | etot = -13.2825375079923 +485000 ekin = 2.37536403472682 | erot = 2.30798475217265 | epot = -17.9658863028417 | etot = -13.2825375159423 +486000 ekin = 2.31029787366189 | erot = 2.2748698765298 | epot = -17.8677052455195 | etot = -13.2825374953278 +487000 ekin = 2.35903895729104 | erot = 2.35840823836807 | epot = -17.999984715744 | etot = -13.2825375200849 +488000 ekin = 2.35207405530543 | erot = 2.45495770512307 | epot = -18.0895692764582 | etot = -13.2825375160297 +489000 ekin = 2.32025825392693 | erot = 2.54616767543756 | epot = -18.1489634454321 | etot = -13.2825375160676 +490000 ekin = 2.29515153865843 | erot = 2.64227715700559 | epot = -18.2199662119985 | etot = -13.2825375163345 +491000 ekin = 2.2772449984618 | erot = 2.73950547065074 | epot = -18.2992879857204 | etot = -13.2825375166078 +492000 ekin = 2.26670396933619 | erot = 2.83351832941017 | epot = -18.3827598156809 | etot = -13.2825375169346 +493000 ekin = 2.26314468313945 | erot = 2.91977614256862 | epot = -18.4654583429805 | etot = -13.2825375172724 +494000 ekin = 2.26577113860128 | erot = 2.99399214337922 | epot = -18.5423007995586 | etot = -13.2825375175781 +495000 ekin = 2.27355094490557 | erot = 3.05259857148999 | epot = -18.6086870342097 | etot = -13.2825375178141 +496000 ekin = 2.28538641730899 | erot = 3.09313022190335 | epot = -18.6610541571706 | etot = -13.2825375179582 +497000 ekin = 2.3002347482288 | erot = 3.1144407210763 | epot = -18.6972129873049 | etot = -13.2825375179998 +498000 ekin = 2.3171936593925 | erot = 3.11678508300488 | epot = -18.7165162603363 | etot = -13.2825375179389 +499000 ekin = 2.33554254161235 | erot = 3.10178716719771 | epot = -18.7198672265934 | etot = -13.2825375177834 +500000 ekin = 2.31317350059265 | erot = 3.05449093047628 | epot = -18.6502019677268 | etot = -13.2825375366579 +501000 ekin = 2.31231722972123 | erot = 3.00810318076113 | epot = -18.6029579372101 | etot = -13.2825375267278 +502000 ekin = 2.3899963895355 | erot = 2.98467042894116 | epot = -18.657204342111 | etot = -13.2825375236343 +503000 ekin = 2.41312387633379 | erot = 2.93091691357846 | epot = -18.6265783132594 | etot = -13.2825375233471 +504000 ekin = 2.43600229237452 | erot = 2.88130858481333 | epot = -18.5998484003212 | etot = -13.2825375231333 +505000 ekin = 2.45757791196529 | erot = 2.8401186666586 | epot = -18.5802341016713 | etot = -13.2825375230474 +506000 ekin = 2.47627134224398 | erot = 2.81025901806717 | epot = -18.5690678834509 | etot = -13.2825375231397 +507000 ekin = 2.48985246050699 | erot = 2.79268587932984 | epot = -18.5650758632795 | etot = -13.2825375234427 +508000 ekin = 2.49542483825493 | erot = 2.78597986937444 | epot = -18.5639422315766 | etot = -13.2825375239472 +509000 ekin = 2.48963204750428 | erot = 2.78630577995571 | epot = -18.5584753520407 | etot = -13.2825375245807 +510000 ekin = 2.4691743887688 | erot = 2.78796571282341 | epot = -18.5396776267959 | etot = -13.2825375252037 +511000 ekin = 2.43159454918128 | erot = 2.78459744696608 | epot = -18.4987295217946 | etot = -13.2825375256472 +512000 ekin = 2.37609227916261 | erot = 2.77073697944887 | epot = -18.4293667843926 | etot = -13.2825375257811 +513000 ekin = 2.30402039322225 | erot = 2.74317280237148 | epot = -18.3297307211636 | etot = -13.2825375255699 +514000 ekin = 2.21884081242786 | erot = 2.7015541486614 | epot = -18.2029324861651 | etot = -13.2825375250758 +515000 ekin = 2.12561338171218 | erot = 2.64810551843191 | epot = -18.056256424559 | etot = -13.2825375244149 +516000 ekin = 2.03029958566718 | erot = 2.58673985991495 | epot = -17.8995769692823 | etot = -13.2825375237002 +517000 ekin = 1.93914577197132 | erot = 2.5220605431355 | epot = -17.7437438381168 | etot = -13.28253752301 +518000 ekin = 1.85826662413893 | erot = 2.45858700715527 | epot = -17.5993911536849 | etot = -13.2825375223908 +519000 ekin = 1.79333215326611 | erot = 2.40035341708905 | epot = -17.476223092216 | etot = -13.2825375218608 +520000 ekin = 1.74929005171215 | erot = 2.35078235677519 | epot = -17.3826099299227 | etot = -13.2825375214353 +521000 ekin = 1.73007209347361 | erot = 2.31266171841647 | epot = -17.3252713330271 | etot = -13.282537521137 +522000 ekin = 1.73822781685003 | erot = 2.28811557190088 | epot = -17.3088809097447 | etot = -13.2825375209937 +523000 ekin = 1.77456624775216 | erot = 2.27850834583591 | epot = -17.3356121146208 | etot = -13.2825375210327 +524000 ekin = 1.8379045851724 | erot = 2.28429322274985 | epot = -17.4047353291923 | etot = -13.28253752127 +525000 ekin = 1.92500868751529 | erot = 2.30484700359158 | epot = -17.5123932128129 | etot = -13.282537521706 +526000 ekin = 2.03075780261764 | erot = 2.33833465322237 | epot = -17.6516299781653 | etot = -13.2825375223253 +527000 ekin = 2.14850843909257 | erot = 2.38164040104111 | epot = -17.8126863632292 | etot = -13.2825375230955 +528000 ekin = 2.2706009665318 | erot = 2.43041424714547 | epot = -17.9835527376429 | etot = -13.2825375239656 +529000 ekin = 2.38896012867467 | erot = 2.47931387509597 | epot = -18.150811528629 | etot = -13.2825375248584 +530000 ekin = 2.4957694053979 | erot = 2.52254117019752 | epot = -18.3008481012612 | etot = -13.2825375256658 +531000 ekin = 2.58420744224834 | erot = 2.55472238423688 | epot = -18.4214673527446 | etot = -13.2825375262593 +532000 ekin = 2.64918587021021 | erot = 2.57201883159204 | epot = -18.5037422283274 | etot = -13.2825375265252 +533000 ekin = 2.68793333158334 | erot = 2.57313230806675 | epot = -18.5436031660632 | etot = -13.2825375264131 +534000 ekin = 2.7002120821811 | erot = 2.55975253143246 | epot = -18.5425021395846 | etot = -13.2825375259711 +535000 ekin = 2.68802701636055 | erot = 2.5361501485681 | epot = -18.5067146902622 | etot = -13.2825375253335 +536000 ekin = 2.65489019113613 | erot = 2.50801671119336 | epot = -18.4454444269979 | etot = -13.2825375246684 +537000 ekin = 2.60490332064252 | erot = 2.481023337825 | epot = -18.3684641825809 | etot = -13.2825375241133 +538000 ekin = 2.54198784535114 | erot = 2.45965628954573 | epot = -18.2841816578421 | etot = -13.2825375229452 +539000 ekin = 2.47150013363699 | erot = 2.44756195577151 | epot = -18.2015996123808 | etot = -13.2825375229723 +540000 ekin = 2.39647534123056 | erot = 2.44525435897827 | epot = -18.124267223265 | etot = -13.2825375230561 +541000 ekin = 2.31786635163547 | erot = 2.45130088246703 | epot = -18.0517047572224 | etot = -13.2825375231199 +542000 ekin = 2.23702678127242 | erot = 2.46423888155736 | epot = -17.9838031859226 | etot = -13.2825375230928 +543000 ekin = 2.15612181944835 | erot = 2.4831366740889 | epot = -17.9217960164714 | etot = -13.2825375229342 +544000 ekin = 2.07836492813028 | erot = 2.50789688702757 | epot = -17.8687993378082 | etot = -13.2825375226504 +545000 ekin = 2.0079425836599 | erot = 2.5391884088184 | epot = -17.8296685147796 | etot = -13.2825375223013 +546000 ekin = 1.94957099406152 | erot = 2.57800819606447 | epot = -17.8101167121046 | etot = -13.2825375219786 +547000 ekin = 1.90776242425117 | erot = 2.62501532095444 | epot = -17.8153152669927 | etot = -13.2825375217871 +548000 ekin = 1.88600984704774 | erot = 2.67988146407457 | epot = -17.8484288329186 | etot = -13.2825375217963 +549000 ekin = 1.88615242684612 | erot = 2.7409037562111 | epot = -17.90959370508 | etot = -13.2825375220228 +550000 ekin = 1.90811801075785 | erot = 2.80501593008068 | epot = -17.9956714632668 | etot = -13.2825375224283 +551000 ekin = 1.95008337619707 | erot = 2.8681680442257 | epot = -18.1007889433631 | etot = -13.2825375229403 +552000 ekin = 2.00893649348012 | erot = 2.92590890431006 | epot = -18.2173829212704 | etot = -13.2825375234803 +553000 ekin = 2.08084803908336 | erot = 2.97396311014114 | epot = -18.3373486732109 | etot = -13.2825375239864 +554000 ekin = 2.16178844740114 | erot = 3.00865361320263 | epot = -18.452979585024 | etot = -13.2825375244202 +555000 ekin = 2.24792031028555 | erot = 3.02713377655537 | epot = -18.5575916115995 | etot = -13.2825375247586 +556000 ekin = 2.3358895304513 | erot = 3.02749801452678 | epot = -18.6459250699588 | etot = -13.2825375249808 +557000 ekin = 2.42273135016537 | erot = 3.0079937814166 | epot = -18.7132626569264 | etot = -13.2825375253445 +558000 ekin = 2.50467530617043 | erot = 2.96457109815147 | epot = -18.7517839296998 | etot = -13.2825375253779 +559000 ekin = 2.57989829545908 | erot = 2.89795083555213 | epot = -18.7603866561733 | etot = -13.2825375251621 +560000 ekin = 2.64819333039288 | erot = 2.81150114191978 | epot = -18.742231997059 | etot = -13.2825375247463 +561000 ekin = 2.7104101471449 | erot = 2.71050571098959 | epot = -18.7034533823758 | etot = -13.2825375242413 +562000 ekin = 2.76764108182985 | erot = 2.60142670489701 | epot = -18.6516053104994 | etot = -13.2825375237726 +563000 ekin = 2.8204133217691 | erot = 2.4909454000306 | epot = -18.5938962452166 | etot = -13.2825375234169 +564000 ekin = 2.86835957175242 | erot = 2.38512022714126 | epot = -18.536017322071 | etot = -13.2825375231773 +565000 ekin = 2.91050556249757 | erot = 2.28886993106156 | epot = -18.481913016576 | etot = -13.2825375230169 +566000 ekin = 2.94583619535282 | erot = 2.20572382115438 | epot = -18.4340975394231 | etot = -13.2825375229159 +567000 ekin = 2.97364576055568 | erot = 2.13764971286302 | epot = -18.3938329963098 | etot = -13.2825375228911 +568000 ekin = 2.99348659090309 | erot = 2.08490808296841 | epot = -18.360932196845 | etot = -13.2825375229735 +569000 ekin = 3.00487691646457 | erot = 2.04604350397463 | epot = -18.3334579436043 | etot = -13.2825375231651 +570000 ekin = 3.00710556181106 | erot = 2.01819764944608 | epot = -18.3078407346813 | etot = -13.2825375234241 +571000 ekin = 2.99930468666728 | erot = 1.99774357921139 | epot = -18.2795857895585 | etot = -13.2825375236798 +572000 ekin = 2.98076231237764 | erot = 1.98107714037278 | epot = -18.2443769766043 | etot = -13.2825375238539 +573000 ekin = 2.95134611354571 | erot = 1.96535938859269 | epot = -18.1992430260208 | etot = -13.2825375238824 +574000 ekin = 2.91190615156914 | erot = 1.94906161393782 | epot = -18.1435052892334 | etot = -13.2825375237264 +575000 ekin = 2.86455063783071 | erot = 1.93223482559859 | epot = -18.079322986811 | etot = -13.2825375233817 +576000 ekin = 2.81270724054619 | erot = 1.91646454104923 | epot = -18.0117093044799 | etot = -13.2825375228844 +577000 ekin = 2.76090536128439 | erot = 1.9045038205141 | epot = -17.9479467041077 | etot = -13.2825375223092 +578000 ekin = 2.71428886858076 | erot = 1.89991544416371 | epot = -17.8967418344083 | etot = -13.2825375216638 +579000 ekin = 2.67747364109253 | erot = 1.90598531718256 | epot = -17.8659964795852 | etot = -13.2825375213101 +580000 ekin = 2.65399321096934 | erot = 1.92422800253644 | epot = -17.8607587346238 | etot = -13.282537521118 +581000 ekin = 2.64614770784911 | erot = 1.95489680824256 | epot = -17.883582037231 | etot = -13.2825375211393 +582000 ekin = 2.65445309232027 | erot = 1.99685469220196 | epot = -17.9338453059165 | etot = -13.2825375213943 +583000 ekin = 2.67733631605306 | erot = 2.04763712313085 | epot = -18.0075109610395 | etot = -13.2825375218556 +584000 ekin = 2.71054840601244 | erot = 2.10372916960457 | epot = -18.0968150982853 | etot = -13.2825375226683 +585000 ekin = 2.74737763681928 | erot = 2.16073411835811 | epot = -18.1906492785603 | etot = -13.282537523383 +586000 ekin = 2.7813786998355 | erot = 2.21419390100359 | epot = -18.2781101248089 | etot = -13.2825375239698 +587000 ekin = 2.80697388603962 | erot = 2.26053952382245 | epot = -18.3500509341984 | etot = -13.2825375243363 +588000 ekin = 2.82026432869703 | erot = 2.29760845660022 | epot = -18.4004103097634 | etot = -13.2825375244661 +589000 ekin = 2.81926713936076 | erot = 2.32471340247167 | epot = -18.4265180662398 | etot = -13.2825375244073 +590000 ekin = 2.80363912211435 | erot = 2.34232144628174 | epot = -18.4284980926317 | etot = -13.2825375242356 +591000 ekin = 2.77414618244973 | erot = 2.35158565792353 | epot = -18.4082693643883 | etot = -13.282537524015 +592000 ekin = 2.73214162068033 | erot = 2.35397672704535 | epot = -18.3686558715069 | etot = -13.2825375237812 +593000 ekin = 2.67919893301821 | erot = 2.35111989741865 | epot = -18.3128563539823 | etot = -13.2825375235455 +594000 ekin = 2.61691997575019 | erot = 2.34478637079319 | epot = -18.2442438698508 | etot = -13.2825375233074 +595000 ekin = 2.54687226698967 | erot = 2.33692048100541 | epot = -18.1663302710608 | etot = -13.2825375230657 +596000 ekin = 2.47060065847364 | erot = 2.32961421031687 | epot = -18.0827523916134 | etot = -13.2825375228228 +597000 ekin = 2.38967001316585 | erot = 2.32500896595718 | epot = -17.9972165017067 | etot = -13.2825375225837 +598000 ekin = 2.30571268082223 | erot = 2.32515834060408 | epot = -17.9134085437803 | etot = -13.282537522354 +599000 ekin = 2.22046028550116 | erot = 2.33189649118178 | epot = -17.8348942988225 | etot = -13.2825375221395 +600000 ekin = 2.13574370490705 | erot = 2.34673734057022 | epot = -17.7650185674242 | etot = -13.2825375219469 +601000 ekin = 2.05345123937653 | erot = 2.37080533030337 | epot = -17.7067940914646 | etot = -13.2825375217847 +602000 ekin = 1.97544542053429 | erot = 2.40478648031343 | epot = -17.6627694225103 | etot = -13.2825375216626 +603000 ekin = 1.9034510520118 | erot = 2.44889273156788 | epot = -17.6348813051703 | etot = -13.2825375215906 +604000 ekin = 1.83893895945378 | erot = 2.50284547570514 | epot = -17.6243219567308 | etot = -13.2825375215719 +605000 ekin = 1.78304137655287 | erot = 2.56590806869957 | epot = -17.6314869668566 | etot = -13.2825375216041 +606000 ekin = 1.736517005622 | erot = 2.63697396084372 | epot = -17.6560284881414 | etot = -13.2825375216757 +607000 ekin = 1.69978182226254 | erot = 2.71471645486191 | epot = -17.6970357988931 | etot = -13.2825375217686 +608000 ekin = 1.67299629743623 | erot = 2.79777529958915 | epot = -17.7533091188892 | etot = -13.2825375218638 +609000 ekin = 1.65617951190665 | erot = 2.88492902630375 | epot = -17.8236460601579 | etot = -13.2825375219475 +610000 ekin = 1.64931072740771 | erot = 2.97519912008037 | epot = -17.9070473695038 | etot = -13.2825375220157 +611000 ekin = 1.65238727025306 | erot = 3.06785620899647 | epot = -18.0027810013235 | etot = -13.2825375220739 +612000 ekin = 1.66542824834998 | erot = 3.16233835695483 | epot = -18.1103041274379 | etot = -13.2825375221331 +613000 ekin = 1.68843555860806 | erot = 3.25812385028217 | epot = -18.229096931095 | etot = -13.2825375222048 +614000 ekin = 1.72133601882631 | erot = 3.35460405562833 | epot = -18.3584775967531 | etot = -13.2825375222984 +615000 ekin = 1.76392386055006 | erot = 3.45098117167973 | epot = -18.4974425546512 | etot = -13.2825375224214 +616000 ekin = 1.81580855352879 | erot = 3.54618284211553 | epot = -18.6445289182269 | etot = -13.2825375225826 +617000 ekin = 1.87635766444892 | erot = 3.63876572292309 | epot = -18.7976609101672 | etot = -13.2825375227952 +618000 ekin = 1.94461656663335 | erot = 3.72678561706335 | epot = -18.9539397067739 | etot = -13.2825375230772 +619000 ekin = 2.01919440946448 | erot = 3.80764383017264 | epot = -19.1093757630845 | etot = -13.2825375234473 +620000 ekin = 2.09812821732459 | erot = 3.87796751089518 | epot = -19.258633252134 | etot = -13.2825375239142 +621000 ekin = 2.17876896452369 | erot = 3.9336243470245 | epot = -19.3949308360123 | etot = -13.2825375244641 +622000 ekin = 2.25776112944306 | erot = 3.96997899371136 | epot = -19.5102776482054 | etot = -13.282537525051 +623000 ekin = 2.33118920319666 | erot = 3.98244070312544 | epot = -19.5961674319216 | etot = -13.2825375255995 +624000 ekin = 2.39492361710553 | erot = 3.96722578269959 | epot = -19.6446869258275 | etot = -13.2825375260223 +625000 ekin = 2.445122210933 | erot = 3.92212025382369 | epot = -19.6497799910047 | etot = -13.282537526248 +626000 ekin = 2.47876984838125 | erot = 3.84697362716387 | epot = -19.6082810017884 | etot = -13.2825375262432 +627000 ekin = 2.49411681790099 | erot = 3.74375083248538 | epot = -19.5204051764041 | etot = -13.2825375260178 +628000 ekin = 2.49092177716844 | erot = 3.61617309043397 | epot = -19.3896323932121 | etot = -13.2825375256096 +629000 ekin = 2.47048208783205 | erot = 3.46915451631132 | epot = -19.2221741292085 | etot = -13.2825375250651 +630000 ekin = 2.43548970061162 | erot = 3.30827690351569 | epot = -19.0263041285523 | etot = -13.282537524425 +631000 ekin = 2.38975948996613 | erot = 3.13944249320995 | epot = -18.8117395069008 | etot = -13.2825375237248 +632000 ekin = 2.33785618698542 | erot = 2.96869689909723 | epot = -18.5890906090837 | etot = -13.2825375230011 +633000 ekin = 2.28462964544115 | erot = 2.80211551086663 | epot = -18.3692826786082 | etot = -13.2825375223005 +634000 ekin = 2.23467746223165 | erot = 2.64563252187923 | epot = -18.1628475057907 | etot = -13.2825375216799 +635000 ekin = 2.15322765543132 | erot = 2.47835094336846 | epot = -17.9141161495184 | etot = -13.2825375507186 +636000 ekin = 2.04549908133069 | erot = 2.31412508405115 | epot = -17.6421616868109 | etot = -13.2825375214291 +637000 ekin = 2.11104805175097 | erot = 2.29419960731515 | epot = -17.6877852052413 | etot = -13.2825375461752 +638000 ekin = 2.16990019917156 | erot = 2.2679567393031 | epot = -17.7203944764658 | etot = -13.2825375379911 +639000 ekin = 2.15825321743296 | erot = 2.17815663923705 | epot = -17.618947382456 | etot = -13.282537525786 +640000 ekin = 2.18911467644369 | erot = 2.15600946831685 | epot = -17.627661668769 | etot = -13.2825375240084 +641000 ekin = 2.26653815123457 | erot = 2.22106973674797 | epot = -17.7701454241734 | etot = -13.2825375361909 +642000 ekin = 2.3144469471055 | erot = 2.28426426145084 | epot = -17.8812487361676 | etot = -13.2825375276113 +643000 ekin = 2.32966846054207 | erot = 2.32625113868682 | epot = -17.9384571273534 | etot = -13.2825375281245 +644000 ekin = 2.33971908606118 | erot = 2.36941556717976 | epot = -17.9916721817351 | etot = -13.2825375284942 +645000 ekin = 2.34497836839587 | erot = 2.40804261253567 | epot = -18.0355585095904 | etot = -13.2825375286589 +646000 ekin = 2.34716147917123 | erot = 2.43809135045114 | epot = -18.0677903582286 | etot = -13.2825375286062 +647000 ekin = 2.34901351981608 | erot = 2.45765540472021 | epot = -18.0892064529145 | etot = -13.2825375283782 +648000 ekin = 2.35429037962735 | erot = 2.46814608869922 | epot = -18.104973996447 | etot = -13.2825375281204 +649000 ekin = 2.36637490476275 | erot = 2.47306901795835 | epot = -18.1219814507637 | etot = -13.2825375280426 +650000 ekin = 2.38594651024424 | erot = 2.47280388235694 | epot = -18.1412879205825 | etot = -13.2825375279813 +651000 ekin = 2.41290732393566 | erot = 2.46797500557286 | epot = -18.1634198574497 | etot = -13.2825375279412 +652000 ekin = 2.44657292409709 | erot = 2.45942209570518 | epot = -18.1885325477104 | etot = -13.2825375279081 +653000 ekin = 2.48591189131261 | erot = 2.44818643125859 | epot = -18.216635850432 | etot = -13.2825375278608 +654000 ekin = 2.52980786353021 | erot = 2.43558904352257 | epot = -18.2479344348361 | etot = -13.2825375277833 +655000 ekin = 2.57725720746836 | erot = 2.42329690336763 | epot = -18.2830916385098 | etot = -13.2825375276738 +656000 ekin = 2.62745567870598 | erot = 2.41329334491405 | epot = -18.3232865511668 | etot = -13.2825375275468 +657000 ekin = 2.67977157736399 | erot = 2.40771681185305 | epot = -18.3700259166474 | etot = -13.2825375274304 +658000 ekin = 2.73363379229086 | erot = 2.40858022061921 | epot = -18.4247515402698 | etot = -13.2825375273597 +659000 ekin = 2.78837854459658 | erot = 2.41741767328155 | epot = -18.4883337452466 | etot = -13.2825375273685 +660000 ekin = 2.84314536322858 | erot = 2.43497153591091 | epot = -18.5606544265713 | etot = -13.2825375274319 +661000 ekin = 2.89550751715279 | erot = 2.46002725149102 | epot = -18.6380722967303 | etot = -13.2825375280865 +662000 ekin = 2.93874528646413 | erot = 2.48685588461621 | epot = -18.708138699778 | etot = -13.2825375286977 +663000 ekin = 2.9687171942415 | erot = 2.51022783071497 | epot = -18.7614825541983 | etot = -13.2825375292419 +664000 ekin = 2.98246138427311 | erot = 2.52516926734448 | epot = -18.7901681812018 | etot = -13.2825375295842 +665000 ekin = 2.97884445494023 | erot = 2.52787955705445 | epot = -18.7892615416123 | etot = -13.2825375296177 +666000 ekin = 2.95920183353605 | erot = 2.51661508434599 | epot = -18.7583544471906 | etot = -13.2825375293085 +667000 ekin = 2.92742550356365 | erot = 2.49210329858316 | epot = -18.702066330864 | etot = -13.2825375287172 +668000 ekin = 2.88934250717656 | erot = 2.45736670750009 | epot = -18.6292467426517 | etot = -13.282537527975 +669000 ekin = 2.85155010044156 | erot = 2.41708074176435 | epot = -18.5511683694359 | etot = -13.28253752723 +670000 ekin = 2.82014314471955 | erot = 2.37673699551223 | epot = -18.4794176668284 | etot = -13.2825375265966 +671000 ekin = 2.79977472961205 | erot = 2.34183940273354 | epot = -18.4241516586146 | etot = -13.282537526269 +672000 ekin = 2.79293252634008 | erot = 2.31695226011576 | epot = -18.3924223124527 | etot = -13.2825375259969 +673000 ekin = 2.80034442408037 | erot = 2.30554472206325 | epot = -18.3884266720798 | etot = -13.2825375259361 +674000 ekin = 2.82129825256449 | erot = 2.30955451981648 | epot = -18.4133902984753 | etot = -13.2825375260944 +675000 ekin = 2.85361934145821 | erot = 2.32878748968739 | epot = -18.4649443576069 | etot = -13.2825375264613 +676000 ekin = 2.89394924995267 | erot = 2.36084337707399 | epot = -18.5373301540152 | etot = -13.2825375269885 +677000 ekin = 2.93819888436731 | erot = 2.40146056805032 | epot = -18.622196980004 | etot = -13.2825375275863 +678000 ekin = 2.98219881046511 | erot = 2.44527797789796 | epot = -18.7100143165049 | etot = -13.2825375281419 +679000 ekin = 3.0224273551935 | erot = 2.48684948025749 | epot = -18.7918143640021 | etot = -13.2825375285511 +680000 ekin = 3.05660821680256 | erot = 2.52163649378434 | epot = -18.8607822393395 | etot = -13.2825375287526 +681000 ekin = 3.08399348184627 | erot = 2.54671087858252 | epot = -18.913241889164 | etot = -13.2825375287352 +682000 ekin = 3.10527370304788 | erot = 2.56103519408599 | epot = -18.9488464256748 | etot = -13.2825375285409 +683000 ekin = 3.12217420783238 | erot = 2.56530128681684 | epot = -18.970013022889 | etot = -13.2825375282398 +684000 ekin = 3.13689854376774 | erot = 2.56147023258304 | epot = -18.9809063042598 | etot = -13.282537527909 +685000 ekin = 3.1516175207619 | erot = 2.55220833199615 | epot = -18.9863633803528 | etot = -13.2825375275947 +686000 ekin = 3.16825656288024 | erot = 2.5404714195813 | epot = -18.9912655098718 | etot = -13.2825375274103 +687000 ekin = 3.18756268898112 | erot = 2.52861508568613 | epot = -18.9987153019925 | etot = -13.2825375273252 +688000 ekin = 3.20935294724633 | erot = 2.51834078646032 | epot = -19.0102312610592 | etot = -13.2825375273526 +689000 ekin = 3.232603857627 | erot = 2.51058529363817 | epot = -19.0257266787599 | etot = -13.2825375274947 +690000 ekin = 3.25550449412986 | erot = 2.50541094760363 | epot = -19.0434529694767 | etot = -13.2825375277432 +691000 ekin = 3.27559454461619 | erot = 2.50196131507165 | epot = -19.0600933877637 | etot = -13.2825375280759 +692000 ekin = 3.29000453529088 | erot = 2.49851988079962 | epot = -19.0710619445408 | etot = -13.2825375284503 +693000 ekin = 3.29579865376218 | erot = 2.49273974858803 | epot = -19.0710759311567 | etot = -13.2825375288065 +694000 ekin = 3.29036742009323 | erot = 2.48207188557003 | epot = -19.0549768347445 | etot = -13.2825375290813 +695000 ekin = 3.27176421105106 | erot = 2.46431581831664 | epot = -19.018617558596 | etot = -13.2825375292283 +696000 ekin = 3.23887890273548 | erot = 2.43812365834886 | epot = -18.9595400903186 | etot = -13.2825375292342 +697000 ekin = 3.19141377377666 | erot = 2.40329594550704 | epot = -18.8772472483983 | etot = -13.2825375291146 +698000 ekin = 3.12971664175668 | erot = 2.36079934043281 | epot = -18.7730535110947 | etot = -13.2825375289052 +699000 ekin = 3.05458980626054 | erot = 2.31258576039904 | epot = -18.6497130952911 | etot = -13.2825375286315 +700000 ekin = 2.96718102298747 | erot = 2.26139197208619 | epot = -18.511110523382 | etot = -13.2825375283083 +701000 ekin = 2.86896613295136 | erot = 2.21057215459575 | epot = -18.3620758154883 | etot = -13.2825375279412 +702000 ekin = 2.76178671337415 | erot = 2.16397434352371 | epot = -18.2082985844344 | etot = -13.2825375275365 +703000 ekin = 2.6478712031048 | erot = 2.12574771744291 | epot = -18.0561564515416 | etot = -13.2825375309939 +704000 ekin = 2.52933762848166 | erot = 2.08674637122766 | epot = -17.8986215283831 | etot = -13.2825375286737 +705000 ekin = 2.41679696536635 | erot = 2.05664012325241 | epot = -17.7559746148874 | etot = -13.2825375262686 +706000 ekin = 2.30501007356423 | erot = 2.0611587655127 | epot = -17.6487063635301 | etot = -13.2825375244532 +707000 ekin = 2.19269241365679 | erot = 2.113750463821 | epot = -17.5889804021149 | etot = -13.2825375246371 +708000 ekin = 2.09960598348176 | erot = 2.19681319891601 | epot = -17.57895670939 | etot = -13.2825375269922 +709000 ekin = 2.01320280623464 | erot = 2.28016876647 | epot = -17.5759090980898 | etot = -13.2825375253852 +710000 ekin = 1.93302644427356 | erot = 2.37473228784994 | epot = -17.5902962580752 | etot = -13.2825375259517 +711000 ekin = 1.85957279067715 | erot = 2.47358324929754 | epot = -17.6156935666084 | etot = -13.2825375266337 +712000 ekin = 1.79282630268912 | erot = 2.56690430142539 | epot = -17.642268131402 | etot = -13.2825375272875 +713000 ekin = 1.73341814876089 | erot = 2.64462400340569 | epot = -17.6605796799123 | etot = -13.2825375277457 +714000 ekin = 1.68328438252143 | erot = 2.69817364688335 | epot = -17.6639955572831 | etot = -13.2825375278783 +715000 ekin = 1.64594117648568 | erot = 2.72207244107394 | epot = -17.6505511452113 | etot = -13.2825375276517 +716000 ekin = 1.62610172701181 | erot = 2.71479815151566 | epot = -17.6234374056764 | etot = -13.282537527149 +717000 ekin = 1.62864489627545 | erot = 2.67867233618631 | epot = -17.589854758993 | etot = -13.2825375265313 +718000 ekin = 1.65730138310094 | erot = 2.6189183926284 | epot = -17.5587573016927 | etot = -13.2825375259634 +719000 ekin = 1.71360335058015 | erot = 2.54235654223589 | epot = -17.5384974183669 | etot = -13.2825375255509 +720000 ekin = 1.79650653909672 | erot = 2.45621436685583 | epot = -17.5352584312718 | etot = -13.2825375253192 +721000 ekin = 1.90273489852489 | erot = 2.36731439641998 | epot = -17.5525868201814 | etot = -13.2825375252366 +722000 ekin = 2.02756635877135 | erot = 2.28163864595547 | epot = -17.5917425299821 | etot = -13.2825375252553 +723000 ekin = 2.16566245424335 | erot = 2.20411346294851 | epot = -17.6523134425365 | etot = -13.2825375253446 +724000 ekin = 2.31164907977026 | erot = 2.13844446404667 | epot = -17.7326310693194 | etot = -13.2825375255025 +725000 ekin = 2.46036017286876 | erot = 2.0869120441014 | epot = -17.8298097427178 | etot = -13.2825375257477 +726000 ekin = 2.60683496355671 | erot = 2.05013619406281 | epot = -17.9395086837224 | etot = -13.2825375261029 +727000 ekin = 2.74622028398704 | erot = 2.02690424050256 | epot = -18.0556620510616 | etot = -13.282537526572 +728000 ekin = 2.87374866259628 | erot = 2.01419303066656 | epot = -18.1704792203877 | etot = -13.2825375271249 +729000 ekin = 2.98490085178579 | erot = 2.00751009694371 | epot = -18.27494847642 | etot = -13.2825375276905 +730000 ekin = 3.07576690667731 | erot = 2.00160558070566 | epot = -18.359910015553 | etot = -13.28253752817 +731000 ekin = 3.14351022574244 | erot = 1.99146923020489 | epot = -18.4175169844133 | etot = -13.282537528466 +732000 ekin = 3.18676307284264 | erot = 1.97337750697634 | epot = -18.4426781083327 | etot = -13.2825375285137 +733000 ekin = 3.20579220152253 | erot = 1.9456870659553 | epot = -18.4340167957808 | etot = -13.282537528303 +734000 ekin = 3.20238921812918 | erot = 1.90917251422492 | epot = -18.3940992602234 | etot = -13.2825375278693 +735000 ekin = 3.17951096479738 | erot = 1.86680153237891 | epot = -18.3288500244819 | etot = -13.2825375273056 +736000 ekin = 3.14073865389039 | erot = 1.8230058759971 | epot = -18.2462820565793 | etot = -13.2825375266918 +737000 ekin = 3.08984658437012 | erot = 1.78292393032115 | epot = -18.1553080407961 | etot = -13.2825375261048 +738000 ekin = 3.03043228101277 | erot = 1.75161934959083 | epot = -18.0645891562027 | etot = -13.2825375255991 +739000 ekin = 2.96566842757407 | erot = 1.73346651117868 | epot = -17.9816724639599 | etot = -13.2825375252071 +740000 ekin = 2.89817088986259 | erot = 1.73175552877345 | epot = -17.912463943576 | etot = -13.28253752494 +741000 ekin = 2.82995232211993 | erot = 1.74850528634245 | epot = -17.8609951332633 | etot = -13.282537524801 +742000 ekin = 2.76247533972923 | erot = 1.78434362386512 | epot = -17.8293564883915 | etot = -13.2825375247972 +743000 ekin = 2.69668176519633 | erot = 1.83847103681881 | epot = -17.8176903269097 | etot = -13.2825375248946 +744000 ekin = 2.6331144461464 | erot = 1.90875045568272 | epot = -17.8244024269328 | etot = -13.2825375251037 +745000 ekin = 2.5719649351672 | erot = 1.99171779991018 | epot = -17.8462202604955 | etot = -13.2825375254181 +746000 ekin = 2.51311596152491 | erot = 2.0826421561814 | epot = -17.8782956435303 | etot = -13.282537525824 +747000 ekin = 2.45621024026481 | erot = 2.17571767245968 | epot = -17.9144654390156 | etot = -13.2825375262911 +748000 ekin = 2.4007641204603 | erot = 2.26445242853415 | epot = -17.9477540757611 | etot = -13.2825375267666 +749000 ekin = 2.34635697390621 | erot = 2.34231237598165 | epot = -17.9712068770626 | etot = -13.2825375271748 +750000 ekin = 2.29290375451926 | erot = 2.40359513867759 | epot = -17.9790364206262 | etot = -13.2825375274293 +751000 ekin = 2.24097207239074 | erot = 2.44437862835496 | epot = -17.9678882282051 | etot = -13.2825375274594 +752000 ekin = 2.19206377659927 | erot = 2.46328788147024 | epot = -17.9378891852944 | etot = -13.2825375272249 +753000 ekin = 2.01910736680425 | erot = 2.37844688257153 | epot = -17.6800917192355 | etot = -13.2825374698597 +754000 ekin = 2.03397419758721 | erot = 2.38379927539831 | epot = -17.7003109699574 | etot = -13.2825374969719 +755000 ekin = 2.10287082583243 | erot = 2.42269050537392 | epot = -17.808098775342 | etot = -13.2825374441357 +756000 ekin = 2.09556625459035 | erot = 2.40575096267731 | epot = -17.7838546607744 | etot = -13.2825374435067 +757000 ekin = 2.11013463605079 | erot = 2.39174642208689 | epot = -17.7844185011481 | etot = -13.2825374430104 +758000 ekin = 2.14991880608121 | erot = 2.38537981475823 | epot = -17.8178360635602 | etot = -13.2825374427207 +759000 ekin = 2.21691275096553 | erot = 2.38948785856312 | epot = -17.8889380522097 | etot = -13.2825374426811 +760000 ekin = 2.31141054899228 | erot = 2.40468264922822 | epot = -17.9986306411391 | etot = -13.2825374429186 +761000 ekin = 2.43175472397619 | erot = 2.42917556867249 | epot = -18.1434677360907 | etot = -13.282537443442 +762000 ekin = 2.57423243283704 | erot = 2.45878794779634 | epot = -18.3155578248644 | etot = -13.2825374442311 +763000 ekin = 2.73317609373997 | erot = 2.48721280702134 | epot = -18.5029263459876 | etot = -13.2825374452263 +764000 ekin = 2.90131643326679 | erot = 2.50663479900723 | epot = -18.690488678594 | etot = -13.28253744632 +765000 ekin = 3.07040159566699 | erot = 2.50879317366612 | epot = -18.8617322166939 | etot = -13.2825374473608 +766000 ekin = 3.23203071048149 | erot = 2.48644536532744 | epot = -19.0010135239876 | etot = -13.2825374481786 +767000 ekin = 3.37856609507255 | erot = 2.43498273995184 | epot = -19.0960862836549 | etot = -13.2825374486305 +768000 ekin = 3.50392633330507 | erot = 2.35374465383522 | epot = -19.1402084357865 | etot = -13.2825374486462 +769000 ekin = 3.60408080015212 | erot = 2.24656658386371 | epot = -19.1331848322651 | etot = -13.2825374482493 +770000 ekin = 3.67731902122504 | erot = 2.12129309978206 | epot = -19.0811495685446 | etot = -13.2825374475374 +771000 ekin = 3.72500466537174 | erot = 1.98803922980452 | epot = -18.9955813418785 | etot = -13.2825374467023 +772000 ekin = 3.73784328897891 | erot = 1.84847100615872 | epot = -18.8688517432933 | etot = -13.2825374481557 +773000 ekin = 3.73518377850858 | erot = 1.74399251375944 | epot = -18.761713737683 | etot = -13.2825374454149 +774000 ekin = 3.73326270400355 | erot = 1.69319142559955 | epot = -18.7089915837464 | etot = -13.2825374541433 +775000 ekin = 3.70600761043796 | erot = 1.6566239979388 | epot = -18.6451690563952 | etot = -13.2825374480184 +776000 ekin = 3.66620956029523 | erot = 1.65229490555453 | epot = -18.6010419136787 | etot = -13.282537447829 +777000 ekin = 3.61649590749819 | erot = 1.68124406448108 | epot = -18.5802774198126 | etot = -13.2825374478333 +778000 ekin = 3.55892172037955 | erot = 1.74156460696009 | epot = -18.5830237753754 | etot = -13.2825374480357 +779000 ekin = 3.49505249872284 | erot = 1.82861083535278 | epot = -18.6062007829277 | etot = -13.2825374488521 +780000 ekin = 3.42606052970244 | erot = 1.93200454593087 | epot = -18.6406025252668 | etot = -13.2825374496335 +781000 ekin = 3.35141348725842 | erot = 2.04005284573706 | epot = -18.6740037834645 | etot = -13.2825374504691 +782000 ekin = 3.2700234367696 | erot = 2.14152553729048 | epot = -18.6940864252466 | etot = -13.2825374511865 +783000 ekin = 3.18141085684875 | erot = 2.22636120811957 | epot = -18.690309516577 | etot = -13.2825374516087 +784000 ekin = 3.08656488529642 | erot = 2.28735807349748 | epot = -18.6564604104105 | etot = -13.2825374516166 +785000 ekin = 2.98843914069599 | erot = 2.32136711573499 | epot = -18.592343707635 | etot = -13.282537451204 +786000 ekin = 2.89178850824096 | erot = 2.3295414984193 | epot = -18.5038674571453 | etot = -13.2825374504851 +787000 ekin = 2.8023307080712 | erot = 2.31656731751225 | epot = -18.4014354752266 | etot = -13.2825374496432 +788000 ekin = 2.72556137551752 | erot = 2.28924565772307 | epot = -18.2973444820957 | etot = -13.2825374488551 +789000 ekin = 2.6656985022175 | erot = 2.25498711354848 | epot = -18.2032230640058 | etot = -13.2825374482399 +790000 ekin = 2.62507547599935 | erot = 2.22062577794683 | epot = -18.1282387017979 | etot = -13.2825374478518 +791000 ekin = 2.60400664952963 | erot = 2.19166523694291 | epot = -18.0782093341748 | etot = -13.2825374477022 +792000 ekin = 2.60095165935059 | erot = 2.17186849882108 | epot = -18.0553576059557 | etot = -13.282537447784 +793000 ekin = 2.61278727243034 | erot = 2.1630579474879 | epot = -18.0583826680031 | etot = -13.2825374480849 +794000 ekin = 2.63509078851047 | erot = 2.16503786006958 | epot = -18.0826660971656 | etot = -13.2825374485855 +795000 ekin = 2.66245645585368 | erot = 2.1756290014367 | epot = -18.1206229065374 | etot = -13.282537449247 +796000 ekin = 2.68895951870523 | erot = 2.19088748025581 | epot = -18.1623844489478 | etot = -13.2825374499868 +797000 ekin = 2.70892452688332 | erot = 2.2056406086122 | epot = -18.197102586158 | etot = -13.2825374506625 +798000 ekin = 2.71873874100197 | erot = 2.21455364270924 | epot = -18.2158298332998 | etot = -13.2825374495886 +799000 ekin = 2.70000299973817 | erot = 2.2105054534633 | epot = -18.1930459030985 | etot = -13.282537449897 +800000 ekin = 2.65392049094459 | erot = 2.17300546859124 | epot = -18.1094633784201 | etot = -13.2825374188843 +801000 ekin = 2.82505345316557 | erot = 2.13616134654269 | epot = -18.2437522542245 | etot = -13.2825374545162 +802000 ekin = 2.90470228885208 | erot = 2.10953657420558 | epot = -18.2967762804394 | etot = -13.2825374173817 +803000 ekin = 2.96775259915972 | erot = 2.08137573430732 | epot = -18.3316657516683 | etot = -13.2825374182013 +804000 ekin = 3.01419864043949 | erot = 2.05336319944923 | epot = -18.3500992582319 | etot = -13.2825374183431 +805000 ekin = 3.03950260644552 | erot = 2.02738087501351 | epot = -18.3494208998051 | etot = -13.2825374183461 +806000 ekin = 3.04147612131243 | erot = 2.00524180159513 | epot = -18.3292553411016 | etot = -13.2825374181941 +807000 ekin = 3.02009152298814 | erot = 1.98876426014739 | epot = -18.2913932010452 | etot = -13.2825374179097 +808000 ekin = 2.97716861753119 | erot = 1.97979280799342 | epot = -18.2394988430722 | etot = -13.2825374175476 +809000 ekin = 2.91576405138726 | erot = 1.98007542312432 | epot = -18.1783768916846 | etot = -13.282537417173 +810000 ekin = 2.83951999042134 | erot = 1.99102014259852 | epot = -18.1130775498589 | etot = -13.282537416839 +811000 ekin = 2.75216924199515 | erot = 2.01344070753323 | epot = -18.0481473661025 | etot = -13.2825374165741 +812000 ekin = 2.65727213726343 | erot = 2.04739495988655 | epot = -17.987204513533 | etot = -13.282537416383 +813000 ekin = 2.55815479837528 | erot = 2.09215794771562 | epot = -17.9328501623443 | etot = -13.2825374162534 +814000 ekin = 2.4579662372483 | erot = 2.14630993623329 | epot = -17.8868135896497 | etot = -13.2825374161681 +815000 ekin = 2.35976627216073 | erot = 2.20788718914275 | epot = -17.8501908774147 | etot = -13.2825374161112 +816000 ekin = 2.26657574981526 | erot = 2.27454135627298 | epot = -17.8236545221636 | etot = -13.2825374160753 +817000 ekin = 2.18134946483051 | erot = 2.3436713345316 | epot = -17.8075582154243 | etot = -13.2825374160622 +818000 ekin = 2.10686415434699 | erot = 2.41251844145424 | epot = -17.8019200118806 | etot = -13.2825374160794 +819000 ekin = 2.04554497125477 | erot = 2.47824070198672 | epot = -17.8063230893767 | etot = -13.2825374161352 +820000 ekin = 1.99927680186843 | erot = 2.53799486411919 | epot = -17.8198090822204 | etot = -13.2825374162328 +821000 ekin = 1.96925307966866 | erot = 2.58905270243613 | epot = -17.840843198472 | etot = -13.2825374163673 +822000 ekin = 1.95590272109404 | erot = 2.62895986973405 | epot = -17.8674000073523 | etot = -13.2825374165242 +823000 ekin = 1.95890926741904 | erot = 2.65572860619527 | epot = -17.8971752902976 | etot = -13.2825374166833 +824000 ekin = 1.977310461331 | erot = 2.66804286174235 | epot = -17.9278907398948 | etot = -13.2825374168215 +825000 ekin = 2.00964945329754 | erot = 2.66544750505568 | epot = -17.9576343752703 | etot = -13.2825374169171 +826000 ekin = 2.0541442314356 | erot = 2.64849047615147 | epot = -17.9851721245422 | etot = -13.2825374169552 +827000 ekin = 2.10884212221679 | erot = 2.61877894563757 | epot = -18.0101584847866 | etot = -13.2825374169322 +828000 ekin = 2.17172935733676 | erot = 2.57890618406652 | epot = -18.0331729582634 | etot = -13.2825374168601 +829000 ekin = 2.24077304904372 | erot = 2.5322165119978 | epot = -18.0555269778081 | etot = -13.2825374167666 +830000 ekin = 2.31389012815757 | erot = 2.48241157684725 | epot = -18.0788391216955 | etot = -13.2825374166907 +831000 ekin = 2.38886546625953 | erot = 2.43305573632076 | epot = -18.104458619251 | etot = -13.2825374166707 +832000 ekin = 2.46326915871406 | erot = 2.38708705021977 | epot = -18.1328936256668 | etot = -13.282537416733 +833000 ekin = 2.53443656409172 | erot = 2.34645691970375 | epot = -18.1634309006758 | etot = -13.2825374168804 +834000 ekin = 2.59956439097001 | erot = 2.31199374937919 | epot = -18.1940955574388 | etot = -13.2825374170896 +835000 ekin = 2.65594316002407 | erot = 2.28352232981187 | epot = -18.2220029071513 | etot = -13.2825374173153 +836000 ekin = 2.70130042716651 | erot = 2.26019210855364 | epot = -18.2440299532235 | etot = -13.2825374175034 +837000 ekin = 2.73418787966583 | erot = 2.24090837049561 | epot = -18.2576336677656 | etot = -13.2825374176041 +838000 ekin = 2.75431729315362 | erot = 2.22474076448287 | epot = -18.2615954752233 | etot = -13.2825374175868 +839000 ekin = 2.76274241572831 | erot = 2.21121141264461 | epot = -18.2564912458202 | etot = -13.2825374174473 +840000 ekin = 2.76179432909388 | erot = 2.20041723497348 | epot = -18.2447489812793 | etot = -13.282537417212 +841000 ekin = 2.75470877418902 | erot = 2.1929795872171 | epot = -18.2302257783439 | etot = -13.2825374169378 +842000 ekin = 2.74495192414829 | erot = 2.18982916717498 | epot = -18.2173185080269 | etot = -13.2825374167036 +843000 ekin = 2.73536701720752 | erot = 2.19185320338424 | epot = -18.2097576371796 | etot = -13.2825374165879 +844000 ekin = 2.72739699207957 | erot = 2.19948517299773 | epot = -18.2094195817172 | etot = -13.2825374166399 +845000 ekin = 2.72069680081942 | erot = 2.2123834314525 | epot = -18.2156176491199 | etot = -13.282537416848 +846000 ekin = 2.71335245842044 | erot = 2.22935501274494 | epot = -18.2252448883063 | etot = -13.2825374171409 +847000 ekin = 2.70267547682563 | erot = 2.24859000802352 | epot = -18.2338029022618 | etot = -13.2825374174127 +848000 ekin = 2.68627674917249 | erot = 2.26812231570546 | epot = -18.2369364824441 | etot = -13.2825374175662 +849000 ekin = 2.66300406346419 | erot = 2.28632293043157 | epot = -18.2318644114456 | etot = -13.2825374175499 +850000 ekin = 2.63341305155328 | erot = 2.30223030137244 | epot = -18.218180770297 | etot = -13.2825374173713 +851000 ekin = 2.59966042962012 | erot = 2.31561676234611 | epot = -18.1978146090528 | etot = -13.2825374170866 +852000 ekin = 2.5649330756416 | erot = 2.32681511046273 | epot = -18.1742856028756 | etot = -13.2825374167712 +853000 ekin = 2.53268458711828 | erot = 2.33642702442706 | epot = -18.1516490280431 | etot = -13.2825374164977 +854000 ekin = 2.50591352350999 | erot = 2.34503055401556 | epot = -18.1334814938378 | etot = -13.2825374163123 +855000 ekin = 2.48667404327569 | erot = 2.3529787337437 | epot = -18.1221901932468 | etot = -13.2825374162274 +856000 ekin = 2.47592780438371 | erot = 2.3603420277346 | epot = -18.1188072483454 | etot = -13.2825374162271 +857000 ekin = 2.47367803113421 | erot = 2.36697110010333 | epot = -18.1231865475261 | etot = -13.2825374162886 +858000 ekin = 2.47922391314762 | erot = 2.37260088410896 | epot = -18.1343622136269 | etot = -13.2825374163703 +859000 ekin = 2.49150776537562 | erot = 2.37701216170971 | epot = -18.1510573435355 | etot = -13.2825374164502 +860000 ekin = 2.50937686487663 | erot = 2.38013993767848 | epot = -18.1720542190715 | etot = -13.2825374165164 +861000 ekin = 2.53170635734158 | erot = 2.382118173112 | epot = -18.1963619470209 | etot = -13.2825374165673 +862000 ekin = 2.55742566397641 | erot = 2.38328933411273 | epot = -18.2232524146946 | etot = -13.2825374166054 +863000 ekin = 2.58549482989182 | erot = 2.38419488615669 | epot = -18.2522271326816 | etot = -13.2825374166331 +864000 ekin = 2.61488040894193 | erot = 2.38555368952377 | epot = -18.2829715151176 | etot = -13.2825374166519 +865000 ekin = 2.64455846197211 | erot = 2.38821849293994 | epot = -18.3153143715761 | etot = -13.282537416664 +866000 ekin = 2.67354800293375 | erot = 2.39309523430222 | epot = -18.3491806539087 | etot = -13.2825374166727 +867000 ekin = 2.70096216873101 | erot = 2.40101926625376 | epot = -18.3845188516697 | etot = -13.282537416685 +868000 ekin = 2.72584498237102 | erot = 2.41260829133849 | epot = -18.4209906905118 | etot = -13.2825374168023 +869000 ekin = 2.74685098517846 | erot = 2.42808376703703 | epot = -18.4574721690819 | etot = -13.2825374168664 +870000 ekin = 2.7633451632292 | erot = 2.44707202924713 | epot = -18.492954609437 | etot = -13.2825374169607 +871000 ekin = 2.77488977650291 | erot = 2.46856883210016 | epot = -18.52599602569 | etot = -13.2825374170869 +872000 ekin = 2.78115731189941 | erot = 2.49101078905502 | epot = -18.5547055181929 | etot = -13.2825374172384 +873000 ekin = 2.78190152481948 | erot = 2.51241399948397 | epot = -18.5768529417016 | etot = -13.2825374173982 +874000 ekin = 2.77696693727655 | erot = 2.53063897251365 | epot = -18.5901433273283 | etot = -13.2825374175381 +875000 ekin = 2.76636320238677 | erot = 2.54374754553387 | epot = -18.5926481655429 | etot = -13.2825374176222 +876000 ekin = 2.75040698328634 | erot = 2.55039472458546 | epot = -18.5833391254864 | etot = -13.2825374176146 +877000 ekin = 2.72989722871737 | erot = 2.55017286738757 | epot = -18.5626075135949 | etot = -13.28253741749 +878000 ekin = 2.70625700359845 | erot = 2.54382115285145 | epot = -18.5326155736941 | etot = -13.2825374172442 +879000 ekin = 2.68156506710304 | erot = 2.5332421375899 | epot = -18.4973446215902 | etot = -13.2825374168973 +880000 ekin = 2.65843100587721 | erot = 2.52132217105652 | epot = -18.4622905934235 | etot = -13.2825374164897 +881000 ekin = 2.63972432917675 | erot = 2.51160592655705 | epot = -18.4338676718058 | etot = -13.282537416072 +882000 ekin = 2.62822235346356 | erot = 2.50790034757638 | epot = -18.4186601167335 | etot = -13.2825374156936 +883000 ekin = 2.62626662018779 | erot = 2.51387422610971 | epot = -18.4226782616929 | etot = -13.2825374153954 +884000 ekin = 2.63550251587674 | erot = 2.53269091102144 | epot = -18.4507308421049 | etot = -13.2825374152068 +885000 ekin = 2.65673814602945 | erot = 2.56668643769325 | epot = -18.5059619988685 | etot = -13.2825374151458 +886000 ekin = 2.68991716922188 | erot = 2.61709355073984 | epot = -18.5895481351839 | etot = -13.2825374152222 +887000 ekin = 2.73417552912835 | erot = 2.6838152242605 | epot = -18.7005281688277 | etot = -13.2825374154388 +888000 ekin = 2.78795008305904 | erot = 2.76526591420808 | epot = -18.8357534130565 | etot = -13.2825374157894 +889000 ekin = 2.84912017691373 | erot = 2.85831711202064 | epot = -18.9899747051915 | etot = -13.2825374162572 +890000 ekin = 2.91517691409144 | erot = 2.95839462905156 | epot = -19.1561089599533 | etot = -13.2825374168103 +891000 ekin = 2.98341766730812 | erot = 3.05976765321724 | epot = -19.325722737928 | etot = -13.2825374174026 +892000 ekin = 3.05115351194122 | erot = 3.15603968509377 | epot = -19.4897306150129 | etot = -13.2825374179779 +893000 ekin = 3.11590366932995 | erot = 3.24080527058909 | epot = -19.6392463583964 | etot = -13.2825374184774 +894000 ekin = 3.17554452677574 | erot = 3.30838806048503 | epot = -19.7664700061104 | etot = -13.2825374188496 +895000 ekin = 3.22839008199059 | erot = 3.35454380329715 | epot = -19.8654713043472 | etot = -13.2825374190595 +896000 ekin = 3.27319974841242 | erot = 3.37700709675264 | epot = -19.9327442642579 | etot = -13.2825374190928 +897000 ekin = 3.30912548213112 | erot = 3.37578333286277 | epot = -19.967446233953 | etot = -13.2825374189591 +898000 ekin = 3.33561719165196 | erot = 3.3531309986516 | epot = -19.9712856089931 | etot = -13.2825374186895 +899000 ekin = 3.35230310065721 | erot = 3.31323476899373 | epot = -19.9480752879843 | etot = -13.2825374183334 +900000 ekin = 3.35886034343544 | erot = 3.26162723368974 | epot = -19.9030249950731 | etot = -13.2825374179479 +901000 ekin = 3.35489762596209 | erot = 3.20446448625264 | epot = -19.8418995298029 | etot = -13.2825374175882 +902000 ekin = 3.33988398696538 | erot = 3.14778460706124 | epot = -19.7702060113224 | etot = -13.2825374172958 +903000 ekin = 3.31316641783821 | erot = 3.09687096396604 | epot = -19.6925747988938 | etot = -13.2825374170895 +904000 ekin = 3.27411465308455 | erot = 3.05580881507587 | epot = -19.6124608851232 | etot = -13.2825374169628 +905000 ekin = 3.22240761769978 | erot = 3.02727711778411 | epot = -19.5322221523689 | etot = -13.282537416885 +906000 ekin = 3.15843123273498 | erot = 3.01257047454492 | epot = -19.4535391240911 | etot = -13.2825374168112 +907000 ekin = 3.08369712964382 | erot = 3.01180553940022 | epot = -19.3780400857413 | etot = -13.2825374166972 +908000 ekin = 3.00113487274611 | erot = 3.02423547951158 | epot = -19.3079077687759 | etot = -13.2825374165182 +909000 ekin = 2.91509126886064 | erot = 3.0485809791401 | epot = -19.2462096642835 | etot = -13.2825374162828 +910000 ekin = 2.83091809167562 | erot = 3.08328866526031 | epot = -19.1967441729738 | etot = -13.2825374160379 +911000 ekin = 2.7541604271422 | erot = 3.1266566210814 | epot = -19.1633544640806 | etot = -13.282537415857 +912000 ekin = 2.68982240100996 | erot = 3.1767030385921 | epot = -19.1490628553551 | etot = -13.2825374157531 +913000 ekin = 2.64026279373643 | erot = 3.23106967523778 | epot = -19.1538698849232 | etot = -13.282537415949 +914000 ekin = 2.60494541465082 | erot = 3.28757760697213 | epot = -19.1750604377642 | etot = -13.2825374161413 +915000 ekin = 2.58331294239456 | erot = 3.34356245911015 | epot = -19.2094128182448 | etot = -13.2825374167401 +916000 ekin = 2.57222527647779 | erot = 3.39542630316431 | epot = -19.2501889969159 | etot = -13.2825374172738 +917000 ekin = 2.56717379817942 | erot = 3.43991413449175 | epot = -19.2896253504428 | etot = -13.2825374177716 +918000 ekin = 2.56366862210109 | erot = 3.47431911616615 | epot = -19.3205251564115 | etot = -13.2825374181443 +919000 ekin = 2.55808580304574 | erot = 3.49688251813148 | epot = -19.3375057395072 | etot = -13.28253741833 +920000 ekin = 2.54828083364558 | erot = 3.5070678678649 | epot = -19.3378861198184 | etot = -13.2825374183079 +921000 ekin = 2.53385837590705 | erot = 3.50557961685233 | epot = -19.3219754108608 | etot = -13.2825374181014 +922000 ekin = 2.51606053239869 | erot = 3.49409623216883 | epot = -19.2926941823441 | etot = -13.2825374177766 +923000 ekin = 2.49728908788132 | erot = 3.47476611576438 | epot = -19.2545926210732 | etot = -13.2825374174275 +924000 ekin = 2.48035717202194 | erot = 3.44958564398511 | epot = -19.2124802331591 | etot = -13.2825374171521 +925000 ekin = 2.46765713254659 | erot = 3.41982437264767 | epot = -19.1700189222178 | etot = -13.2825374170235 +926000 ekin = 2.46048446158288 | erot = 3.38566546873097 | epot = -19.1286873473806 | etot = -13.2825374170668 +927000 ekin = 2.45872404317125 | erot = 3.34617863031278 | epot = -19.0874400907354 | etot = -13.2825374172514 +928000 ekin = 2.46097855171065 | erot = 3.29964380838023 | epot = -19.0431597775946 | etot = -13.2825374175038 +929000 ekin = 2.46505358069594 | erot = 3.24413140257229 | epot = -18.991722401002 | etot = -13.2825374177338 +930000 ekin = 2.46859437787823 | erot = 3.17816487157566 | epot = -18.9292966673187 | etot = -13.2825374178649 +931000 ekin = 2.46965047267191 | erot = 3.10127887080617 | epot = -18.8534667613313 | etot = -13.2825374178532 +932000 ekin = 2.4670173255647 | erot = 3.01434778959557 | epot = -18.7639025328451 | etot = -13.2825374176848 +933000 ekin = 2.46031519134382 | erot = 2.9197399878057 | epot = -18.6625925965562 | etot = -13.2825374174067 +934000 ekin = 2.44985996562476 | erot = 2.82081794784481 | epot = -18.5532153305218 | etot = -13.2825374170523 +935000 ekin = 2.436420580333 | erot = 2.72162862765433 | epot = -18.4405866246576 | etot = -13.2825374166703 +936000 ekin = 2.42095423708767 | erot = 2.62651830215161 | epot = -18.3300099555418 | etot = -13.2825374163026 +937000 ekin = 2.40438434932027 | erot = 2.53973621279557 | epot = -18.226657978095 | etot = -13.2825374159791 +938000 ekin = 2.38744919935998 | erot = 2.4651292336249 | epot = -18.135115848703 | etot = -13.2825374157181 +939000 ekin = 2.37062067073867 | erot = 2.40593643839711 | epot = -18.0590945246642 | etot = -13.2825374155285 +940000 ekin = 2.35407564445261 | erot = 2.36465978724872 | epot = -18.0012728471164 | etot = -13.2825374154151 +941000 ekin = 2.33770002396805 | erot = 2.3429775907629 | epot = -17.9632150301122 | etot = -13.2825374153812 +942000 ekin = 2.3211100477539 | erot = 2.34167204177044 | epot = -17.9453195049536 | etot = -13.2825374154293 +943000 ekin = 2.30368578977883 | erot = 2.36056240878928 | epot = -17.9467856141281 | etot = -13.28253741556 +944000 ekin = 2.28462216192276 | erot = 2.39846175869457 | epot = -17.965621336385 | etot = -13.2825374157677 +945000 ekin = 2.2630091294477 | erot = 2.45319770839139 | epot = -17.9987442538757 | etot = -13.2825374160366 +946000 ekin = 2.23795189081835 | erot = 2.52174524491464 | epot = -18.0422345520714 | etot = -13.2825374163384 +947000 ekin = 2.20873145000821 | erot = 2.60050188215201 | epot = -18.0917707487932 | etot = -13.282537416633 +948000 ekin = 2.17498954570766 | erot = 2.68569096156255 | epot = -18.1432179241464 | etot = -13.2825374168762 +949000 ekin = 2.13690579381781 | erot = 2.77382147859291 | epot = -18.1932646894412 | etot = -13.2825374170305 +950000 ekin = 2.09532426392926 | erot = 2.86208910103834 | epot = -18.2399507820441 | etot = -13.2825374170765 +951000 ekin = 2.05179334892108 | erot = 2.94860198731117 | epot = -18.2829327532513 | etot = -13.282537417019 +952000 ekin = 2.00850116617196 | erot = 3.03236285196215 | epot = -18.3234014350193 | etot = -13.2825374168852 +953000 ekin = 1.96811370411823 | erot = 3.11301524923778 | epot = -18.3636663700751 | etot = -13.2825374167191 +954000 ekin = 1.93354422096465 | erot = 3.19043207950452 | epot = -18.4065137170385 | etot = -13.2825374165694 +955000 ekin = 1.90769299354898 | erot = 3.26426019429227 | epot = -18.4544906043215 | etot = -13.2825374164802 +956000 ekin = 1.89319483668346 | erot = 3.3335310510213 | epot = -18.5092633041882 | etot = -13.2825374164834 +957000 ekin = 1.89220136687493 | erot = 3.39641763043281 | epot = -18.5711564139026 | etot = -13.2825374165948 +958000 ekin = 1.90621184327196 | erot = 3.45018116338437 | epot = -18.6389304234696 | etot = -13.2825374168133 +959000 ekin = 1.93595602572738 | erot = 3.49131884016615 | epot = -18.7098122830149 | etot = -13.2825374171214 +960000 ekin = 1.98132739808155 | erot = 3.51589596586286 | epot = -18.7797607814332 | etot = -13.2825374174888 +961000 ekin = 2.04135467404736 | erot = 3.52022622800403 | epot = -18.8441183199515 | etot = -13.2825374179001 +962000 ekin = 2.11395441310799 | erot = 3.50134462367084 | epot = -18.8978364550807 | etot = -13.2825374183019 +963000 ekin = 2.19624676899701 | erot = 3.45688460164827 | epot = -18.9356687892675 | etot = -13.2825374186222 +964000 ekin = 2.28502253915305 | erot = 3.38607259923977 | epot = -18.9536325572173 | etot = -13.2825374188245 +965000 ekin = 2.37703902445876 | erot = 3.290048679397 | epot = -18.9496251223776 | etot = -13.2825374185219 +966000 ekin = 2.47063968725093 | erot = 3.1723513983338 | epot = -18.9255285040288 | etot = -13.2825374184441 +967000 ekin = 2.56372995923146 | erot = 3.03797961445187 | epot = -18.8842469918799 | etot = -13.2825374181965 +968000 ekin = 2.65424153344269 | erot = 2.89333166097639 | epot = -18.8301106122161 | etot = -13.282537417797 +969000 ekin = 2.74102206186552 | erot = 2.74597895251273 | epot = -18.7695384316796 | etot = -13.2825374173014 +970000 ekin = 2.82317857356224 | erot = 2.604190086995 | epot = -18.7099060774559 | etot = -13.2825374168987 +971000 ekin = 2.8994689638118 | erot = 2.4760495859706 | epot = -18.6580559662902 | etot = -13.2825374165078 +972000 ekin = 2.9692788351105 | erot = 2.36783972481189 | epot = -18.6196559761964 | etot = -13.282537416274 +973000 ekin = 3.03160430536472 | erot = 2.2837390116559 | epot = -18.5978807332491 | etot = -13.2825374162285 +974000 ekin = 3.08487810189262 | erot = 2.22552920107224 | epot = -18.5929447193212 | etot = -13.2825374163564 +975000 ekin = 3.12708218339791 | erot = 2.19270938701088 | epot = -18.6023289870154 | etot = -13.2825374166067 +976000 ekin = 3.15606698313496 | erot = 2.18294126797245 | epot = -18.6215456680199 | etot = -13.2825374169125 +977000 ekin = 3.16994500148915 | erot = 2.19267118134068 | epot = -18.6451536000414 | etot = -13.2825374172116 +978000 ekin = 3.16742946230438 | erot = 2.21776877388408 | epot = -18.6677356536463 | etot = -13.2825374174579 +979000 ekin = 3.14804045634032 | erot = 2.25406876454721 | epot = -18.6846466385122 | etot = -13.2825374176247 +980000 ekin = 3.11216367300116 | erot = 2.29776911310777 | epot = -18.6924702038109 | etot = -13.282537417702 +981000 ekin = 3.06099214892659 | erot = 2.3456929996696 | epot = -18.6892225662862 | etot = -13.28253741769 +982000 ekin = 2.99639964718071 | erot = 2.39544433336442 | epot = -18.6743813981403 | etot = -13.2825374175951 +983000 ekin = 2.92078844001815 | erot = 2.44547840699747 | epot = -18.6488042644435 | etot = -13.2825374174279 +984000 ekin = 2.83693459158518 | erot = 2.49508912549767 | epot = -18.6145611342876 | etot = -13.2825374172048 +985000 ekin = 2.74783419632812 | erot = 2.5443043349293 | epot = -18.574675948205 | etot = -13.2825374169476 +986000 ekin = 2.65654531631453 | erot = 2.59369131479764 | epot = -18.5327740477957 | etot = -13.2825374166835 +987000 ekin = 2.56602543639744 | erot = 2.64409903932047 | epot = -18.4926618921587 | etot = -13.2825374164408 +988000 ekin = 2.47897321242724 | erot = 2.69638105728562 | epot = -18.4578916859573 | etot = -13.2825374162445 +989000 ekin = 2.39763961356463 | erot = 2.75059396001095 | epot = -18.4307709898088 | etot = -13.2825374162332 +990000 ekin = 2.32368779513216 | erot = 2.8060334288419 | epot = -18.4122586401602 | etot = -13.2825374161862 +991000 ekin = 2.25825301239778 | erot = 2.86226671700632 | epot = -18.403057145624 | etot = -13.2825374162199 +992000 ekin = 2.20187988804497 | erot = 2.91825634883864 | epot = -18.40267365322 | etot = -13.2825374163364 +993000 ekin = 2.15452775813786 | erot = 2.97231721272995 | epot = -18.4093823873994 | etot = -13.2825374165316 +994000 ekin = 2.1156117684003 | erot = 3.02214023540268 | epot = -18.4202894205965 | etot = -13.2825374167935 +995000 ekin = 2.0840816135671 | erot = 3.0648940369717 | epot = -18.4315130676401 | etot = -13.2825374171013 +996000 ekin = 2.05854312781033 | erot = 3.09743221589021 | epot = -18.4385127611221 | etot = -13.2825374174216 +997000 ekin = 2.03742523644506 | erot = 3.11662356541409 | epot = -18.4365862195703 | etot = -13.2825374177112 +998000 ekin = 2.0191844917443 | erot = 3.11978989754515 | epot = -18.4215118072117 | etot = -13.2825374179223 +999000 ekin = 2.00252382756565 | erot = 3.10518925660486 | epot = -18.3902505021827 | etot = -13.2825374180121 +1000000 ekin = 1.98658902728357 | erot = 3.07244218051013 | epot = -18.341568625748 | etot = -13.2825374179543 + 1000000 0.088292846 -1.1874188 0.041070751 -1.0221862 -7.1515284e-05 +Loop time of 31.8631 on 4 procs for 1000000 steps with 16 atoms + +Performance: 27116.007 tau/day, 31384.268 timesteps/s +99.5% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 4.7557 | 14.198 | 24.52 | 210.8 | 44.56 +Bond | 0.22678 | 0.45105 | 0.74273 | 29.9 | 1.42 +Neigh | 0.00012 | 0.00012675 | 0.00013 | 0.0 | 0.00 +Comm | 2.6837 | 2.8338 | 3.0258 | 7.8 | 8.89 +Output | 2e-05 | 2.75e-05 | 3e-05 | 0.0 | 0.00 +Modify | 0.43472 | 0.8763 | 1.3871 | 38.7 | 2.75 +Other | | 13.5 | | | 42.38 + +Nlocal: 4 ave 7 max 1 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +Nghost: 10.5 ave 12 max 9 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 38.75 ave 63 max 11 min +Histogram: 1 0 0 0 0 1 1 0 0 1 + +Total # of neighbors = 155 +Ave neighs/atom = 9.6875 +Ave special neighs/atom = 3.75 +Neighbor list builds = 6 +Dangerous builds = 0 + +#write_restart config.${number}.* +Total wall time: 0:00:31 diff --git a/src/USER-CGDNA/README b/src/USER-CGDNA/README deleted file mode 100644 index 48d6178d13..0000000000 --- a/src/USER-CGDNA/README +++ /dev/null @@ -1,87 +0,0 @@ -This package contains a LAMMPS implementation of coarse-grained -models of DNA, which can be used to model sequence-specific -DNA strands. - -Please cite [1] and the relevant oxDNA articles in any publication -that uses this package. - -See the doc pages and [2,3,4] for the individual bond and pair styles. -The packages contains also a new Langevin-type rigid-body integrator, -which has also its own doc page and is explained in [5]. - -[1] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, -"Coarse-grained simulation of DNA using LAMMPS", -Eur. Phys. J. E 41, 57 (2018). - -[2] T. Ouldridge, A. Louis, J. Doye, "Structural, mechanical, -and thermodynamic properties of a coarse-grained DNA model", -J. Chem. Phys. 134, 085101 (2011). - -[3] T.E. Ouldridge, Coarse-grained modelling of DNA and DNA -self-assembly, DPhil. University of Oxford (2011). - -[4] B.E. Snodin, F. Randisi, M. Mosayebi, et al., Introducing -Improved Structural Properties and Salt Dependence into a Coarse-Grained -Model of DNA, J. Chem. Phys. 142, 234901 (2015). - -[5] R. Davidchack, T. Ouldridge, M. Tretyakov, "New Langevin and -gradient thermostats for rigid body dynamics", J. Chem. Phys. 142, -144114 (2015). - -Example input and data files can be found in -/examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/. Python setup -tools which create single straight or helical DNA strands as -well as DNA duplexes or arrays of duplexes can be found in -/examples/USER/cgdna/util/. A technical report with more information -on the models, the structure of the input and data file, the setup tool -and the performance of the LAMMPS-implementation of oxDNA can be found -in /doc/src/PDF/USER-CGDNA.pdf. - -IMPORTANT NOTE: This package can only be used if LAMMPS is compiled -with the MOLECULE and ASPHERE packages. These should be included in -the LAMMPS build by typing "make yes-asphere yes-molecule" prior to -the usual compilation (see the "Including/excluding packages" section -of the LAMMPS manual). - -The creator of this package is: - -Dr Oliver Henrich -University of Strathclyde, Glasgow, UK -oliver d o t henrich a t strath d o t ac d o t uk - - --------------------------------------------------------------------------- - -** Bond styles provided by this package: - -bond_oxdna_fene.cpp: backbone connectivity, a modified FENE potential - -bond_oxdna2_fene.cpp: corresponding bond style in oxDNA2 (see [3]) - -** Pair styles provided by this package: - -pair_oxdna_excv.cpp: excluded volume interaction between the nucleotides - -pair_oxdna_stk.cpp: stacking interaction between consecutive nucleotides - on the same strand - -pair_oxdna_hbond.cpp: hydrogen-bonding interaction between complementary - nucleotides on different strands, e.g. A-T and C-G - -pair_oxdna_xstk.cpp: cross-stacking interaction between nucleotides - -pair_oxdna_coaxstk.cpp: coaxial stacking interaction between nucleotides - - -pair_oxdna2_excv.cpp, pair_oxdna2_coaxstk.cpp: - corresponding pair styles in oxDNA2 (see [3]) - -pair_oxdna2_dh.cpp: Debye-Hueckel electrostatic interaction between backbone - sites - -** Fixes provided by this package: - -fix_nve_dotc_langevin.cpp: fix for Langevin-type rigid body integrator "C" - in above Ref. [3] - -fix_nve_dot.cpp: NVE-type rigid body integrator without noise diff --git a/src/USER-CGDNA/README.md b/src/USER-CGDNA/README.md new file mode 100644 index 0000000000..138638525e --- /dev/null +++ b/src/USER-CGDNA/README.md @@ -0,0 +1,105 @@ +This package contains a LAMMPS implementation of coarse-grained +models of DNA, which can be used to model sequence-specific +DNA strands. + +Please cite + +[![DOI](https://zenodo.org/badge/132764768.svg)](https://zenodo.org/badge/latestdoi/132764768) + +as well as [1] and the relevant oxDNA, oxDNA2 and oxRNA2 articles +in any publication that uses this package. + +See the doc pages and [2,3,4,5,6] for the individual bond and pair styles. +The packages contains also a new Langevin-type rigid-body integrator, +which has also its own doc page and is explained in [7]. + +[1] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, +"Coarse-grained simulation of DNA using LAMMPS", +Eur. Phys. J. E 41, 57 (2018). + +[2] T. Ouldridge, A. Louis, J. Doye, "Structural, mechanical, +and thermodynamic properties of a coarse-grained DNA model", +J. Chem. Phys. 134, 085101 (2011). + +[3] T.E. Ouldridge, "Coarse-grained modelling of DNA and DNA +self-assembly", DPhil. University of Oxford (2011). + +[4] B.E. Snodin, F. Randisi, M. Mosayebi, et al., "Introducing +Improved structural properties and salt dependence into a coarse-grained +model of DNA", J. Chem. Phys. 142, 234901 (2015). + +[5] P. Sulc, F. Romano, T.E. Ouldridge, et al., "A nucleotide-level +coarse-grained model of RNA", J. Chem. Phys. 140, 235102 (2014). + +[6] P. Sulc, F. Romano, T.E. Ouldridge, et al., "Sequence-dependent +thermodynamics of a coarse-grained DNA model", +J. Chem. Phys. 137, 135101 (2012). + +[7] R. Davidchack, T. Ouldridge, M. Tretyakov, "New Langevin and +gradient thermostats for rigid body dynamics", J. Chem. Phys. 142, +144114 (2015). + +Example input and data files can be found in +/examples/USER/cgdna/examples/oxDNA/, /oxDNA2/ and /oxRNA2/. +Python setup tools which create single straight or helical DNA or RNA +strands as well as DNA or RNA duplexes or arrays of duplexes can be +found in /examples/USER/cgdna/util/. A technical report with more +general information on the model, its implementation and performance +as well as the structure of the data and input file can be found +in /doc/src/PDF/USER-CGDNA.pdf. + +IMPORTANT NOTE: This package can only be used if LAMMPS is compiled +with the MOLECULE and ASPHERE packages. These should be included in +the LAMMPS build by typing "make yes-asphere yes-molecule" prior to +the usual compilation (see the "Including/excluding packages" section +of the LAMMPS manual). + +The creator of this package is: + +Dr Oliver Henrich +University of Strathclyde, Glasgow, UK +oliver d o t henrich a t strath d o t ac d o t uk + + +-------------------------------------------------------------------------- + +** Bond styles provided by this package: + +bond_oxdna_fene.cpp: backbone connectivity, + a modified FENE potential (see [2,3]) + +bond_oxdna2_fene.cpp: corresponding bond style in oxDNA2 (see [4]) + +bond_oxrna2_fene.cpp: corresponding bond style in oxRNA2 (see [5]) + +** Pair styles provided by this package: + +pair_oxdna_excv.cpp: excluded volume interaction between the nucleotides + +pair_oxdna_stk.cpp: stacking interaction between consecutive nucleotides + on the same strand + +pair_oxdna_hbond.cpp: hydrogen-bonding interaction between complementary + nucleotides on different strands, e.g. A-T and C-G + +pair_oxdna_xstk.cpp: cross-stacking interaction between nucleotides + +pair_oxdna_coaxstk.cpp: coaxial stacking interaction between nucleotides + +pair_oxdna2_excv.cpp, pair_oxdna2_coaxstk.cpp: + corresponding pair styles in oxDNA2 (see [4]) + +pair_oxrna2_excv.cpp, pair_oxrna2_stk.cpp, pair_oxrna2_hbond.cpp, +pair_oxrna2_xstk.cpp: + corresponding pair styles in oxDNA2 (see [5]) + +pair_oxdna2_dh.cpp, pair_oxrna2_dh.cpp: + Debye-Hueckel electrostatic interaction between backbone sites + + +** Fixes provided by this package: + +fix_nve_dotc_langevin.cpp: fix for Langevin-type rigid body integrator "C" + in above Ref. [7] + +fix_nve_dot.cpp: NVE-type rigid body integrator without noise diff --git a/src/USER-CGDNA/bond_oxrna2_fene.cpp b/src/USER-CGDNA/bond_oxrna2_fene.cpp new file mode 100644 index 0000000000..bdddccda87 --- /dev/null +++ b/src/USER-CGDNA/bond_oxrna2_fene.cpp @@ -0,0 +1,49 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- + Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) +------------------------------------------------------------------------- */ + +#include +#include +#include "bond_oxrna2_fene.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +BondOxrna2Fene::BondOxrna2Fene(LAMMPS *lmp) : BondOxdnaFene(lmp) +{ + +} + +/* ---------------------------------------------------------------------- */ + +BondOxrna2Fene::~BondOxrna2Fene() +{ + +} + +/* ---------------------------------------------------------------------- + compute vector COM-sugar-phosphate backbone interaction site in oxRNA2 +------------------------------------------------------------------------- */ +void BondOxrna2Fene::compute_interaction_sites(double e1[3], double /*e2*/[3], + double e3[3], double r[3]) +{ + double d_cs_x=-0.4, d_cs_z=+0.2; + + r[0] = d_cs_x*e1[0] + d_cs_z*e3[0]; + r[1] = d_cs_x*e1[1] + d_cs_z*e3[1]; + r[2] = d_cs_x*e1[2] + d_cs_z*e3[2]; + +} diff --git a/src/USER-CGDNA/bond_oxrna2_fene.h b/src/USER-CGDNA/bond_oxrna2_fene.h new file mode 100644 index 0000000000..585a253eb5 --- /dev/null +++ b/src/USER-CGDNA/bond_oxrna2_fene.h @@ -0,0 +1,65 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef BOND_CLASS + +BondStyle(oxrna2/fene,BondOxrna2Fene) + +#else + +#ifndef LMP_BOND_OXRNA2_FENE_H +#define LMP_BOND_OXRNA2_FENE_H + +#include "bond_oxdna_fene.h" + +namespace LAMMPS_NS { + +class BondOxrna2Fene : public BondOxdnaFene { + public: + BondOxrna2Fene(class LAMMPS *); + virtual ~BondOxrna2Fene(); + virtual void compute_interaction_sites(double *, double *, double *, + double *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +W: FENE bond too long: %ld %d %d %g + +A FENE bond has stretched dangerously far. It's interaction strength +will be truncated to attempt to prevent the bond from blowing up. + +E: Bad FENE bond + +Two atoms in a FENE bond have become so far apart that the bond cannot +be computed. + +E: Incorrect args for bond coefficients + +Self-explanatory. Check the input script or data file. + +W: Use special bonds = 0,1,1 with bond style oxrna + +Most FENE models need this setting for the special_bonds command. + +W: FENE bond too long: %ld %g + +A FENE bond has stretched dangerously far. It's interaction strength +will be truncated to attempt to prevent the bond from blowing up. + +*/ diff --git a/src/USER-CGDNA/pair_oxdna2_dh.cpp b/src/USER-CGDNA/pair_oxdna2_dh.cpp index 44413ee7f1..e698d8d906 100644 --- a/src/USER-CGDNA/pair_oxdna2_dh.cpp +++ b/src/USER-CGDNA/pair_oxdna2_dh.cpp @@ -64,7 +64,7 @@ PairOxdna2Dh::~PairOxdna2Dh() compute vector COM-sugar-phosphate backbone interaction site in oxDNA2 ------------------------------------------------------------------------- */ void PairOxdna2Dh::compute_interaction_sites(double e1[3], - double e2[3], double r[3]) + double e2[3], double /*e3*/[3], double r[3]) { double d_cs_x=-0.34, d_cs_y=+0.3408; @@ -125,7 +125,7 @@ void PairOxdna2Dh::compute(int eflag, int vflag) MathExtra::q_to_exyz(qa,ax,ay,az); // vector COM-backbone site a - compute_interaction_sites(ax,ay,ra_cs); + compute_interaction_sites(ax,ay,az,ra_cs); rtmp_s[0] = x[a][0] + ra_cs[0]; rtmp_s[1] = x[a][1] + ra_cs[1]; @@ -145,7 +145,7 @@ void PairOxdna2Dh::compute(int eflag, int vflag) MathExtra::q_to_exyz(qb,bx,by,bz); // vector COM-backbone site b - compute_interaction_sites(bx,by,rb_cs); + compute_interaction_sites(bx,by,bz,rb_cs); // vector backbone site b to a delr[0] = rtmp_s[0] - x[b][0] - rb_cs[0]; diff --git a/src/USER-CGDNA/pair_oxdna2_dh.h b/src/USER-CGDNA/pair_oxdna2_dh.h index 7c907168e3..2a41524126 100644 --- a/src/USER-CGDNA/pair_oxdna2_dh.h +++ b/src/USER-CGDNA/pair_oxdna2_dh.h @@ -28,7 +28,8 @@ class PairOxdna2Dh : public Pair { public: PairOxdna2Dh(class LAMMPS *); virtual ~PairOxdna2Dh(); - virtual void compute_interaction_sites(double *, double *, double *); + virtual void compute_interaction_sites(double *, double *, double *, + double *); virtual void compute(int, int); void settings(int, char **); void coeff(int, char **); diff --git a/src/USER-CGDNA/pair_oxdna_coaxstk.h b/src/USER-CGDNA/pair_oxdna_coaxstk.h index e89e9bdbaa..79c8fa24ed 100644 --- a/src/USER-CGDNA/pair_oxdna_coaxstk.h +++ b/src/USER-CGDNA/pair_oxdna_coaxstk.h @@ -14,6 +14,7 @@ #ifdef PAIR_CLASS PairStyle(oxdna/coaxstk,PairOxdnaCoaxstk) +PairStyle(oxrna2/coaxstk,PairOxdnaCoaxstk) #else diff --git a/src/USER-CGDNA/pair_oxrna2_dh.cpp b/src/USER-CGDNA/pair_oxrna2_dh.cpp new file mode 100644 index 0000000000..045a6aa6bc --- /dev/null +++ b/src/USER-CGDNA/pair_oxrna2_dh.cpp @@ -0,0 +1,47 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- + Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) +------------------------------------------------------------------------- */ + +#include "pair_oxrna2_dh.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +PairOxrna2Dh::PairOxrna2Dh(LAMMPS *lmp) : PairOxdna2Dh(lmp) +{ + +} + +/* ---------------------------------------------------------------------- */ + +PairOxrna2Dh::~PairOxrna2Dh() +{ + +} + +/* ---------------------------------------------------------------------- + compute vector COM-sugar-phosphate backbone interaction site in oxRNA2 +------------------------------------------------------------------------- */ +void PairOxrna2Dh::compute_interaction_sites(double e1[3], double /*e2*/[3], + double e3[3], double r[3]) +{ + double d_cs_x=-0.4, d_cs_z=+0.2; + + r[0] = d_cs_x*e1[0] + d_cs_z*e3[0]; + r[1] = d_cs_x*e1[1] + d_cs_z*e3[1]; + r[2] = d_cs_x*e1[2] + d_cs_z*e3[2]; + +} diff --git a/src/USER-CGDNA/pair_oxrna2_dh.h b/src/USER-CGDNA/pair_oxrna2_dh.h new file mode 100644 index 0000000000..8ff4010113 --- /dev/null +++ b/src/USER-CGDNA/pair_oxrna2_dh.h @@ -0,0 +1,53 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(oxrna2/dh,PairOxrna2Dh) + +#else + +#ifndef LMP_PAIR_OXRNA2_DH_H +#define LMP_PAIR_OXRNA2_DH_H + +#include "pair_oxdna2_dh.h" + +namespace LAMMPS_NS { + +class PairOxrna2Dh : public PairOxdna2Dh { + public: + PairOxrna2Dh(class LAMMPS *); + virtual ~PairOxrna2Dh(); + virtual void compute_interaction_sites(double *, double *, double *, + double *); + +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +*/ diff --git a/src/USER-CGDNA/pair_oxrna2_excv.cpp b/src/USER-CGDNA/pair_oxrna2_excv.cpp new file mode 100644 index 0000000000..3c0194d636 --- /dev/null +++ b/src/USER-CGDNA/pair_oxrna2_excv.cpp @@ -0,0 +1,55 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- + Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) +------------------------------------------------------------------------- */ + +#include +#include +#include +#include +#include "pair_oxrna2_excv.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +PairOxrna2Excv::PairOxrna2Excv(LAMMPS *lmp) : PairOxdnaExcv(lmp) +{ + +} + +/* ---------------------------------------------------------------------- */ + +PairOxrna2Excv::~PairOxrna2Excv() +{ + +} + +/* ---------------------------------------------------------------------- + compute vector COM-excluded volume interaction sites in oxRNA2 +------------------------------------------------------------------------- */ +void PairOxrna2Excv::compute_interaction_sites(double e1[3], double /*e2*/[3], + double e3[3], double rs[3], double rb[3]) +{ + double d_cs_x=-0.4, d_cs_z=+0.2, d_cb=+0.4; + + rs[0] = d_cs_x*e1[0] + d_cs_z*e3[0]; + rs[1] = d_cs_x*e1[1] + d_cs_z*e3[1]; + rs[2] = d_cs_x*e1[2] + d_cs_z*e3[2]; + + rb[0] = d_cb*e1[0]; + rb[1] = d_cb*e1[1]; + rb[2] = d_cb*e1[2]; + +} diff --git a/src/USER-CGDNA/pair_oxrna2_excv.h b/src/USER-CGDNA/pair_oxrna2_excv.h new file mode 100644 index 0000000000..2dfb356203 --- /dev/null +++ b/src/USER-CGDNA/pair_oxrna2_excv.h @@ -0,0 +1,52 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(oxrna2/excv,PairOxrna2Excv) + +#else + +#ifndef LMP_PAIR_OXRNA2_EXCV_H +#define LMP_PAIR_OXRNA2_EXCV_H + +#include "pair_oxdna_excv.h" + +namespace LAMMPS_NS { + +class PairOxrna2Excv : public PairOxdnaExcv { + public: + PairOxrna2Excv(class LAMMPS *); + virtual ~PairOxrna2Excv(); + virtual void compute_interaction_sites(double *, double *, + double *, double *, double *); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +*/ diff --git a/src/USER-CGDNA/pair_oxrna2_hbond.cpp b/src/USER-CGDNA/pair_oxrna2_hbond.cpp new file mode 100644 index 0000000000..65f266ba36 --- /dev/null +++ b/src/USER-CGDNA/pair_oxrna2_hbond.cpp @@ -0,0 +1,58 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- + Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) +------------------------------------------------------------------------- */ + +#include "pair_oxrna2_hbond.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +PairOxrna2Hbond::PairOxrna2Hbond(LAMMPS *lmp) : PairOxdnaHbond(lmp) +{ + single_enable = 0; + writedata = 1; + + // sequence-specific base-pairing strength + // A:0 C:1 G:2 U:3, 5'- [i][j] -3' + + alpha_hb[0][0] = 1.00000; + alpha_hb[0][1] = 1.00000; + alpha_hb[0][2] = 1.00000; + alpha_hb[0][3] = 0.94253; + + alpha_hb[1][0] = 1.00000; + alpha_hb[1][1] = 1.00000; + alpha_hb[1][2] = 1.22288; + alpha_hb[1][3] = 1.00000; + + alpha_hb[2][0] = 1.00000; + alpha_hb[2][1] = 1.22288; + alpha_hb[2][2] = 1.00000; + alpha_hb[2][3] = 0.58655; + + alpha_hb[3][0] = 0.94253; + alpha_hb[3][1] = 1.00000; + alpha_hb[3][2] = 0.58655; + alpha_hb[3][3] = 1.00000; + +} + +/* ---------------------------------------------------------------------- */ + +PairOxrna2Hbond::~PairOxrna2Hbond() +{ + +} diff --git a/src/USER-CGDNA/pair_oxrna2_hbond.h b/src/USER-CGDNA/pair_oxrna2_hbond.h new file mode 100644 index 0000000000..3386cc23ec --- /dev/null +++ b/src/USER-CGDNA/pair_oxrna2_hbond.h @@ -0,0 +1,50 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(oxrna2/hbond,PairOxrna2Hbond) + +#else + +#ifndef LMP_PAIR_OXRNA2_HBOND_H +#define LMP_PAIR_OXRNA2_HBOND_H + +#include "pair_oxdna_hbond.h" + +namespace LAMMPS_NS { + +class PairOxrna2Hbond : public PairOxdnaHbond { + public: + PairOxrna2Hbond(class LAMMPS *); + virtual ~PairOxrna2Hbond(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +*/ diff --git a/src/USER-CGDNA/pair_oxrna2_stk.cpp b/src/USER-CGDNA/pair_oxrna2_stk.cpp new file mode 100644 index 0000000000..5fd32099f3 --- /dev/null +++ b/src/USER-CGDNA/pair_oxrna2_stk.cpp @@ -0,0 +1,1435 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- + Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) +------------------------------------------------------------------------- */ + +#include +#include +#include +#include +#include "pair_oxrna2_stk.h" +#include "mf_oxdna.h" +#include "atom.h" +#include "comm.h" +#include "force.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "update.h" +#include "integrate.h" +#include "math_const.h" +#include "memory.h" +#include "error.h" +#include "utils.h" +#include "atom_vec_ellipsoid.h" +#include "math_extra.h" + +using namespace LAMMPS_NS; +using namespace MathConst; +using namespace MFOxdna; + +/* ---------------------------------------------------------------------- */ + +PairOxrna2Stk::PairOxrna2Stk(LAMMPS *lmp) : Pair(lmp) +{ + single_enable = 0; + writedata = 1; + + // sequence-specific stacking strength + // A:0 C:1 G:2 U:3, 5'- [i][j] -3' + + eta_st[0][0] = 0.93851; + eta_st[0][1] = 1.12901; + eta_st[0][2] = 1.15626; + eta_st[0][3] = 0.88850; + + eta_st[1][0] = 0.86331; + eta_st[1][1] = 1.05060; + eta_st[1][2] = 0.90982; + eta_st[1][3] = 0.83252; + + eta_st[2][0] = 0.99407; + eta_st[2][1] = 1.14333; + eta_st[2][2] = 1.06573; + eta_st[2][3] = 0.91705; + + eta_st[3][0] = 0.98804; + eta_st[3][1] = 1.04949; + eta_st[3][2] = 1.12063; + eta_st[3][3] = 0.83818; + +} + +/* ---------------------------------------------------------------------- */ + +PairOxrna2Stk::~PairOxrna2Stk() +{ + if (allocated) { + + memory->destroy(setflag); + memory->destroy(cutsq); + + memory->destroy(epsilon_st); + memory->destroy(a_st); + memory->destroy(cut_st_0); + memory->destroy(cut_st_c); + memory->destroy(cut_st_lo); + memory->destroy(cut_st_hi); + memory->destroy(cut_st_lc); + memory->destroy(cut_st_hc); + memory->destroy(b_st_lo); + memory->destroy(b_st_hi); + memory->destroy(shift_st); + memory->destroy(cutsq_st_hc); + + memory->destroy(a_st5); + memory->destroy(theta_st5_0); + memory->destroy(dtheta_st5_ast); + memory->destroy(b_st5); + memory->destroy(dtheta_st5_c); + + memory->destroy(a_st6); + memory->destroy(theta_st6_0); + memory->destroy(dtheta_st6_ast); + memory->destroy(b_st6); + memory->destroy(dtheta_st6_c); + + memory->destroy(a_st9); + memory->destroy(theta_st9_0); + memory->destroy(dtheta_st9_ast); + memory->destroy(b_st9); + memory->destroy(dtheta_st9_c); + + memory->destroy(a_st10); + memory->destroy(theta_st10_0); + memory->destroy(dtheta_st10_ast); + memory->destroy(b_st10); + memory->destroy(dtheta_st10_c); + + memory->destroy(a_st1); + memory->destroy(cosphi_st1_ast); + memory->destroy(b_st1); + memory->destroy(cosphi_st1_c); + memory->destroy(a_st2); + memory->destroy(cosphi_st2_ast); + memory->destroy(b_st2); + memory->destroy(cosphi_st2_c); + + } +} + +/* ---------------------------------------------------------------------- + tally energy and virial into global and per-atom accumulators + + NOTE: Although this is a pair style interaction, the algorithm below + follows the virial incrementation of the bond style. This is because + the bond topology is used in the main compute loop. +------------------------------------------------------------------------- */ + +void PairOxrna2Stk::ev_tally_xyz(int i, int j, int nlocal, int newton_bond, + double evdwl, + double fx, double fy, double fz, + double delx, double dely, double delz) +{ + double evdwlhalf,v[6]; + + if (eflag_either) { + if (eflag_global) { + if (newton_bond) eng_vdwl += evdwl; + else { + evdwlhalf = 0.5*evdwl; + if (i < nlocal) eng_vdwl += evdwlhalf; + if (j < nlocal) eng_vdwl += evdwlhalf; + } + } + if (eflag_atom) { + evdwlhalf = 0.5*evdwl; + if (newton_bond || i < nlocal) eatom[i] += evdwlhalf; + if (newton_bond || j < nlocal) eatom[j] += evdwlhalf; + } + } + + if (vflag_either) { + v[0] = delx*fx; + v[1] = dely*fy; + v[2] = delz*fz; + v[3] = delx*fy; + v[4] = delx*fz; + v[5] = dely*fz; + + if (vflag_global) { + if (newton_bond) { + virial[0] += v[0]; + virial[1] += v[1]; + virial[2] += v[2]; + virial[3] += v[3]; + virial[4] += v[4]; + virial[5] += v[5]; + } else { + if (i < nlocal) { + virial[0] += 0.5*v[0]; + virial[1] += 0.5*v[1]; + virial[2] += 0.5*v[2]; + virial[3] += 0.5*v[3]; + virial[4] += 0.5*v[4]; + virial[5] += 0.5*v[5]; + } + if (j < nlocal) { + virial[0] += 0.5*v[0]; + virial[1] += 0.5*v[1]; + virial[2] += 0.5*v[2]; + virial[3] += 0.5*v[3]; + virial[4] += 0.5*v[4]; + virial[5] += 0.5*v[5]; + } + } + } + + if (vflag_atom) { + if (newton_bond || i < nlocal) { + vatom[i][0] += 0.5*v[0]; + vatom[i][1] += 0.5*v[1]; + vatom[i][2] += 0.5*v[2]; + vatom[i][3] += 0.5*v[3]; + vatom[i][4] += 0.5*v[4]; + vatom[i][5] += 0.5*v[5]; + } + if (newton_bond || j < nlocal) { + vatom[j][0] += 0.5*v[0]; + vatom[j][1] += 0.5*v[1]; + vatom[j][2] += 0.5*v[2]; + vatom[j][3] += 0.5*v[3]; + vatom[j][4] += 0.5*v[4]; + vatom[j][5] += 0.5*v[5]; + } + } + } +} + +/* ---------------------------------------------------------------------- + compute function for oxRNA2 pair interactions + s=sugar-phosphate backbone site, b=base site, st=stacking site +------------------------------------------------------------------------- */ + +void PairOxrna2Stk::compute(int eflag, int vflag) +{ + + double delf[3],delta[3],deltb[3]; // force, torque increment; + double evdwl,fpair,finc,tpair; + double delr_ss[3],delr_ss_norm[3],rsq_ss,r_ss,rinv_ss; + double delr_st[3],delr_st_norm[3],rsq_st,r_st,rinv_st; + double theta5p,t5pdir[3],cost5p; + double theta6p,t6pdir[3],cost6p; + double theta9,t9dir[3],cost9; + double theta10,t10dir[3],cost10; + double cosphi1,cosphi2,cosphi1dir[3],cosphi2dir[3]; + + // distances COM-backbone site, COM-3' and COM-5' stacking site + double d_cs_x=-0.4, d_cs_z=+0.2; + double d_cst_x_3p=+0.4, d_cst_y_3p=+0.1; + double d_cst_x_5p=+0.124906078525, d_cst_y_5p=-0.00866274917473; + + // 3' and p5' auxiliary vectors + double d3p_x=-0.462510,d3p_y=-0.528218,d3p_z=+0.712089; + double d5p_x=-0.104402,d5p_y=-0.841783,d5p_z=+0.529624; + double aux3p[3], aux5p[3]; + + // vectors COM-backbone site, COM-stacking site in lab frame + double ra_cs[3],ra_cst[3]; + double rb_cs[3],rb_cst[3]; + + // quaternions and Cartesian unit vectors in lab frame + double *qa,ax[3],ay[3],az[3]; + double *qb,bx[3],by[3],bz[3]; + + double **x = atom->x; + double **f = atom->f; + double **torque = atom->torque; + int *type = atom->type; + + int nlocal = atom->nlocal; + int newton_bond = force->newton_bond; + + int **bondlist = neighbor->bondlist; + int nbondlist = neighbor->nbondlist; + + AtomVecEllipsoid *avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid"); + AtomVecEllipsoid::Bonus *bonus = avec->bonus; + + int a,b,in,atype,btype; + + double f1,f4t5,f4t6,f4t9,f4t10,f5c1,f5c2; + double df1,df4t5,df4t6,df4t9,df4t10,df5c1,df5c2; + double tptofp; + + evdwl = 0.0; + ev_init(eflag,vflag); + + // loop over stacking interaction neighbors using bond topology + + for (in = 0; in < nbondlist; in++) { + + a = bondlist[in][1]; + b = bondlist[in][0]; + + qa=bonus[a].quat; + MathExtra::q_to_exyz(qa,ax,ay,az); + qb=bonus[b].quat; + MathExtra::q_to_exyz(qb,bx,by,bz); + + // vector COM a - 3'-stacking site a + ra_cst[0] = d_cst_x_3p*ax[0] + d_cst_y_3p*ay[0]; + ra_cst[1] = d_cst_x_3p*ax[1] + d_cst_y_3p*ay[1]; + ra_cst[2] = d_cst_x_3p*ax[2] + d_cst_y_3p*ay[2]; + + // vector COM b - 5'-stacking site b + rb_cst[0] = d_cst_x_5p*bx[0] + d_cst_y_5p*by[0]; + rb_cst[1] = d_cst_x_5p*bx[1] + d_cst_y_5p*by[1]; + rb_cst[2] = d_cst_x_5p*bx[2] + d_cst_y_5p*by[2]; + + // vector 5'-stacking site b to 3'-stacking site a + delr_st[0] = x[a][0] + ra_cst[0] - x[b][0] - rb_cst[0]; + delr_st[1] = x[a][1] + ra_cst[1] - x[b][1] - rb_cst[1]; + delr_st[2] = x[a][2] + ra_cst[2] - x[b][2] - rb_cst[2]; + + // test for directionality of vector b to a + tptofp = MFOxdna::is_3pto5p(delr_st,bz); + + // if b to a is 5' to 3' we need to swap roles of a and b + if (tptofp == -1) { + + std::swap(a,b); + std::swap(ax,bx); + std::swap(ay,by); + std::swap(az,bz); + + } + + // a now in 5' direction, b in 3' direction + atype = type[a]; + btype = type[b]; + + // calculate again + // vector COM a - 3'-stacking site a + ra_cst[0] = d_cst_x_3p*ax[0] + d_cst_y_3p*ay[0]; + ra_cst[1] = d_cst_x_3p*ax[1] + d_cst_y_3p*ay[1]; + ra_cst[2] = d_cst_x_3p*ax[2] + d_cst_y_3p*ay[2]; + + // vector COM b - 5'-stacking site b + rb_cst[0] = d_cst_x_5p*bx[0] + d_cst_y_5p*by[0]; + rb_cst[1] = d_cst_x_5p*bx[1] + d_cst_y_5p*by[1]; + rb_cst[2] = d_cst_x_5p*bx[2] + d_cst_y_5p*by[2]; + + // vector 5'-stacking site b to 3'-stacking site a + delr_st[0] = x[a][0] + ra_cst[0] - x[b][0] - rb_cst[0]; + delr_st[1] = x[a][1] + ra_cst[1] - x[b][1] - rb_cst[1]; + delr_st[2] = x[a][2] + ra_cst[2] - x[b][2] - rb_cst[2]; + + rsq_st = delr_st[0]*delr_st[0] + delr_st[1]*delr_st[1] + delr_st[2]*delr_st[2]; + r_st = sqrt(rsq_st); + rinv_st = 1.0/r_st; + + delr_st_norm[0] = delr_st[0] * rinv_st; + delr_st_norm[1] = delr_st[1] * rinv_st; + delr_st_norm[2] = delr_st[2] * rinv_st; + + // vector COM a - backbone site a + ra_cs[0] = d_cs_x*ax[0] + d_cs_z*az[0]; + ra_cs[1] = d_cs_x*ax[1] + d_cs_z*az[1]; + ra_cs[2] = d_cs_x*ax[2] + d_cs_z*az[2]; + + // vector COM b - backbone site b + rb_cs[0] = d_cs_x*bx[0] + d_cs_z*bz[0]; + rb_cs[1] = d_cs_x*bx[1] + d_cs_z*bz[1]; + rb_cs[2] = d_cs_x*bx[2] + d_cs_z*bz[2]; + + // vector backbone site b to a + delr_ss[0] = (x[a][0] + ra_cs[0] - x[b][0] - rb_cs[0]); + delr_ss[1] = (x[a][1] + ra_cs[1] - x[b][1] - rb_cs[1]); + delr_ss[2] = (x[a][2] + ra_cs[2] - x[b][2] - rb_cs[2]); + + rsq_ss = delr_ss[0]*delr_ss[0] + delr_ss[1]*delr_ss[1] + delr_ss[2]*delr_ss[2]; + r_ss = sqrt(rsq_ss); + rinv_ss = 1.0/r_ss; + + delr_ss_norm[0] = delr_ss[0] * rinv_ss; + delr_ss_norm[1] = delr_ss[1] * rinv_ss; + delr_ss_norm[2] = delr_ss[2] * rinv_ss; + + f1 = F1(r_st, epsilon_st[atype][btype], a_st[atype][btype], cut_st_0[atype][btype], + cut_st_lc[atype][btype], cut_st_hc[atype][btype], cut_st_lo[atype][btype], cut_st_hi[atype][btype], + b_st_lo[atype][btype], b_st_hi[atype][btype], shift_st[atype][btype]); + + // early rejection criterium + if (f1) { + + // theta5 angle and correction + cost5p = MathExtra::dot3(delr_st_norm,az); + if (cost5p > 1.0) cost5p = 1.0; + if (cost5p < -1.0) cost5p = -1.0; + theta5p = acos(cost5p); + + f4t5 = F4(theta5p, a_st5[atype][btype], theta_st5_0[atype][btype], dtheta_st5_ast[atype][btype], + b_st5[atype][btype], dtheta_st5_c[atype][btype]); + + // early rejection criterium + if (f4t5) { + + cost6p = MathExtra::dot3(delr_st_norm,bz); + if (cost6p > 1.0) cost6p = 1.0; + if (cost6p < -1.0) cost6p = -1.0; + theta6p = acos(cost6p); + + aux3p[0] = d3p_x * ax[0] + d3p_y * ay[0] + d3p_z * az[0]; + aux3p[1] = d3p_x * ax[1] + d3p_y * ay[1] + d3p_z * az[1]; + aux3p[2] = d3p_x * ax[2] + d3p_y * ay[2] + d3p_z * az[2]; + + aux5p[0] = d5p_x * bx[0] + d5p_y * by[0] + d5p_z * bz[0]; + aux5p[1] = d5p_x * bx[1] + d5p_y * by[1] + d5p_z * bz[1]; + aux5p[2] = d5p_x * bx[2] + d5p_y * by[2] + d5p_z * bz[2]; + + cost9 = MathExtra::dot3(delr_ss_norm,aux3p); + if (cost9 > 1.0) cost9 = 1.0; + if (cost9 < -1.0) cost9 = -1.0; + theta9 = acos(cost9); + + cost10 = MathExtra::dot3(delr_ss_norm,aux5p); + if (cost10 > 1.0) cost10 = 1.0; + if (cost10 < -1.0) cost10 = -1.0; + theta10 = acos(cost10); + + cosphi1 = MathExtra::dot3(delr_ss_norm,ay); + if (cosphi1 > 1.0) cosphi1 = 1.0; + if (cosphi1 < -1.0) cosphi1 = -1.0; + + cosphi2 = MathExtra::dot3(delr_ss_norm,by); + if (cosphi2 > 1.0) cosphi2 = 1.0; + if (cosphi2 < -1.0) cosphi2 = -1.0; + + f4t6 = F4(theta6p, a_st6[atype][btype], theta_st6_0[atype][btype], dtheta_st6_ast[atype][btype], + b_st6[atype][btype], dtheta_st6_c[atype][btype]); + + f4t9 = F4(theta9, a_st9[atype][btype], theta_st9_0[atype][btype], dtheta_st9_ast[atype][btype], + b_st9[atype][btype], dtheta_st9_c[atype][btype]); + + f4t10 = F4(theta10, a_st10[atype][btype], theta_st10_0[atype][btype], dtheta_st10_ast[atype][btype], + b_st10[atype][btype], dtheta_st10_c[atype][btype]); + + f5c1 = F5(-cosphi1, a_st1[atype][btype], -cosphi_st1_ast[atype][btype], b_st1[atype][btype], + cosphi_st1_c[atype][btype]); + + f5c2 = F5(-cosphi2, a_st2[atype][btype], -cosphi_st2_ast[atype][btype], b_st2[atype][btype], + cosphi_st2_c[atype][btype]); + + + evdwl = f1 * f4t5 * f4t6 * f4t9 * f4t10 * f5c1 * f5c2; + + // early rejection criterium + if (evdwl) { + + df1 = DF1(r_st, epsilon_st[atype][btype], a_st[atype][btype], cut_st_0[atype][btype], + cut_st_lc[atype][btype], cut_st_hc[atype][btype], cut_st_lo[atype][btype], cut_st_hi[atype][btype], + b_st_lo[atype][btype], b_st_hi[atype][btype]); + + df4t5 = DF4(theta5p, a_st5[atype][btype], theta_st5_0[atype][btype], dtheta_st5_ast[atype][btype], + b_st5[atype][btype], dtheta_st5_c[atype][btype])/sin(theta5p); + + df4t6 = DF4(theta6p, a_st6[atype][btype], theta_st6_0[atype][btype], dtheta_st6_ast[atype][btype], + b_st6[atype][btype], dtheta_st6_c[atype][btype])/sin(theta6p); + + df4t9 = DF4(theta9, a_st9[atype][btype], theta_st9_0[atype][btype], dtheta_st9_ast[atype][btype], + b_st9[atype][btype], dtheta_st9_c[atype][btype])/sin(theta9); + + df4t10 = DF4(theta10, a_st10[atype][btype], theta_st10_0[atype][btype], dtheta_st10_ast[atype][btype], + b_st10[atype][btype], dtheta_st10_c[atype][btype])/sin(theta10); + + df5c1 = DF5(-cosphi1, a_st1[atype][btype], -cosphi_st1_ast[atype][btype], b_st1[atype][btype], + cosphi_st1_c[atype][btype]); + + df5c2 = DF5(-cosphi2, a_st2[atype][btype], -cosphi_st2_ast[atype][btype], b_st2[atype][btype], + cosphi_st2_c[atype][btype]); + + + // force, torque and virial contribution for forces between stacking sites + + fpair = 0.0; + + delf[0] = 0.0; + delf[1] = 0.0; + delf[2] = 0.0; + + delta[0] = 0.0; + delta[1] = 0.0; + delta[2] = 0.0; + + deltb[0] = 0.0; + deltb[1] = 0.0; + deltb[2] = 0.0; + + // radial force + finc = -df1 * f4t5 * f4t6 * f4t9 * f4t10 * f5c1 * f5c2; + fpair += finc; + + delf[0] += delr_st[0] * finc; + delf[1] += delr_st[1] * finc; + delf[2] += delr_st[2] * finc; + + // theta5p force + if (theta5p) { + + finc = -f1 * df4t5 * f4t6 * f4t9 * f4t10 * f5c1 * f5c2 * rinv_st; + fpair += finc; + + delf[0] += (delr_st_norm[0]*cost5p - az[0]) * finc; + delf[1] += (delr_st_norm[1]*cost5p - az[1]) * finc; + delf[2] += (delr_st_norm[2]*cost5p - az[2]) * finc; + + } + + // theta6p force + if (theta6p) { + + finc = -f1 * f4t5 * df4t6 * f4t9 * f4t10 * f5c1 * f5c2 * rinv_st; + fpair += finc; + + delf[0] += (delr_st_norm[0]*cost6p - bz[0]) * finc; + delf[1] += (delr_st_norm[1]*cost6p - bz[1]) * finc; + delf[2] += (delr_st_norm[2]*cost6p - bz[2]) * finc; + + } + + // increment forces and torques + + if (newton_bond || a < nlocal) { + + f[a][0] += delf[0]; + f[a][1] += delf[1]; + f[a][2] += delf[2]; + + MathExtra::cross3(ra_cst,delf,delta); + + } + if (newton_bond || b < nlocal) { + + f[b][0] -= delf[0]; + f[b][1] -= delf[1]; + f[b][2] -= delf[2]; + + MathExtra::cross3(rb_cst,delf,deltb); + + } + + if (newton_bond || a < nlocal) { + + torque[a][0] += delta[0]; + torque[a][1] += delta[1]; + torque[a][2] += delta[2]; + + } + if (newton_bond || b < nlocal) { + + torque[b][0] -= deltb[0]; + torque[b][1] -= deltb[1]; + torque[b][2] -= deltb[2]; + + } + + // increment energy and virial + // NOTE: The virial is calculated on the 'molecular' basis. + // (see G. Ciccotti and J.P. Ryckaert, Comp. Phys. Rep. 4, 345-392 (1986)) + + if (evflag) ev_tally_xyz(a,b,nlocal,newton_bond,evdwl, + delf[0],delf[1],delf[2],x[a][0]-x[b][0],x[a][1]-x[b][1],x[a][2]-x[b][2]); + + // force, torque and virial contribution for forces between backbone sites + + fpair = 0.0; + + delf[0] = 0.0; + delf[1] = 0.0; + delf[2] = 0.0; + + delta[0] = 0.0; + delta[1] = 0.0; + delta[2] = 0.0; + + deltb[0] = 0.0; + deltb[1] = 0.0; + deltb[2] = 0.0; + + // theta9 force + if (theta9) { + + finc = -f1 * f4t5 * f4t6 * df4t9 * f4t10 * f5c1 * f5c2 * rinv_ss; + fpair += finc; + + delf[0] += (delr_ss_norm[0]*cost9 - aux3p[0]) * finc; + delf[1] += (delr_ss_norm[1]*cost9 - aux3p[1]) * finc; + delf[2] += (delr_ss_norm[2]*cost9 - aux3p[2]) * finc; + + } + + // theta10 force + if (theta10) { + + finc = -f1 * f4t5 * f4t6 * f4t9 * df4t10 * f5c1 * f5c2 * rinv_ss; + fpair += finc; + + delf[0] += (delr_ss_norm[0]*cost10 - aux5p[0]) * finc; + delf[1] += (delr_ss_norm[1]*cost10 - aux5p[1]) * finc; + delf[2] += (delr_ss_norm[2]*cost10 - aux5p[2]) * finc; + + } + + // cosphi1 force + if (cosphi1) { + + finc = -f1 * f4t5 * f4t6 * f4t9 * f4t10 * df5c1 * f5c2 * rinv_ss; + fpair += finc; + + delf[0] += (delr_ss_norm[0]*cosphi1 - ay[0]) * finc; + delf[1] += (delr_ss_norm[1]*cosphi1 - ay[1]) * finc; + delf[2] += (delr_ss_norm[2]*cosphi1 - ay[2]) * finc; + + } + + // cosphi2 force + if (cosphi2) { + + finc = -f1 * f4t5 * f4t6 * f4t9 * f4t10 * f5c1 * df5c2 * rinv_ss; + fpair += finc; + + delf[0] += (delr_ss_norm[0]*cosphi2 - by[0]) * finc; + delf[1] += (delr_ss_norm[1]*cosphi2 - by[1]) * finc; + delf[2] += (delr_ss_norm[2]*cosphi2 - by[2]) * finc; + + } + + // increment forces and torques + + if (newton_bond || a < nlocal) { + + f[a][0] += delf[0]; + f[a][1] += delf[1]; + f[a][2] += delf[2]; + + MathExtra::cross3(ra_cs,delf,delta); + + } + if (newton_bond || b < nlocal) { + + f[b][0] -= delf[0]; + f[b][1] -= delf[1]; + f[b][2] -= delf[2]; + + MathExtra::cross3(rb_cs,delf,deltb); + + } + + if (newton_bond || a < nlocal) { + + torque[a][0] += delta[0]; + torque[a][1] += delta[1]; + torque[a][2] += delta[2]; + + } + if (newton_bond || b < nlocal) { + + torque[b][0] -= deltb[0]; + torque[b][1] -= deltb[1]; + torque[b][2] -= deltb[2]; + + } + + // increment virial only + if (evflag) ev_tally_xyz(a,b,nlocal,newton_bond,0.0, + delf[0],delf[1],delf[2],x[a][0]-x[b][0],x[a][1]-x[b][1],x[a][2]-x[b][2]); + + // pure torques not expressible as r x f + + delta[0] = 0.0; + delta[1] = 0.0; + delta[2] = 0.0; + deltb[0] = 0.0; + deltb[1] = 0.0; + deltb[2] = 0.0; + + // theta5p torque + if (theta5p) { + + tpair = -f1 * df4t5 * f4t6 * f4t9 * f4t10 * f5c1 * f5c2; + MathExtra::cross3(delr_st_norm,az,t5pdir); + + delta[0] += t5pdir[0] * tpair; + delta[1] += t5pdir[1] * tpair; + delta[2] += t5pdir[2] * tpair; + + } + + // theta6p torque + if (theta6p) { + + tpair = -f1 * f4t5 * df4t6 * f4t9 * f4t10 * f5c1 * f5c2; + MathExtra::cross3(delr_st_norm,bz,t6pdir); + + deltb[0] -= t6pdir[0] * tpair; + deltb[1] -= t6pdir[1] * tpair; + deltb[2] -= t6pdir[2] * tpair; + + } + + // theta9 torque + if (theta9) { + + tpair = -f1 * f4t5 * f4t6 * df4t9 * f4t10 * f5c1 * f5c2; + MathExtra::cross3(delr_ss_norm,aux3p,t9dir); + + delta[0] += t9dir[0] * tpair; + delta[1] += t9dir[1] * tpair; + delta[2] += t9dir[2] * tpair; + + } + + // theta10 torque + if (theta10) { + + tpair = -f1 * f4t5 * f4t6 * f4t9 * df4t10 * f5c1 * f5c2; + MathExtra::cross3(delr_ss_norm,aux5p,t10dir); + + deltb[0] -= t10dir[0] * tpair; + deltb[1] -= t10dir[1] * tpair; + deltb[2] -= t10dir[2] * tpair; + + } + + // cosphi1 torque + if (cosphi1) { + + tpair = -f1 * f4t5 * f4t6 * f4t9 * f4t10 * df5c1 * f5c2; + MathExtra::cross3(delr_ss_norm,ay,cosphi1dir); + + delta[0] += cosphi1dir[0] * tpair; + delta[1] += cosphi1dir[1] * tpair; + delta[2] += cosphi1dir[2] * tpair; + + } + + // cosphi2 torque + if (cosphi2) { + + tpair = -f1 * f4t5 * f4t6 * f4t9 * f4t10 * f5c1 * df5c2; + MathExtra::cross3(delr_ss_norm,by,cosphi2dir); + + deltb[0] -= cosphi2dir[0] * tpair; + deltb[1] -= cosphi2dir[1] * tpair; + deltb[2] -= cosphi2dir[2] * tpair; + + } + + // increment torques + if (newton_bond || a < nlocal) { + + torque[a][0] += delta[0]; + torque[a][1] += delta[1]; + torque[a][2] += delta[2]; + + } + if (newton_bond || b < nlocal) { + + torque[b][0] -= deltb[0]; + torque[b][1] -= deltb[1]; + torque[b][2] -= deltb[2]; + + } + + } + } + } + // end early rejection criteria + + } + // end stacking interaction + + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairOxrna2Stk::allocate() +{ + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag,n+1,n+1,"pair:setflag"); + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; + + memory->create(cutsq,n+1,n+1,"pair:cutsq"); + + memory->create(epsilon_st,n+1,n+1,"pair:epsilon_st"); + memory->create(a_st,n+1,n+1,"pair:a_st"); + memory->create(cut_st_0,n+1,n+1,"pair:cut_st_0"); + memory->create(cut_st_c,n+1,n+1,"pair:cut_st_c"); + memory->create(cut_st_lo,n+1,n+1,"pair:cut_st_lo"); + memory->create(cut_st_hi,n+1,n+1,"pair:cut_st_hi"); + memory->create(cut_st_lc,n+1,n+1,"pair:cut_st_lc"); + memory->create(cut_st_hc,n+1,n+1,"pair:cut_st_hc"); + memory->create(b_st_lo,n+1,n+1,"pair:b_st_lo"); + memory->create(b_st_hi,n+1,n+1,"pair:b_st_hi"); + memory->create(shift_st,n+1,n+1,"pair:shift_st"); + memory->create(cutsq_st_hc,n+1,n+1,"pair:cutsq_st_hc"); + + memory->create(a_st5,n+1,n+1,"pair:a_st5"); + memory->create(theta_st5_0,n+1,n+1,"pair:theta_st5_0"); + memory->create(dtheta_st5_ast,n+1,n+1,"pair:dtheta_st5_ast"); + memory->create(b_st5,n+1,n+1,"pair:b_st5"); + memory->create(dtheta_st5_c,n+1,n+1,"pair:dtheta_st5_c"); + + memory->create(a_st6,n+1,n+1,"pair:a_st6"); + memory->create(theta_st6_0,n+1,n+1,"pair:theta_st6_0"); + memory->create(dtheta_st6_ast,n+1,n+1,"pair:dtheta_st6_ast"); + memory->create(b_st6,n+1,n+1,"pair:b_st6"); + memory->create(dtheta_st6_c,n+1,n+1,"pair:dtheta_st6_c"); + + memory->create(a_st9,n+1,n+1,"pair:a_st9"); + memory->create(theta_st9_0,n+1,n+1,"pair:theta_st9_0"); + memory->create(dtheta_st9_ast,n+1,n+1,"pair:dtheta_st9_ast"); + memory->create(b_st9,n+1,n+1,"pair:b_st9"); + memory->create(dtheta_st9_c,n+1,n+1,"pair:dtheta_st9_c"); + + memory->create(a_st10,n+1,n+1,"pair:a_st10"); + memory->create(theta_st10_0,n+1,n+1,"pair:theta_st10_0"); + memory->create(dtheta_st10_ast,n+1,n+1,"pair:dtheta_st10_ast"); + memory->create(b_st10,n+1,n+1,"pair:b_st10"); + memory->create(dtheta_st10_c,n+1,n+1,"pair:dtheta_st10_c"); + + memory->create(a_st1,n+1,n+1,"pair:a_st1"); + memory->create(cosphi_st1_ast,n+1,n+1,"pair:cosphi_st1_ast"); + memory->create(b_st1,n+1,n+1,"pair:b_st1"); + memory->create(cosphi_st1_c,n+1,n+1,"pair:cosphi_st1_c"); + memory->create(a_st2,n+1,n+1,"pair:a_st2"); + memory->create(cosphi_st2_ast,n+1,n+1,"pair:cosphi_st2_ast"); + memory->create(b_st2,n+1,n+1,"pair:b_st2"); + memory->create(cosphi_st2_c,n+1,n+1,"pair:cosphi_st2_c"); + +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairOxrna2Stk::settings(int narg, char **/*arg*/) +{ + if (narg != 0) error->all(FLERR,"Illegal pair_style command"); + +} + +/* ---------------------------------------------------------------------- + return temperature dependent oxRNA stacking strength +------------------------------------------------------------------------- */ + +double PairOxrna2Stk::stacking_strength(double xi_st, double kappa_st, double T) +{ + double eps; + + eps = xi_st + kappa_st * T; + + return eps; +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairOxrna2Stk::coeff(int narg, char **arg) +{ + int count; + + if (narg != 27) error->all(FLERR,"Incorrect args for pair coefficients in oxrna2/stk"); + if (!allocated) allocate(); + + int ilo,ihi,jlo,jhi; + force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi); + force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi); + + // stacking interaction + count = 0; + + double T, epsilon_st_one, xi_st_one, kappa_st_one, a_st_one, b_st_lo_one, b_st_hi_one; + double cut_st_0_one, cut_st_c_one, cut_st_lo_one, cut_st_hi_one; + double cut_st_lc_one, cut_st_hc_one, tmp, shift_st_one; + + double a_st5_one, theta_st5_0_one, dtheta_st5_ast_one; + double b_st5_one, dtheta_st5_c_one; + + double a_st6_one, theta_st6_0_one, dtheta_st6_ast_one; + double b_st6_one, dtheta_st6_c_one; + + double a_st9_one, theta_st9_0_one, dtheta_st9_ast_one; + double b_st9_one, dtheta_st9_c_one; + + double a_st10_one, theta_st10_0_one, dtheta_st10_ast_one; + double b_st10_one, dtheta_st10_c_one; + + double a_st1_one, cosphi_st1_ast_one, b_st1_one, cosphi_st1_c_one; + double a_st2_one, cosphi_st2_ast_one, b_st2_one, cosphi_st2_c_one; + + if (strcmp(arg[2], "seqav") != 0 && strcmp(arg[2], "seqdep") != 0) { + error->all(FLERR,"Incorrect setting, select seqav or seqdep in oxrna2/stk"); + } + if (strcmp(arg[2],"seqav") == 0) seqdepflag = 0; + if (strcmp(arg[2],"seqdep") == 0) seqdepflag = 1; + + T = force->numeric(FLERR,arg[3]); + xi_st_one = force->numeric(FLERR,arg[4]); + kappa_st_one = force->numeric(FLERR,arg[5]); + epsilon_st_one = stacking_strength(xi_st_one, kappa_st_one, T); + + a_st_one = force->numeric(FLERR,arg[6]); + cut_st_0_one = force->numeric(FLERR,arg[7]); + cut_st_c_one = force->numeric(FLERR,arg[8]); + cut_st_lo_one = force->numeric(FLERR,arg[9]); + cut_st_hi_one = force->numeric(FLERR,arg[10]); + + a_st5_one = force->numeric(FLERR,arg[11]); + theta_st5_0_one = force->numeric(FLERR,arg[12]); + dtheta_st5_ast_one = force->numeric(FLERR,arg[13]); + a_st6_one = force->numeric(FLERR,arg[14]); + theta_st6_0_one = force->numeric(FLERR,arg[15]); + dtheta_st6_ast_one = force->numeric(FLERR,arg[16]); + + a_st9_one = force->numeric(FLERR,arg[17]); + theta_st9_0_one = force->numeric(FLERR,arg[18]); + dtheta_st9_ast_one = force->numeric(FLERR,arg[19]); + a_st10_one = force->numeric(FLERR,arg[20]); + theta_st10_0_one = force->numeric(FLERR,arg[21]); + dtheta_st10_ast_one = force->numeric(FLERR,arg[22]); + + a_st1_one = force->numeric(FLERR,arg[23]); + cosphi_st1_ast_one = force->numeric(FLERR,arg[24]); + a_st2_one = force->numeric(FLERR,arg[25]); + cosphi_st2_ast_one = force->numeric(FLERR,arg[26]); + + b_st_lo_one = 2*a_st_one*exp(-a_st_one*(cut_st_lo_one-cut_st_0_one))* + 2*a_st_one*exp(-a_st_one*(cut_st_lo_one-cut_st_0_one))* + (1-exp(-a_st_one*(cut_st_lo_one-cut_st_0_one)))* + (1-exp(-a_st_one*(cut_st_lo_one-cut_st_0_one)))/ + (4*((1-exp(-a_st_one*(cut_st_lo_one -cut_st_0_one)))* + (1-exp(-a_st_one*(cut_st_lo_one-cut_st_0_one)))- + (1-exp(-a_st_one*(cut_st_c_one -cut_st_0_one)))* + (1-exp(-a_st_one*(cut_st_c_one-cut_st_0_one))))); + + cut_st_lc_one = cut_st_lo_one - a_st_one*exp(-a_st_one*(cut_st_lo_one-cut_st_0_one))* + (1-exp(-a_st_one*(cut_st_lo_one-cut_st_0_one)))/b_st_lo_one; + + b_st_hi_one = 2*a_st_one*exp(-a_st_one*(cut_st_hi_one-cut_st_0_one))* + 2*a_st_one*exp(-a_st_one*(cut_st_hi_one-cut_st_0_one))* + (1-exp(-a_st_one*(cut_st_hi_one-cut_st_0_one)))* + (1-exp(-a_st_one*(cut_st_hi_one-cut_st_0_one)))/ + (4*((1-exp(-a_st_one*(cut_st_hi_one -cut_st_0_one)))* + (1-exp(-a_st_one*(cut_st_hi_one-cut_st_0_one)))- + (1-exp(-a_st_one*(cut_st_c_one -cut_st_0_one)))* + (1-exp(-a_st_one*(cut_st_c_one-cut_st_0_one))))); + + cut_st_hc_one = cut_st_hi_one - a_st_one*exp(-a_st_one*(cut_st_hi_one-cut_st_0_one))* + (1-exp(-a_st_one*(cut_st_hi_one-cut_st_0_one)))/b_st_hi_one; + + tmp = 1 - exp(-(cut_st_c_one-cut_st_0_one) * a_st_one); + shift_st_one = epsilon_st_one * tmp * tmp; + + b_st5_one = a_st5_one*a_st5_one*dtheta_st5_ast_one*dtheta_st5_ast_one/(1-a_st5_one*dtheta_st5_ast_one*dtheta_st5_ast_one); + dtheta_st5_c_one = 1/(a_st5_one*dtheta_st5_ast_one); + + b_st6_one = a_st6_one*a_st6_one*dtheta_st6_ast_one*dtheta_st6_ast_one/(1-a_st6_one*dtheta_st6_ast_one*dtheta_st6_ast_one); + dtheta_st6_c_one = 1/(a_st6_one*dtheta_st6_ast_one); + + b_st9_one = a_st9_one*a_st9_one*dtheta_st9_ast_one*dtheta_st9_ast_one/(1-a_st9_one*dtheta_st9_ast_one*dtheta_st9_ast_one); + dtheta_st9_c_one = 1/(a_st9_one*dtheta_st9_ast_one); + + b_st10_one = a_st10_one*a_st10_one*dtheta_st10_ast_one*dtheta_st10_ast_one/(1-a_st10_one*dtheta_st10_ast_one*dtheta_st10_ast_one); + dtheta_st10_c_one = 1/(a_st10_one*dtheta_st10_ast_one); + + b_st1_one = a_st1_one*a_st1_one*cosphi_st1_ast_one*cosphi_st1_ast_one/(1-a_st1_one*cosphi_st1_ast_one*cosphi_st1_ast_one); + cosphi_st1_c_one=1/(a_st1_one*cosphi_st1_ast_one); + + b_st2_one = a_st2_one*a_st2_one*cosphi_st2_ast_one*cosphi_st2_ast_one/(1-a_st2_one*cosphi_st2_ast_one*cosphi_st2_ast_one); + cosphi_st2_c_one=1/(a_st2_one*cosphi_st2_ast_one); + + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j <= jhi; j++) { + + epsilon_st[i][j] = epsilon_st_one; + if (seqdepflag) epsilon_st[i][j] *= eta_st[i-1][j-1]; + a_st[i][j] = a_st_one; + cut_st_0[i][j] = cut_st_0_one; + cut_st_c[i][j] = cut_st_c_one; + cut_st_lo[i][j] = cut_st_lo_one; + cut_st_hi[i][j] = cut_st_hi_one; + cut_st_lc[i][j] = cut_st_lc_one; + cut_st_hc[i][j] = cut_st_hc_one; + b_st_lo[i][j] = b_st_lo_one; + b_st_hi[i][j] = b_st_hi_one; + shift_st[i][j] = shift_st_one; + if (seqdepflag) shift_st[i][j] *= eta_st[i-1][j-1]; + + a_st5[i][j] = a_st5_one; + theta_st5_0[i][j] = theta_st5_0_one; + dtheta_st5_ast[i][j] = dtheta_st5_ast_one; + b_st5[i][j] = b_st5_one; + dtheta_st5_c[i][j] = dtheta_st5_c_one; + + a_st6[i][j] = a_st6_one; + theta_st6_0[i][j] = theta_st6_0_one; + dtheta_st6_ast[i][j] = dtheta_st6_ast_one; + b_st6[i][j] = b_st6_one; + dtheta_st6_c[i][j] = dtheta_st6_c_one; + + a_st9[i][j] = a_st9_one; + theta_st9_0[i][j] = theta_st9_0_one; + dtheta_st9_ast[i][j] = dtheta_st9_ast_one; + b_st9[i][j] = b_st9_one; + dtheta_st9_c[i][j] = dtheta_st9_c_one; + + a_st10[i][j] = a_st10_one; + theta_st10_0[i][j] = theta_st10_0_one; + dtheta_st10_ast[i][j] = dtheta_st10_ast_one; + b_st10[i][j] = b_st10_one; + dtheta_st10_c[i][j] = dtheta_st10_c_one; + + a_st1[i][j] = a_st1_one; + cosphi_st1_ast[i][j] = cosphi_st1_ast_one; + b_st1[i][j] = b_st1_one; + cosphi_st1_c[i][j] = cosphi_st1_c_one; + + a_st2[i][j] = a_st2_one; + cosphi_st2_ast[i][j] = cosphi_st2_ast_one; + b_st2[i][j] = b_st2_one; + cosphi_st2_c[i][j] = cosphi_st2_c_one; + + setflag[i][j] = 1; + count++; + } + } + + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/stk"); + +} + +/* ---------------------------------------------------------------------- + neighbor callback to inform pair style of neighbor list to use regular +------------------------------------------------------------------------- */ + +void PairOxrna2Stk::init_list(int id, NeighList *ptr) +{ + if (id == 0) list = ptr; + if (id > 0) error->all(FLERR,"Respa not supported"); + +} + + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairOxrna2Stk::init_one(int i, int j) +{ + + if (setflag[i][j] == 0) { + error->all(FLERR,"Coefficient mixing not defined in oxRNA"); + } + if (offset_flag) { + error->all(FLERR,"Offset not supported in oxRNA"); + } + + if (seqdepflag) { + epsilon_st[j][i] = epsilon_st[i][j] / eta_st[i-1][j-1] * eta_st[j-1][i-1]; + } + else { + epsilon_st[j][i] = epsilon_st[i][j]; + } + a_st[j][i] = a_st[i][j]; + b_st_lo[j][i] = b_st_lo[i][j]; + b_st_hi[j][i] = b_st_hi[i][j]; + cut_st_0[j][i] = cut_st_0[i][j]; + cut_st_c[j][i] = cut_st_c[i][j]; + cut_st_lo[j][i] = cut_st_lo[i][j]; + cut_st_hi[j][i] = cut_st_hi[i][j]; + cut_st_lc[j][i] = cut_st_lc[i][j]; + cut_st_hc[j][i] = cut_st_hc[i][j]; + if (seqdepflag) { + shift_st[j][i] = shift_st[i][j] / eta_st[i-1][j-1] * eta_st[j-1][i-1]; + } + else { + shift_st[j][i] = shift_st[i][j]; + } + + a_st5[j][i] = a_st5[i][j]; + theta_st5_0[j][i] = theta_st5_0[i][j]; + dtheta_st5_ast[j][i] = dtheta_st5_ast[i][j]; + b_st5[j][i] = b_st5[i][j]; + dtheta_st5_c[j][i] = dtheta_st5_c[i][j]; + + a_st6[j][i] = a_st6[i][j]; + theta_st6_0[j][i] = theta_st6_0[i][j]; + dtheta_st6_ast[j][i] = dtheta_st6_ast[i][j]; + b_st6[j][i] = b_st6[i][j]; + dtheta_st6_c[j][i] = dtheta_st6_c[i][j]; + + a_st9[j][i] = a_st9[i][j]; + theta_st9_0[j][i] = theta_st9_0[i][j]; + dtheta_st9_ast[j][i] = dtheta_st9_ast[i][j]; + b_st9[j][i] = b_st9[i][j]; + dtheta_st9_c[j][i] = dtheta_st9_c[i][j]; + + a_st10[j][i] = a_st10[i][j]; + theta_st10_0[j][i] = theta_st10_0[i][j]; + dtheta_st10_ast[j][i] = dtheta_st10_ast[i][j]; + b_st10[j][i] = b_st10[i][j]; + dtheta_st10_c[j][i] = dtheta_st10_c[i][j]; + + a_st1[j][i] = a_st1[i][j]; + cosphi_st1_ast[j][i] = cosphi_st1_ast[i][j]; + b_st1[j][i] = b_st1[i][j]; + cosphi_st1_c[j][i] = cosphi_st1_c[i][j]; + + a_st2[j][i] = a_st2[i][j]; + cosphi_st2_ast[j][i] = cosphi_st2_ast[i][j]; + b_st2[j][i] = b_st2[i][j]; + cosphi_st2_c[j][i] = cosphi_st2_c[i][j]; + + cutsq_st_hc[i][j] = cut_st_hc[i][j]*cut_st_hc[i][j]; + cutsq_st_hc[j][i] = cutsq_st_hc[i][j]; + + // set the master list distance cutoff + return cut_st_hc[i][j]; + +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairOxrna2Stk::write_restart(FILE *fp) +{ + write_restart_settings(fp); + + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + fwrite(&setflag[i][j],sizeof(int),1,fp); + if (setflag[i][j]) { + + fwrite(&epsilon_st[i][j],sizeof(double),1,fp); + fwrite(&a_st[i][j],sizeof(double),1,fp); + fwrite(&cut_st_0[i][j],sizeof(double),1,fp); + fwrite(&cut_st_c[i][j],sizeof(double),1,fp); + fwrite(&cut_st_lo[i][j],sizeof(double),1,fp); + fwrite(&cut_st_hi[i][j],sizeof(double),1,fp); + fwrite(&cut_st_lc[i][j],sizeof(double),1,fp); + fwrite(&cut_st_hc[i][j],sizeof(double),1,fp); + fwrite(&b_st_lo[i][j],sizeof(double),1,fp); + fwrite(&b_st_hi[i][j],sizeof(double),1,fp); + fwrite(&shift_st[i][j],sizeof(double),1,fp); + + fwrite(&a_st5[i][j],sizeof(double),1,fp); + fwrite(&theta_st5_0[i][j],sizeof(double),1,fp); + fwrite(&dtheta_st5_ast[i][j],sizeof(double),1,fp); + fwrite(&b_st5[i][j],sizeof(double),1,fp); + fwrite(&dtheta_st5_c[i][j],sizeof(double),1,fp); + + fwrite(&a_st6[i][j],sizeof(double),1,fp); + fwrite(&theta_st6_0[i][j],sizeof(double),1,fp); + fwrite(&dtheta_st6_ast[i][j],sizeof(double),1,fp); + fwrite(&b_st6[i][j],sizeof(double),1,fp); + fwrite(&dtheta_st6_c[i][j],sizeof(double),1,fp); + + fwrite(&a_st9[i][j],sizeof(double),1,fp); + fwrite(&theta_st9_0[i][j],sizeof(double),1,fp); + fwrite(&dtheta_st9_ast[i][j],sizeof(double),1,fp); + fwrite(&b_st9[i][j],sizeof(double),1,fp); + fwrite(&dtheta_st9_c[i][j],sizeof(double),1,fp); + + fwrite(&a_st10[i][j],sizeof(double),1,fp); + fwrite(&theta_st10_0[i][j],sizeof(double),1,fp); + fwrite(&dtheta_st10_ast[i][j],sizeof(double),1,fp); + fwrite(&b_st10[i][j],sizeof(double),1,fp); + fwrite(&dtheta_st10_c[i][j],sizeof(double),1,fp); + + fwrite(&a_st1[i][j],sizeof(double),1,fp); + fwrite(&cosphi_st1_ast[i][j],sizeof(double),1,fp); + fwrite(&b_st1[i][j],sizeof(double),1,fp); + fwrite(&cosphi_st1_c[i][j],sizeof(double),1,fp); + fwrite(&a_st2[i][j],sizeof(double),1,fp); + fwrite(&cosphi_st2_ast[i][j],sizeof(double),1,fp); + fwrite(&b_st2[i][j],sizeof(double),1,fp); + fwrite(&cosphi_st2_c[i][j],sizeof(double),1,fp); + + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairOxrna2Stk::read_restart(FILE *fp) +{ + read_restart_settings(fp); + allocate(); + + int i,j; + int me = comm->me; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); + MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); + if (setflag[i][j]) { + if (me == 0) { + + utils::sfread(FLERR,&epsilon_st[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&a_st[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_st_0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_st_c[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_st_lo[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_st_hi[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_st_lc[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_st_hc[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&b_st_lo[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&b_st_hi[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&shift_st[i][j],sizeof(double),1,fp,NULL,error); + + utils::sfread(FLERR,&a_st5[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&theta_st5_0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_st5_ast[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&b_st5[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_st5_c[i][j],sizeof(double),1,fp,NULL,error); + + utils::sfread(FLERR,&a_st6[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&theta_st6_0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_st6_ast[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&b_st6[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_st6_c[i][j],sizeof(double),1,fp,NULL,error); + + utils::sfread(FLERR,&a_st9[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&theta_st9_0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_st9_ast[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&b_st9[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_st9_c[i][j],sizeof(double),1,fp,NULL,error); + + utils::sfread(FLERR,&a_st10[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&theta_st10_0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_st10_ast[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&b_st10[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_st10_c[i][j],sizeof(double),1,fp,NULL,error); + + utils::sfread(FLERR,&a_st1[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cosphi_st1_ast[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&b_st1[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cosphi_st1_c[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&a_st2[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cosphi_st2_ast[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&b_st2[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cosphi_st2_c[i][j],sizeof(double),1,fp,NULL,error); + + } + + MPI_Bcast(&epsilon_st[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&a_st[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_st_0[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_st_c[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_st_lo[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_st_hi[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_st_lc[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_st_hc[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&b_st_lo[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&b_st_hi[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&shift_st[i][j],1,MPI_DOUBLE,0,world); + + MPI_Bcast(&a_st5[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&theta_st5_0[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&dtheta_st5_ast[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&b_st5[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&dtheta_st5_c[i][j],1,MPI_DOUBLE,0,world); + + MPI_Bcast(&a_st6[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&theta_st6_0[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&dtheta_st6_ast[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&b_st6[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&dtheta_st6_c[i][j],1,MPI_DOUBLE,0,world); + + MPI_Bcast(&a_st9[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&theta_st9_0[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&dtheta_st9_ast[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&b_st9[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&dtheta_st9_c[i][j],1,MPI_DOUBLE,0,world); + + MPI_Bcast(&a_st10[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&theta_st10_0[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&dtheta_st10_ast[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&b_st10[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&dtheta_st10_c[i][j],1,MPI_DOUBLE,0,world); + + MPI_Bcast(&a_st1[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cosphi_st1_ast[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&b_st1[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cosphi_st1_c[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&a_st2[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cosphi_st2_ast[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&b_st2[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cosphi_st2_c[i][j],1,MPI_DOUBLE,0,world); + + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairOxrna2Stk::write_restart_settings(FILE *fp) +{ + fwrite(&offset_flag,sizeof(int),1,fp); + fwrite(&mix_flag,sizeof(int),1,fp); + fwrite(&tail_flag,sizeof(int),1,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairOxrna2Stk::read_restart_settings(FILE *fp) +{ + int me = comm->me; + if (me == 0) { + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error); + } + MPI_Bcast(&offset_flag,1,MPI_INT,0,world); + MPI_Bcast(&mix_flag,1,MPI_INT,0,world); + MPI_Bcast(&tail_flag,1,MPI_INT,0,world); +} + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void PairOxrna2Stk::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + fprintf(fp,"%d\ + %g %g %g %g %g %g\ + %g %g %g %g %g\ + %g %g %g %g %g\ + %g %g %g %g %g\ + %g %g %g %g %g\ + %g %g %g %g %g\ + %g %g %g %g\ + %g %g %g %g\ + \n",i, + epsilon_st[i][i],a_st[i][i],cut_st_0[i][i],cut_st_c[i][i],cut_st_lo[i][i],cut_st_hi[i][i], + cut_st_lc[i][i],cut_st_hc[i][i],b_st_lo[i][i],b_st_hi[i][i],shift_st[i][i], + a_st5[i][i],theta_st5_0[i][i],dtheta_st5_ast[i][i],b_st5[i][i],dtheta_st5_c[i][i], + a_st6[i][i],theta_st6_0[i][i],dtheta_st6_ast[i][i],b_st6[i][i],dtheta_st6_c[i][i], + a_st9[i][i],theta_st9_0[i][i],dtheta_st9_ast[i][i],b_st9[i][i],dtheta_st9_c[i][i], + a_st10[i][i],theta_st10_0[i][i],dtheta_st10_ast[i][i],b_st10[i][i],dtheta_st10_c[i][i], + a_st1[i][i],cosphi_st1_ast[i][i],b_st1[i][i], cosphi_st1_c[i][i], + a_st2[i][i],cosphi_st2_ast[i][i],b_st2[i][i], cosphi_st2_c[i][i]); +} + +/* ---------------------------------------------------------------------- + proc 0 writes all pairs to data file +------------------------------------------------------------------------- */ + +void PairOxrna2Stk::write_data_all(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + for (int j = i; j <= atom->ntypes; j++) + fprintf(fp,"%d %d\ + %g %g %g %g %g %g\ + %g %g %g %g %g\ + %g %g %g %g %g\ + %g %g %g %g %g\ + %g %g %g %g %g\ + %g %g %g %g %g\ + %g %g %g %g\ + %g %g %g %g\ + \n",i,j, + epsilon_st[i][j],a_st[i][j],cut_st_0[i][j],cut_st_c[i][j],cut_st_lo[i][j],cut_st_hi[i][j], + cut_st_lc[i][j],cut_st_hc[i][j],b_st_lo[i][j],b_st_hi[i][j],shift_st[i][j], + a_st5[i][j],theta_st5_0[i][j],dtheta_st5_ast[i][j],b_st5[i][j],dtheta_st5_c[i][j], + a_st6[i][j],theta_st6_0[i][j],dtheta_st6_ast[i][j],b_st6[i][j],dtheta_st6_c[i][j], + a_st9[i][j],theta_st9_0[i][j],dtheta_st9_ast[i][j],b_st9[i][j],dtheta_st9_c[i][j], + a_st10[i][j],theta_st10_0[i][j],dtheta_st10_ast[i][j],b_st10[i][j],dtheta_st10_c[i][j], + a_st1[i][j],cosphi_st1_ast[i][j],b_st1[i][j],cosphi_st1_c[i][j], + a_st2[i][j],cosphi_st2_ast[i][j],b_st2[i][j],cosphi_st2_c[i][j]); +} + +/* ---------------------------------------------------------------------- */ + +void *PairOxrna2Stk::extract(const char *str, int &dim) +{ + dim = 2; + + if (strcmp(str,"epsilon_st") == 0) return (void *) epsilon_st; + if (strcmp(str,"a_st") == 0) return (void *) a_st; + if (strcmp(str,"cut_st_0") == 0) return (void *) cut_st_0; + if (strcmp(str,"cut_st_c") == 0) return (void *) cut_st_c; + if (strcmp(str,"cut_st_lo") == 0) return (void *) cut_st_lo; + if (strcmp(str,"cut_st_hi") == 0) return (void *) cut_st_hi; + if (strcmp(str,"cut_st_lc") == 0) return (void *) cut_st_lc; + if (strcmp(str,"cut_st_hc") == 0) return (void *) cut_st_hc; + if (strcmp(str,"b_st_lo") == 0) return (void *) b_st_lo; + if (strcmp(str,"b_st_hi") == 0) return (void *) b_st_hi; + if (strcmp(str,"shift_st") == 0) return (void *) shift_st; + + if (strcmp(str,"a_st5") == 0) return (void *) a_st5; + if (strcmp(str,"theta_st5_0") == 0) return (void *) theta_st5_0; + if (strcmp(str,"dtheta_st5_ast") == 0) return (void *) dtheta_st5_ast; + if (strcmp(str,"b_st5") == 0) return (void *) b_st5; + if (strcmp(str,"dtheta_st5_c") == 0) return (void *) dtheta_st5_c; + + if (strcmp(str,"a_st6") == 0) return (void *) a_st6; + if (strcmp(str,"theta_st6_0") == 0) return (void *) theta_st6_0; + if (strcmp(str,"dtheta_st6_ast") == 0) return (void *) dtheta_st6_ast; + if (strcmp(str,"b_st6") == 0) return (void *) b_st6; + if (strcmp(str,"dtheta_st6_c") == 0) return (void *) dtheta_st6_c; + + if (strcmp(str,"a_st9") == 0) return (void *) a_st9; + if (strcmp(str,"theta_st9_0") == 0) return (void *) theta_st9_0; + if (strcmp(str,"dtheta_st9_ast") == 0) return (void *) dtheta_st9_ast; + if (strcmp(str,"b_st9") == 0) return (void *) b_st9; + if (strcmp(str,"dtheta_st9_c") == 0) return (void *) dtheta_st9_c; + + if (strcmp(str,"a_st10") == 0) return (void *) a_st10; + if (strcmp(str,"theta_st10_0") == 0) return (void *) theta_st10_0; + if (strcmp(str,"dtheta_st10_ast") == 0) return (void *) dtheta_st10_ast; + if (strcmp(str,"b_st10") == 0) return (void *) b_st10; + if (strcmp(str,"dtheta_st10_c") == 0) return (void *) dtheta_st10_c; + + if (strcmp(str,"a_st1") == 0) return (void *) a_st1; + if (strcmp(str,"cosphi_st1_ast") == 0) return (void *) cosphi_st1_ast; + if (strcmp(str,"b_st1") == 0) return (void *) b_st1; + if (strcmp(str,"cosphi_st1_c") == 0) return (void *) cosphi_st1_c; + + if (strcmp(str,"a_st2") == 0) return (void *) a_st2; + if (strcmp(str,"cosphi_st2_ast") == 0) return (void *) cosphi_st2_ast; + if (strcmp(str,"b_st2") == 0) return (void *) b_st2; + if (strcmp(str,"cosphi_st2_c") == 0) return (void *) cosphi_st2_c; + + return NULL; +} diff --git a/src/USER-CGDNA/pair_oxrna2_stk.h b/src/USER-CGDNA/pair_oxrna2_stk.h new file mode 100644 index 0000000000..519f7c0707 --- /dev/null +++ b/src/USER-CGDNA/pair_oxrna2_stk.h @@ -0,0 +1,86 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(oxrna2/stk,PairOxrna2Stk) + +#else + +#ifndef LMP_PAIR_OXRNA2_STK_H +#define LMP_PAIR_OXRNA2_STK_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairOxrna2Stk : public Pair { + public: + PairOxrna2Stk(class LAMMPS *); + virtual ~PairOxrna2Stk(); + virtual void compute(int, int); + void settings(int, char **); + void coeff(int, char **); + void init_list(int, class NeighList *); + double init_one(int, int); + void write_restart(FILE *); + void read_restart(FILE *); + void write_restart_settings(FILE *); + void read_restart_settings(FILE *); + void write_data(FILE *); + void write_data_all(FILE *); + void *extract(const char *, int &); + + protected: + // stacking interaction + double eta_st[4][4]; + double stacking_strength(double, double, double); + double **epsilon_st, **a_st, **cut_st_0, **cut_st_c; + double **cut_st_lo, **cut_st_hi; + double **cut_st_lc, **cut_st_hc, **b_st_lo, **b_st_hi, **shift_st; + double **cutsq_st_hc; + double **a_st5, **theta_st5_0, **dtheta_st5_ast; + double **b_st5, **dtheta_st5_c; + double **a_st6, **theta_st6_0, **dtheta_st6_ast; + double **b_st6, **dtheta_st6_c; + double **a_st9, **theta_st9_0, **dtheta_st9_ast; + double **b_st9, **dtheta_st9_c; + double **a_st10, **theta_st10_0, **dtheta_st10_ast; + double **b_st10, **dtheta_st10_c; + double **a_st1, **cosphi_st1_ast, **b_st1, **cosphi_st1_c; + double **a_st2, **cosphi_st2_ast, **b_st2, **cosphi_st2_c; + + int seqdepflag; + + virtual void allocate(); + void ev_tally_xyz(int, int, int, int, double, double, double, double, double, double, double); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +*/ diff --git a/src/USER-CGDNA/pair_oxrna2_xstk.cpp b/src/USER-CGDNA/pair_oxrna2_xstk.cpp new file mode 100644 index 0000000000..f5207c53e7 --- /dev/null +++ b/src/USER-CGDNA/pair_oxrna2_xstk.cpp @@ -0,0 +1,1079 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- + Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) +------------------------------------------------------------------------- */ + +#include "pair_oxrna2_xstk.h" +#include +#include +#include +#include "mf_oxdna.h" +#include "atom.h" +#include "comm.h" +#include "force.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "math_const.h" +#include "memory.h" +#include "error.h" +#include "utils.h" +#include "atom_vec_ellipsoid.h" +#include "math_extra.h" + +using namespace LAMMPS_NS; +using namespace MathConst; +using namespace MFOxdna; + +/* ---------------------------------------------------------------------- */ + +PairOxrna2Xstk::PairOxrna2Xstk(LAMMPS *lmp) : Pair(lmp) +{ + single_enable = 0; + writedata = 1; +} + +/* ---------------------------------------------------------------------- */ + +PairOxrna2Xstk::~PairOxrna2Xstk() +{ + if (allocated) { + + memory->destroy(setflag); + memory->destroy(cutsq); + + memory->destroy(k_xst); + memory->destroy(cut_xst_0); + memory->destroy(cut_xst_c); + memory->destroy(cut_xst_lo); + memory->destroy(cut_xst_hi); + memory->destroy(cut_xst_lc); + memory->destroy(cut_xst_hc); + memory->destroy(cutsq_xst_hc); + memory->destroy(b_xst_lo); + memory->destroy(b_xst_hi); + + memory->destroy(a_xst1); + memory->destroy(theta_xst1_0); + memory->destroy(dtheta_xst1_ast); + memory->destroy(b_xst1); + memory->destroy(dtheta_xst1_c); + + memory->destroy(a_xst2); + memory->destroy(theta_xst2_0); + memory->destroy(dtheta_xst2_ast); + memory->destroy(b_xst2); + memory->destroy(dtheta_xst2_c); + + memory->destroy(a_xst3); + memory->destroy(theta_xst3_0); + memory->destroy(dtheta_xst3_ast); + memory->destroy(b_xst3); + memory->destroy(dtheta_xst3_c); + + memory->destroy(a_xst7); + memory->destroy(theta_xst7_0); + memory->destroy(dtheta_xst7_ast); + memory->destroy(b_xst7); + memory->destroy(dtheta_xst7_c); + + memory->destroy(a_xst8); + memory->destroy(theta_xst8_0); + memory->destroy(dtheta_xst8_ast); + memory->destroy(b_xst8); + memory->destroy(dtheta_xst8_c); + + } +} + +/* ---------------------------------------------------------------------- + compute function for oxDNA pair interactions + hb=hydrogen bonding site + + NOTE: The cross-stacking interaction takes place between hb sites +------------------------------------------------------------------------- */ + +void PairOxrna2Xstk::compute(int eflag, int vflag) +{ + + double delf[3],delta[3],deltb[3]; // force, torque increment; + double evdwl,fpair,finc,tpair,factor_lj; + double delr_hb[3],delr_hb_norm[3],rsq_hb,r_hb,rinv_hb; + double theta1,t1dir[3],cost1; + double theta2,t2dir[3],cost2; + double theta3,t3dir[3],cost3; + double theta4,theta4p,t4dir[3],cost4; + double theta7,theta7p,t7dir[3],cost7; + double theta8,theta8p,t8dir[3],cost8; + + // distance COM-h-bonding site + double d_chb=+0.4; + // vectors COM-h-bonding site in lab frame + double ra_chb[3],rb_chb[3]; + + // quaternions and Cartesian unit vectors in lab frame + double *qa,ax[3],ay[3],az[3]; + double *qb,bx[3],by[3],bz[3]; + + double **x = atom->x; + double **f = atom->f; + double **torque = atom->torque; + int *type = atom->type; + + int nlocal = atom->nlocal; + int newton_pair = force->newton_pair; + int *alist,*blist,*numneigh,**firstneigh; + double *special_lj = force->special_lj; + + AtomVecEllipsoid *avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid"); + AtomVecEllipsoid::Bonus *bonus = avec->bonus; + + int a,b,ia,ib,anum,bnum,atype,btype; + + double f2,f4t1,f4t2,f4t3,f4t7,f4t8; + double df2,df4t1,df4t2,df4t3,df4t7,df4t8,rsint; + + evdwl = 0.0; + ev_init(eflag,vflag); + + anum = list->inum; + alist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // loop over pair interaction neighbors of my atoms + + for (ia = 0; ia < anum; ia++) { + + a = alist[ia]; + atype = type[a]; + + qa=bonus[a].quat; + MathExtra::q_to_exyz(qa,ax,ay,az); + + ra_chb[0] = d_chb*ax[0]; + ra_chb[1] = d_chb*ax[1]; + ra_chb[2] = d_chb*ax[2]; + + blist = firstneigh[a]; + bnum = numneigh[a]; + + for (ib = 0; ib < bnum; ib++) { + + b = blist[ib]; + factor_lj = special_lj[sbmask(b)]; // = 0 for nearest neighbors + b &= NEIGHMASK; + + btype = type[b]; + + qb=bonus[b].quat; + MathExtra::q_to_exyz(qb,bx,by,bz); + + rb_chb[0] = d_chb*bx[0]; + rb_chb[1] = d_chb*bx[1]; + rb_chb[2] = d_chb*bx[2]; + + // vector h-bonding site b to a + delr_hb[0] = x[a][0] + ra_chb[0] - x[b][0] - rb_chb[0]; + delr_hb[1] = x[a][1] + ra_chb[1] - x[b][1] - rb_chb[1]; + delr_hb[2] = x[a][2] + ra_chb[2] - x[b][2] - rb_chb[2]; + + rsq_hb = delr_hb[0]*delr_hb[0] + delr_hb[1]*delr_hb[1] + delr_hb[2]*delr_hb[2]; + r_hb = sqrt(rsq_hb); + rinv_hb = 1.0/r_hb; + + delr_hb_norm[0] = delr_hb[0] * rinv_hb; + delr_hb_norm[1] = delr_hb[1] * rinv_hb; + delr_hb_norm[2] = delr_hb[2] * rinv_hb; + + f2 = F2(r_hb, k_xst[atype][btype], cut_xst_0[atype][btype], + cut_xst_lc[atype][btype], cut_xst_hc[atype][btype], cut_xst_lo[atype][btype], cut_xst_hi[atype][btype], + b_xst_lo[atype][btype], b_xst_hi[atype][btype], cut_xst_c[atype][btype]); + + // early rejection criterium + if (f2) { + + cost1 = -1.0*MathExtra::dot3(ax,bx); + if (cost1 > 1.0) cost1 = 1.0; + if (cost1 < -1.0) cost1 = -1.0; + theta1 = acos(cost1); + + f4t1 = F4(theta1, a_xst1[atype][btype], theta_xst1_0[atype][btype], dtheta_xst1_ast[atype][btype], + b_xst1[atype][btype], dtheta_xst1_c[atype][btype]); + + // early rejection criterium + if (f4t1) { + + cost2 = -1.0*MathExtra::dot3(ax,delr_hb_norm); + if (cost2 > 1.0) cost2 = 1.0; + if (cost2 < -1.0) cost2 = -1.0; + theta2 = acos(cost2); + + f4t2 = F4(theta2, a_xst2[atype][btype], theta_xst2_0[atype][btype], dtheta_xst2_ast[atype][btype], + b_xst2[atype][btype], dtheta_xst2_c[atype][btype]); + + // early rejection criterium + if (f4t2) { + + cost3 = MathExtra::dot3(bx,delr_hb_norm); + if (cost3 > 1.0) cost3 = 1.0; + if (cost3 < -1.0) cost3 = -1.0; + theta3 = acos(cost3); + + f4t3 = F4(theta3, a_xst3[atype][btype], theta_xst3_0[atype][btype], dtheta_xst3_ast[atype][btype], + b_xst3[atype][btype], dtheta_xst3_c[atype][btype]); + + // early rejection criterium + if (f4t3) { + + cost7 = -1.0*MathExtra::dot3(az,delr_hb_norm); + if (cost7 > 1.0) cost7 = 1.0; + if (cost7 < -1.0) cost7 = -1.0; + theta7 = acos(cost7); + theta7p = MY_PI - theta7; + + f4t7 = F4(theta7, a_xst7[atype][btype], theta_xst7_0[atype][btype], dtheta_xst7_ast[atype][btype], + b_xst7[atype][btype], dtheta_xst7_c[atype][btype]) + + F4(theta7p, a_xst7[atype][btype], theta_xst7_0[atype][btype], dtheta_xst7_ast[atype][btype], + b_xst7[atype][btype], dtheta_xst7_c[atype][btype]); + + // early rejection criterium + if (f4t7) { + + cost8 = MathExtra::dot3(bz,delr_hb_norm); + if (cost8 > 1.0) cost8 = 1.0; + if (cost8 < -1.0) cost8 = -1.0; + theta8 = acos(cost8); + theta8p = MY_PI -theta8; + + f4t8 = F4(theta8, a_xst8[atype][btype], theta_xst8_0[atype][btype], dtheta_xst8_ast[atype][btype], + b_xst8[atype][btype], dtheta_xst8_c[atype][btype]) + + F4(theta8p, a_xst8[atype][btype], theta_xst8_0[atype][btype], dtheta_xst8_ast[atype][btype], + b_xst8[atype][btype], dtheta_xst8_c[atype][btype]); + + + evdwl = f2 * f4t1 * f4t2 * f4t3 * f4t7 * f4t8 * factor_lj; + + + // early rejection criterium + if (evdwl) { + + df2 = DF2(r_hb, k_xst[atype][btype], cut_xst_0[atype][btype], + cut_xst_lc[atype][btype], cut_xst_hc[atype][btype], cut_xst_lo[atype][btype], cut_xst_hi[atype][btype], + b_xst_lo[atype][btype], b_xst_hi[atype][btype]); + + df4t1 = DF4(theta1, a_xst1[atype][btype], theta_xst1_0[atype][btype], dtheta_xst1_ast[atype][btype], + b_xst1[atype][btype], dtheta_xst1_c[atype][btype])/sin(theta1); + + df4t2 = DF4(theta2, a_xst2[atype][btype], theta_xst2_0[atype][btype], dtheta_xst2_ast[atype][btype], + b_xst2[atype][btype], dtheta_xst2_c[atype][btype])/sin(theta2); + + df4t3 = DF4(theta3, a_xst3[atype][btype], theta_xst3_0[atype][btype], dtheta_xst3_ast[atype][btype], + b_xst3[atype][btype], dtheta_xst3_c[atype][btype])/sin(theta3); + + rsint = 1.0/sin(theta7); + df4t7 = DF4(theta7, a_xst7[atype][btype], theta_xst7_0[atype][btype], dtheta_xst7_ast[atype][btype], + b_xst7[atype][btype], dtheta_xst7_c[atype][btype])*rsint - + DF4(theta7p, a_xst7[atype][btype], theta_xst7_0[atype][btype], dtheta_xst7_ast[atype][btype], + b_xst7[atype][btype], dtheta_xst7_c[atype][btype])*rsint; + + rsint = 1.0/sin(theta8); + df4t8 = DF4(theta8, a_xst8[atype][btype], theta_xst8_0[atype][btype], dtheta_xst8_ast[atype][btype], + b_xst8[atype][btype], dtheta_xst8_c[atype][btype])*rsint - + DF4(theta8p, a_xst8[atype][btype], theta_xst8_0[atype][btype], dtheta_xst8_ast[atype][btype], + b_xst8[atype][btype], dtheta_xst8_c[atype][btype])*rsint; + + // force, torque and virial contribution for forces between h-bonding sites + + fpair = 0.0; + + delf[0] = 0.0; + delf[1] = 0.0; + delf[2] = 0.0; + + delta[0] = 0.0; + delta[1] = 0.0; + delta[2] = 0.0; + + deltb[0] = 0.0; + deltb[1] = 0.0; + deltb[2] = 0.0; + + // radial force + finc = -df2 * f4t1 * f4t2 * f4t3 * f4t7 * f4t8 * rinv_hb *factor_lj; + fpair += finc; + + delf[0] += delr_hb[0] * finc; + delf[1] += delr_hb[1] * finc; + delf[2] += delr_hb[2] * finc; + + // theta2 force + if (theta2) { + + finc = -f2 * f4t1 * df4t2 * f4t3 * f4t7 * f4t8 * rinv_hb * factor_lj; + fpair += finc; + + delf[0] += (delr_hb_norm[0]*cost2 + ax[0]) * finc; + delf[1] += (delr_hb_norm[1]*cost2 + ax[1]) * finc; + delf[2] += (delr_hb_norm[2]*cost2 + ax[2]) * finc; + + } + + // theta3 force + if (theta3) { + + finc = -f2 * f4t1 * f4t2 * df4t3 * f4t7 * f4t8 * rinv_hb * factor_lj; + fpair += finc; + + delf[0] += (delr_hb_norm[0]*cost3 - bx[0]) * finc; + delf[1] += (delr_hb_norm[1]*cost3 - bx[1]) * finc; + delf[2] += (delr_hb_norm[2]*cost3 - bx[2]) * finc; + + } + + // theta7 force + if (theta7) { + + finc = -f2 * f4t1 * f4t2 * f4t3 * df4t7 * f4t8 * rinv_hb * factor_lj; + fpair += finc; + + delf[0] += (delr_hb_norm[0]*cost7 + az[0]) * finc; + delf[1] += (delr_hb_norm[1]*cost7 + az[1]) * finc; + delf[2] += (delr_hb_norm[2]*cost7 + az[2]) * finc; + + } + + // theta8 force + if (theta8) { + + finc = -f2 * f4t1 * f4t2 * f4t3 * f4t7 * df4t8 * rinv_hb * factor_lj; + fpair += finc; + + delf[0] += (delr_hb_norm[0]*cost8 - bz[0]) * finc; + delf[1] += (delr_hb_norm[1]*cost8 - bz[1]) * finc; + delf[2] += (delr_hb_norm[2]*cost8 - bz[2]) * finc; + + } + + // increment forces and torques + + f[a][0] += delf[0]; + f[a][1] += delf[1]; + f[a][2] += delf[2]; + + MathExtra::cross3(ra_chb,delf,delta); + + torque[a][0] += delta[0]; + torque[a][1] += delta[1]; + torque[a][2] += delta[2]; + + if (newton_pair || b < nlocal) { + + f[b][0] -= delf[0]; + f[b][1] -= delf[1]; + f[b][2] -= delf[2]; + + + MathExtra::cross3(rb_chb,delf,deltb); + + torque[b][0] -= deltb[0]; + torque[b][1] -= deltb[1]; + torque[b][2] -= deltb[2]; + + } + + // increment energy and virial + // NOTE: The virial is calculated on the 'molecular' basis. + // (see G. Ciccotti and J.P. Ryckaert, Comp. Phys. Rep. 4, 345-392 (1986)) + + if (evflag) ev_tally_xyz(a,b,nlocal,newton_pair,evdwl,0.0, + delf[0],delf[1],delf[2],x[a][0]-x[b][0],x[a][1]-x[b][1],x[a][2]-x[b][2]); + + // pure torques not expressible as r x f + + delta[0] = 0.0; + delta[1] = 0.0; + delta[2] = 0.0; + deltb[0] = 0.0; + deltb[1] = 0.0; + deltb[2] = 0.0; + + // theta1 torque + if (theta1) { + + tpair = -f2 * df4t1 * f4t2 * f4t3 * f4t7 * f4t8 * factor_lj; + MathExtra::cross3(ax,bx,t1dir); + + delta[0] += t1dir[0]*tpair; + delta[1] += t1dir[1]*tpair; + delta[2] += t1dir[2]*tpair; + + deltb[0] += t1dir[0]*tpair; + deltb[1] += t1dir[1]*tpair; + deltb[2] += t1dir[2]*tpair; + + } + + // theta2 torque + if (theta2) { + + tpair = -f2 * f4t1 * df4t2 * f4t3 * f4t7 * f4t8 * factor_lj; + MathExtra::cross3(ax,delr_hb_norm,t2dir); + + delta[0] += t2dir[0]*tpair; + delta[1] += t2dir[1]*tpair; + delta[2] += t2dir[2]*tpair; + + } + + // theta3 torque + if (theta3) { + + tpair = -f2 * f4t1 * f4t2 * df4t3 * f4t7 * f4t8 * factor_lj; + MathExtra::cross3(bx,delr_hb_norm,t3dir); + + deltb[0] += t3dir[0]*tpair; + deltb[1] += t3dir[1]*tpair; + deltb[2] += t3dir[2]*tpair; + + } + + // theta7 torque + if (theta7) { + + tpair = -f2 * f4t1 * f4t2 * f4t3 * df4t7 * f4t8 * factor_lj; + MathExtra::cross3(az,delr_hb_norm,t7dir); + + delta[0] += t7dir[0]*tpair; + delta[1] += t7dir[1]*tpair; + delta[2] += t7dir[2]*tpair; + + } + + // theta8 torque + if (theta8) { + + tpair = -f2 * f4t1 * f4t2 * f4t3 * f4t7 * df4t8 * factor_lj; + MathExtra::cross3(bz,delr_hb_norm,t8dir); + + deltb[0] += t8dir[0]*tpair; + deltb[1] += t8dir[1]*tpair; + deltb[2] += t8dir[2]*tpair; + + } + + // increment torques + + torque[a][0] += delta[0]; + torque[a][1] += delta[1]; + torque[a][2] += delta[2]; + + if (newton_pair || b < nlocal) { + + torque[b][0] -= deltb[0]; + torque[b][1] -= deltb[1]; + torque[b][2] -= deltb[2]; + + } + + + } + } + } + } + } + }// end early rejection criteria + + } + } + + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairOxrna2Xstk::allocate() +{ + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag,n+1,n+1,"pair:setflag"); + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; + + memory->create(cutsq,n+1,n+1,"pair:cutsq"); + + memory->create(k_xst,n+1,n+1,"pair:k_xst"); + memory->create(cut_xst_0,n+1,n+1,"pair:cut_xst_0"); + memory->create(cut_xst_c,n+1,n+1,"pair:cut_xst_c"); + memory->create(cut_xst_lo,n+1,n+1,"pair:cut_xst_lo"); + memory->create(cut_xst_hi,n+1,n+1,"pair:cut_xst_hi"); + memory->create(cut_xst_lc,n+1,n+1,"pair:cut_xst_lc"); + memory->create(cut_xst_hc,n+1,n+1,"pair:cut_xst_hc"); + memory->create(b_xst_lo,n+1,n+1,"pair:b_xst_lo"); + memory->create(b_xst_hi,n+1,n+1,"pair:b_xst_hi"); + memory->create(cutsq_xst_hc,n+1,n+1,"pair:cutsq_xst_hc"); + + memory->create(a_xst1,n+1,n+1,"pair:a_xst1"); + memory->create(theta_xst1_0,n+1,n+1,"pair:theta_xst1_0"); + memory->create(dtheta_xst1_ast,n+1,n+1,"pair:dtheta_xst1_ast"); + memory->create(b_xst1,n+1,n+1,"pair:b_xst1"); + memory->create(dtheta_xst1_c,n+1,n+1,"pair:dtheta_xst1_c"); + + memory->create(a_xst2,n+1,n+1,"pair:a_xst2"); + memory->create(theta_xst2_0,n+1,n+1,"pair:theta_xst2_0"); + memory->create(dtheta_xst2_ast,n+1,n+1,"pair:dtheta_xst2_ast"); + memory->create(b_xst2,n+1,n+1,"pair:b_xst2"); + memory->create(dtheta_xst2_c,n+1,n+1,"pair:dtheta_xst2_c"); + + memory->create(a_xst3,n+1,n+1,"pair:a_xst3"); + memory->create(theta_xst3_0,n+1,n+1,"pair:theta_xst3_0"); + memory->create(dtheta_xst3_ast,n+1,n+1,"pair:dtheta_xst3_ast"); + memory->create(b_xst3,n+1,n+1,"pair:b_xst3"); + memory->create(dtheta_xst3_c,n+1,n+1,"pair:dtheta_xst3_c"); + + memory->create(a_xst7,n+1,n+1,"pair:a_xst7"); + memory->create(theta_xst7_0,n+1,n+1,"pair:theta_xst7_0"); + memory->create(dtheta_xst7_ast,n+1,n+1,"pair:dtheta_xst7_ast"); + memory->create(b_xst7,n+1,n+1,"pair:b_xst7"); + memory->create(dtheta_xst7_c,n+1,n+1,"pair:dtheta_xst7_c"); + + memory->create(a_xst8,n+1,n+1,"pair:a_xst8"); + memory->create(theta_xst8_0,n+1,n+1,"pair:theta_xst8_0"); + memory->create(dtheta_xst8_ast,n+1,n+1,"pair:dtheta_xst8_ast"); + memory->create(b_xst8,n+1,n+1,"pair:b_xst8"); + memory->create(dtheta_xst8_c,n+1,n+1,"pair:dtheta_xst8_c"); + +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairOxrna2Xstk::settings(int narg, char **/*arg*/) +{ + if (narg != 0) error->all(FLERR,"Illegal pair_style command"); + +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairOxrna2Xstk::coeff(int narg, char **arg) +{ + int count; + + if (narg != 22) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/xstk"); + if (!allocated) allocate(); + + int ilo,ihi,jlo,jhi; + force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi); + force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi); + + // cross-stacking interaction + count = 0; + + double k_xst_one, cut_xst_0_one, cut_xst_c_one, cut_xst_lo_one, cut_xst_hi_one; + double b_xst_lo_one, b_xst_hi_one, cut_xst_lc_one, cut_xst_hc_one; + + double a_xst1_one, theta_xst1_0_one, dtheta_xst1_ast_one; + double b_xst1_one, dtheta_xst1_c_one; + + double a_xst2_one, theta_xst2_0_one, dtheta_xst2_ast_one; + double b_xst2_one, dtheta_xst2_c_one; + + double a_xst3_one, theta_xst3_0_one, dtheta_xst3_ast_one; + double b_xst3_one, dtheta_xst3_c_one; + + double a_xst7_one, theta_xst7_0_one, dtheta_xst7_ast_one; + double b_xst7_one, dtheta_xst7_c_one; + + double a_xst8_one, theta_xst8_0_one, dtheta_xst8_ast_one; + double b_xst8_one, dtheta_xst8_c_one; + + k_xst_one = force->numeric(FLERR,arg[2]); + cut_xst_0_one = force->numeric(FLERR,arg[3]); + cut_xst_c_one = force->numeric(FLERR,arg[4]); + cut_xst_lo_one = force->numeric(FLERR,arg[5]); + cut_xst_hi_one = force->numeric(FLERR,arg[6]); + + a_xst1_one = force->numeric(FLERR,arg[7]); + theta_xst1_0_one = force->numeric(FLERR,arg[8]); + dtheta_xst1_ast_one = force->numeric(FLERR,arg[9]); + + a_xst2_one = force->numeric(FLERR,arg[10]); + theta_xst2_0_one = force->numeric(FLERR,arg[11]); + dtheta_xst2_ast_one = force->numeric(FLERR,arg[12]); + + a_xst3_one = force->numeric(FLERR,arg[13]); + theta_xst3_0_one = force->numeric(FLERR,arg[14]); + dtheta_xst3_ast_one = force->numeric(FLERR,arg[15]); + + a_xst7_one = force->numeric(FLERR,arg[16]); + theta_xst7_0_one = force->numeric(FLERR,arg[17]); + dtheta_xst7_ast_one = force->numeric(FLERR,arg[18]); + + a_xst8_one = force->numeric(FLERR,arg[19]); + theta_xst8_0_one = force->numeric(FLERR,arg[20]); + dtheta_xst8_ast_one = force->numeric(FLERR,arg[21]); + + + b_xst_lo_one = 0.25 * (cut_xst_lo_one - cut_xst_0_one) * (cut_xst_lo_one - cut_xst_0_one)/ + (0.5 * (cut_xst_lo_one - cut_xst_0_one) * (cut_xst_lo_one - cut_xst_0_one) - + k_xst_one * 0.5 * (cut_xst_0_one -cut_xst_c_one) * (cut_xst_0_one - cut_xst_c_one)/k_xst_one); + + cut_xst_lc_one = cut_xst_lo_one - 0.5 * (cut_xst_lo_one - cut_xst_0_one)/b_xst_lo_one;; + + b_xst_hi_one = 0.25 * (cut_xst_hi_one - cut_xst_0_one) * (cut_xst_hi_one - cut_xst_0_one)/ + (0.5 * (cut_xst_hi_one - cut_xst_0_one) * (cut_xst_hi_one - cut_xst_0_one) - + k_xst_one * 0.5 * (cut_xst_0_one -cut_xst_c_one) * (cut_xst_0_one - cut_xst_c_one)/k_xst_one); + + cut_xst_hc_one = cut_xst_hi_one - 0.5* (cut_xst_hi_one - cut_xst_0_one)/b_xst_hi_one; + + + b_xst1_one = a_xst1_one*a_xst1_one*dtheta_xst1_ast_one*dtheta_xst1_ast_one/(1-a_xst1_one*dtheta_xst1_ast_one*dtheta_xst1_ast_one); + dtheta_xst1_c_one = 1/(a_xst1_one*dtheta_xst1_ast_one); + + b_xst2_one = a_xst2_one*a_xst2_one*dtheta_xst2_ast_one*dtheta_xst2_ast_one/(1-a_xst2_one*dtheta_xst2_ast_one*dtheta_xst2_ast_one); + dtheta_xst2_c_one = 1/(a_xst2_one*dtheta_xst2_ast_one); + + b_xst3_one = a_xst3_one*a_xst3_one*dtheta_xst3_ast_one*dtheta_xst3_ast_one/(1-a_xst3_one*dtheta_xst3_ast_one*dtheta_xst3_ast_one); + dtheta_xst3_c_one = 1/(a_xst3_one*dtheta_xst3_ast_one); + + b_xst7_one = a_xst7_one*a_xst7_one*dtheta_xst7_ast_one*dtheta_xst7_ast_one/(1-a_xst7_one*dtheta_xst7_ast_one*dtheta_xst7_ast_one); + dtheta_xst7_c_one = 1/(a_xst7_one*dtheta_xst7_ast_one); + + b_xst8_one = a_xst8_one*a_xst8_one*dtheta_xst8_ast_one*dtheta_xst8_ast_one/(1-a_xst8_one*dtheta_xst8_ast_one*dtheta_xst8_ast_one); + dtheta_xst8_c_one = 1/(a_xst8_one*dtheta_xst8_ast_one); + + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j <= jhi; j++) { + + k_xst[i][j] = k_xst_one; + cut_xst_0[i][j] = cut_xst_0_one; + cut_xst_c[i][j] = cut_xst_c_one; + cut_xst_lo[i][j] = cut_xst_lo_one; + cut_xst_hi[i][j] = cut_xst_hi_one; + cut_xst_lc[i][j] = cut_xst_lc_one; + cut_xst_hc[i][j] = cut_xst_hc_one; + b_xst_lo[i][j] = b_xst_lo_one; + b_xst_hi[i][j] = b_xst_hi_one; + + a_xst1[i][j] = a_xst1_one; + theta_xst1_0[i][j] = theta_xst1_0_one; + dtheta_xst1_ast[i][j] = dtheta_xst1_ast_one; + b_xst1[i][j] = b_xst1_one; + dtheta_xst1_c[i][j] = dtheta_xst1_c_one; + + a_xst2[i][j] = a_xst2_one; + theta_xst2_0[i][j] = theta_xst2_0_one; + dtheta_xst2_ast[i][j] = dtheta_xst2_ast_one; + b_xst2[i][j] = b_xst2_one; + dtheta_xst2_c[i][j] = dtheta_xst2_c_one; + + a_xst3[i][j] = a_xst3_one; + theta_xst3_0[i][j] = theta_xst3_0_one; + dtheta_xst3_ast[i][j] = dtheta_xst3_ast_one; + b_xst3[i][j] = b_xst3_one; + dtheta_xst3_c[i][j] = dtheta_xst3_c_one; + + a_xst7[i][j] = a_xst7_one; + theta_xst7_0[i][j] = theta_xst7_0_one; + dtheta_xst7_ast[i][j] = dtheta_xst7_ast_one; + b_xst7[i][j] = b_xst7_one; + dtheta_xst7_c[i][j] = dtheta_xst7_c_one; + + a_xst8[i][j] = a_xst8_one; + theta_xst8_0[i][j] = theta_xst8_0_one; + dtheta_xst8_ast[i][j] = dtheta_xst8_ast_one; + b_xst8[i][j] = b_xst8_one; + dtheta_xst8_c[i][j] = dtheta_xst8_c_one; + + setflag[i][j] = 1; + count++; + } + } + + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/xstk"); + +} + +/* ---------------------------------------------------------------------- + neighbor callback to inform pair style of neighbor list to use regular +------------------------------------------------------------------------- */ + +void PairOxrna2Xstk::init_list(int id, NeighList *ptr) +{ + if (id == 0) list = ptr; + if (id > 0) error->all(FLERR,"Respa not supported"); + +} + + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairOxrna2Xstk::init_one(int i, int j) +{ + + if (setflag[i][j] == 0) { + error->all(FLERR,"Coefficient mixing not defined in oxDNA"); + } + if (offset_flag) { + error->all(FLERR,"Offset not supported in oxDNA"); + } + + k_xst[j][i] = k_xst[i][j]; + cut_xst_0[j][i] = cut_xst_0[i][j]; + cut_xst_c[j][i] = cut_xst_c[i][j]; + cut_xst_lo[j][i] = cut_xst_lo[i][j]; + cut_xst_hi[j][i] = cut_xst_hi[i][j]; + b_xst_lo[j][i] = b_xst_lo[i][j]; + b_xst_hi[j][i] = b_xst_hi[i][j]; + cut_xst_lc[j][i] = cut_xst_lc[i][j]; + cut_xst_hc[j][i] = cut_xst_hc[i][j]; + + a_xst1[j][i] = a_xst1[i][j]; + theta_xst1_0[j][i] = theta_xst1_0[i][j]; + dtheta_xst1_ast[j][i] = dtheta_xst1_ast[i][j]; + b_xst1[j][i] = b_xst1[i][j]; + dtheta_xst1_c[j][i] = dtheta_xst1_c[i][j]; + + a_xst2[j][i] = a_xst2[i][j]; + theta_xst2_0[j][i] = theta_xst2_0[i][j]; + dtheta_xst2_ast[j][i] = dtheta_xst2_ast[i][j]; + b_xst2[j][i] = b_xst2[i][j]; + dtheta_xst2_c[j][i] = dtheta_xst2_c[i][j]; + + a_xst3[j][i] = a_xst3[i][j]; + theta_xst3_0[j][i] = theta_xst3_0[i][j]; + dtheta_xst3_ast[j][i] = dtheta_xst3_ast[i][j]; + b_xst3[j][i] = b_xst3[i][j]; + dtheta_xst3_c[j][i] = dtheta_xst3_c[i][j]; + + a_xst7[j][i] = a_xst7[i][j]; + theta_xst7_0[j][i] = theta_xst7_0[i][j]; + dtheta_xst7_ast[j][i] = dtheta_xst7_ast[i][j]; + b_xst7[j][i] = b_xst7[i][j]; + dtheta_xst7_c[j][i] = dtheta_xst7_c[i][j]; + + a_xst8[j][i] = a_xst8[i][j]; + theta_xst8_0[j][i] = theta_xst8_0[i][j]; + dtheta_xst8_ast[j][i] = dtheta_xst8_ast[i][j]; + b_xst8[j][i] = b_xst8[i][j]; + dtheta_xst8_c[j][i] = dtheta_xst8_c[i][j]; + + cutsq_xst_hc[i][j] = cut_xst_hc[i][j]*cut_xst_hc[i][j]; + cutsq_xst_hc[j][i] = cutsq_xst_hc[i][j]; + + // set the master list distance cutoff + return cut_xst_hc[i][j]; + +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairOxrna2Xstk::write_restart(FILE *fp) +{ + write_restart_settings(fp); + + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + fwrite(&setflag[i][j],sizeof(int),1,fp); + if (setflag[i][j]) { + + fwrite(&k_xst[i][j],sizeof(double),1,fp); + fwrite(&cut_xst_0[i][j],sizeof(double),1,fp); + fwrite(&cut_xst_c[i][j],sizeof(double),1,fp); + fwrite(&cut_xst_lo[i][j],sizeof(double),1,fp); + fwrite(&cut_xst_hi[i][j],sizeof(double),1,fp); + fwrite(&cut_xst_lc[i][j],sizeof(double),1,fp); + fwrite(&cut_xst_hc[i][j],sizeof(double),1,fp); + fwrite(&b_xst_lo[i][j],sizeof(double),1,fp); + fwrite(&b_xst_hi[i][j],sizeof(double),1,fp); + + fwrite(&a_xst1[i][j],sizeof(double),1,fp); + fwrite(&theta_xst1_0[i][j],sizeof(double),1,fp); + fwrite(&dtheta_xst1_ast[i][j],sizeof(double),1,fp); + fwrite(&b_xst1[i][j],sizeof(double),1,fp); + fwrite(&dtheta_xst1_c[i][j],sizeof(double),1,fp); + + fwrite(&a_xst2[i][j],sizeof(double),1,fp); + fwrite(&theta_xst2_0[i][j],sizeof(double),1,fp); + fwrite(&dtheta_xst2_ast[i][j],sizeof(double),1,fp); + fwrite(&b_xst2[i][j],sizeof(double),1,fp); + fwrite(&dtheta_xst2_c[i][j],sizeof(double),1,fp); + + fwrite(&a_xst3[i][j],sizeof(double),1,fp); + fwrite(&theta_xst3_0[i][j],sizeof(double),1,fp); + fwrite(&dtheta_xst3_ast[i][j],sizeof(double),1,fp); + fwrite(&b_xst3[i][j],sizeof(double),1,fp); + fwrite(&dtheta_xst3_c[i][j],sizeof(double),1,fp); + + fwrite(&a_xst7[i][j],sizeof(double),1,fp); + fwrite(&theta_xst7_0[i][j],sizeof(double),1,fp); + fwrite(&dtheta_xst7_ast[i][j],sizeof(double),1,fp); + fwrite(&b_xst7[i][j],sizeof(double),1,fp); + fwrite(&dtheta_xst7_c[i][j],sizeof(double),1,fp); + + fwrite(&a_xst8[i][j],sizeof(double),1,fp); + fwrite(&theta_xst8_0[i][j],sizeof(double),1,fp); + fwrite(&dtheta_xst8_ast[i][j],sizeof(double),1,fp); + fwrite(&b_xst8[i][j],sizeof(double),1,fp); + fwrite(&dtheta_xst8_c[i][j],sizeof(double),1,fp); + + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairOxrna2Xstk::read_restart(FILE *fp) +{ + read_restart_settings(fp); + allocate(); + + int i,j; + int me = comm->me; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); + MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); + if (setflag[i][j]) { + if (me == 0) { + + utils::sfread(FLERR,&k_xst[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_xst_0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_xst_c[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_xst_lo[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_xst_hi[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_xst_lc[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_xst_hc[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&b_xst_lo[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&b_xst_hi[i][j],sizeof(double),1,fp,NULL,error); + + utils::sfread(FLERR,&a_xst1[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&theta_xst1_0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_xst1_ast[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&b_xst1[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_xst1_c[i][j],sizeof(double),1,fp,NULL,error); + + utils::sfread(FLERR,&a_xst2[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&theta_xst2_0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_xst2_ast[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&b_xst2[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_xst2_c[i][j],sizeof(double),1,fp,NULL,error); + + utils::sfread(FLERR,&a_xst3[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&theta_xst3_0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_xst3_ast[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&b_xst3[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_xst3_c[i][j],sizeof(double),1,fp,NULL,error); + + utils::sfread(FLERR,&a_xst7[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&theta_xst7_0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_xst7_ast[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&b_xst7[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_xst7_c[i][j],sizeof(double),1,fp,NULL,error); + + utils::sfread(FLERR,&a_xst8[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&theta_xst8_0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_xst8_ast[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&b_xst8[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_xst8_c[i][j],sizeof(double),1,fp,NULL,error); + + } + + MPI_Bcast(&k_xst[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_xst_0[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_xst_c[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_xst_lo[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_xst_hi[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_xst_lc[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_xst_hc[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&b_xst_lo[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&b_xst_hi[i][j],1,MPI_DOUBLE,0,world); + + MPI_Bcast(&a_xst1[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&theta_xst1_0[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&dtheta_xst1_ast[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&b_xst1[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&dtheta_xst1_c[i][j],1,MPI_DOUBLE,0,world); + + MPI_Bcast(&a_xst2[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&theta_xst2_0[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&dtheta_xst2_ast[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&b_xst2[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&dtheta_xst2_c[i][j],1,MPI_DOUBLE,0,world); + + MPI_Bcast(&a_xst3[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&theta_xst3_0[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&dtheta_xst3_ast[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&b_xst3[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&dtheta_xst3_c[i][j],1,MPI_DOUBLE,0,world); + + MPI_Bcast(&a_xst7[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&theta_xst7_0[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&dtheta_xst7_ast[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&b_xst7[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&dtheta_xst7_c[i][j],1,MPI_DOUBLE,0,world); + + MPI_Bcast(&a_xst8[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&theta_xst8_0[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&dtheta_xst8_ast[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&b_xst8[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&dtheta_xst8_c[i][j],1,MPI_DOUBLE,0,world); + + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairOxrna2Xstk::write_restart_settings(FILE *fp) +{ + fwrite(&offset_flag,sizeof(int),1,fp); + fwrite(&mix_flag,sizeof(int),1,fp); + fwrite(&tail_flag,sizeof(int),1,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairOxrna2Xstk::read_restart_settings(FILE *fp) +{ + int me = comm->me; + if (me == 0) { + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error); + } + MPI_Bcast(&offset_flag,1,MPI_INT,0,world); + MPI_Bcast(&mix_flag,1,MPI_INT,0,world); + MPI_Bcast(&tail_flag,1,MPI_INT,0,world); +} + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void PairOxrna2Xstk::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + fprintf(fp,"%d\ + %g %g %g %g %g\ + %g %g %g %g\ + %g %g %g %g %g\ + %g %g %g %g %g\ + %g %g %g %g %g\ + %g %g %g %g %g\ + %g %g %g %g %g\ + \n",i, + k_xst[i][i],cut_xst_0[i][i],cut_xst_c[i][i],cut_xst_lo[i][i],cut_xst_hi[i][i], + cut_xst_lc[i][i],cut_xst_hc[i][i],b_xst_lo[i][i],b_xst_hi[i][i], + a_xst1[i][i],theta_xst1_0[i][i],dtheta_xst1_ast[i][i],b_xst1[i][i],dtheta_xst1_c[i][i], + a_xst2[i][i],theta_xst2_0[i][i],dtheta_xst2_ast[i][i],b_xst2[i][i],dtheta_xst2_c[i][i], + a_xst3[i][i],theta_xst3_0[i][i],dtheta_xst3_ast[i][i],b_xst3[i][i],dtheta_xst3_c[i][i], + a_xst7[i][i],theta_xst7_0[i][i],dtheta_xst7_ast[i][i],b_xst7[i][i],dtheta_xst7_c[i][i], + a_xst8[i][i],theta_xst8_0[i][i],dtheta_xst8_ast[i][i],b_xst8[i][i],dtheta_xst8_c[i][i]); + +} + +/* ---------------------------------------------------------------------- + proc 0 writes all pairs to data file +------------------------------------------------------------------------- */ + +void PairOxrna2Xstk::write_data_all(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + for (int j = i; j <= atom->ntypes; j++) + fprintf(fp,"%d %d\ + %g %g %g %g %g\ + %g %g %g %g\ + %g %g %g %g %g\ + %g %g %g %g %g\ + %g %g %g %g %g\ + %g %g %g %g %g\ + %g %g %g %g %g\ + \n",i,j, + k_xst[i][j],cut_xst_0[i][j],cut_xst_c[i][j],cut_xst_lo[i][j],cut_xst_hi[i][j], + cut_xst_lc[i][j],cut_xst_hc[i][j],b_xst_lo[i][j],b_xst_hi[i][j], + a_xst1[i][j],theta_xst1_0[i][j],dtheta_xst1_ast[i][j],b_xst1[i][j],dtheta_xst1_c[i][j], + a_xst2[i][j],theta_xst2_0[i][j],dtheta_xst2_ast[i][j],b_xst2[i][j],dtheta_xst2_c[i][j], + a_xst3[i][j],theta_xst3_0[i][j],dtheta_xst3_ast[i][j],b_xst3[i][j],dtheta_xst3_c[i][j], + a_xst7[i][j],theta_xst7_0[i][j],dtheta_xst7_ast[i][j],b_xst7[i][j],dtheta_xst7_c[i][j], + a_xst8[i][j],theta_xst8_0[i][j],dtheta_xst8_ast[i][j],b_xst8[i][j],dtheta_xst8_c[i][j]); + +} + +/* ---------------------------------------------------------------------- */ + +void *PairOxrna2Xstk::extract(const char *str, int &dim) +{ + dim = 2; + + if (strcmp(str,"k_xst") == 0) return (void *) k_xst; + if (strcmp(str,"cut_xst_0") == 0) return (void *) cut_xst_0; + if (strcmp(str,"cut_xst_c") == 0) return (void *) cut_xst_c; + if (strcmp(str,"cut_xst_lo") == 0) return (void *) cut_xst_lo; + if (strcmp(str,"cut_xst_hi") == 0) return (void *) cut_xst_hi; + if (strcmp(str,"cut_xst_lc") == 0) return (void *) cut_xst_lc; + if (strcmp(str,"cut_xst_hc") == 0) return (void *) cut_xst_hc; + if (strcmp(str,"b_xst_lo") == 0) return (void *) b_xst_lo; + if (strcmp(str,"b_xst_hi") == 0) return (void *) b_xst_hi; + + if (strcmp(str,"a_xst1") == 0) return (void *) a_xst1; + if (strcmp(str,"theta_xst1_0") == 0) return (void *) theta_xst1_0; + if (strcmp(str,"dtheta_xst1_ast") == 0) return (void *) dtheta_xst1_ast; + if (strcmp(str,"b_xst1") == 0) return (void *) b_xst1; + if (strcmp(str,"dtheta_xst1_c") == 0) return (void *) dtheta_xst1_c; + + if (strcmp(str,"a_xst2") == 0) return (void *) a_xst2; + if (strcmp(str,"theta_xst2_0") == 0) return (void *) theta_xst2_0; + if (strcmp(str,"dtheta_xst2_ast") == 0) return (void *) dtheta_xst2_ast; + if (strcmp(str,"b_xst2") == 0) return (void *) b_xst2; + if (strcmp(str,"dtheta_xst2_c") == 0) return (void *) dtheta_xst2_c; + + if (strcmp(str,"a_xst3") == 0) return (void *) a_xst3; + if (strcmp(str,"theta_xst3_0") == 0) return (void *) theta_xst3_0; + if (strcmp(str,"dtheta_xst3_ast") == 0) return (void *) dtheta_xst3_ast; + if (strcmp(str,"b_xst3") == 0) return (void *) b_xst3; + if (strcmp(str,"dtheta_xst3_c") == 0) return (void *) dtheta_xst3_c; + + if (strcmp(str,"a_xst7") == 0) return (void *) a_xst7; + if (strcmp(str,"theta_xst7_0") == 0) return (void *) theta_xst7_0; + if (strcmp(str,"dtheta_xst7_ast") == 0) return (void *) dtheta_xst7_ast; + if (strcmp(str,"b_xst7") == 0) return (void *) b_xst7; + if (strcmp(str,"dtheta_xst7_c") == 0) return (void *) dtheta_xst7_c; + + if (strcmp(str,"a_xst8") == 0) return (void *) a_xst8; + if (strcmp(str,"theta_xst8_0") == 0) return (void *) theta_xst8_0; + if (strcmp(str,"dtheta_xst8_ast") == 0) return (void *) dtheta_xst8_ast; + if (strcmp(str,"b_xst8") == 0) return (void *) b_xst8; + if (strcmp(str,"dtheta_xst8_c") == 0) return (void *) dtheta_xst8_c; + + return NULL; +} diff --git a/src/USER-CGDNA/pair_oxrna2_xstk.h b/src/USER-CGDNA/pair_oxrna2_xstk.h new file mode 100644 index 0000000000..97e878c342 --- /dev/null +++ b/src/USER-CGDNA/pair_oxrna2_xstk.h @@ -0,0 +1,85 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(oxrna2/xstk,PairOxrna2Xstk) + +#else + +#ifndef LMP_PAIR_OXRNA2_XSTK_H +#define LMP_PAIR_OXRNA2_XSTK_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairOxrna2Xstk : public Pair { + public: + PairOxrna2Xstk(class LAMMPS *); + virtual ~PairOxrna2Xstk(); + virtual void compute(int, int); + void settings(int, char **); + void coeff(int, char **); + void init_list(int, class NeighList *); + double init_one(int, int); + void write_restart(FILE *); + void read_restart(FILE *); + void write_restart_settings(FILE *); + void read_restart_settings(FILE *); + void write_data(FILE *); + void write_data_all(FILE *); + void *extract(const char *, int &); + + protected: + // cross-stacking interaction + double **k_xst, **cut_xst_0, **cut_xst_c, **cut_xst_lo, **cut_xst_hi; + double **cut_xst_lc, **cut_xst_hc, **b_xst_lo, **b_xst_hi; + double **cutsq_xst_hc; + + double **a_xst1, **theta_xst1_0, **dtheta_xst1_ast; + double **b_xst1, **dtheta_xst1_c; + + double **a_xst2, **theta_xst2_0, **dtheta_xst2_ast; + double **b_xst2, **dtheta_xst2_c; + + double **a_xst3, **theta_xst3_0, **dtheta_xst3_ast; + double **b_xst3, **dtheta_xst3_c; + + double **a_xst7, **theta_xst7_0, **dtheta_xst7_ast; + double **b_xst7, **dtheta_xst7_c; + + double **a_xst8, **theta_xst8_0, **dtheta_xst8_ast; + double **b_xst8, **dtheta_xst8_c; + + virtual void allocate(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +*/